commit/galaxy-central: guerler: Charts: Allow switching chart types without reset, fix resizing
by commits-noreplyï¼ bitbucket.org 10 Apr '14
by commits-noreplyï¼ bitbucket.org 10 Apr '14
10 Apr '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b887ef428f8f/
Changeset: b887ef428f8f
User: guerler
Date: 2014-04-10 02:50:45
Summary: Charts: Allow switching chart types without reset, fix resizing
Affected #: 8 files
diff -r f0651cd048cb4ba8a472361d9e7cc8413d9dcd2b -r b887ef428f8f99685878df3cfe61531e3b4a26a2 config/plugins/visualizations/charts/static/app.js
--- a/config/plugins/visualizations/charts/static/app.js
+++ b/config/plugins/visualizations/charts/static/app.js
@@ -51,7 +51,8 @@
// append views
this.$el.append(this.viewer_view.$el);
this.$el.append(this.editor_view.$el);
-
+ this.$el.css('height', 'inherit');
+
// pick start screen
if (!this.storage.load()) {
// show editor
diff -r f0651cd048cb4ba8a472361d9e7cc8413d9dcd2b -r b887ef428f8f99685878df3cfe61531e3b4a26a2 config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
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t=this.buttonList[e];this.$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.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-portlet",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find("#content"),this.$title=this.$el.find("#title-text"),this.options.height&&(this.$el.find("#body").css("height",this.options.height),this.$el.find("#content").css("overflow",this.options.overflow)),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var n=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),n.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var n=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),n.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="toolForm portlet-view no-highlight">';if(e.title||e.icon)t+='<div id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var n=this;this.options.onchange&&this.$select.on("change",function(){n.value(n.$select.val())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return"<label><b>"+e.title+"</b></label>"},value:function(){return options.title}}),r=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<div class="'+e.cls+'">'+e.title+"</div>"},value:function(){return options.title}}),i=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),s=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),o=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),u=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),a=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),f=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:i,Icon:s,ButtonIcon:o,Input:h,Anchor:u,Message:a,Searchbox:f,Title:l,Text:r,Select:t,ButtonMenu:c}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},cleanup:function(t){var n=t.get("dataset_id_job");if(n!=""){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()}),t.set("dataset_id_job","")}},submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"chartskit",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","Job has been queued..."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._loop(n.id,function(e){switch(e.state){case"ok":return t.state("wait","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),s&&s(),!0;case"running":return t.state("wait","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the Charts-Kit. Please make sure it is installed. "+n),s&&s()})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups;for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh")},ready:function(){return this.counter==0?!0:!1}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._create_canvas("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=e.find("#icon");t.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var n=r.chart.get("state");switch(n){case"ok":e.hide();break;case"failed":t.addClass("fa fa-warning");break;default:t.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_create_canvas:function(e){this.canvas&&this.canvas.remove(),this.$el.append($(this._template_canvas(e)));var t=this.$el.find(".canvas");e=="svg"?this.canvas=d3.select(t[0]):this.canvas=t},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r),this._create_canvas(this.chart_settings.element),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/"+r],function(r){var i=new r(t.app,{canvas:t.canvas});t.chart_settings.execute?e.get("dataset_id_job")==""?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e)):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){for(var i in r.chart_settings.columns)t+=i+"_"+ ++n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns)i[s]=e.get(s);t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div style="height: 100%; min-height: 50px;"><div id="info" style="position: absolute; margin-left: 10px; margin-top: 10px; margin-bottom: 50px;"><span id="icon" style="font-size: 1.2em; display: inline-block;"/><span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/></div></div>'},_template_canvas:function(e){return"<"+e+' class="canvas" style="height: calc(100% - 80px)"/>'}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Customize",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show();r.chart.state("wait","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(s,o){var u=this;this.app=s,this.chart=this.app.chart,this.options=i.merge(o,this.optionsDefault),this.portlet=new r.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){u.app.go("viewer"),u._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){u.app.go("viewer"),u.app.storage.load()}})}}),this.table=new t.View({header:!1,onconfirm:function(e){u.chart.groups.length>0?u.app.modal.show({title:"Switching to another chart type?",body:"If you continue your settings and selections will be cleared.",buttons:{Cancel:function(){u.app.modal.hide()},Continue:function(){u.app.modal.hide(),u.table.value(e)}}}):u.table.value(e)},onchange:function(e){u.chart.groups.reset(),u.chart.settings.clear(),u.chart.set({type:e})},ondblclick:function(e){u.tabs.show("settings")},content:"No chart types available"}),this.table.addHeader("No."),this.table.addHeader("Type"),this.table.addHeader("Library"),this.table.addHeader("Processing*"),this.table.appendHeader();var f=0,l=s.types.attributes;for(var c in l){var h=l[c];this.table.add(++f+"."),this.table.add(h.title),this.table.add(h.library,"10%"),h.execute?this.table.add((new n.Icon({icon:"fa-check"})).$el,"10%","center"):this.table.add(""),this.table.append(c)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=u._addGroupModel();u.tabs.show(e.id)}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){u.chart.set("title",u.title.value())}});var p=$("<div/>");p.append(i.wrap((new n.Label({title:"Provide a chart title:"})).$el)),p.append(i.wrap(this.title.$el)),p.append(i.wrap((new n.Label({title:"Select a chart type:"})).$el)),p.append(i.wrap(this.table.$el)),p.append((new n.Text({title:"*Certain chart types pre-process data before rendering the visualization. The pre-processing is done using the chartskit available in the Toolshed.",cls:"toolParamHelp"})).$el),this.tabs.add({id:"main",title:"Start",$el:p}),this.settings=new a(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var 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onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),c=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:i,Icon:s,ButtonIcon:o,Input:h,Anchor:u,Message:a,Searchbox:f,Title:l,Text:r,Select:t,ButtonMenu:c}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},cleanup:function(t){var n=t.get("dataset_id_job");if(n!=""){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()}),t.set("dataset_id_job","")}},submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=this.app.types.get(a);data={tool_id:"chartskit",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","Job has been queued..."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._loop(n.id,function(e){switch(e.state){case"ok":return t.state("wait","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),s&&s(),!0;case"running":return t.state("wait","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the Charts-Kit. Please make sure it is installed. "+n),s&&s()})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups;for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r},l=!1;for(var c in a.columns){var h=a.columns[c],d=u[h],v=s[d];isNaN(v)&&(l=!0),f[c]=v}l||p[o].values.push(f)}}n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){if(this.counter==0)for(var e in this.queue)this.queue[e](),this.queue.splice(e,1)})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh")},ready:function(){return this.counter==0?!0:!1}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","plugin/library/deferred","mvc/visualization/visualization-model"],function(e,t){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(n){this.groups=new e,this.settings=new Backbone.Model,this.deferred=new t},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.set("modified",!1),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,80),this._create_canvas("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=e.find("#icon");t.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var n=r.chart.get("state");switch(n){case"ok":e.hide();break;case"failed":t.addClass("fa fa-warning");break;default:t.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_create_canvas:function(e){this.canvas&&this.canvas.remove(),this.$el.append($(this._template_canvas(e)));var t=this.$el.find(".canvas");e=="svg"?this.canvas=d3.select(t[0]):this.canvas=t},_draw:function(e){var t=this,n=e.deferred.register(),r=e.get("type");this.chart_settings=this.app.types.get(r),this._create_canvas(this.chart_settings.element),e.state("wait","Please wait...");if(!this.chart_settings.execute||this.chart_settings.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+r+"/"+r],function(r){var i=new r(t.app,{canvas:t.canvas});t.chart_settings.execute?e.get("dataset_id_job")==""?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(n,e,t._defaultRequestDictionary(e))},function(){e.deferred.done(n)}):i.draw(n,e,t._defaultRequestDictionary(e)):i.draw(n,e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){for(var i in r.chart_settings.columns)t+=i+"_"+ ++n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_settings.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var n=0,r=this;return e.groups.each(function(e){var i={};for(var s in r.chart_settings.columns)i[s]=e.get(s);t.groups.push({key:++n+":"+e.get("key"),columns:i})}),t},_template:function(){return'<div style="height: inherit; min-height: 50px;"><div id="info" style="position: absolute; margin-left: 10px; margin-top: 10px; margin-bottom: 50px;"><span id="icon" style="font-size: 1.2em; display: inline-block;"/><span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/></div></div>'},_template_canvas:function(e){return"<"+e+' class="canvas" style="height: 100%;"/>'}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){s._wait(s.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_screenshot:function(){var e=new XMLSerializer,t=e.serializeToString(this.viewport_view.svg.node()),n="data:image/svg+xml;base64,"+btoa(t);window.location.href="data:application/x-download/;charset=utf-8,"+encodeURIComponent(t)},_wait:function(e,t){if(e.deferred.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e),r.chart.set("modified",!0)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata...");var l=this.chart.deferred.register();this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show();r.chart.state("wait","Metadata initialized..."),r.chart.deferred.done(l)})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({list:[],initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll(),this.list=[];for(var n in e)this._add(n,e[n],t);for(var n in this.list){var r=this.list[n].options.onchange;r&&r()}},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:e,placeholder:n.placeholder,onchange:function(){r.set(e,s.value())}});break;case"select":s=new t.Select.View({id:e,data:n.data,onchange:function(){var t=s.value();r.set(e,t);var o=_.findWhere(n.data,{value:t});o&&(o.show&&i.$el.find("#"+o.show).fadeIn("fast"),o.hide&&i.$el.find("#"+o.hide).fadeOut("fast"))}});break;case"separator":s=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),u.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(u)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(s,o){var u=this;this.app=s,this.chart=this.app.chart,this.options=i.merge(o,this.optionsDefault),this.portlet=new r.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){u.app.go("viewer"),u._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){u.app.go("viewer"),u.app.storage.load()}})}}),this.table=new t.View({header:!1,onchange:function(e){u.chart.settings.clear(),u.chart.set({type:e}),u.chart.set("modified",!0)},ondblclick:function(e){u.tabs.show("settings")},content:"No chart types available"}),this.table.addHeader("No."),this.table.addHeader("Type"),this.table.addHeader("Library"),this.table.addHeader("Processing*"),this.table.appendHeader();var f=0,l=s.types.attributes;for(var c in l){var h=l[c];this.table.add(++f+"."),this.table.add(h.title),this.table.add(h.library,"10%"),h.execute?this.table.add((new n.Icon({icon:"fa-check"})).$el,"10%","center"):this.table.add(""),this.table.append(c)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=u._addGroupModel();u.tabs.show(e.id)}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){u.chart.set("title",u.title.value())}});var p=$("<div/>");p.append(i.wrap((new n.Label({title:"Provide a chart title:"})).$el)),p.append(i.wrap(this.title.$el)),p.append(i.wrap((new n.Label({title:"Select a chart type:"})).$el)),p.append(i.wrap(this.table.$el)),p.append((new n.Text({title:"*Certain chart types pre-process data before rendering the visualization. The pre-processing is done using the chartskit available in the Toolshed.",cls:"toolParamHelp"})).$el),this.tabs.add({id:"main",title:"Start",$el:p}),this.settings=new a(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var u=this;this.chart.on("change:title",function(e){u._refreshTitle()}),this.chart.on("change:type",function(e){u.table.value(e.get("type"))}),this.chart.on("reset",function(e){u._resetChart()}),this.app.chart.on("redraw",function(e){u.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){u._addGroup(e)}),this.app.chart.groups.on("remove",function(e){u._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){u._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){u._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new o({id:i.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new u(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",i.uuid()),this.chart.set("type","nvd3_bardiagram"),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.table.value(),title:this.title.value(),date:i.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this;this.chart.deferred.execute(function(){e.app.storage.save(),e.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:500}})}),define("plugin/charts/nvd3/config",[],function(){return{title:"",library:"nvd3.js",element:"svg",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"x_axis_tick"},{label:"Auto",value:"auto",hide:"x_axis_tick"},{label:"Float",value:"f",show:"x_axis_tick"},{label:"Exponent",value:"e",show:"x_axis_tick"},{label:"Integer",value:"d",hide:"x_axis_tick"},{label:"Percentage",value:"p",show:"x_axis_tick"},{label:"Rounded",value:"r",show:"x_axis_tick"},{label:"SI-prefix",value:"s",show:"x_axis_tick"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",hide:"y_axis_tick"},{label:"Auto",value:"auto",hide:"y_axis_tick"},{label:"Float",value:"f",show:"y_axis_tick"},{label:"Exponent",value:"e",show:"y_axis_tick"},{label:"Integer",value:"d",hide:"y_axis_tick"},{label:"Percentage",value:"p",show:"y_axis_tick"},{label:"Rounded",value:"r",show:"y_axis_tick"},{label:"SI-prefix",value:"s",show:"y_axis_tick"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/nvd3_bardiagram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/nvd3_histogram/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:"histogram",columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"}}})}),define("plugin/charts/nvd3_horizontal/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/nvd3_line/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/nvd3_linewithfocus/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/nvd3_piechart/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Pie chart"})}),define("plugin/charts/nvd3_scatterplot/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/nvd3_stackedarea/config",["plugin/charts/nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked area"})}),define("plugin/charts/highcharts_boxplot/config",[],function(){return{title:"Box plot",library:"highcharts.js",element:"div",execute:"boxplot",columns:{y:{title:"Observations"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"}}}}),define("plugin/charts/types",["plugin/charts/nvd3_bardiagram/config","plugin/charts/nvd3_histogram/config","plugin/charts/nvd3_horizontal/config","plugin/charts/nvd3_line/config","plugin/charts/nvd3_linewithfocus/config","plugin/charts/nvd3_piechart/config","plugin/charts/nvd3_scatterplot/config","plugin/charts/nvd3_stackedarea/config","plugin/charts/highcharts_boxplot/config"],function(e,t,n,r,i,s,o,u,a){return Backbone.Model.extend({defaults:{nvd3_bardiagram:e,nvd3_horizontal:n,nvd3_histogram:t,nvd3_line:r,nvd3_linewithfocus:i,nvd3_piechart:s,nvd3_scatterplot:o,nvd3_stackedarea:u,highcharts_boxplot:a}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el),this.$el.css("height","inherit");if(!this.storage.load())this.go("editor");else{this.go("viewer");var n=this;this.chart.deferred.execute(function(){n.chart.trigger("redraw")})}},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})});
\ No newline at end of file
diff -r f0651cd048cb4ba8a472361d9e7cc8413d9dcd2b -r b887ef428f8f99685878df3cfe61531e3b4a26a2 config/plugins/visualizations/charts/static/charts/highcharts_boxplot/highcharts_boxplot.js
--- a/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/highcharts_boxplot.js
+++ b/config/plugins/visualizations/charts/static/charts/highcharts_boxplot/highcharts_boxplot.js
@@ -104,7 +104,7 @@
// update data
self.hc_config.series[0].data = data;
-
+
// draw plot
self.options.canvas.highcharts(self.hc_config);
diff -r f0651cd048cb4ba8a472361d9e7cc8413d9dcd2b -r b887ef428f8f99685878df3cfe61531e3b4a26a2 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
@@ -118,6 +118,7 @@
};
// fill value
+ var skip = false;
for (var key in group.columns) {
// get column
var column = group.columns[key];
@@ -127,8 +128,8 @@
// read value from row
var v = row[index];
- if(isNaN(v) || !v) {
- v = 0;
+ if(isNaN(v)) {
+ skip = true;
}
// add value to dictionary
@@ -136,7 +137,9 @@
}
// add to result
- result[j].values.push(value);
+ if (!skip) {
+ result[j].values.push(value);
+ }
}
}
diff -r f0651cd048cb4ba8a472361d9e7cc8413d9dcd2b -r b887ef428f8f99685878df3cfe61531e3b4a26a2 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
@@ -120,6 +120,7 @@
if (response && response.message && response.message.data && response.message.data.input) {
message = response.message.data.input + '.';
}
+
// update state
chart.state('failed', 'This visualization requires the Charts-Kit. Please make sure it is installed. ' + message);
diff -r f0651cd048cb4ba8a472361d9e7cc8413d9dcd2b -r b887ef428f8f99685878df3cfe61531e3b4a26a2 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
@@ -65,38 +65,15 @@
//
this.table = new Table.View({
header : false,
- onconfirm : function(type) {
- if (self.chart.groups.length > 0) {
- // show modal
- self.app.modal.show({
- title : 'Switching to another chart type?',
- body : 'If you continue your settings and selections will be cleared.',
- buttons : {
- 'Cancel' : function() {
- // hide modal
- self.app.modal.hide();
- },
- 'Continue' : function() {
- // hide modal
- self.app.modal.hide();
-
- // confirm
- self.table.value(type);
- }
- }
- });
- } else {
- // confirm
- self.table.value(type);
- }
- },
onchange : function(type) {
// reset type relevant chart content
- self.chart.groups.reset();
self.chart.settings.clear();
// update chart type
self.chart.set({type: type});
+
+ // set modified flag
+ self.chart.set('modified', true);
},
ondblclick : function(chart_id) {
self.tabs.show('settings');
diff -r f0651cd048cb4ba8a472361d9e7cc8413d9dcd2b -r b887ef428f8f99685878df3cfe61531e3b4a26a2 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
@@ -29,7 +29,7 @@
edit_button: new Ui.ButtonIcon({
icon : 'fa-edit',
tooltip : 'Customize this chart',
- title : 'Customize',
+ title : 'Editor',
onclick : function() {
// attempt to load chart editor
self._wait (self.chart, function() {
diff -r f0651cd048cb4ba8a472361d9e7cc8413d9dcd2b -r b887ef428f8f99685878df3cfe61531e3b4a26a2 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
@@ -3,11 +3,9 @@
function(Portlet, Ui, Utils) {
// widget
-return Backbone.View.extend(
-{
+return Backbone.View.extend({
// initialize
- initialize: function(app, options)
- {
+ initialize: function(app, options) {
// link app
this.app = app;
@@ -20,6 +18,9 @@
// create element
this.setElement($(this._template()));
+ // use full screen for viewer
+ this._fullscreen(this.$el, 80);
+
// create canvas element
this._create_canvas('div');
@@ -69,6 +70,17 @@
this.$el.hide();
},
+ // resize to fullscreen
+ _fullscreen: function($el, margin) {
+ // fix size
+ $el.css('height', $(window).height() - margin);
+
+ // catch window resize event
+ $(window).resize(function () {
+ $el.css('height', $(window).height() - margin);
+ });
+ },
+
// create
_create_canvas: function(element) {
// clear canvas
@@ -219,7 +231,7 @@
// template
_template: function() {
- return '<div style="height: 100%; min-height: 50px;">' +
+ return '<div style="height: inherit; min-height: 50px;">' +
'<div id="info" style="position: absolute; margin-left: 10px; margin-top: 10px; margin-bottom: 50px;">' +
'<span id="icon" style="font-size: 1.2em; display: inline-block;"/>' +
'<span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/>' +
@@ -229,7 +241,7 @@
// template svg/div element
_template_canvas: function(element) {
- return '<' + element + ' class="canvas" style="height: calc(100% - 80px)"/>';
+ return '<' + element + ' class="canvas" style="height: 100%;"/>';
}
});
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dan: Improve handling of invalid/expired GenomeSpace tokens in GenomeSpace export tool.
by commits-noreplyï¼ bitbucket.org 10 Apr '14
by commits-noreplyï¼ bitbucket.org 10 Apr '14
10 Apr '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f0651cd048cb/
Changeset: f0651cd048cb
User: dan
Date: 2014-04-09 23:24:56
Summary: Improve handling of invalid/expired GenomeSpace tokens in GenomeSpace export tool.
Affected #: 2 files
diff -r 63a81f21363325ebbefc321350315804b15bc79e -r f0651cd048cb4ba8a472361d9e7cc8413d9dcd2b tools/genomespace/genomespace_exporter.py
--- a/tools/genomespace/genomespace_exporter.py
+++ b/tools/genomespace/genomespace_exporter.py
@@ -11,6 +11,7 @@
import os
import urllib
import urllib2
+from urlparse import urljoin
log = logging.getLogger( "tools.genomespace.genomespace_exporter" )#( __name__ )
@@ -117,7 +118,7 @@
break
return webtools
-def galaxy_code_get_genomespace_folders( genomespace_site='prod', trans=None, value=None, **kwd ):
+def galaxy_code_get_genomespace_folders( genomespace_site='prod', trans=None, value=None, base_url=None, **kwd ):
if value:
value = value[0]#single select, only 1 value
def recurse_directory_dict( url_opener, cur_options, url ):
@@ -142,19 +143,19 @@
if trans and trans.user:
username = trans.user.preferences.get( 'genomespace_username', None )
token = trans.user.preferences.get( 'genomespace_token', None )
- if None in ( username, token ):
- return []
- url_opener = get_cookie_opener( username, token )
- genomespace_site_dict = get_genomespace_site_urls()[ genomespace_site ]
- dm_url = genomespace_site_dict['dmServer']
- #get export root directory
- #directory_dict = get_default_directory( url_opener, dm_url ).get( 'directory', None ) #This directory contains shares and other items outside of the users home
- directory_dict = get_personal_directory( url_opener, dm_url ).get( 'directory', None ) #Limit export list to only user's home dir
- if directory_dict is None:
- return []
- #what directory to stuff this in
- recurse_directory_dict( url_opener, rval, directory_dict.get( 'url' ) )
-
+ if None not in ( username, token ):
+ url_opener = get_cookie_opener( username, token )
+ genomespace_site_dict = get_genomespace_site_urls()[ genomespace_site ]
+ dm_url = genomespace_site_dict['dmServer']
+ #get export root directory
+ #directory_dict = get_default_directory( url_opener, dm_url ).get( 'directory', None ) #This directory contains shares and other items outside of the users home
+ directory_dict = get_personal_directory( url_opener, dm_url ).get( 'directory', None ) #Limit export list to only user's home dir
+ if directory_dict is not None:
+ recurse_directory_dict( url_opener, rval, directory_dict.get( 'url' ) )
+ if not rval:
+ if not base_url:
+ base_url = '..'
+ rval = [ { 'name':'Your GenomeSpace token appears to be <strong>expired</strong>, please <a href="%s">reauthenticate</a>.' % ( urljoin( base_url, 'user/openid_auth?openid_provider=genomespace&auto_associate=True' ) ), 'value': '', 'options':[], 'selected': False } ]
return rval
diff -r 63a81f21363325ebbefc321350315804b15bc79e -r f0651cd048cb4ba8a472361d9e7cc8413d9dcd2b tools/genomespace/genomespace_exporter.xml
--- a/tools/genomespace/genomespace_exporter.xml
+++ b/tools/genomespace/genomespace_exporter.xml
@@ -35,14 +35,18 @@
<inputs><param format="data" name="input1" type="data" label="Send this dataset to GenomeSpace" /><param name="base_url" type="baseurl" />
- <param name="subdirectory" type="drill_down" display="radio" hierarchy="exact" multiple="False" optional="True" label="Choose Target Directory" dynamic_options="galaxy_code_get_genomespace_folders( genomespace_site = 'prod', trans=__trans__, value=__value__, input_dataset=input1 )" help="Leave blank to generate automatically"/>
+ <param name="subdirectory" type="drill_down" display="radio" hierarchy="exact" multiple="False" optional="True" label="Choose Target Directory" dynamic_options="galaxy_code_get_genomespace_folders( genomespace_site = 'prod', trans=__trans__, value=__value__, input_dataset=input1, base_url=base_url )" help="Leave blank to generate automatically"/><param name="filename" type="text" size="80" help="Leave blank to generate automatically" /></inputs><outputs><data format="html" name="output_log" /></outputs><help>
- This Tool allows you to export data to GenomeSpace. You must have logged in using your GenomeSpace OpenID. You can associate your OpenID credentials under the User Preferences panel.
+This Tool allows you to export data to GenomeSpace. You must have logged in using your GenomeSpace OpenID. You can associate your OpenID credentials under the User Preferences panel.
+
+If you are having trouble with this tool, click here_ to refresh your GenomeSpace token before reporting errors.
+
+.. _here: ${static_path}/../user/openid_auth?openid_provider=genomespace&auto_associate=True
</help><options refresh="True"/><code file="genomespace_exporter.py" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: Metrics API: allow posting of metrics sending to app.trace_logger.log if available
by commits-noreplyï¼ bitbucket.org 10 Apr '14
by commits-noreplyï¼ bitbucket.org 10 Apr '14
10 Apr '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/63a81f213633/
Changeset: 63a81f213633
User: carlfeberhard
Date: 2014-04-09 22:15:00
Summary: Metrics API: allow posting of metrics sending to app.trace_logger.log if available
Affected #: 2 files
diff -r fbe5f3970ac2f1fe32710a4962a175de7264c2be -r 63a81f21363325ebbefc321350315804b15bc79e lib/galaxy/webapps/galaxy/api/metrics.py
--- /dev/null
+++ b/lib/galaxy/webapps/galaxy/api/metrics.py
@@ -0,0 +1,131 @@
+"""
+API operations for for querying and recording user metrics from some client
+(typically a user's browser).
+"""
+#TODO: facade or adapter to fluentd
+
+import datetime
+
+from galaxy import exceptions
+from galaxy import web
+from galaxy.web import require_admin
+from galaxy.web import _future_expose_api as expose_api
+from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous
+
+from galaxy.web.base.controller import BaseAPIController
+
+from galaxy.util import json
+
+import logging
+log = logging.getLogger( __name__ )
+
+
+class MetricsController( BaseAPIController ):
+
+ def __init__( self, app ):
+ super( MetricsController, self ).__init__( app )
+ #: set to true to send additional debugging info to the log
+ self.debugging = True
+
+ #def _decode_id( self, trans, id ):
+ # try:
+ # return trans.security.decode_id( id )
+ # except:
+ # raise exceptions.MalformedId( "Malformed id ( %s ) specified, unable to decode"
+ # % ( str( id ) ), type='error' )
+
+ def _deserialize_isoformat_date( self, datestring ):
+ """
+ Convert ISO formatted date string into python datetime.
+ """
+ return datetime.datetime.strptime( datestring, "%Y-%m-%dT%H:%M:%S.%fZ" )
+
+ #@expose_api
+ #@require_admin
+ #def index( self, trans, **kwd ):
+ # """
+ # """
+ # returned = []
+ # return returned
+
+ #@expose_api
+ #@require_admin
+ #def show( self, trans, id, **kwd ):
+ # """
+ # """
+ # returned = {}
+ # return returned
+
+ @expose_api_anonymous
+ def create( self, trans, payload, **kwd ):
+ """
+ create( trans, payload )
+ * POST /api/metrics:
+ record any metrics sent and return some status object
+
+ .. note:: Anonymous users can post metrics
+
+ :type payload: dict
+ :param payload: (optional) dictionary structure containing:
+ * metrics: a list containing dictionaries of the form:
+ ** namespace: label indicating the source of the metric
+ ** time: isoformat datetime when the metric was recorded
+ ** level: an integer representing the metric's log level
+ ** args: a json string containing an array of extra data
+
+ :rtype: dict
+ :returns: status object
+ """
+ user_id = trans.user.id if trans.user else None
+ session_id = trans.galaxy_session.id if trans.galaxy_session else None
+ parsed_gen = self._parse_metrics( payload.get( 'metrics', None ), user_id, session_id )
+ self._send_metrics( trans, parsed_gen )
+ response = self._get_server_pong( trans )
+ return response
+
+ #TODO: move the following to DAO/Manager object
+ def _parse_metrics( self, metrics, user_id=None, session_id=None ):
+ """
+ Return a generator yielding the each given metric as a tuple:
+ * label: the namespace of the metric
+ * time: datetime of the metric's creation
+ * kwargs: a dictionary containing:
+ ** level: the log level of the metric
+ ** user: the user associated with the metric
+ (will be None if anonymous user)
+ ** session: the session of the current user
+ """
+ metrics = metrics or []
+ for metric in metrics:
+ label = metric[ 'namespace' ]
+ time = self._deserialize_isoformat_date( metric[ 'time' ] )
+ kwargs = {
+ 'level' : metric[ 'level' ],
+ 'args' : json.from_json_string( metric[ 'args' ] ),
+ 'user' : user_id,
+ 'session' : session_id
+ }
+ yield ( label, time, kwargs )
+
+ def _send_metrics( self, trans, metrics ):
+ """
+ Send metrics to the app's `trace_logger` if set and
+ send to `log.debug` if this controller if `self.debugging`.
+
+ Precondition: metrics are parsed and in proper format.
+ """
+ if trans.app.trace_logger:
+ for label, time, kwargs in metrics:
+ trans.app.trace_logger.log( label, time=int( time ), **kwargs )
+ elif self.debugging:
+ for label, time, kwargs in metrics:
+ log.debug( '%s %s %s', label, time, kwargs )
+
+ def _get_server_pong( self, trans ):
+ """
+ Return some status message or object.
+
+ For future use.
+ """
+ return {}
+
diff -r fbe5f3970ac2f1fe32710a4962a175de7264c2be -r 63a81f21363325ebbefc321350315804b15bc79e lib/galaxy/webapps/galaxy/buildapp.py
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -304,10 +304,22 @@
new={ 'install_repository_revision' : 'POST' },
parent_resources=dict( member_name='tool_shed_repository', collection_name='tool_shed_repositories' ) )
+
+ # ==== Trace/Metrics Logger
# Connect logger from app
if app.trace_logger:
webapp.trace_logger = app.trace_logger
+ # metrics logging API
+ #webapp.mapper.connect( "index", "/api/metrics",
+ # controller="metrics", action="index", conditions=dict( method=["GET"] ) )
+ #webapp.mapper.connect( "show", "/api/metrics/{id}",
+ # controller="metrics", action="show", conditions=dict( method=["GET"] ) )
+ webapp.mapper.connect( "create", "/api/metrics",
+ controller="metrics", action="create", conditions=dict( method=["POST"] ) )
+
+
+ # ==== Done
# Indicate that all configuration settings have been provided
webapp.finalize_config()
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/6a85e1496b98/
Changeset: 6a85e1496b98
Branch: next-stable
User: Jeremy Goecks
Date: 2014-04-09 16:47:22
Summary: Genome data provider: (a) handle regions with no mapped reads and (b) clean up trailing whitespace.
Affected #: 1 file
diff -r 44f5b4a2091bc6e552e0c79a0a761cfc8759a36f -r 6a85e1496b98ac05cdfff0b6940877c19bc37cd8 lib/galaxy/visualization/data_providers/genome.py
--- a/lib/galaxy/visualization/data_providers/genome.py
+++ b/lib/galaxy/visualization/data_providers/genome.py
@@ -965,18 +965,23 @@
# -- Choose iterator. --
# Calculate threshold for non-sequential iterators based on mean_depth and read length.
- first_read = next( iterator )
+ try:
+ first_read = next( iterator )
+ except StopIteration:
+ # no reads.
+ return { 'data': [], 'message': None, 'max_low': start, 'max_high': start }
+
read_len = len( first_read.seq )
num_reads = ( end - start ) * mean_depth / float ( read_len )
threshold = float( max_vals )/ num_reads
iterator = itertools.chain( iter( [ first_read ] ), iterator )
# Use specified iterator type, save for when threshold is >= 1.
- # A threshold of >= 1 indicates all reads are to be returned, so no
+ # A threshold of >= 1 indicates all reads are to be returned, so no
# sampling needed and seqential iterator will be used.
if iterator_type == 'sequential' or threshold >= 1:
read_iterator = iterator
- elif iterator_type == 'random':
+ elif iterator_type == 'random':
read_iterator = _random_read_iterator( iterator, threshold )
elif iterator_type == 'nth':
read_iterator = _nth_read_iterator( iterator, threshold )
https://bitbucket.org/galaxy/galaxy-central/commits/376ffdb91bd1/
Changeset: 376ffdb91bd1
Branch: next-stable
User: Jeremy Goecks
Date: 2014-04-09 18:53:34
Summary: SAM/BAM data provider: fix bug and streamline code to support both genomes with reference data and those without.
Affected #: 1 file
diff -r 6a85e1496b98ac05cdfff0b6940877c19bc37cd8 -r 376ffdb91bd1c1a7881e72c5cb6da8dea0e0534f lib/galaxy/visualization/data_providers/genome.py
--- a/lib/galaxy/visualization/data_providers/genome.py
+++ b/lib/galaxy/visualization/data_providers/genome.py
@@ -1063,45 +1063,48 @@
# Clean up. TODO: is this needed? If so, we'll need a cleanup function after processing the data.
# bamfile.close()
- # If there are results and reference data, transform read sequence and cigar.
- if len( results ) != 0 and ref_seq:
- def process_read( read, start_field, cigar_field, seq_field ):
- '''
- Process a read using the designated fields.
- '''
- read_seq, read_cigar = get_ref_based_read_seq_and_cigar( read[ seq_field ].upper(),
- read[ start_field ],
- ref_seq,
- start,
- read[ cigar_field ] )
- read[ seq_field ] = read_seq
- read[ cigar_field ] = read_cigar
+ def compress_seq_and_cigar( read, start_field, cigar_field, seq_field ):
+ '''
+ Use reference-based compression to compress read sequence and cigar.
+ '''
+ read_seq, read_cigar = get_ref_based_read_seq_and_cigar( read[ seq_field ].upper(),
+ read[ start_field ],
+ ref_seq,
+ start,
+ read[ cigar_field ] )
+ read[ seq_field ] = read_seq
+ read[ cigar_field ] = read_cigar
- def process_se_read( read ):
- '''
- Process single-end read.
- '''
- process_read( read, 1, 4, 6)
+ def convert_cigar( read, start_field, cigar_field, seq_field ):
+ '''
+ Convert read cigar from pysam format to string format.
+ '''
+ cigar_ops = 'MIDNSHP=X'
+ read_cigar = ''
+ for op_tuple in read[ cigar_field ]:
+ read_cigar += '%i%s' % ( op_tuple[1], cigar_ops[ op_tuple[0] ] )
+ read[ cigar_field ] = read_cigar
- def process_pe_read( read ):
- '''
- Process paired-end read.
- '''
+ # Choose method for processing reads. Use reference-based compression
+ # if possible. Otherwise, convert cigar.
+ if ref_seq:
+ # Uppercase for easy comparison.
+ ref_seq = ref_seq.upper()
+ process_read = compress_seq_and_cigar
+ else:
+ process_read = convert_cigar
+
+ # Process reads.
+ for read in results:
+ if isinstance( read[ 5 ], list ):
+ # Paired-end read.
if len( read[4] ) > 2:
process_read( read[4], 0, 2, 4 )
if len( read[5] ) > 2:
process_read( read[5], 0, 2, 4 )
-
- # Uppercase for easy comparison.
- ref_seq = ref_seq.upper()
-
- # Process reads.
- for read in results:
- # Use correct function for processing reads.
- if isinstance( read[ 5 ], list ):
- process_pe_read( read )
- else:
- process_se_read( read )
+ else:
+ # Single-end read.
+ process_read( read, 1, 4, 6)
max_low, max_high = get_bounds( results, 1, 2 )
https://bitbucket.org/galaxy/galaxy-central/commits/fbe5f3970ac2/
Changeset: fbe5f3970ac2
User: Jeremy Goecks
Date: 2014-04-09 18:53:57
Summary: Automated merge of next-stable to default.
Affected #: 1 file
diff -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 -r fbe5f3970ac2f1fe32710a4962a175de7264c2be lib/galaxy/visualization/data_providers/genome.py
--- a/lib/galaxy/visualization/data_providers/genome.py
+++ b/lib/galaxy/visualization/data_providers/genome.py
@@ -965,18 +965,23 @@
# -- Choose iterator. --
# Calculate threshold for non-sequential iterators based on mean_depth and read length.
- first_read = next( iterator )
+ try:
+ first_read = next( iterator )
+ except StopIteration:
+ # no reads.
+ return { 'data': [], 'message': None, 'max_low': start, 'max_high': start }
+
read_len = len( first_read.seq )
num_reads = ( end - start ) * mean_depth / float ( read_len )
threshold = float( max_vals )/ num_reads
iterator = itertools.chain( iter( [ first_read ] ), iterator )
# Use specified iterator type, save for when threshold is >= 1.
- # A threshold of >= 1 indicates all reads are to be returned, so no
+ # A threshold of >= 1 indicates all reads are to be returned, so no
# sampling needed and seqential iterator will be used.
if iterator_type == 'sequential' or threshold >= 1:
read_iterator = iterator
- elif iterator_type == 'random':
+ elif iterator_type == 'random':
read_iterator = _random_read_iterator( iterator, threshold )
elif iterator_type == 'nth':
read_iterator = _nth_read_iterator( iterator, threshold )
@@ -1058,45 +1063,48 @@
# Clean up. TODO: is this needed? If so, we'll need a cleanup function after processing the data.
# bamfile.close()
- # If there are results and reference data, transform read sequence and cigar.
- if len( results ) != 0 and ref_seq:
- def process_read( read, start_field, cigar_field, seq_field ):
- '''
- Process a read using the designated fields.
- '''
- read_seq, read_cigar = get_ref_based_read_seq_and_cigar( read[ seq_field ].upper(),
- read[ start_field ],
- ref_seq,
- start,
- read[ cigar_field ] )
- read[ seq_field ] = read_seq
- read[ cigar_field ] = read_cigar
+ def compress_seq_and_cigar( read, start_field, cigar_field, seq_field ):
+ '''
+ Use reference-based compression to compress read sequence and cigar.
+ '''
+ read_seq, read_cigar = get_ref_based_read_seq_and_cigar( read[ seq_field ].upper(),
+ read[ start_field ],
+ ref_seq,
+ start,
+ read[ cigar_field ] )
+ read[ seq_field ] = read_seq
+ read[ cigar_field ] = read_cigar
- def process_se_read( read ):
- '''
- Process single-end read.
- '''
- process_read( read, 1, 4, 6)
+ def convert_cigar( read, start_field, cigar_field, seq_field ):
+ '''
+ Convert read cigar from pysam format to string format.
+ '''
+ cigar_ops = 'MIDNSHP=X'
+ read_cigar = ''
+ for op_tuple in read[ cigar_field ]:
+ read_cigar += '%i%s' % ( op_tuple[1], cigar_ops[ op_tuple[0] ] )
+ read[ cigar_field ] = read_cigar
- def process_pe_read( read ):
- '''
- Process paired-end read.
- '''
+ # Choose method for processing reads. Use reference-based compression
+ # if possible. Otherwise, convert cigar.
+ if ref_seq:
+ # Uppercase for easy comparison.
+ ref_seq = ref_seq.upper()
+ process_read = compress_seq_and_cigar
+ else:
+ process_read = convert_cigar
+
+ # Process reads.
+ for read in results:
+ if isinstance( read[ 5 ], list ):
+ # Paired-end read.
if len( read[4] ) > 2:
process_read( read[4], 0, 2, 4 )
if len( read[5] ) > 2:
process_read( read[5], 0, 2, 4 )
-
- # Uppercase for easy comparison.
- ref_seq = ref_seq.upper()
-
- # Process reads.
- for read in results:
- # Use correct function for processing reads.
- if isinstance( read[ 5 ], list ):
- process_pe_read( read )
- else:
- process_se_read( read )
+ else:
+ # Single-end read.
+ process_read( read, 1, 4, 6)
max_low, max_high = get_bounds( results, 1, 2 )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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09 Apr '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/4aee689e69da/
Changeset: 4aee689e69da
User: greg
Date: 2014-04-09 16:11:48
Summary: The basis of this change set is to provide some fixes to certain Tool Shed functions for supporting changing HTTP protocols over time (ie.e, https <-> http). In doing this, I've refactored several functions and moved most of the Tool Shed <-> Galaxy URL munging functions to the Tool Shed's common_util.py module. Ive renamed the munging functions to clarify what each of them does. Several duplicate functions have been eliminated from the code as well.
Affected #: 28 files
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 lib/galaxy/model/tool_shed_install/__init__.py
--- a/lib/galaxy/model/tool_shed_install/__init__.py
+++ b/lib/galaxy/model/tool_shed_install/__init__.py
@@ -123,12 +123,8 @@
self.shed_config_filename = name
return shed_tool_conf_dict
if self.includes_datatypes:
- #we need to search by filepaths here, which is less desirable
- tool_shed_url = self.tool_shed
- if tool_shed_url.find( ':' ) > 0:
- # Eliminate the port, if any, since it will result in an invalid directory name.
- tool_shed_url = tool_shed_url.split( ':' )[ 0 ]
- tool_shed = tool_shed_url.rstrip( '/' )
+ # We need to search by file paths here, which is less desirable.
+ tool_shed = common_util.remove_protocol_and_port_from_tool_shed_url( self.tool_shed )
for shed_tool_conf_dict in app.toolbox.shed_tool_confs:
tool_path = shed_tool_conf_dict[ 'tool_path' ]
relative_path = os.path.join( tool_path, tool_shed, 'repos', self.owner, self.name, self.installed_changeset_revision )
@@ -271,11 +267,7 @@
return None
def repo_path( self, app ):
- tool_shed_url = self.tool_shed
- if tool_shed_url.find( ':' ) > 0:
- # Eliminate the port, if any, since it will result in an invalid directory name.
- tool_shed_url = tool_shed_url.split( ':' )[ 0 ]
- tool_shed = tool_shed_url.rstrip( '/' )
+ tool_shed = common_util.remove_protocol_and_port_from_tool_shed_url( self.tool_shed )
for index, shed_tool_conf_dict in enumerate( app.toolbox.shed_tool_confs ):
tool_path = shed_tool_conf_dict[ 'tool_path' ]
relative_path = os.path.join( tool_path, tool_shed, 'repos', self.owner, self.name, self.installed_changeset_revision )
@@ -339,7 +331,7 @@
be installed in order for this repository to function correctly. However, those repository dependencies that are defined for this
repository with prior_installation_required set to True place them in a special category in that the required repositories must be
installed before this repository is installed. Among other things, this enables these "special" repository dependencies to include
- information that enables the successful intallation of this repository. This method is not used during the initial installation of
+ information that enables the successful installation of this repository. This method is not used during the initial installation of
this repository, but only after it has been installed (metadata must be set for this repository in order for this method to be useful).
"""
required_rd_tups_that_must_be_installed = []
@@ -347,12 +339,14 @@
rd_tups = self.metadata[ 'repository_dependencies' ][ 'repository_dependencies' ]
for rd_tup in rd_tups:
if len( rd_tup ) == 5:
- tool_shed, name, owner, changeset_revision, prior_installation_required = rd_tup
+ tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
+ common_util.parse_repository_dependency_tuple( rd_tup, contains_error=False )
if asbool( prior_installation_required ):
required_rd_tups_that_must_be_installed.append( ( tool_shed, name, owner, changeset_revision, 'True', 'False' ) )
elif len( rd_tup ) == 6:
- tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = rd_tup
- # The repository dependency will only be required to be previsously installed if it does not fall into the category of
+ tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
+ common_util.parse_repository_dependency_tuple( rd_tup, contains_error=False )
+ # The repository dependency will only be required to be previously installed if it does not fall into the category of
# a repository that must be installed only so that it's contained tool dependency can be used for compiling the tool
# dependency of the dependent repository.
if not asbool( only_if_compiling_contained_td ):
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -63,6 +63,7 @@
from galaxy.web.form_builder import SelectField
from galaxy.model.item_attrs import Dictifiable
from galaxy.model import Workflow
+from tool_shed.util import common_util
from tool_shed.util import shed_util_common as suc
from .loader import load_tool, template_macro_params
from .wrappers import (
@@ -467,6 +468,8 @@
.first()
def __get_tool_shed_repository( self, tool_shed, name, owner, installed_changeset_revision ):
+ # We store only the port, if one exists, in the database.
+ tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed )
return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ) \
.filter( and_( self.app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed,
self.app.install_model.ToolShedRepository.table.c.name == name,
@@ -532,7 +535,10 @@
# Backward compatibility issue - the tag used to be named 'changeset_revision'.
installed_changeset_revision_elem = elem.find( "changeset_revision" )
installed_changeset_revision = installed_changeset_revision_elem.text
- tool_shed_repository = self.__get_tool_shed_repository( tool_shed, repository_name, repository_owner, installed_changeset_revision )
+ tool_shed_repository = self.__get_tool_shed_repository( tool_shed,
+ repository_name,
+ repository_owner,
+ installed_changeset_revision )
if tool_shed_repository:
# Only load tools if the repository is not deactivated or uninstalled.
can_load_into_panel_dict = not tool_shed_repository.deleted
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 lib/galaxy/tools/data_manager/manager.py
--- a/lib/galaxy/tools/data_manager/manager.py
+++ b/lib/galaxy/tools/data_manager/manager.py
@@ -6,6 +6,7 @@
from galaxy.util.odict import odict
from galaxy.util.template import fill_template
from galaxy.tools.data import TabularToolDataTable
+from tool_shed.util import common_util
import tool_shed.util.shed_util_common as suc
#set up logger
@@ -16,6 +17,7 @@
VALUE_TRANSLATION_FUNCTIONS = dict( abspath=os.path.abspath )
DEFAULT_VALUE_TRANSLATION_TYPE = 'template'
+
class DataManagers( object ):
def __init__( self, app, xml_filename=None ):
self.app = app
@@ -26,6 +28,7 @@
self.load_from_xml( self.filename )
if self.app.config.shed_data_manager_config_file:
self.load_from_xml( self.app.config.shed_data_manager_config_file, store_tool_path=False, replace_existing=True )
+
def load_from_xml( self, xml_filename, store_tool_path=True, replace_existing=False ):
try:
tree = util.parse_xml( xml_filename )
@@ -45,6 +48,7 @@
self.tool_path = tool_path
for data_manager_elem in root.findall( 'data_manager' ):
self.load_manager_from_elem( data_manager_elem, replace_existing=replace_existing )
+
def load_manager_from_elem( self, data_manager_elem, tool_path=None, add_manager=True, replace_existing=False ):
try:
data_manager = DataManager( self, data_manager_elem, tool_path=tool_path )
@@ -55,6 +59,7 @@
self.add_manager( data_manager, replace_existing=replace_existing )
log.debug( 'Loaded Data Manager: %s' % ( data_manager.id ) )
return data_manager
+
def add_manager( self, data_manager, replace_existing=False ):
if not replace_existing:
assert data_manager.id not in self.data_managers, "A data manager has been defined twice: %s" % ( data_manager.id )
@@ -67,8 +72,10 @@
if data_table_name not in self.managed_data_tables:
self.managed_data_tables[ data_table_name ] = []
self.managed_data_tables[ data_table_name ].append( data_manager )
+
def get_manager( self, *args, **kwds ):
return self.data_managers.get( *args, **kwds )
+
def remove_manager( self, manager_ids ):
if not isinstance( manager_ids, list ):
manager_ids = [ manager_ids ]
@@ -89,6 +96,7 @@
if remove_data_table_tracking and data_table_name in self.managed_data_tables:
del self.managed_data_tables[ data_table_name ]
+
class DataManager( object ):
GUID_TYPE = 'data_manager'
DEFAULT_VERSION = "0.0.1"
@@ -108,6 +116,7 @@
self.tool_shed_repository_info_dict = None
if elem is not None:
self.load_from_element( elem, tool_path or self.data_managers.tool_path )
+
def load_from_element( self, elem, tool_path ):
assert elem.tag == 'data_manager', 'A data manager configuration must have a "data_manager" tag as the root. "%s" is present' % ( elem.tag )
self.declared_id = elem.get( 'id', None )
@@ -122,14 +131,24 @@
path = tool_elem.get( "file", None )
tool_guid = tool_elem.get( "guid", None )
#need to determine repository info so that dependencies will work correctly
- tool_shed = tool_elem.find( 'tool_shed' ).text
+ tool_shed_url = tool_elem.find( 'tool_shed' ).text
+ # Handle protocol changes.
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.data_managers.app, tool_shed_url )
repository_name = tool_elem.find( 'repository_name' ).text
repository_owner = tool_elem.find( 'repository_owner' ).text
installed_changeset_revision = tool_elem.find( 'installed_changeset_revision' ).text
- #save repository info here
- self.tool_shed_repository_info_dict = dict( tool_shed=tool_shed, name=repository_name, owner=repository_owner, installed_changeset_revision=installed_changeset_revision )
- #get tool_shed repo id
- tool_shed_repository = suc.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( self.data_managers.app, tool_shed, repository_name, repository_owner, installed_changeset_revision )
+ self.tool_shed_repository_info_dict = dict( tool_shed_url=tool_shed_url,
+ name=repository_name,
+ owner=repository_owner,
+ installed_changeset_revision=installed_changeset_revision )
+ # The protocol is not stored in the database.
+ tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url )
+ tool_shed_repository = \
+ suc.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( self.data_managers.app,
+ tool_shed,
+ repository_name,
+ repository_owner,
+ installed_changeset_revision )
if tool_shed_repository is None:
log.warning( 'Could not determine tool shed repository from database. This should only ever happen when running tests.' )
#we'll set tool_path manually here from shed_conf_file
@@ -147,7 +166,10 @@
if shed_conf:
tool_path = shed_conf.get( "tool_path", tool_path )
assert path is not None, "A tool file path could not be determined:\n%s" % ( util.xml_to_string( elem ) )
- self.load_tool( os.path.join( tool_path, path ), guid=tool_guid, data_manager_id=self.id, tool_shed_repository_id=tool_shed_repository_id )
+ self.load_tool( os.path.join( tool_path, path ),
+ guid=tool_guid,
+ data_manager_id=self.id,
+ tool_shed_repository_id=tool_shed_repository_id )
self.name = elem.get( 'name', self.tool.name )
self.description = elem.get( 'description', self.tool.description )
@@ -206,12 +228,23 @@
target_value = target_elem.text
if data_table_name not in self.move_by_data_table_column:
self.move_by_data_table_column[ data_table_name ] = {}
- self.move_by_data_table_column[ data_table_name ][ data_table_coumn_name ] = dict( type=move_type, source_base=source_base, source_value=source_value, target_base=target_base, target_value=target_value, relativize_symlinks=relativize_symlinks )
+ self.move_by_data_table_column[ data_table_name ][ data_table_coumn_name ] = \
+ dict( type=move_type,
+ source_base=source_base,
+ source_value=source_value,
+ target_base=target_base,
+ target_value=target_value,
+ relativize_symlinks=relativize_symlinks )
+
@property
def id( self ):
return self.guid or self.declared_id #if we have a guid, we will use that as the data_manager id
+
def load_tool( self, tool_filename, guid=None, data_manager_id=None, tool_shed_repository_id=None ):
- tool = self.data_managers.app.toolbox.load_tool( tool_filename, guid=guid, data_manager_id=data_manager_id, repository_id=tool_shed_repository_id )
+ tool = self.data_managers.app.toolbox.load_tool( tool_filename,
+ guid=guid,
+ data_manager_id=data_manager_id,
+ repository_id=tool_shed_repository_id )
self.data_managers.app.toolbox.data_manager_tools[ tool.id ] = tool
self.data_managers.app.toolbox.tools_by_id[ tool.id ] = tool
self.tool = tool
@@ -294,7 +327,6 @@
except OSError, e:
if e.errno != errno.EEXIST:
raise e
- #log.debug( 'Error creating directory "%s": %s' % ( dirs, e ) )
#moving a directory and the target already exists, we move the contents instead
util.move_merge( source, target )
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 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
@@ -207,9 +207,9 @@
# Keep track of all repositories that are installed - there may be more than one if repository dependencies are installed.
installed_tool_shed_repositories = []
# Get all of the information necessary for installing the repository from the specified tool shed.
- url = suc.url_join( tool_shed_url,
- 'api/repositories/get_repository_revision_install_info?name=%s&owner=%s&changeset_revision=%s' % \
- ( name, owner, changeset_revision ) )
+ params = '?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision )
+ url = common_util.url_join( tool_shed_url,
+ 'api/repositories/get_repository_revision_install_info%s' % params )
try:
raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
except Exception, e:
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 lib/galaxy/webapps/galaxy/controllers/admin.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin.py
@@ -20,46 +20,74 @@
log = logging.getLogger( __name__ )
+
class UserListGrid( grids.Grid ):
+
+
class EmailColumn( grids.TextColumn ):
+
def get_value( self, trans, grid, user ):
return user.email
+
+
class UserNameColumn( grids.TextColumn ):
+
def get_value( self, trans, grid, user ):
if user.username:
return user.username
return 'not set'
+
+
class StatusColumn( grids.GridColumn ):
+
def get_value( self, trans, grid, user ):
if user.purged:
return "purged"
elif user.deleted:
return "deleted"
return ""
+
+
class GroupsColumn( grids.GridColumn ):
+
def get_value( self, trans, grid, user ):
if user.groups:
return len( user.groups )
return 0
+
+
class RolesColumn( grids.GridColumn ):
+
def get_value( self, trans, grid, user ):
if user.roles:
return len( user.roles )
return 0
+
+
class ExternalColumn( grids.GridColumn ):
+
def get_value( self, trans, grid, user ):
if user.external:
return 'yes'
return 'no'
+
+
class LastLoginColumn( grids.GridColumn ):
+
def get_value( self, trans, grid, user ):
if user.galaxy_sessions:
return self.format( user.galaxy_sessions[ 0 ].update_time )
return 'never'
+
+
class TimeCreatedColumn( grids.GridColumn ):
+
def get_value( self, trans, grid, user ):
return user.create_time.strftime('%x')
+
+
class ActivatedColumn( grids.GridColumn ):
+
def get_value( self, trans, grid, user ):
if user.active:
return 'Y'
@@ -121,32 +149,53 @@
num_rows_per_page = 50
preserve_state = False
use_paging = True
+
def get_current_item( self, trans, **kwargs ):
return trans.user
+
class RoleListGrid( grids.Grid ):
+
+
class NameColumn( grids.TextColumn ):
+
def get_value( self, trans, grid, role ):
return role.name
+
+
class DescriptionColumn( grids.TextColumn ):
+
def get_value( self, trans, grid, role ):
if role.description:
return role.description
return ''
+
+
class TypeColumn( grids.TextColumn ):
+
def get_value( self, trans, grid, role ):
return role.type
+
+
class StatusColumn( grids.GridColumn ):
+
def get_value( self, trans, grid, role ):
if role.deleted:
return "deleted"
return ""
+
+
class GroupsColumn( grids.GridColumn ):
+
def get_value( self, trans, grid, role ):
if role.groups:
return len( role.groups )
return 0
+
+
class UsersColumn( grids.GridColumn ):
+
+
def get_value( self, trans, grid, role ):
if role.users:
return len( role.users )
@@ -212,24 +261,38 @@
num_rows_per_page = 50
preserve_state = False
use_paging = True
+
def apply_query_filter( self, trans, query, **kwargs ):
return query.filter( model.Role.type != model.Role.types.PRIVATE )
+
class GroupListGrid( grids.Grid ):
+
+
class NameColumn( grids.TextColumn ):
+
def get_value( self, trans, grid, group ):
return group.name
+
+
class StatusColumn( grids.GridColumn ):
+
def get_value( self, trans, grid, group ):
if group.deleted:
return "deleted"
return ""
+
+
class RolesColumn( grids.GridColumn ):
+
def get_value( self, trans, grid, group ):
if group.roles:
return len( group.roles )
return 0
+
+
class UsersColumn( grids.GridColumn ):
+
def get_value( self, trans, grid, group ):
if group.members:
return len( group.members )
@@ -287,30 +350,48 @@
use_paging = True
class QuotaListGrid( grids.Grid ):
+
+
class NameColumn( grids.TextColumn ):
+
def get_value( self, trans, grid, quota ):
return quota.name
+
+
class DescriptionColumn( grids.TextColumn ):
+
def get_value( self, trans, grid, quota ):
if quota.description:
return quota.description
return ''
+
+
class AmountColumn( grids.TextColumn ):
+
def get_value( self, trans, grid, quota ):
return quota.operation + quota.display_amount
+
+
class StatusColumn( grids.GridColumn ):
+
def get_value( self, trans, grid, quota ):
if quota.deleted:
return "deleted"
elif quota.default:
return "<strong>default for %s users</strong>" % quota.default[0].type
return ""
+
+
class UsersColumn( grids.GridColumn ):
+
def get_value( self, trans, grid, quota ):
if quota.users:
return len( quota.users )
return 0
+
+
class GroupsColumn( grids.GridColumn ):
+
def get_value( self, trans, grid, quota ):
if quota.groups:
return len( quota.groups )
@@ -397,15 +478,22 @@
preserve_state = False
use_paging = True
+
class ToolVersionListGrid( grids.Grid ):
+
+
class ToolIdColumn( grids.TextColumn ):
+
def get_value( self, trans, grid, tool_version ):
if tool_version.tool_id in trans.app.toolbox.tools_by_id:
link = url_for( controller='tool_runner', tool_id=tool_version.tool_id )
link_str = '<a href="%s">' % link
return '<div class="count-box state-color-ok">%s%s</a></div>' % ( link_str, tool_version.tool_id )
return tool_version.tool_id
+
+
class ToolVersionsColumn( grids.TextColumn ):
+
def get_value( self, trans, grid, tool_version ):
tool_ids_str = ''
for tool_id in tool_version.get_version_ids( trans.app ):
@@ -443,6 +531,7 @@
def build_initial_query( self, trans, **kwd ):
return trans.install_model.context.query( self.model_class )
+
class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuotaMixin, QuotaParamParser ):
user_list_grid = UserListGrid()
@@ -479,6 +568,7 @@
return self.edit_quota( trans, **kwargs )
# Render the list view
return self.quota_list_grid( trans, **kwargs )
+
@web.expose
@web.require_admin
def create_quota( self, trans, **kwd ):
@@ -525,6 +615,7 @@
out_groups=params.out_groups,
message=params.message,
status=params.status )
+
@web.expose
@web.require_admin
def rename_quota( self, trans, **kwd ):
@@ -538,6 +629,7 @@
webapp=params.webapp,
message=params.message,
status=params.status )
+
@web.expose
@web.require_admin
def manage_users_and_groups_for_quota( self, trans, **kwd ):
@@ -572,6 +664,7 @@
webapp=params.webapp,
message=params.message,
status=params.status )
+
@web.expose
@web.require_admin
def edit_quota( self, trans, **kwd ):
@@ -585,6 +678,7 @@
webapp=params.webapp,
message=params.message,
status=params.status )
+
@web.expose
@web.require_admin
def set_quota_default( self, trans, **kwd ):
@@ -603,6 +697,7 @@
webapp=params.webapp,
message=params.message,
status=params.status )
+
@web.expose
@web.require_admin
def unset_quota_default( self, trans, **kwd ):
@@ -614,6 +709,7 @@
webapp=params.webapp,
message=sanitize_text( params.message ),
status='error' ) )
+
@web.expose
@web.require_admin
def mark_quota_deleted( self, trans, **kwd ):
@@ -625,6 +721,7 @@
webapp=params.webapp,
message=sanitize_text( params.message ),
status='error' ) )
+
@web.expose
@web.require_admin
def undelete_quota( self, trans, **kwd ):
@@ -636,6 +733,7 @@
webapp=params.webapp,
message=sanitize_text( params.message ),
status='error' ) )
+
@web.expose
@web.require_admin
def purge_quota( self, trans, **kwd ):
@@ -647,6 +745,7 @@
webapp=params.webapp,
message=sanitize_text( params.message ),
status='error' ) )
+
def _quota_op( self, trans, do_op, op_method, kwd, listify=False ):
params = self.get_quota_params( kwd )
if listify:
@@ -684,6 +783,7 @@
params.message = e.err_msg
params.status = e.type
return quota, params
+
@web.expose
@web.require_admin
def impersonate( self, trans, email=None, **kwd ):
@@ -705,21 +805,14 @@
if emails is None:
emails = [ u.email for u in trans.sa_session.query( trans.app.model.User ).enable_eagerloads( False ).all() ]
return trans.fill_template( 'admin/impersonate.mako', emails=emails, message=message, status=status )
- def get_tool_shed_url_from_tools_xml_file_path( self, trans, tool_shed ):
- search_str = '://%s' % tool_shed
- for shed_name, shed_url in trans.app.tool_shed_registry.tool_sheds.items():
- if shed_url.find( search_str ) >= 0:
- if shed_url.endswith( '/' ):
- shed_url = shed_url.rstrip( '/' )
- return shed_url
- return None
+
def check_for_tool_dependencies( self, trans, migration_stage ):
# Get the 000x_tools.xml file associated with migration_stage.
tools_xml_file_path = os.path.abspath( os.path.join( trans.app.config.root, 'scripts', 'migrate_tools', '%04d_tools.xml' % migration_stage ) )
tree = galaxy.util.parse_xml( tools_xml_file_path )
root = tree.getroot()
tool_shed = root.get( 'name' )
- tool_shed_url = self.get_tool_shed_url_from_tools_xml_file_path( trans, tool_shed )
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed )
repo_name_dependency_tups = []
if tool_shed_url:
for elem in root:
@@ -741,6 +834,7 @@
tool_dependencies.append( ( tool_dependency_name, tool_dependency_version, tool_dependency_type, tool_dependency_readme ) )
repo_name_dependency_tups.append( ( repository_name, tool_dependencies ) )
return repo_name_dependency_tups
+
@web.expose
@web.require_admin
def review_tool_migration_stages( self, trans, **kwd ):
@@ -772,12 +866,14 @@
migration_stages_dict=migration_stages_dict,
message=message,
status=status )
+
@web.expose
@web.require_admin
def view_datatypes_registry( self, trans, **kwd ):
message = galaxy.util.restore_text( kwd.get( 'message', '' ) )
status = galaxy.util.restore_text( kwd.get( 'status', 'done' ) )
return trans.fill_template( 'admin/view_datatypes_registry.mako', message=message, status=status )
+
@web.expose
@web.require_admin
def view_tool_data_tables( self, trans, **kwd ):
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -180,9 +180,10 @@
@web.expose
@web.require_admin
def browse_tool_shed( self, trans, **kwd ):
- tool_shed_url = kwd[ 'tool_shed_url' ]
+ tool_shed_url = kwd.get( 'tool_shed_url', '' )
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url )
galaxy_url = web.url_for( '/', qualified=True )
- url = suc.url_join( tool_shed_url, 'repository/browse_valid_categories?galaxy_url=%s' % ( galaxy_url ) )
+ url = common_util.url_join( tool_shed_url, 'repository/browse_valid_categories?galaxy_url=%s' % ( galaxy_url ) )
return trans.response.send_redirect( url )
@web.expose
@@ -200,13 +201,13 @@
"""Send a request to the relevant tool shed to see if there are any updates."""
repository_id = kwd.get( 'id', None )
repository = suc.get_installed_tool_shed_repository( trans, repository_id )
- tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) )
params = '?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \
( web.url_for( '/', qualified=True ),
str( repository.name ),
str( repository.owner ),
str( repository.changeset_revision ) )
- url = suc.url_join( tool_shed_url,
+ url = common_util.url_join( tool_shed_url,
'repository/check_for_updates%s' % params )
return trans.response.send_redirect( url )
@@ -340,17 +341,19 @@
@web.expose
@web.require_admin
def find_tools_in_tool_shed( self, trans, **kwd ):
- tool_shed_url = kwd[ 'tool_shed_url' ]
+ tool_shed_url = kwd.get( 'tool_shed_url', '' )
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url )
galaxy_url = web.url_for( '/', qualified=True )
- url = suc.url_join( tool_shed_url, 'repository/find_tools?galaxy_url=%s' % galaxy_url )
+ url = common_util.url_join( tool_shed_url, 'repository/find_tools?galaxy_url=%s' % galaxy_url )
return trans.response.send_redirect( url )
@web.expose
@web.require_admin
def find_workflows_in_tool_shed( self, trans, **kwd ):
- tool_shed_url = kwd[ 'tool_shed_url' ]
+ tool_shed_url = kwd.get( 'tool_shed_url', '' )
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url )
galaxy_url = web.url_for( '/', qualified=True )
- url = suc.url_join( tool_shed_url, 'repository/find_workflows?galaxy_url=%s' % galaxy_url )
+ url = common_util.url_join( tool_shed_url, 'repository/find_workflows?galaxy_url=%s' % galaxy_url )
return trans.response.send_redirect( url )
@web.expose
@@ -377,10 +380,10 @@
it was installed.
"""
repository = suc.get_installed_tool_shed_repository( trans, repository_id )
- tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
- url = suc.url_join( tool_shed_url,
- 'repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s' % \
- ( repository_name, repository_owner, changeset_revision ) )
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) )
+ params = '?name=%s&owner=%s&changeset_revision=%s' % ( repository_name, repository_owner, changeset_revision )
+ url = common_util.url_join( tool_shed_url,
+ 'repository/get_tool_dependencies%s' % params )
raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
if len( raw_text ) > 2:
encoded_text = json.from_json_string( raw_text )
@@ -397,10 +400,12 @@
an updated revision of an uninstalled tool shed repository.
"""
repository = suc.get_installed_tool_shed_repository( trans, repository_id )
- tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
- url = suc.url_join( tool_shed_url,
- 'repository/get_updated_repository_information?name=%s&owner=%s&changeset_revision=%s' % \
- ( repository_name, repository_owner, changeset_revision ) )
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) )
+ params = '?name=%s&owner=%s&changeset_revision=%s' % ( str( repository_name ),
+ str( repository_owner ),
+ changeset_revision )
+ url = common_util.url_join( tool_shed_url,
+ 'repository/get_updated_repository_information%s' % params )
raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
repo_information_dict = json.from_json_string( raw_text )
return repo_information_dict
@@ -479,12 +484,12 @@
if repository_id is not None:
repository = suc.get_installed_tool_shed_repository( trans, repository_id )
if repository is not None:
- tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) )
name = str( repository.name )
owner = str( repository.owner )
- url = suc.url_join( tool_shed_url,
- 'repository/get_latest_downloadable_changeset_revision?galaxy_url=%s&name=%s&owner=%s' % \
- ( web.url_for( '/', qualified=True ), name, owner ) )
+ params = '?galaxy_url=%s&name=%s&owner=%s' % ( web.url_for( '/', qualified=True ), name, owner )
+ url = common_util.url_join( tool_shed_url,
+ 'repository/get_latest_downloadable_changeset_revision%s' % params )
raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
latest_downloadable_revision = json.from_json_string( raw_text )
if latest_downloadable_revision == suc.INITIAL_CHANGELOG_HASH:
@@ -496,7 +501,7 @@
# appropriate repository revision if one exists. We need to create a temporary repo_info_tuple
# with the following entries to handle this.
# ( description, clone_url, changeset_revision, ctx_rev, owner, repository_dependencies, tool_dependencies )
- tmp_clone_url = suc.url_join( tool_shed_url, 'repos', owner, name )
+ tmp_clone_url = common_util.url_join( tool_shed_url, 'repos', owner, name )
tmp_repo_info_tuple = ( None, tmp_clone_url, latest_downloadable_revision, None, owner, None, None )
installed_repository, installed_changeset_revision = \
suc.repository_was_previously_installed( trans, tool_shed_url, name, tmp_repo_info_tuple )
@@ -509,10 +514,12 @@
status = 'error'
else:
# Install the latest downloadable revision of the repository.
- params = '?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \
- ( name, owner, str( latest_downloadable_revision ), web.url_for( '/', qualified=True ) )
- url = suc.url_join( tool_shed_url,
- 'repository/install_repositories_by_revision%s' % params )
+ params = '?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % ( name,
+ owner,
+ str( latest_downloadable_revision ),
+ web.url_for( '/', qualified=True ) )
+ url = common_util.url_join( tool_shed_url,
+ 'repository/install_repositories_by_revision%s' % params )
return trans.response.send_redirect( url )
else:
message = 'Cannot locate installed tool shed repository with encoded id <b>%s</b>.' % str( repository_id )
@@ -713,7 +720,7 @@
repository = suc.get_installed_tool_shed_repository( trans, repository_id )
if repository is None:
return trans.show_error_message( 'Invalid repository specified.' )
- tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) )
name = str( repository.name )
owner = str( repository.owner )
installed_changeset_revision = str( repository.installed_changeset_revision )
@@ -724,9 +731,12 @@
tool_shed_repository_ids=tool_shed_repository_ids ) )
if repository.can_install and operation == 'install':
# Send a request to the tool shed to install the repository.
- url = suc.url_join( tool_shed_url,
- 'repository/install_repositories_by_revision?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \
- ( name, owner, installed_changeset_revision, ( web.url_for( '/', qualified=True ) ) ) )
+ params = '?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % ( name,
+ owner,
+ installed_changeset_revision,
+ web.url_for( '/', qualified=True ) )
+ url = common_util.url_join( tool_shed_url,
+ 'repository/install_repositories_by_revision%s' % params )
return trans.response.send_redirect( url )
description = kwd.get( 'description', repository.description )
shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository )
@@ -938,7 +948,8 @@
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
shed_tool_conf = kwd.get( 'shed_tool_conf', None )
- tool_shed_url = kwd.get( 'tool_shed_url', None )
+ tool_shed_url = kwd.get( 'tool_shed_url', '' )
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url )
# Handle repository dependencies, which do not include those that are required only for compiling a dependent
# repository's tool dependencies.
has_repository_dependencies = util.string_as_bool( kwd.get( 'has_repository_dependencies', False ) )
@@ -978,9 +989,9 @@
repository = suc.get_tool_shed_repository_by_id( trans, updating_repository_id )
# For backward compatibility to the 12/20/12 Galaxy release.
try:
- url = suc.url_join( tool_shed_url,
- 'repository/get_repository_id?name=%s&owner=%s' % \
- ( str( repository.name ), str( repository.owner ) ) )
+ params = '?name=%s&owner=%s' % ( str( repository.name ), str( repository.owner ) )
+ url = common_util.url_join( tool_shed_url,
+ 'repository/get_repository_id%s' % params )
repository_ids = common_util.tool_shed_get( trans.app, tool_shed_url, url )
except Exception, e:
# The Tool Shed cannot handle the get_repository_id request, so the code must be older than the
@@ -999,9 +1010,9 @@
else:
changeset_revisions = kwd.get( 'changeset_revisions', None )
# Get the information necessary to install each repository.
- url = suc.url_join( tool_shed_url,
- 'repository/get_repository_information?repository_ids=%s&changeset_revisions=%s' % \
- ( str( repository_ids ), str( changeset_revisions ) ) )
+ params = '?repository_ids=%s&changeset_revisions=%s' % ( str( repository_ids ), str( changeset_revisions ) )
+ url = common_util.url_join( tool_shed_url,
+ 'repository/get_repository_information%s' % params )
raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
repo_information_dict = json.from_json_string( raw_text )
for encoded_repo_info_dict in repo_information_dict.get( 'repo_info_dicts', [] ):
@@ -1245,12 +1256,12 @@
install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) )
shed_tool_conf, tool_path, relative_install_dir = \
suc.get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository )
- repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository )
+ repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository )
clone_dir = os.path.join( tool_path,
suc.generate_tool_shed_repository_install_dir( repository_clone_url,
tool_shed_repository.installed_changeset_revision ) )
relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name )
- tool_shed_url = suc.get_url_from_tool_shed( trans.app, tool_shed_repository.tool_shed )
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_repository.tool_shed )
tool_section = None
tool_panel_section_id = kwd.get( 'tool_panel_section_id', '' )
new_tool_panel_section_label = kwd.get( 'new_tool_panel_section_label', '' )
@@ -1328,8 +1339,8 @@
install_repository_dependencies=install_repository_dependencies,
no_changes_checked=no_changes_checked,
tool_panel_section_id=tool_panel_section_id )
- # Default the selected tool panel location for loading tools included in each newly installed required tool shed repository to the location
- # selected for the repository selected for reinstallation.
+ # Default the selected tool panel location for loading tools included in each newly installed required
+ # tool shed repository to the location selected for the repository selected for re-installation.
for index, tps_key in enumerate( tool_panel_section_keys ):
if tps_key is None:
tool_panel_section_keys[ index ] = tool_panel_section_key
@@ -1463,9 +1474,9 @@
latest_changeset_revision = kwd.get( 'latest_changeset_revision', None )
latest_ctx_rev = kwd.get( 'latest_ctx_rev', None )
tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id )
- repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository )
+ repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository )
metadata = tool_shed_repository.metadata
- tool_shed_url = suc.get_url_from_tool_shed( trans.app, tool_shed_repository.tool_shed )
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( tool_shed_repository.tool_shed ) )
tool_path, relative_install_dir = tool_shed_repository.get_tool_relative_path( trans.app )
if latest_changeset_revision and latest_ctx_rev:
# There are updates available in the tool shed for the repository, so use the receieved dependency information which was retrieved from
@@ -1510,9 +1521,11 @@
if 'workflows' in metadata:
includes_workflows = True
# Since we're reinstalling, we need to send a request to the tool shed to get the README files.
- url = suc.url_join( tool_shed_url,
- 'repository/get_readme_files?name=%s&owner=%s&changeset_revision=%s' % \
- ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) )
+ params = '?name=%s&owner=%s&changeset_revision=%s' % ( str( tool_shed_repository.name ),
+ str( tool_shed_repository.owner ),
+ str( tool_shed_repository.installed_changeset_revision ) )
+ url = common_util.url_join( tool_shed_url,
+ 'repository/get_readme_files%s' % params )
raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
readme_files_dict = json.from_json_string( raw_text )
tool_dependencies = metadata.get( 'tool_dependencies', None )
@@ -1647,8 +1660,7 @@
def reset_repository_metadata( self, trans, id ):
"""Reset all metadata on a single installed tool shed repository."""
repository = suc.get_installed_tool_shed_repository( trans, id )
- tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
- repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, repository )
+ repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, repository )
tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app )
if relative_install_dir:
original_metadata_dict = repository.metadata
@@ -1713,10 +1725,12 @@
repository and update the metadata for the repository's revision in the Galaxy database.
"""
repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] )
- tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
- url = suc.url_join( tool_shed_url,
- 'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \
- ( repository.name, repository.owner, repository.changeset_revision ) )
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) )
+ params = '?name=%s&owner=%s&changeset_revision=%s' % ( str( repository.name ),
+ str( repository.owner ),
+ str( repository.changeset_revision ) )
+ url = common_util.url_join( tool_shed_url,
+ 'repository/get_tool_versions%s' % params )
text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
if text:
tool_version_dicts = json.from_json_string( text )
@@ -1814,7 +1828,9 @@
"""Update a cloned repository to the latest revision possible."""
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
- tool_shed_url = kwd.get( 'tool_shed_url', None )
+ tool_shed_url = kwd.get( 'tool_shed_url', '' )
+ # Handle protocol changes over time.
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url )
name = kwd.get( 'name', None )
owner = kwd.get( 'owner', None )
changeset_revision = kwd.get( 'changeset_revision', None )
@@ -1839,7 +1855,6 @@
repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name )
repository_util.pull_repository( repo, repository_clone_url, latest_ctx_rev )
suc.update_repository( repo, latest_ctx_rev )
- tool_shed = suc.clean_tool_shed_url( tool_shed_url )
# Remove old Data Manager entries
if repository.includes_data_managers:
data_manager_util.remove_from_data_manager( trans.app, repository )
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 lib/galaxy/webapps/tool_shed/controllers/repository.py
--- a/lib/galaxy/webapps/tool_shed/controllers/repository.py
+++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py
@@ -793,7 +793,7 @@
def browse_valid_categories( self, trans, **kwd ):
"""Filter repositories per category by those that are valid for installing into Galaxy."""
# The request came from Galaxy, so restrict category links to display only valid repository changeset revisions.
- galaxy_url = suc.handle_galaxy_url( trans, **kwd )
+ galaxy_url = common_util.handle_galaxy_url( trans, **kwd )
if galaxy_url:
kwd[ 'galaxy_url' ] = galaxy_url
if 'f-free-text-search' in kwd:
@@ -831,7 +831,7 @@
@web.expose
def browse_valid_repositories( self, trans, **kwd ):
"""Filter repositories to those that are installable into Galaxy."""
- galaxy_url = suc.handle_galaxy_url( trans, **kwd )
+ galaxy_url = common_util.handle_galaxy_url( trans, **kwd )
if galaxy_url:
kwd[ 'galaxy_url' ] = galaxy_url
repository_id = kwd.get( 'id', None )
@@ -885,7 +885,7 @@
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
# If the request originated with the UpdateManager, it will not include a galaxy_url.
- galaxy_url = suc.handle_galaxy_url( trans, **kwd )
+ galaxy_url = common_util.handle_galaxy_url( trans, **kwd )
name = kwd.get( 'name', None )
owner = kwd.get( 'owner', None )
changeset_revision = kwd.get( 'changeset_revision', None )
@@ -902,9 +902,12 @@
elif galaxy_url:
# Start building up the url to redirect back to the calling Galaxy instance.
params = '?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \
- ( web.url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision )
- url = suc.url_join( galaxy_url,
- 'admin_toolshed/update_to_changeset_revision%s' % params )
+ ( web.url_for( '/', qualified=True ),
+ str( repository.name ),
+ str( repository.user.username ),
+ changeset_revision )
+ url = common_util.url_join( galaxy_url,
+ 'admin_toolshed/update_to_changeset_revision%s' % params )
else:
message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. ' % galaxy_url
message += 'You may need to enable third-party cookies in your browser. '
@@ -1145,7 +1148,12 @@
repository.times_downloaded += 1
trans.sa_session.add( repository )
trans.sa_session.flush()
- download_url = suc.url_join( '/', 'repos', repository.user.username, repository.name, 'archive', file_type_str )
+ download_url = common_util.url_join( '/',
+ 'repos',
+ str( repository.user.username ),
+ str( repository.name ),
+ 'archive',
+ file_type_str )
return trans.response.send_redirect( download_url )
@web.expose
@@ -1233,7 +1241,7 @@
def find_tools( self, trans, **kwd ):
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
- galaxy_url = suc.handle_galaxy_url( trans, **kwd )
+ galaxy_url = common_util.handle_galaxy_url( trans, **kwd )
if 'operation' in kwd:
item_id = kwd.get( 'id', '' )
if item_id:
@@ -1321,7 +1329,7 @@
def find_workflows( self, trans, **kwd ):
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
- galaxy_url = suc.handle_galaxy_url( trans, **kwd )
+ galaxy_url = common_util.handle_galaxy_url( trans, **kwd )
if 'operation' in kwd:
item_id = kwd.get( 'id', '' )
if item_id:
@@ -1615,7 +1623,11 @@
# section 5.1, e.g. Sat, 07 Sep 2002 00:00:01 UT
time_tested = repository_metadata.time_last_tested.strftime( '%a, %d %b %Y %H:%M:%S UT' )
# Generate a citable URL for this repository with owner and changeset revision.
- repository_citable_url = suc.url_join( tool_shed_url, 'view', user.username, repository.name, repository_metadata.changeset_revision )
+ repository_citable_url = common_util.url_join( tool_shed_url,
+ 'view',
+ str( user.username ),
+ str( repository.name ),
+ str( repository_metadata.changeset_revision ) )
passed_tests = len( tool_test_results.get( 'passed_tests', [] ) )
failed_tests = len( tool_test_results.get( 'failed_tests', [] ) )
missing_test_components = len( tool_test_results.get( 'missing_test_components', [] ) )
@@ -1866,7 +1878,7 @@
"""
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository_id = trans.security.encode_id( repository.id )
- repository_clone_url = suc.generate_clone_url_for_repository_in_tool_shed( trans, repository )
+ repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository )
repo_dir = repository.repo_path( trans.app )
repo = hg.repository( suc.get_configured_ui(), repo_dir )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
@@ -2051,15 +2063,15 @@
if not repository_ids:
repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository_ids = trans.security.encode_id( repository.id )
- galaxy_url = suc.handle_galaxy_url( trans, **kwd )
+ galaxy_url = common_util.handle_galaxy_url( trans, **kwd )
if galaxy_url:
# Redirect back to local Galaxy to perform install.
params = '?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \
( web.url_for( '/', qualified=True ),
','.join( util.listify( repository_ids ) ),
','.join( util.listify( changeset_revisions ) ) )
- url = suc.url_join( galaxy_url,
- 'admin_toolshed/prepare_for_install%s' % params )
+ url = common_util.url_join( galaxy_url,
+ 'admin_toolshed/prepare_for_install%s' % params )
return trans.response.send_redirect( url )
else:
message = 'Repository installation is not possible due to an invalid Galaxy URL: <b>%s</b>. ' % galaxy_url
@@ -2560,8 +2572,8 @@
if invalid:
message += 'The repository dependency definitions for this repository are invalid and will be ignored. '
message += 'The complete dependency hierarchy could not be determined. The cause of repository dependency '
- message += 'definition errors like this can usually be seen when viewing the repository directly from the'
- message += 'Tool Shed. The exact cause cannot be determined when visiting the Tool Shed from Galaxy to'
+ message += 'definition errors like this can usually be seen when viewing the repository directly from the '
+ message += 'Tool Shed. The exact cause cannot be determined when visiting the Tool Shed from Galaxy to '
message += 'install the repository.'
status = 'error'
else:
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 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
@@ -58,8 +58,8 @@
else:
root = tree.getroot()
defined_tool_shed_url = root.get( 'name' )
- self.tool_shed_url = suc.get_url_from_tool_shed( self.app, defined_tool_shed_url )
- self.tool_shed = suc.clean_tool_shed_url( defined_tool_shed_url )
+ self.tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, defined_tool_shed_url )
+ self.tool_shed = common_util.remove_protocol_and_port_from_tool_shed_url( self.tool_shed_url )
self.repository_owner = common_util.REPOSITORY_OWNER
index, self.shed_config_dict = suc.get_shed_tool_conf_dict( app, self.migrated_tools_config )
# Since tool migration scripts can be executed any number of times, we need to make sure the appropriate tools are defined in
@@ -101,7 +101,11 @@
name = repository_elem.get( 'name' )
changeset_revision = repository_elem.get( 'changeset_revision' )
tool_shed_accessible, repository_dependencies_dict = \
- common_util.get_repository_dependencies( app, self.tool_shed_url, name, self.repository_owner, changeset_revision )
+ common_util.get_repository_dependencies( app,
+ self.tool_shed_url,
+ name,
+ self.repository_owner,
+ changeset_revision )
# Make sure all repository dependency records exist (as tool_shed_repository table rows) in the Galaxy database.
created_tool_shed_repositories = self.create_or_update_tool_shed_repository_records( name,
changeset_revision,
@@ -155,12 +159,15 @@
def create_or_update_tool_shed_repository_records( self, name, changeset_revision, repository_dependencies_dict ):
"""
- Make sure the repository defined by name and changeset_revision and all of it's repository dependencies have associated tool_shed_repository
- table rows in the Galaxy database.
+ Make sure the repository defined by name and changeset_revision and all of it's repository dependencies have
+ associated tool_shed_repository table rows in the Galaxy database.
"""
created_tool_shed_repositories = []
description = repository_dependencies_dict.get( 'description', None )
- tool_shed_repository = self.create_or_update_tool_shed_repository_record( name, self.repository_owner, changeset_revision, description=description )
+ tool_shed_repository = self.create_or_update_tool_shed_repository_record( name,
+ self.repository_owner,
+ changeset_revision,
+ description=description )
if tool_shed_repository:
created_tool_shed_repositories.append( tool_shed_repository )
for rd_key, rd_tups in repository_dependencies_dict.items():
@@ -170,7 +177,10 @@
parsed_rd_tup = common_util.parse_repository_dependency_tuple( rd_tup )
rd_tool_shed, rd_name, rd_owner, rd_changeset_revision = parsed_rd_tup[ 0:4 ]
# TODO: Make sure the repository description is applied to the new repository record during installation.
- tool_shed_repository = self.create_or_update_tool_shed_repository_record( rd_name, rd_owner, rd_changeset_revision, description=None )
+ tool_shed_repository = self.create_or_update_tool_shed_repository_record( rd_name,
+ rd_owner,
+ rd_changeset_revision,
+ description=None )
if tool_shed_repository:
created_tool_shed_repositories.append( tool_shed_repository )
return created_tool_shed_repositories
@@ -451,7 +461,7 @@
converter_path, display_path = datatype_util.alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, repo_install_dir, override=False ) #repo_install_dir was relative_install_dir
if converter_path or display_path:
# Create a dictionary of tool shed repository related information.
- repository_dict = datatype_util.create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed,
+ repository_dict = datatype_util.create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed_url,
name=tool_shed_repository.name,
owner=self.repository_owner,
installed_changeset_revision=tool_shed_repository.installed_changeset_revision,
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 lib/tool_shed/galaxy_install/installed_repository_manager.py
--- a/lib/tool_shed/galaxy_install/installed_repository_manager.py
+++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py
@@ -3,7 +3,7 @@
"""
import logging
import os
-import tool_shed.util.shed_util_common as suc
+from tool_shed.util import common_util
from tool_shed.util import datatype_util
from tool_shed.util import repository_dependency_util
from tool_shed.util import tool_dependency_util
@@ -175,7 +175,7 @@
root = tree.getroot()
tool_path = root.get( 'tool_path', None )
if tool_path:
- ts = suc.clean_tool_shed_url( tool_shed_repository.tool_shed )
+ ts = common_util.remove_port_from_tool_shed_url( str( tool_shed_repository.tool_shed ) )
relative_path = os.path.join( tool_path,
ts,
'repos',
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 lib/tool_shed/galaxy_install/repository_util.py
--- a/lib/tool_shed/galaxy_install/repository_util.py
+++ b/lib/tool_shed/galaxy_install/repository_util.py
@@ -64,13 +64,13 @@
if repository_metadata:
metadata = repository_metadata.metadata
if metadata:
- toolshed_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' )
+ tool_shed_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' )
# Get a dictionary of all repositories upon which the contents of the received repository depends.
repository_dependencies = \
repository_dependency_util.get_repository_dependencies_for_changeset_revision( trans=trans,
repository=repository,
repository_metadata=repository_metadata,
- toolshed_base_url=toolshed_url,
+ toolshed_base_url=tool_shed_url,
key_rd_dicts_to_be_processed=None,
all_repository_dependencies=None,
handled_key_rd_dicts=None,
@@ -187,7 +187,7 @@
repository = suc.get_repository_in_tool_shed( trans, repository_id )
repo_dir = repository.repo_path( trans.app )
repo = hg.repository( suc.get_configured_ui(), repo_dir )
- repository_clone_url = suc.generate_clone_url_for_repository_in_tool_shed( trans, repository )
+ repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans,
repository_id,
changeset_revision )
@@ -241,20 +241,23 @@
def get_repo_info_dict_for_repair( trans, repository ):
tool_panel_section_key = None
- repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, repository )
- repository_dependencies = repository_dependency_util.get_repository_dependencies_for_installed_tool_shed_repository( trans, repository )
+ repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, repository )
+ repository_dependencies = \
+ repository_dependency_util.get_repository_dependencies_for_installed_tool_shed_repository( trans, repository )
metadata = repository.metadata
if metadata:
tool_dependencies = metadata.get( 'tool_dependencies', None )
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> : [{ 'id':<section id>, 'name':<section name>, 'version':<section version>, 'tool_config':<tool config file name> }]}
+ # {<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":
- # [{"id": "filter_and_sort", "name": "Filter and Sort", "tool_config": "filtering.xml", "version": ""}]}
- # Currently all tools contained within an installed tool shed repository must be loaded into the same section in the tool panel, so we can
- # get the section id of the first guid in the tool_panel_section_dict. In the future, we'll have to handle different sections per guid.
+ # [{"id": "filter_and_sort", "name": "Filter and Sort", "tool_config": "filtering.xml", "version": ""}]}
+ # Currently all tools contained within an installed tool shed repository must be loaded into the same
+ # section in the tool panel, so we can get the section id of the first guid in the tool_panel_section_dict.
+ # In the future, we'll have to handle different sections per guid.
guid = tool_panel_section_dict.keys()[ 0 ]
section_dicts = tool_panel_section_dict[ guid ]
section_dict = section_dicts[ 0 ]
@@ -315,9 +318,11 @@
def get_update_to_changeset_revision_and_ctx_rev( trans, repository ):
"""Return the changeset revision hash to which the repository can be updated."""
changeset_revision_dict = {}
- tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
- url = suc.url_join( tool_shed_url, 'repository/get_changeset_revision_and_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % \
- ( repository.name, repository.owner, repository.installed_changeset_revision ) )
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) )
+ params = '?name=%s&owner=%s&changeset_revision=%s' % ( str( repository.name ),
+ str( repository.owner ),
+ str( repository.installed_changeset_revision ) )
+ url = common_util.url_join( tool_shed_url, 'repository/get_changeset_revision_and_ctx_rev%s' % params )
try:
encoded_update_dict = common_util.tool_shed_get( trans.app, tool_shed_url, url )
if encoded_update_dict:
@@ -588,10 +593,12 @@
suc.update_tool_shed_repository_status( trans.app,
tool_shed_repository,
trans.install_model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS )
- tool_shed_url = suc.get_url_from_tool_shed( trans.app, tool_shed_repository.tool_shed )
- url = suc.url_join( tool_shed_url,
- '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' %
- ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) )
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( tool_shed_repository.tool_shed ) )
+ params = '?name=%s&owner=%s&changeset_revision=%s' % ( str( tool_shed_repository.name ),
+ str( tool_shed_repository.owner ),
+ str( tool_shed_repository.changeset_revision ) )
+ url = common_util.url_join( tool_shed_url,
+ '/repository/get_tool_versions%s' % params )
text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
if text:
tool_version_dicts = json.from_json_string( text )
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py
@@ -22,8 +22,10 @@
def create_temporary_tool_dependencies_config( app, tool_shed_url, name, owner, changeset_revision ):
"""Make a call to the tool shed to get the required repository's tool_dependencies.xml file."""
- url = url_join( tool_shed_url,
- 'repository/get_tool_dependencies_config_contents?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision ) )
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
+ params = '?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision )
+ url = common_util.url_join( tool_shed_url,
+ 'repository/get_tool_dependencies_config_contents%s' % params )
text = common_util.tool_shed_get( app, tool_shed_url, url )
if text:
# Write the contents to a temporary file on disk so it can be reloaded and parsed.
@@ -132,7 +134,8 @@
def get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( app, tool_shed_url, name, owner, changeset_revision ):
sa_session = app.install_model.context
- tool_shed = td_common_util.clean_tool_shed_url( tool_shed_url )
+ # The protocol is not stored, but the port is if it exists.
+ tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url )
tool_shed_repository = sa_session.query( app.install_model.ToolShedRepository ) \
.filter( and_( app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed,
app.install_model.ToolShedRepository.table.c.name == name,
@@ -165,8 +168,10 @@
Get all appropriate newer changeset revisions for the repository defined by
the received tool_shed_url / name / owner combination.
"""
- url = suc.url_join( tool_shed_url,
- 'repository/updated_changeset_revisions?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision ) )
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed_url )
+ params = '?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision )
+ url = common_util.url_join( tool_shed_url,
+ 'repository/updated_changeset_revisions%s' % params )
text = common_util.tool_shed_get( app, tool_shed_url, url )
return text
@@ -180,6 +185,8 @@
"""
handled_tool_dependencies = []
tool_shed = elem.attrib[ 'toolshed' ]
+ # The protocol is not stored, but the port is if it exists.
+ tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed )
required_repository_name = elem.attrib[ 'name' ]
required_repository_owner = elem.attrib[ 'owner' ]
default_required_repository_changeset_revision = elem.attrib[ 'changeset_revision' ]
@@ -950,9 +957,3 @@
except:
file_name = fpath
return file_name
-
-def url_join( *args ):
- parts = []
- for arg in args:
- parts.append( arg.strip( '/' ) )
- return '/'.join( parts )
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py
@@ -9,6 +9,7 @@
import urllib2
import zipfile
from string import Template
+from tool_shed.util import common_util
import tool_shed.util.shed_util_common as suc
from galaxy.datatypes import checkers
@@ -108,19 +109,6 @@
def open_zip( self, filepath, mode ):
return zipfile.ZipFile( filepath, mode )
-def clean_tool_shed_url( base_url ):
- if base_url:
- if base_url.find( '://' ) > -1:
- try:
- protocol, base = base_url.split( '://' )
- except ValueError, e:
- # The received base_url must be an invalid url.
- log.debug( "Returning unchanged invalid base_url from td_common_util.clean_tool_shed_url: %s" % str( base_url ) )
- return base_url
- return base.rstrip( '/' )
- return base_url.rstrip( '/' )
- return base_url
-
def create_env_var_dict( elem, tool_dependency_install_dir=None, tool_shed_repository_install_dir=None ):
env_var_name = elem.get( 'name', 'PATH' )
env_var_action = elem.get( 'action', 'prepend_to' )
@@ -192,7 +180,8 @@
repository_owner = elem.get( 'owner', None )
changeset_revision = elem.get( 'changeset_revision', None )
if toolshed and repository_name and repository_owner and changeset_revision:
- toolshed = clean_tool_shed_url( toolshed )
+ # The protocol is not stored, but the port is if it exists.
+ toolshed = common_util.remove_protocol_from_tool_shed_url( toolshed )
repository = suc.get_repository_for_dependency_relationship( app, toolshed, repository_name, repository_owner, changeset_revision )
if repository:
for sub_elem in elem:
@@ -203,7 +192,9 @@
# Get the tool_dependency so we can get it's installation directory.
tool_dependency = None
for tool_dependency in repository.tool_dependencies:
- if tool_dependency.type == tool_dependency_type and tool_dependency.name == tool_dependency_name and tool_dependency.version == tool_dependency_version:
+ if tool_dependency.type == tool_dependency_type and \
+ tool_dependency.name == tool_dependency_name and \
+ tool_dependency.version == tool_dependency_version:
break
if tool_dependency:
tool_dependency_key = '%s/%s' % ( tool_dependency_name, tool_dependency_version )
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 lib/tool_shed/scripts/api/common.py
--- a/lib/tool_shed/scripts/api/common.py
+++ b/lib/tool_shed/scripts/api/common.py
@@ -9,6 +9,7 @@
sys.path = new_path
import tool_shed.util.shed_util_common as suc
+from tool_shed.util import common_util
from galaxy import eggs
import pkg_resources
@@ -90,7 +91,7 @@
parts.insert( 0, 'api' )
elif 'api' not in parts:
parts.insert( 0, 'api' )
- url = suc.url_join( base, *parts )
+ url = common_util.url_join( base, *parts )
if params is not None:
try:
query_string = urllib.urlencode( params )
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
--- a/lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
+++ b/lib/tool_shed/scripts/deprecate_repositories_without_metadata.py
@@ -20,7 +20,7 @@
from optparse import OptionParser
from galaxy.tools import parameters
-from tool_shed.util.shed_util_common import url_join
+from tool_shed.util.common_util import url_join
import galaxy.webapps.tool_shed.config as tool_shed_config
import galaxy.webapps.tool_shed.model.mapping
import sqlalchemy as sa
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 lib/tool_shed/util/common_install_util.py
--- a/lib/tool_shed/util/common_install_util.py
+++ b/lib/tool_shed/util/common_install_util.py
@@ -24,7 +24,7 @@
def activate_repository( trans, repository ):
"""Activate an installed tool shed repository that has been marked as deactivated."""
- repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, repository )
+ repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, repository )
shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository )
repository.deleted = False
repository.status = trans.install_model.ToolShedRepository.installation_status.INSTALLED
@@ -90,7 +90,7 @@
# Inspect the tool_dependencies dictionary to separate the installed and missing tool dependencies.
# We don't add to installed_td and missing_td here because at this point they are empty.
installed_td, missing_td = \
- get_installed_and_missing_tool_dependencies_for_repository( trans, tool_shed_url, tool_dependencies )
+ get_installed_and_missing_tool_dependencies_for_repository( trans, tool_dependencies )
# In cases where a repository dependency is required only for compiling a dependent repository's
# tool dependency, the value of repository_dependencies will be an empty dictionary here.
if repository_dependencies:
@@ -130,9 +130,7 @@
if required_tool_dependencies:
# Discover and categorize all tool dependencies defined for this repository's repository dependencies.
required_installed_td, required_missing_td = \
- get_installed_and_missing_tool_dependencies_for_repository( trans,
- tool_shed_url,
- required_tool_dependencies )
+ get_installed_and_missing_tool_dependencies_for_repository( trans, required_tool_dependencies )
if required_installed_td:
if not includes_tool_dependencies:
includes_tool_dependencies = True
@@ -189,7 +187,7 @@
installed_rd_tups = []
missing_rd_tups = []
for tsr in repository.repository_dependencies:
- prior_installation_required = suc.set_prior_installation_required( repository, tsr )
+ prior_installation_required = suc.set_prior_installation_required( trans.app, repository, tsr )
only_if_compiling_contained_td = suc.set_only_if_compiling_contained_td( repository, tsr )
rd_tup = [ tsr.tool_shed,
tsr.name,
@@ -261,7 +259,7 @@
# that includes the correct repository owner which we get from the current rd_tup. The current
# tuple looks like: ( description, repository_clone_url, changeset_revision, ctx_rev, repository_owner,
# repository_dependencies, installed_td )
- tmp_clone_url = suc.generate_clone_url_from_repo_info_tup( rd_tup )
+ tmp_clone_url = common_util.generate_clone_url_from_repo_info_tup( trans, rd_tup )
tmp_repo_info_tuple = ( None, tmp_clone_url, changeset_revision, None, owner, None, None )
repository, installed_changeset_revision = suc.repository_was_previously_installed( trans,
tool_shed,
@@ -312,7 +310,7 @@
missing_repository_dependencies[ 'description' ] = description
return installed_repository_dependencies, missing_repository_dependencies
-def get_installed_and_missing_tool_dependencies_for_repository( trans, tool_shed_url, tool_dependencies_dict ):
+def get_installed_and_missing_tool_dependencies_for_repository( trans, tool_dependencies_dict ):
"""
Return the lists of installed tool dependencies and missing tool dependencies for a set of repositories
being installed into Galaxy.
@@ -439,7 +437,10 @@
encoded_required_repository_tups.append( encoding_util.encoding_sep.join( required_repository_tup ) )
encoded_required_repository_str = encoding_util.encoding_sep2.join( encoded_required_repository_tups )
encoded_required_repository_str = encoding_util.tool_shed_encode( encoded_required_repository_str )
- url = suc.url_join( tool_shed_url, '/repository/get_required_repo_info_dict' )
+ if trans.webapp.name == 'galaxy':
+ # Handle secure / insecure Tool Shed URL protocol changes and port changes.
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url )
+ url = common_util.url_join( tool_shed_url, '/repository/get_required_repo_info_dict' )
request = urllib2.Request( url, data=urllib.urlencode( dict( encoded_str=encoded_required_repository_str ) ) )
response = urllib2.urlopen( request ).read()
if response:
@@ -569,7 +570,10 @@
tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = rd_tup
# TODO: we may discover that we need to check more than just installed_changeset_revision and changeset_revision here, in which
# case we'll need to contact the tool shed to get the list of all possible changeset_revisions.
- if repository_dependency.tool_shed == tool_shed and \
+ cleaned_tool_shed = common_util.remove_protocol_and_port_from_tool_shed_url( tool_shed )
+ cleaned_repository_dependency_tool_shed = \
+ common_util.remove_protocol_and_port_from_tool_shed_url( str( repository_dependency.tool_shed ) )
+ if cleaned_repository_dependency_tool_shed == cleaned_tool_shed and \
repository_dependency.name == name and \
repository_dependency.owner == owner and \
( repository_dependency.installed_changeset_revision == changeset_revision or \
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 lib/tool_shed/util/common_util.py
--- a/lib/tool_shed/util/common_util.py
+++ b/lib/tool_shed/util/common_util.py
@@ -3,6 +3,7 @@
import urllib2
from galaxy.util import json
from galaxy.util.odict import odict
+from galaxy.web import url_for
from tool_shed.util import encoding_util
from tool_shed.util import xml_util
@@ -28,7 +29,7 @@
return False, odict()
root = tree.getroot()
tool_shed = root.get( 'name' )
- tool_shed_url = get_tool_shed_url_from_tools_xml_file_path( app, tool_shed )
+ tool_shed_url = get_tool_shed_url_from_tool_shed_registry( app, tool_shed )
# The default behavior is that the tool shed is down.
tool_shed_accessible = False
missing_tool_configs_dict = odict()
@@ -52,7 +53,7 @@
tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
parse_repository_dependency_tuple( rd_tup )
tool_shed_accessible, tool_dependencies = get_tool_dependencies( app,
- tool_shed,
+ tool_shed_url,
name,
owner,
changeset_revision )
@@ -96,6 +97,30 @@
missing_tool_configs_dict[ name ] = migrated_tool_configs_dict[ migrated_tool_config ]
return missing_tool_configs_dict
+def generate_clone_url_for_installed_repository( app, repository ):
+ """Generate the URL for cloning a repository that has been installed into a Galaxy instance."""
+ tool_shed_url = get_tool_shed_url_from_tool_shed_registry( app, str( repository.tool_shed ) )
+ return url_join( tool_shed_url, 'repos', repository.owner, repository.name )
+
+def generate_clone_url_for_repository_in_tool_shed( trans, repository ):
+ """Generate the URL for cloning a repository that is in the tool shed."""
+ base_url = url_for( '/', qualified=True ).rstrip( '/' )
+ if trans and trans.user:
+ protocol, base = base_url.split( '://' )
+ username = '%s@' % trans.user.username
+ return '%s://%s%s/repos/%s/%s' % ( protocol, username, base, repository.user.username, repository.name )
+ else:
+ return '%s/repos/%s/%s' % ( base_url, repository.user.username, repository.name )
+
+def generate_clone_url_from_repo_info_tup( trans, repo_info_tup ):
+ """Generate the URL for cloning a repository given a tuple of toolshed, name, owner, changeset_revision."""
+ # Example tuple: ['http://localhost:9009', 'blast_datatypes', 'test', '461a4216e8ab', False]
+ toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
+ parse_repository_dependency_tuple( repo_info_tup )
+ tool_shed_url = get_tool_shed_url_from_tool_shed_registry( trans.app, toolshed )
+ # Don't include the changeset_revision in clone urls.
+ return url_join( tool_shed_url, 'repos', owner, name )
+
def get_non_shed_tool_panel_configs( app ):
"""Get the non-shed related tool panel configs - there can be more than one, and the default is tool_conf.xml."""
config_filenames = []
@@ -149,15 +174,44 @@
tool_dependencies.append( ( tool_dependency_name, tool_dependency_version, tool_dependency_type ) )
return tool_shed_accessible, tool_dependencies
-def get_tool_shed_url_from_tools_xml_file_path( app, tool_shed ):
- search_str = '://%s' % tool_shed
+def get_tool_shed_url_from_tool_shed_registry( app, tool_shed ):
+ """
+ The value of tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is
+ something like: http://toolshed.g2.bx.psu.edu/
+ """
+ cleaned_tool_shed = remove_protocol_from_tool_shed_url( tool_shed )
for shed_name, shed_url in app.tool_shed_registry.tool_sheds.items():
- if shed_url.find( search_str ) >= 0:
+ if shed_url.find( cleaned_tool_shed ) >= 0:
if shed_url.endswith( '/' ):
shed_url = shed_url.rstrip( '/' )
return shed_url
+ # The tool shed from which the repository was originally installed must no longer be configured in tool_sheds_conf.xml.
return None
+def handle_galaxy_url( trans, **kwd ):
+ galaxy_url = kwd.get( 'galaxy_url', None )
+ if galaxy_url:
+ trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' )
+ else:
+ galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
+ return galaxy_url
+
+def handle_tool_shed_url_protocol( app, shed_url ):
+ """Handle secure and insecure HTTP protocol since they may change over time."""
+ try:
+ if app.name == 'galaxy':
+ url = remove_protocol_from_tool_shed_url( shed_url )
+ tool_shed_url = get_tool_shed_url_from_tool_shed_registry( app, url )
+ else:
+ tool_shed_url = str( url_for( '/', qualified=True ) ).rstrip( '/' )
+ return tool_shed_url
+ except Exception, e:
+ # We receive a lot of calls here where the tool_shed_url is None. The container_util uses
+ # that value when creating a header row. If the tool_shed_url is not None, we have a problem.
+ if shed_url is not None:
+ log.exception( "Handled exception removing protocol from URL %s:\n%s" % ( str( shed_url ), str( e ) ) )
+ return shed_url
+
def parse_repository_dependency_tuple( repository_dependency_tuple, contains_error=False ):
# Default both prior_installation_required and only_if_compiling_contained_td to False in cases where metadata should be reset on the
# repository containing the repository_dependency definition.
@@ -167,10 +221,11 @@
if len( repository_dependency_tuple ) == 5:
tool_shed, name, owner, changeset_revision, error = repository_dependency_tuple
elif len( repository_dependency_tuple ) == 6:
- toolshed, name, owner, changeset_revision, prior_installation_required, error = repository_dependency_tuple
+ tool_shed, name, owner, changeset_revision, prior_installation_required, error = repository_dependency_tuple
elif len( repository_dependency_tuple ) == 7:
- toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error = repository_dependency_tuple
- return toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error
+ tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error = \
+ repository_dependency_tuple
+ return tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error
else:
if len( repository_dependency_tuple ) == 4:
tool_shed, name, owner, changeset_revision = repository_dependency_tuple
@@ -180,6 +235,59 @@
tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = repository_dependency_tuple
return tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td
+def remove_port_from_tool_shed_url( tool_shed_url ):
+ """Return a partial Tool Shed URL, eliminating the port if it exists."""
+ try:
+ if tool_shed_url.find( ':' ) > 0:
+ # Eliminate the port, if any, since it will result in an invalid directory name.
+ new_tool_shed_url = tool_shed_url.split( ':' )[ 0 ]
+ else:
+ new_tool_shed_url = tool_shed_url
+ return new_tool_shed_url.rstrip( '/' )
+ except Exception, e:
+ # We receive a lot of calls here where the tool_shed_url is None. The container_util uses
+ # that value when creating a header row. If the tool_shed_url is not None, we have a problem.
+ if tool_shed_url is not None:
+ log.exception( "Handled exception removing the port from Tool Shed URL %s:\n%s" % ( str( tool_shed_url ), str( e ) ) )
+ return tool_shed_url
+
+def remove_protocol_and_port_from_tool_shed_url( tool_shed_url ):
+ """Return a partial Tool Shed URL, eliminating the protocol and/or port if either exists."""
+ tool_shed = remove_protocol_from_tool_shed_url( tool_shed_url )
+ tool_shed = remove_port_from_tool_shed_url( tool_shed )
+ return tool_shed
+
+def remove_protocol_and_user_from_clone_url( repository_clone_url ):
+ """Return a URL that can be used to clone a repository, eliminating the protocol and user if either exists."""
+ if repository_clone_url.find( '@' ) > 0:
+ # We have an url that includes an authenticated user, something like:
+ # http://test@bx.psu.edu:9009/repos/some_username/column
+ items = repository_clone_url.split( '@' )
+ tmp_url = items[ 1 ]
+ elif repository_clone_url.find( '//' ) > 0:
+ # We have an url that includes only a protocol, something like:
+ # http://bx.psu.edu:9009/repos/some_username/column
+ items = repository_clone_url.split( '//' )
+ tmp_url = items[ 1 ]
+ else:
+ tmp_url = repository_clone_url
+ return tmp_url.rstrip( '/' )
+
+def remove_protocol_from_tool_shed_url( tool_shed_url ):
+ """Return a partial Tool Shed URL, eliminating the protocol if it exists."""
+ try:
+ if tool_shed_url.find( '://' ) > 0:
+ new_tool_shed_url = tool_shed_url.split( '://' )[1]
+ else:
+ new_tool_shed_url = tool_shed_url
+ return new_tool_shed_url.rstrip( '/' )
+ except Exception, e:
+ # We receive a lot of calls here where the tool_shed_url is None. The container_util uses
+ # that value when creating a header row. If the tool_shed_url is not None, we have a problem.
+ if tool_shed_url is not None:
+ log.exception( "Handled exception removing the protocol from Tool Shed URL %s:\n%s" % ( str( tool_shed_url ), str( e ) ) )
+ return tool_shed_url
+
def tool_shed_get( app, tool_shed_url, uri ):
"""Make contact with the tool shed via the uri provided."""
registry = app.tool_shed_registry
@@ -196,3 +304,10 @@
content = response.read()
response.close()
return content
+
+def url_join( *args ):
+ """Return a valid URL produced by appending a base URL and a set of request parameters."""
+ parts = []
+ for arg in args:
+ parts.append( arg.strip( '/' ) )
+ return '/'.join( parts )
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 lib/tool_shed/util/container_util.py
--- a/lib/tool_shed/util/container_util.py
+++ b/lib/tool_shed/util/container_util.py
@@ -65,17 +65,6 @@
if contained_repository_dependency.listify == listified_repository_dependency:
self.repository_dependencies.remove( contained_repository_dependency )
- def to_repository_dependency( self, repository_dependency_id ):
- toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
- common_util.parse_repository_dependency_tuple( self.key.split( STRSEP ) )
- return RepositoryDependency( id=repository_dependency_id,
- toolshed=toolshed,
- repository_name=name,
- repository_owner=owner,
- changeset_revision=changeset_revision,
- prior_installation_required=galaxy.util.asbool( prior_installation_required ),
- only_if_compiling_contained_td=galaxy.util.asbool( only_if_compiling_contained_td ) )
-
class DataManager( object ):
"""Data Manager object"""
@@ -1525,22 +1514,6 @@
return True
return False
-def cast_empty_repository_dependency_folders( folder, repository_dependency_id ):
- """
- Change any empty folders contained within the repository dependencies container into a repository dependency
- since it has no repository dependencies of it's own. This method is not used (and may not be needed), but here
- it is just in case.
- """
- if not folder.folders and not folder.repository_dependencies:
- repository_dependency_id += 1
- repository_dependency = folder.to_repository_dependency( repository_dependency_id )
- if not folder.parent.contains_repository_dependency( repository_dependency ):
- folder.parent.repository_dependencies.append( repository_dependency )
- folder.parent.folders.remove( folder )
- for sub_folder in folder.folders:
- return cast_empty_repository_dependency_folders( sub_folder, repository_dependency_id )
- return folder, repository_dependency_id
-
def generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision,
prior_installation_required, only_if_compiling_contained_td, key ):
"""Return a repository dependency label based on the repository dependency key."""
@@ -1562,17 +1535,21 @@
def generate_repository_dependencies_key_for_repository( toolshed_base_url, repository_name, repository_owner, changeset_revision,
prior_installation_required, only_if_compiling_contained_td ):
"""Assumes tool shed is current tool shed since repository dependencies across tool sheds is not yet supported."""
- return '%s%s%s%s%s%s%s%s%s%s%s' % ( str( toolshed_base_url ).rstrip( '/' ),
- STRSEP,
- str( repository_name ),
- STRSEP,
- str( repository_owner ),
- STRSEP,
- str( changeset_revision ),
- STRSEP,
- str( prior_installation_required ),
- STRSEP,
- str( only_if_compiling_contained_td ) )
+ # The tool_shed portion of the key must be the value that is stored in the tool_shed_repository.tool_shed column
+ # of the Galaxy database for an installed repository. This value does not include the protocol, but does include
+ # the port if there is one.
+ tool_shed = common_util.remove_protocol_from_tool_shed_url( toolshed_base_url )
+ return '%s%s%s%s%s%s%s%s%s%s%s' % ( tool_shed,
+ STRSEP,
+ str( repository_name ),
+ STRSEP,
+ str( repository_owner ),
+ STRSEP,
+ str( changeset_revision ),
+ STRSEP,
+ str( prior_installation_required ),
+ STRSEP,
+ str( only_if_compiling_contained_td ) )
def generate_tool_dependencies_key( name, version, type ):
return '%s%s%s%s%s' % ( str( name ), STRSEP, str( version ), STRSEP, str( type ) )
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 lib/tool_shed/util/export_util.py
--- a/lib/tool_shed/util/export_util.py
+++ b/lib/tool_shed/util/export_util.py
@@ -12,6 +12,7 @@
from galaxy.util.odict import odict
from tool_shed.util import commit_util
from tool_shed.util import common_install_util
+from tool_shed.util import common_util
from tool_shed.util import encoding_util
from tool_shed.util import repository_dependency_util
from tool_shed.util import xml_util
@@ -49,12 +50,6 @@
log.exception( error_message )
return return_code, error_message
-def clean_tool_shed_url( base_url ):
- protocol, base = base_url.split( '://' )
- base = base.replace( ':', '_colon_' )
- base = base.rstrip( '/' )
- return base
-
def export_repository( trans, tool_shed_url, repository_id, repository_name, changeset_revision, file_type,
export_repository_dependencies, api=False ):
repository = suc.get_repository_in_tool_shed( trans, repository_id )
@@ -124,8 +119,9 @@
repositories_archive.close()
if api:
encoded_repositories_archive_name = encoding_util.tool_shed_encode( repositories_archive_filename )
- download_url = suc.url_join( web.url_for( '/', qualified=True ),
- 'repository/export_via_api?encoded_repositories_archive_name=%s' % encoded_repositories_archive_name )
+ params = '?encoded_repositories_archive_name=%s' % encoded_repositories_archive_name
+ download_url = common_util.url_join( web.url_for( '/', qualified=True ),
+ 'repository/export_via_api%s' % params )
return dict( download_url=download_url, error_messages=error_messages )
return repositories_archive, error_messages
@@ -171,7 +167,7 @@
return repository_archive, error_message
def generate_repository_archive_filename( tool_shed_url, name, owner, changeset_revision, file_type, export_repository_dependencies=False, use_tmp_archive_dir=False ):
- tool_shed = clean_tool_shed_url( tool_shed_url )
+ tool_shed = remove_protocol_from_tool_shed_url( tool_shed_url )
file_type_str = suc.get_file_type_str( changeset_revision, file_type )
if export_repository_dependencies:
repositories_archive_filename = '%s_%s_%s_%s_%s' % ( CAPSULE_WITH_DEPENDENCIES_FILENAME, tool_shed, name, owner, file_type_str )
@@ -242,7 +238,7 @@
repo_info_dict = {}
# Cast unicode to string.
repo_info_dict[ str( repository.name ) ] = ( str( repository.description ),
- suc.generate_clone_url_for_repository_in_tool_shed( trans, repository ),
+ common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository ),
str( changeset_revision ),
str( ctx.rev() ),
str( repository.user.username ),
@@ -343,3 +339,9 @@
ordered_repositories.append( repository )
ordered_changeset_revisions.append( changeset_revision )
return ordered_repository_ids, ordered_repositories, ordered_changeset_revisions
+
+def remove_protocol_from_tool_shed_url( base_url ):
+ protocol, base = base_url.split( '://' )
+ base = base.replace( ':', '_colon_' )
+ base = base.rstrip( '/' )
+ return base
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 lib/tool_shed/util/import_util.py
--- a/lib/tool_shed/util/import_util.py
+++ b/lib/tool_shed/util/import_util.py
@@ -343,7 +343,6 @@
return_dict[ 'error_message' ] = error_message
return_dict[ 'status' ] = 'error'
uploaded_file.close()
- tar_archive.close()
return return_dict
return_dict[ 'tar_archive' ] = tar_archive
return_dict[ 'capsule_file_name' ] = uploaded_file_filename
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 lib/tool_shed/util/metadata_util.py
--- a/lib/tool_shed/util/metadata_util.py
+++ b/lib/tool_shed/util/metadata_util.py
@@ -206,11 +206,13 @@
for ancestor_tup in ancestor_repository_dependencies:
a_tool_shed, a_repo_name, a_repo_owner, a_changeset_revision, a_prior_installation_required, a_only_if_compiling_contained_td = \
ancestor_tup
+ cleaned_a_tool_shed = common_util.remove_protocol_from_tool_shed_url( a_tool_shed )
found_in_current = False
for current_tup in current_repository_dependencies:
c_tool_shed, c_repo_name, c_repo_owner, c_changeset_revision, c_prior_installation_required, c_only_if_compiling_contained_td = \
current_tup
- if c_tool_shed == a_tool_shed and \
+ cleaned_c_tool_shed = common_util.remove_protocol_from_tool_shed_url( c_tool_shed )
+ if cleaned_c_tool_shed == cleaned_a_tool_shed and \
c_repo_name == a_repo_name and \
c_repo_owner == a_repo_owner and \
c_changeset_revision == a_changeset_revision and \
@@ -369,15 +371,18 @@
def different_revision_defines_tip_only_repository_dependency( trans, rd_tup, repository_dependencies ):
"""
- Determine if the only difference between rd_tup and a dependency definition in the list of repository_dependencies is the changeset_revision value.
+ Determine if the only difference between rd_tup and a dependency definition in the list of
+ repository_dependencies is the changeset_revision value.
"""
new_metadata_required = False
rd_tool_shed, rd_name, rd_owner, rd_changeset_revision, rd_prior_installation_required, rd_only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple( rd_tup )
+ cleaned_rd_tool_shed = common_util.remove_protocol_from_tool_shed_url( rd_tool_shed )
for repository_dependency in repository_dependencies:
tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
common_util.parse_repository_dependency_tuple( repository_dependency )
- if rd_tool_shed == tool_shed and rd_name == name and rd_owner == owner:
+ cleaned_tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed )
+ if cleaned_rd_tool_shed == cleaned_tool_shed and rd_name == name and rd_owner == owner:
# Determine if the repository represented by the dependency tuple is an instance of the repository type TipOnly.
required_repository = suc.get_repository_by_name_and_owner( trans.app, name, owner )
repository_type_class = trans.app.repository_types_registry.get_class_by_label( required_repository.type )
@@ -393,11 +398,11 @@
# Galaxy Side.
repo_files_directory = repository.repo_files_directory( app )
repo_dir = repo_files_directory
- repository_clone_url = suc.generate_clone_url_for_installed_repository( app, repository )
+ repository_clone_url = common_util.generate_clone_url_for_installed_repository( app, repository )
except AttributeError:
# Tool Shed side.
repo_files_directory = repo_path
- repository_clone_url = suc.generate_clone_url_for_repository_in_tool_shed( None, repository )
+ repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( None, repository )
relative_data_manager_dir = util.relpath( os.path.split( data_manager_config_filename )[0], repo_dir )
rel_data_manager_config_filename = os.path.join( relative_data_manager_dir, os.path.split( data_manager_config_filename )[1] )
data_managers = {}
@@ -572,7 +577,7 @@
return valid_tool_dependencies_dict
def generate_guid_for_object( repository_clone_url, guid_type, obj_id, version ):
- tmp_url = suc.clean_repository_clone_url( repository_clone_url )
+ tmp_url = common_util.remove_protocol_and_user_from_clone_url( repository_clone_url )
return '%s/%s/%s/%s' % ( tmp_url, guid_type, obj_id, version )
def generate_metadata_for_changeset_revision( app, repository, changeset_revision, repository_clone_url,
@@ -1217,16 +1222,16 @@
changeset_revision,
prior_installation_required,
str( only_if_compiling_contained_td ) ]
- cleaned_toolshed = td_common_util.clean_tool_shed_url( toolshed )
user = None
repository = None
+ toolshed = common_util.remove_protocol_from_tool_shed_url( toolshed )
if app.name == 'galaxy':
# We're in Galaxy. We reach here when we're generating the metadata for a tool dependencies package defined
# for a repository or when we're generating metadata for an installed repository. See if we can locate the
# installed repository via the changeset_revision defined in the repository_elem (it may be outdated). If we're
# successful in locating an installed repository with the attributes defined in the repository_elem, we know it
# is valid.
- repository = suc.get_repository_for_dependency_relationship( app, cleaned_toolshed, name, owner, changeset_revision )
+ repository = suc.get_repository_for_dependency_relationship( app, toolshed, name, owner, changeset_revision )
if repository:
return repository_dependency_tup, is_valid, error_message
else:
@@ -1237,7 +1242,7 @@
updated_changeset_revisions = util.listify( text )
for updated_changeset_revision in updated_changeset_revisions:
repository = suc.get_repository_for_dependency_relationship( app,
- cleaned_toolshed,
+ toolshed,
name,
owner,
updated_changeset_revision )
@@ -1648,9 +1653,12 @@
if reinstalling or repository.status not in [ trans.install_model.ToolShedRepository.installation_status.DEACTIVATED,
trans.install_model.ToolShedRepository.installation_status.INSTALLED ]:
# Since we're reinstalling, we need to send a request to the tool shed to get the README files.
- url = suc.url_join( tool_shed_url,
- 'repository/get_readme_files?name=%s&owner=%s&changeset_revision=%s' % \
- ( repository.name, repository.owner, repository.installed_changeset_revision ) )
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url )
+ params = '?name=%s&owner=%s&changeset_revision=%s' % ( str( repository.name ),
+ str( repository.owner ),
+ str( repository.installed_changeset_revision ) )
+ url = common_util.url_join( tool_shed_url,
+ 'repository/get_readme_files%s' % params )
raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
readme_files_dict = json.from_json_string( raw_text )
else:
@@ -1722,8 +1730,7 @@
def reset_all_metadata_on_installed_repository( trans, id ):
"""Reset all metadata on a single tool shed repository installed into a Galaxy instance."""
repository = suc.get_installed_tool_shed_repository( trans, id )
- tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed )
- repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, repository )
+ repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, repository )
tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app )
if relative_install_dir:
original_metadata_dict = repository.metadata
@@ -1791,7 +1798,7 @@
log.debug( "Resetting all metadata on repository: %s" % repository.name )
repo_dir = repository.repo_path( trans.app )
repo = hg.repository( suc.get_configured_ui(), repo_dir )
- repository_clone_url = suc.generate_clone_url_for_repository_in_tool_shed( trans, repository )
+ repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository )
# The list of changeset_revisions refers to repository_metadata records that have been created or updated. When the following loop
# completes, we'll delete all repository_metadata records for this repository that do not have a changeset_revision value in this list.
changeset_revisions = []
@@ -1969,7 +1976,7 @@
message = ''
status = 'done'
encoded_id = trans.security.encode_id( repository.id )
- repository_clone_url = suc.generate_clone_url_for_repository_in_tool_shed( trans, repository )
+ repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( trans, repository )
repo_dir = repository.repo_path( trans.app )
repo = hg.repository( suc.get_configured_ui(), repo_dir )
metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app,
diff -r 47b3011ebe653f7218c70e0b458252783ef6f255 -r 4aee689e69dac57676de7f9ceb0a31f227bc0dd2 lib/tool_shed/util/readme_util.py
--- a/lib/tool_shed/util/readme_util.py
+++ b/lib/tool_shed/util/readme_util.py
@@ -95,9 +95,11 @@
repo_info_tuple = repo_info_dict[ name ]
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td = \
suc.get_repo_info_tuple_contents( repo_info_tuple )
- # Handle README files.
- url = suc.url_join( tool_shed_url,
- 'repository/get_readme_files?name=%s&owner=%s&changeset_revision=%s' % ( name, repository_owner, changeset_revision ) )
+ # Handle changing HTTP protocols over time.
+ tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url )
+ params = '?name=%s&owner=%s&changeset_revision=%s' % ( name, repository_owner, changeset_revision )
+ url = common_util.url_join( tool_shed_url,
+ 'repository/get_readme_files%s' % params )
raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
readme_files_dict = json.from_json_string( raw_text )
return readme_files_dict
This diff is so big that we needed to truncate the remainder.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
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this because you have the service enabled, addressing the recipient of
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1
0
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/44f5b4a2091b/
Changeset: 44f5b4a2091b
Branch: next-stable
User: dan
Date: 2014-04-08 23:05:09
Summary: fix tab spaces in javascript
Affected #: 1 file
diff -r dbfcb1b570763f3e1617ed493d9f1c44e108360e -r 44f5b4a2091bc6e552e0c79a0a761cfc8759a36f templates/webapps/galaxy/dataset/errors.mako
--- a/templates/webapps/galaxy/dataset/errors.mako
+++ b/templates/webapps/galaxy/dataset/errors.mako
@@ -35,10 +35,10 @@
}
var hiddenInput = document.createElement('input');
- hiddenInput.type = 'hidden';
- hiddenInput.name = button.name;
- hiddenInput.value = button.value;
- form.appendChild( hiddenInput );
+ hiddenInput.type = 'hidden';
+ hiddenInput.name = button.name;
+ hiddenInput.value = button.value;
+ form.appendChild( hiddenInput );
return true;
}
return false;
https://bitbucket.org/galaxy/galaxy-central/commits/47b3011ebe65/
Changeset: 47b3011ebe65
User: dan
Date: 2014-04-08 23:05:21
Summary: merge next-stable
Affected #: 1 file
diff -r 2a7447a1d3a23571eb390a0c7cf8a035428ce42b -r 47b3011ebe653f7218c70e0b458252783ef6f255 templates/webapps/galaxy/dataset/errors.mako
--- a/templates/webapps/galaxy/dataset/errors.mako
+++ b/templates/webapps/galaxy/dataset/errors.mako
@@ -35,10 +35,10 @@
}
var hiddenInput = document.createElement('input');
- hiddenInput.type = 'hidden';
- hiddenInput.name = button.name;
- hiddenInput.value = button.value;
- form.appendChild( hiddenInput );
+ hiddenInput.type = 'hidden';
+ hiddenInput.name = button.name;
+ hiddenInput.value = button.value;
+ form.appendChild( hiddenInput );
return true;
}
return false;
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/dbfcb1b57076/
Changeset: dbfcb1b57076
Branch: next-stable
User: dan
Date: 2014-04-08 23:03:19
Summary: When submiting bug reports disable submit buttons while form is being submitted. When submiting bug report to Biostar, have user confirm that they are posting to a public forum.
Affected #: 1 file
diff -r 6eb680d500b14753d7db2efd552613e531541495 -r dbfcb1b570763f3e1617ed493d9f1c44e108360e templates/webapps/galaxy/dataset/errors.mako
--- a/templates/webapps/galaxy/dataset/errors.mako
+++ b/templates/webapps/galaxy/dataset/errors.mako
@@ -14,6 +14,36 @@
padding: 10px;
}
</style>
+
+ <script type="text/javascript">
+ function sendReport( button, form, target, doConfirm )
+ {
+ var doIt = true;
+ if ( doConfirm==true )
+ {
+ doIt = confirm( 'You are about to submit to a public forum, do you want to continue?' );
+ }
+ if ( doIt==true )
+ {
+ form.setAttribute( 'target', target );
+ for( i=0; i<form.elements.length; i++ )
+ {
+ if ( form.elements[i].type == 'submit' )
+ {
+ form.elements[i].disabled = true;
+ }
+
+ }
+ var hiddenInput = document.createElement('input');
+ hiddenInput.type = 'hidden';
+ hiddenInput.name = button.name;
+ hiddenInput.value = button.value;
+ form.appendChild( hiddenInput );
+ return true;
+ }
+ return false;
+ }
+ </script></head><body>
@@ -71,9 +101,9 @@
<textarea name="message" rows="10" cols="40"></textarea></div><div class="form-row">
- <input type="submit" name="submit_error_report" value="Report" onclick="form.setAttribute('target', '_self');"/>
+ <input type="submit" name="submit_error_report" value="Report" onclick="return sendReport( this, this.form, '_self' );"/>
%if trans.app.config.biostar_url:
- <input type="submit" name="submit_error_report" value="Post on Biostar" onclick="form.setAttribute('target', '_blank');"/>
+ <input type="submit" name="submit_error_report" value="Post on Biostar" onclick="return sendReport( this, this.form, '_blank', true );"/>
%endif
</div></form>
https://bitbucket.org/galaxy/galaxy-central/commits/2a7447a1d3a2/
Changeset: 2a7447a1d3a2
User: dan
Date: 2014-04-08 23:03:38
Summary: merge next-stable
Affected #: 1 file
diff -r d79eccd2d0beae713abe1f44b6d2584c8528b03e -r 2a7447a1d3a23571eb390a0c7cf8a035428ce42b templates/webapps/galaxy/dataset/errors.mako
--- a/templates/webapps/galaxy/dataset/errors.mako
+++ b/templates/webapps/galaxy/dataset/errors.mako
@@ -14,6 +14,36 @@
padding: 10px;
}
</style>
+
+ <script type="text/javascript">
+ function sendReport( button, form, target, doConfirm )
+ {
+ var doIt = true;
+ if ( doConfirm==true )
+ {
+ doIt = confirm( 'You are about to submit to a public forum, do you want to continue?' );
+ }
+ if ( doIt==true )
+ {
+ form.setAttribute( 'target', target );
+ for( i=0; i<form.elements.length; i++ )
+ {
+ if ( form.elements[i].type == 'submit' )
+ {
+ form.elements[i].disabled = true;
+ }
+
+ }
+ var hiddenInput = document.createElement('input');
+ hiddenInput.type = 'hidden';
+ hiddenInput.name = button.name;
+ hiddenInput.value = button.value;
+ form.appendChild( hiddenInput );
+ return true;
+ }
+ return false;
+ }
+ </script></head><body>
@@ -71,9 +101,9 @@
<textarea name="message" rows="10" cols="40"></textarea></div><div class="form-row">
- <input type="submit" name="submit_error_report" value="Report" onclick="form.setAttribute('target', '_self');"/>
+ <input type="submit" name="submit_error_report" value="Report" onclick="return sendReport( this, this.form, '_self' );"/>
%if trans.app.config.biostar_url:
- <input type="submit" name="submit_error_report" value="Post on Biostar" onclick="form.setAttribute('target', '_blank');"/>
+ <input type="submit" name="submit_error_report" value="Post on Biostar" onclick="return sendReport( this, this.form, '_blank', true );"/>
%endif
</div></form>
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/6eb680d500b1/
Changeset: 6eb680d500b1
Branch: next-stable
User: carlfeberhard
Date: 2014-04-08 20:14:17
Summary: Remove debugging statements
Affected #: 4 files
diff -r a4d225dbfc8f2d3e7384ab206ecc30c4368b7c94 -r 6eb680d500b14753d7db2efd552613e531541495 static/scripts/galaxy.pages.js
--- a/static/scripts/galaxy.pages.js
+++ b/static/scripts/galaxy.pages.js
@@ -462,7 +462,6 @@
item_info.singular.toLowerCase(), " when it is displayed.]",
"</p>",
"</div>" ].join( '' );
- console.debug( item_embed_html );
// Insert embedded item into document.
//wym.insert(" "); // Needed to prevent insertion from occurring in child element in webkit browsers.
diff -r a4d225dbfc8f2d3e7384ab206ecc30c4368b7c94 -r 6eb680d500b14753d7db2efd552613e531541495 static/scripts/mvc/dataset/hda-base.js
--- a/static/scripts/mvc/dataset/hda-base.js
+++ b/static/scripts/mvc/dataset/hda-base.js
@@ -194,7 +194,6 @@
// add frame manager option onclick event
var self = this;
displayBtnData.onclick = function( ev ){
- console.debug( 'displayBtn onclick', ev );
if( Galaxy.frame && Galaxy.frame.active ){
Galaxy.frame.add({
title : "Data Viewer: " + self.model.get('name'),
diff -r a4d225dbfc8f2d3e7384ab206ecc30c4368b7c94 -r 6eb680d500b14753d7db2efd552613e531541495 static/scripts/packed/galaxy.pages.js
--- a/static/scripts/packed/galaxy.pages.js
+++ b/static/scripts/packed/galaxy.pages.js
@@ -1,1 +1,1 @@
-var Galaxy={ITEM_HISTORY:"item_history",ITEM_DATASET:"item_dataset",ITEM_WORKFLOW:"item_workflow",ITEM_PAGE:"item_page",ITEM_VISUALIZATION:"item_visualization",DIALOG_HISTORY_LINK:"link_history",DIALOG_DATASET_LINK:"link_dataset",DIALOG_WORKFLOW_LINK:"link_workflow",DIALOG_PAGE_LINK:"link_page",DIALOG_VISUALIZATION_LINK:"link_visualization",DIALOG_EMBED_HISTORY:"embed_history",DIALOG_EMBED_DATASET:"embed_dataset",DIALOG_EMBED_WORKFLOW:"embed_workflow",DIALOG_EMBED_PAGE:"embed_page",DIALOG_EMBED_VISUALIZATION:"embed_visualization",DIALOG_HISTORY_ANNOTATE:"history_annotate",};function init_galaxy_elts(a){$(".annotation",a._doc.body).each(function(){$(this).click(function(){var b=a._doc.createRange();b.selectNodeContents(this);var d=window.getSelection();d.removeAllRanges();d.addRange(b);var c=""})})}function get_item_info(d){var f,c,b;switch(d){case (Galaxy.ITEM_HISTORY):f="History";c="Histories";b="history";item_class="History";break;case (Galaxy.ITEM_DATASET):f="Dataset";c="Datasets";b="dataset";item_class="HistoryDatasetAssociation";break;case (Galaxy.ITEM_WORKFLOW):f="Workflow";c="Workflows";b="workflow";item_class="StoredWorkflow";break;case (Galaxy.ITEM_PAGE):f="Page";c="Pages";b="page";item_class="Page";break;case (Galaxy.ITEM_VISUALIZATION):f="Visualization";c="Visualizations";b="visualization";item_class="Visualization";break}var e="list_"+c.toLowerCase()+"_for_selection";var a=list_objects_url.replace("LIST_ACTION",e);return{singular:f,plural:c,controller:b,iclass:item_class,list_ajax_url:a}}function make_item_importable(a,c,b){ajax_url=set_accessible_url.replace("ITEM_CONTROLLER",a);$.ajax({type:"POST",url:ajax_url,data:{id:c,accessible:"True"},error:function(){alert("Making "+b+" accessible failed")}})}WYMeditor.editor.prototype.dialog=function(i,e,g){var a=this;var b=a.uniqueStamp();var f=a.selected();function h(){$("#set_link_id").click(function(){$("#link_attribute_label").text("ID/Name");var k=$(".wym_href");k.addClass("wym_id").removeClass("wym_href");if(f){k.val($(f).attr("id"))}$(this).remove()})}if(i==WYMeditor.DIALOG_LINK){if(f){$(a._options.hrefSelector).val($(f).attr(WYMeditor.HREF));$(a._options.srcSelector).val($(f).attr(WYMeditor.SRC));$(a._options.titleSelector).val($(f).attr(WYMeditor.TITLE));$(a._options.altSelector).val($(f).attr(WYMeditor.ALT))}var c,d;if(f){c=$(f).attr("href");if(c==undefined){c=""}d=$(f).attr("title");if(d==undefined){d=""}}show_modal("Create Link","<div><div><label id='link_attribute_label'>URL <span style='float: right; font-size: 90%'><a href='#' id='set_link_id'>Create in-page anchor</a></span></label><br><input type='text' class='wym_href' value='"+c+"' size='40' /></div><div><label>Title</label><br><input type='text' class='wym_title' value='"+d+"' size='40' /></div><div>",{"Make link":function(){var m=$(a._options.hrefSelector).val()||"",k=$(".wym_id").val()||"",n=$(a._options.titleSelector).val()||"";if(m||k){a._exec(WYMeditor.CREATE_LINK,b);var l=$("a[href="+b+"]",a._doc.body);l.attr(WYMeditor.HREF,m).attr(WYMeditor.TITLE,n).attr("id",k);if(l.text().indexOf("wym-")===0){l.text(n)}}hide_modal()},Cancel:function(){hide_modal()}},{},h)}if(i==WYMeditor.DIALOG_IMAGE){if(a._selected_image){$(a._options.dialogImageSelector+" "+a._options.srcSelector).val($(a._selected_image).attr(WYMeditor.SRC));$(a._options.dialogImageSelector+" "+a._options.titleSelector).val($(a._selected_image).attr(WYMeditor.TITLE));$(a._options.dialogImageSelector+" "+a._options.altSelector).val($(a._selected_image).attr(WYMeditor.ALT))}show_modal("Image","<div class='row'><label>URL</label><br><input type='text' class='wym_src' value='' size='40' /></div><div class='row'><label>Alt text</label><br><input type='text' class='wym_alt' value='' size='40' /></div><div class='row'><label>Title</label><br><input type='text' class='wym_title' value='' size='40' /></div>",{Insert:function(){var k=$(a._options.srcSelector).val();if(k.length>0){a._exec(WYMeditor.INSERT_IMAGE,b);$("img[src$="+b+"]",a._doc.body).attr(WYMeditor.SRC,k).attr(WYMeditor.TITLE,$(a._options.titleSelector).val()).attr(WYMeditor.ALT,$(a._options.altSelector).val())}hide_modal()},Cancel:function(){hide_modal()}});return}if(i==WYMeditor.DIALOG_TABLE){show_modal("Table","<div class='row'><label>Caption</label><br><input type='text' class='wym_caption' value='' size='40' /></div><div class='row'><label>Summary</label><br><input type='text' class='wym_summary' value='' size='40' /></div><div class='row'><label>Number Of Rows<br></label><input type='text' class='wym_rows' value='3' size='3' /></div><div class='row'><label>Number Of Cols<br></label><input type='text' class='wym_cols' value='2' size='3' /></div>",{Insert:function(){var o=$(a._options.rowsSelector).val();var r=$(a._options.colsSelector).val();if(o>0&&r>0){var n=a._doc.createElement(WYMeditor.TABLE);var l=null;var q=null;var k=$(a._options.captionSelector).val();var p=n.createCaption();p.innerHTML=k;for(x=0;x<o;x++){l=n.insertRow(x);for(y=0;y<r;y++){l.insertCell(y)}}$(n).attr("summary",$(a._options.summarySelector).val());var m=$(a.findUp(a.container(),WYMeditor.MAIN_CONTAINERS)).get(0);if(!m||!m.parentNode){$(a._doc.body).append(n)}else{$(m).after(n)}}hide_modal()},Cancel:function(){hide_modal()}})}if(i==Galaxy.DIALOG_HISTORY_LINK||i==Galaxy.DIALOG_DATASET_LINK||i==Galaxy.DIALOG_WORKFLOW_LINK||i==Galaxy.DIALOG_PAGE_LINK||i==Galaxy.DIALOG_VISUALIZATION_LINK){var j;switch(i){case (Galaxy.DIALOG_HISTORY_LINK):j=get_item_info(Galaxy.ITEM_HISTORY);break;case (Galaxy.DIALOG_DATASET_LINK):j=get_item_info(Galaxy.ITEM_DATASET);break;case (Galaxy.DIALOG_WORKFLOW_LINK):j=get_item_info(Galaxy.ITEM_WORKFLOW);break;case (Galaxy.DIALOG_PAGE_LINK):j=get_item_info(Galaxy.ITEM_PAGE);break;case (Galaxy.DIALOG_VISUALIZATION_LINK):j=get_item_info(Galaxy.ITEM_VISUALIZATION);break}$.ajax({url:j.list_ajax_url,data:{},error:function(){alert("Failed to list "+j.plural.toLowerCase()+" for selection")},success:function(k){show_modal("Insert Link to "+j.singular,k+"<div><input id='make-importable' type='checkbox' checked/>Make the selected "+j.plural.toLowerCase()+" accessible so that they can viewed by everyone.</div>",{Insert:function(){var m=false;if($("#make-importable:checked").val()!==null){m=true}var l=new Array();$("input[name=id]:checked").each(function(){var n=$(this).val();if(m){make_item_importable(j.controller,n,j.singular)}url_template=get_name_and_link_url+n;ajax_url=url_template.replace("ITEM_CONTROLLER",j.controller);$.getJSON(ajax_url,function(p){a._exec(WYMeditor.CREATE_LINK,b);var o=$("a[href="+b+"]",a._doc.body).text();if(o==""||o==b){a.insert("<a href='"+p.link+"'>"+j.singular+" '"+p.name+"'</a>")}else{$("a[href="+b+"]",a._doc.body).attr(WYMeditor.HREF,p.link).attr(WYMeditor.TITLE,j.singular+n)}})});hide_modal()},Cancel:function(){hide_modal()}})}})}if(i==Galaxy.DIALOG_EMBED_HISTORY||i==Galaxy.DIALOG_EMBED_DATASET||i==Galaxy.DIALOG_EMBED_WORKFLOW||i==Galaxy.DIALOG_EMBED_PAGE||i==Galaxy.DIALOG_EMBED_VISUALIZATION){var j;switch(i){case (Galaxy.DIALOG_EMBED_HISTORY):j=get_item_info(Galaxy.ITEM_HISTORY);break;case (Galaxy.DIALOG_EMBED_DATASET):j=get_item_info(Galaxy.ITEM_DATASET);break;case (Galaxy.DIALOG_EMBED_WORKFLOW):j=get_item_info(Galaxy.ITEM_WORKFLOW);break;case (Galaxy.DIALOG_EMBED_PAGE):j=get_item_info(Galaxy.ITEM_PAGE);break;case (Galaxy.DIALOG_EMBED_VISUALIZATION):j=get_item_info(Galaxy.ITEM_VISUALIZATION);break}$.ajax({url:j.list_ajax_url,data:{},error:function(){alert("Failed to list "+j.plural.toLowerCase()+" for selection")},success:function(k){if(i==Galaxy.DIALOG_EMBED_HISTORY||i==Galaxy.DIALOG_EMBED_WORKFLOW||i==Galaxy.DIALOG_EMBED_VISUALIZATION){k=k+"<div><input id='make-importable' type='checkbox' checked/>Make the selected "+j.plural.toLowerCase()+" accessible so that they can viewed by everyone.</div>"}show_modal("Embed "+j.plural,k,{Embed:function(){var l=false;if($("#make-importable:checked").val()!=null){l=true}$("input[name=id]:checked").each(function(){var m=$(this).val();var p=$("label[for='"+m+"']:first").text();if(l){make_item_importable(j.controller,m,j.singular)}var n=j.iclass+"-"+m;var o=["<div id='",n,"' class='embedded-item ",j.singular.toLowerCase()," placeholder'>","<p class='title'>","Embedded Galaxy ",j.singular," '",p,"'","</p>","<p class='content'>","[Do not edit this block; Galaxy will fill it in with the annotated ",j.singular.toLowerCase()," when it is displayed.]","</p>","</div>"].join("");console.debug(o);a.insert(o)});hide_modal()},Cancel:function(){hide_modal()}})}})}if(i==Galaxy.DIALOG_ANNOTATE_HISTORY){$.ajax({url:list_histories_for_selection_url,data:{},error:function(){alert("Grid refresh failed")},success:function(k){show_modal("Insert Link to History",k,{Annotate:function(){var l=new Array();$("input[name=id]:checked").each(function(){var m=$(this).val();$.ajax({url:get_history_annotation_table_url,data:{id:m},error:function(){alert("Grid refresh failed")},success:function(n){a.insert(n);init_galaxy_elts(a)}})});hide_modal()},Cancel:function(){hide_modal()}})}})}};$(function(){$(document).ajaxError(function(i,g){var h=g.responseText||g.statusText||"Could not connect to server";show_modal("Server error",h,{"Ignore error":hide_modal});return false});$("[name=page_content]").wymeditor({skin:"galaxy",basePath:editor_base_path,iframeBasePath:iframe_base_path,boxHtml:"<table class='wym_box' width='100%' height='100%'><tr><td><div class='wym_area_top'>"+WYMeditor.TOOLS+"</div></td></tr><tr height='100%'><td><div class='wym_area_main' style='height: 100%;'>"+WYMeditor.IFRAME+WYMeditor.STATUS+"</div></div></td></tr></table>",toolsItems:[{name:"Bold",title:"Strong",css:"wym_tools_strong"},{name:"Italic",title:"Emphasis",css:"wym_tools_emphasis"},{name:"Superscript",title:"Superscript",css:"wym_tools_superscript"},{name:"Subscript",title:"Subscript",css:"wym_tools_subscript"},{name:"InsertOrderedList",title:"Ordered_List",css:"wym_tools_ordered_list"},{name:"InsertUnorderedList",title:"Unordered_List",css:"wym_tools_unordered_list"},{name:"Indent",title:"Indent",css:"wym_tools_indent"},{name:"Outdent",title:"Outdent",css:"wym_tools_outdent"},{name:"Undo",title:"Undo",css:"wym_tools_undo"},{name:"Redo",title:"Redo",css:"wym_tools_redo"},{name:"CreateLink",title:"Link",css:"wym_tools_link"},{name:"Unlink",title:"Unlink",css:"wym_tools_unlink"},{name:"InsertImage",title:"Image",css:"wym_tools_image"},{name:"InsertTable",title:"Table",css:"wym_tools_table"},]});var d=$.wymeditors(0);var f=function(g){show_modal("Saving page","progress");$.ajax({url:save_url,type:"POST",data:{id:page_id,content:d.xhtml(),annotations:JSON.stringify(new Object()),_:"true"},success:function(){g()}})};$("#save-button").click(function(){f(function(){hide_modal()})});$("#close-button").click(function(){var h=false;if(h){var g=function(){window.onbeforeunload=undefined;window.document.location=page_list_url};show_modal("Close editor","There are unsaved changes to your page which will be lost.",{Cancel:hide_modal,"Save Changes":function(){f(g)}},{"Don't Save":g})}else{window.document.location=page_list_url}});var a=$("<div class='galaxy-page-editor-button'><a id='insert-galaxy-link' class='action-button popup' href='#'>Paragraph type</a></div>");$(".wym_area_top").append(a);var b={};$.each(d._options.containersItems,function(h,g){var i=g.name;b[g.title.replace("_"," ")]=function(){d.container(i)}});make_popupmenu(a,b);var c=$("<div><a id='insert-galaxy-link' class='action-button popup' href='#'>Insert Link to Galaxy Object</a></div>").addClass("galaxy-page-editor-button");$(".wym_area_top").append(c);make_popupmenu(c,{"Insert History Link":function(){d.dialog(Galaxy.DIALOG_HISTORY_LINK)},"Insert Dataset Link":function(){d.dialog(Galaxy.DIALOG_DATASET_LINK)},"Insert Workflow Link":function(){d.dialog(Galaxy.DIALOG_WORKFLOW_LINK)},"Insert Page Link":function(){d.dialog(Galaxy.DIALOG_PAGE_LINK)},"Insert Visualization Link":function(){d.dialog(Galaxy.DIALOG_VISUALIZATION_LINK)},});var e=$("<div><a id='embed-galaxy-object' class='action-button popup' href='#'>Embed Galaxy Object</a></div>").addClass("galaxy-page-editor-button");$(".wym_area_top").append(e);make_popupmenu(e,{"Embed History":function(){d.dialog(Galaxy.DIALOG_EMBED_HISTORY)},"Embed Dataset":function(){d.dialog(Galaxy.DIALOG_EMBED_DATASET)},"Embed Workflow":function(){d.dialog(Galaxy.DIALOG_EMBED_WORKFLOW)},"Embed Visualization":function(){d.dialog(Galaxy.DIALOG_EMBED_VISUALIZATION)},})});
\ No newline at end of file
+var Galaxy={ITEM_HISTORY:"item_history",ITEM_DATASET:"item_dataset",ITEM_WORKFLOW:"item_workflow",ITEM_PAGE:"item_page",ITEM_VISUALIZATION:"item_visualization",DIALOG_HISTORY_LINK:"link_history",DIALOG_DATASET_LINK:"link_dataset",DIALOG_WORKFLOW_LINK:"link_workflow",DIALOG_PAGE_LINK:"link_page",DIALOG_VISUALIZATION_LINK:"link_visualization",DIALOG_EMBED_HISTORY:"embed_history",DIALOG_EMBED_DATASET:"embed_dataset",DIALOG_EMBED_WORKFLOW:"embed_workflow",DIALOG_EMBED_PAGE:"embed_page",DIALOG_EMBED_VISUALIZATION:"embed_visualization",DIALOG_HISTORY_ANNOTATE:"history_annotate",};function init_galaxy_elts(a){$(".annotation",a._doc.body).each(function(){$(this).click(function(){var b=a._doc.createRange();b.selectNodeContents(this);var d=window.getSelection();d.removeAllRanges();d.addRange(b);var c=""})})}function get_item_info(d){var f,c,b;switch(d){case (Galaxy.ITEM_HISTORY):f="History";c="Histories";b="history";item_class="History";break;case (Galaxy.ITEM_DATASET):f="Dataset";c="Datasets";b="dataset";item_class="HistoryDatasetAssociation";break;case (Galaxy.ITEM_WORKFLOW):f="Workflow";c="Workflows";b="workflow";item_class="StoredWorkflow";break;case (Galaxy.ITEM_PAGE):f="Page";c="Pages";b="page";item_class="Page";break;case (Galaxy.ITEM_VISUALIZATION):f="Visualization";c="Visualizations";b="visualization";item_class="Visualization";break}var e="list_"+c.toLowerCase()+"_for_selection";var a=list_objects_url.replace("LIST_ACTION",e);return{singular:f,plural:c,controller:b,iclass:item_class,list_ajax_url:a}}function make_item_importable(a,c,b){ajax_url=set_accessible_url.replace("ITEM_CONTROLLER",a);$.ajax({type:"POST",url:ajax_url,data:{id:c,accessible:"True"},error:function(){alert("Making "+b+" accessible failed")}})}WYMeditor.editor.prototype.dialog=function(i,e,g){var a=this;var b=a.uniqueStamp();var f=a.selected();function h(){$("#set_link_id").click(function(){$("#link_attribute_label").text("ID/Name");var k=$(".wym_href");k.addClass("wym_id").removeClass("wym_href");if(f){k.val($(f).attr("id"))}$(this).remove()})}if(i==WYMeditor.DIALOG_LINK){if(f){$(a._options.hrefSelector).val($(f).attr(WYMeditor.HREF));$(a._options.srcSelector).val($(f).attr(WYMeditor.SRC));$(a._options.titleSelector).val($(f).attr(WYMeditor.TITLE));$(a._options.altSelector).val($(f).attr(WYMeditor.ALT))}var c,d;if(f){c=$(f).attr("href");if(c==undefined){c=""}d=$(f).attr("title");if(d==undefined){d=""}}show_modal("Create Link","<div><div><label id='link_attribute_label'>URL <span style='float: right; font-size: 90%'><a href='#' id='set_link_id'>Create in-page anchor</a></span></label><br><input type='text' class='wym_href' value='"+c+"' size='40' /></div><div><label>Title</label><br><input type='text' class='wym_title' value='"+d+"' size='40' /></div><div>",{"Make link":function(){var 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\ No newline at end of file
diff -r a4d225dbfc8f2d3e7384ab206ecc30c4368b7c94 -r 6eb680d500b14753d7db2efd552613e531541495 static/scripts/packed/mvc/dataset/hda-base.js
--- a/static/scripts/packed/mvc/dataset/hda-base.js
+++ b/static/scripts/packed/mvc/dataset/hda-base.js
@@ -1,1 +1,1 @@
-define(["mvc/dataset/hda-model","mvc/base-mvc"],function(d,b){var c=Backbone.View.extend(b.LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(f){if(f.logger){this.logger=this.model.logger=f.logger}this.log(this+".initialize:",f);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=f.linkTarget||"_blank";this.selectable=f.selectable||false;this.selected=f.selected||false;this.expanded=f.expanded||false;this.draggable=f.draggable||false;this._setUpListeners()},_setUpListeners:function(){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)},render:function(h){h=(h===undefined)?(true):(h);var f=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var g=this._buildNewRender();if(h){$(f).queue(function(i){this.$el.fadeOut(f.fxSpeed,i)})}$(f).queue(function(i){this.$el.empty().attr("class",f.className).addClass("state-"+f.model.get("state")).append(g.children());if(this.selectable){this.showSelector(0)}i()});if(h){$(f).queue(function(i){this.$el.fadeIn(f.fxSpeed,i)})}$(f).queue(function(i){this.trigger("rendered",f);if(this.model.inReadyState()){this.trigger("rendered:ready",f)}if(this.draggable){this.draggableOn()}i()});return this},_buildNewRender:function(){var f=$(c.templates.skeleton(this.model.toJSON()));f.find(".dataset-primary-actions").append(this._render_titleButtons());f.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(f);return f},_setUpBehaviors:function(f){f=f||this.$el;make_popup_menus(f);f.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var g={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){g.disabled=true;g.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){g.disabled=true;g.title=_l("This dataset must finish uploading before it can be viewed")}else{g.title=_l("View data");g.href=this.urls.display;var f=this;g.onclick=function(h){console.debug("displayBtn onclick",h);if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+f.model.get("name"),type:"url",content:f.urls.display});h.preventDefault()}}}}g.faIcon="fa-eye";return faIconButton(g)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var g=this.urls,h=this.model.get("meta_files");if(_.isEmpty(h)){return $(['<a href="'+g.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var i="dataset-"+this.model.get("id")+"-popup",f=['<div popupmenu="'+i+'">','<a href="'+g.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(h,function(j){return['<a class="action-button" href="',g.meta_download+j.file_type,'">',_l("Download")," ",j.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+g.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+i+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(f)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var g=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),f=this["_render_body_"+this.model.get("state")];if(_.isFunction(f)){g=f.call(this)}this._setUpBehaviors(g);if(this.expanded){g.show()}return g},_render_stateBodyHelper:function(f,i){i=i||[];var g=this,h=$(c.templates.body(_.extend(this.model.toJSON(),{body:f})));h.find(".dataset-actions .left").append(_.map(i,function(j){return j.call(g)}));return h},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var f=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){f="<div>"+this.model.get("misc_blurb")+"</div>"+f}return this._render_stateBodyHelper(f,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var f=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),g=this._render_body_ok();g.prepend(f);return g},_render_body_ok:function(){var f=this,h=$(c.templates.body(this.model.toJSON())),g=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);h.find(".dataset-actions .left").append(_.map(g,function(i){return i.call(f)}));if(this.model.isDeletedOrPurged()){return h}return h},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(i,g){var f=32,h=13;if(i&&(i.type==="keydown")&&!(i.keyCode===f||i.keyCode===h)){return true}var j=this.$el.find(".dataset-body");g=(g===undefined)?(!j.is(":visible")):(g);if(g){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var f=this;function g(){f.$el.children(".dataset-body").replaceWith(f._render_body());f.$el.children(".dataset-body").slideDown(f.fxSpeed,function(){f.expanded=true;f.trigger("body-expanded",f.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(h){f.urls=f.model.urls();g()})}else{g()}},collapseBody:function(){var f=this;this.$el.children(".dataset-body").slideUp(f.fxSpeed,function(){f.expanded=false;f.trigger("body-collapsed",f.model.get("id"))})},showSelector:function(){if(this.selected){this.select(null,true)}this.selectable=true;this.trigger("selectable",true,this);this.$(".dataset-primary-actions").hide();this.$(".dataset-selector").show()},hideSelector:function(){this.selectable=false;this.trigger("selectable",false,this);this.$(".dataset-selector").hide();this.$(".dataset-primary-actions").show()},toggleSelector:function(){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector()}else{this.hideSelector()}},select:function(f){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(f){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(f){if(this.selected){this.deselect(f)}else{this.select(f)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var f=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);f.addEventListener("dragstart",this.dragStartHandler,false);f.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var f=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);f.removeEventListener("dragstart",this.dragStartHandler,false);f.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(f){this.trigger("dragstart",this);f.dataTransfer.effectAllowed="move";f.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(f){this.trigger("dragend",this);return false},remove:function(g){var f=this;this.$el.fadeOut(f.fxSpeed,function(){f.$el.remove();f.off();if(g){g()}})},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+f+")"}});var a=['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',_l("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',_l("This dataset has been deleted and removed from disk."),"</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',_l("This dataset has been deleted."),"</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',_l("This dataset has been hidden."),"</strong></div>","<% } %>","</div>",'<div class="dataset-selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join("");var e=['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',_l("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',_l("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_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>","<% }); %>","<% _.each( hda.display_types, 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>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join("");c.templates={skeleton:function(f){return _.template(a,f,{variable:"hda"})},body:function(f){return _.template(e,f,{variable:"hda"})}};return{HDABaseView:c}});
\ No newline at end of file
+define(["mvc/dataset/hda-model","mvc/base-mvc"],function(d,b){var c=Backbone.View.extend(b.LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(f){if(f.logger){this.logger=this.model.logger=f.logger}this.log(this+".initialize:",f);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=f.linkTarget||"_blank";this.selectable=f.selectable||false;this.selected=f.selected||false;this.expanded=f.expanded||false;this.draggable=f.draggable||false;this._setUpListeners()},_setUpListeners:function(){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)},render:function(h){h=(h===undefined)?(true):(h);var f=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var g=this._buildNewRender();if(h){$(f).queue(function(i){this.$el.fadeOut(f.fxSpeed,i)})}$(f).queue(function(i){this.$el.empty().attr("class",f.className).addClass("state-"+f.model.get("state")).append(g.children());if(this.selectable){this.showSelector(0)}i()});if(h){$(f).queue(function(i){this.$el.fadeIn(f.fxSpeed,i)})}$(f).queue(function(i){this.trigger("rendered",f);if(this.model.inReadyState()){this.trigger("rendered:ready",f)}if(this.draggable){this.draggableOn()}i()});return this},_buildNewRender:function(){var f=$(c.templates.skeleton(this.model.toJSON()));f.find(".dataset-primary-actions").append(this._render_titleButtons());f.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(f);return f},_setUpBehaviors:function(f){f=f||this.$el;make_popup_menus(f);f.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var g={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){g.disabled=true;g.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){g.disabled=true;g.title=_l("This dataset must finish uploading before it can be viewed")}else{g.title=_l("View data");g.href=this.urls.display;var f=this;g.onclick=function(h){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+f.model.get("name"),type:"url",content:f.urls.display});h.preventDefault()}}}}g.faIcon="fa-eye";return faIconButton(g)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var g=this.urls,h=this.model.get("meta_files");if(_.isEmpty(h)){return $(['<a href="'+g.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var i="dataset-"+this.model.get("id")+"-popup",f=['<div popupmenu="'+i+'">','<a href="'+g.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(h,function(j){return['<a class="action-button" href="',g.meta_download+j.file_type,'">',_l("Download")," ",j.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+g.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+i+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(f)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var g=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),f=this["_render_body_"+this.model.get("state")];if(_.isFunction(f)){g=f.call(this)}this._setUpBehaviors(g);if(this.expanded){g.show()}return g},_render_stateBodyHelper:function(f,i){i=i||[];var g=this,h=$(c.templates.body(_.extend(this.model.toJSON(),{body:f})));h.find(".dataset-actions .left").append(_.map(i,function(j){return j.call(g)}));return h},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var f=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){f="<div>"+this.model.get("misc_blurb")+"</div>"+f}return this._render_stateBodyHelper(f,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var f=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),g=this._render_body_ok();g.prepend(f);return g},_render_body_ok:function(){var f=this,h=$(c.templates.body(this.model.toJSON())),g=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);h.find(".dataset-actions .left").append(_.map(g,function(i){return i.call(f)}));if(this.model.isDeletedOrPurged()){return h}return h},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(i,g){var f=32,h=13;if(i&&(i.type==="keydown")&&!(i.keyCode===f||i.keyCode===h)){return true}var j=this.$el.find(".dataset-body");g=(g===undefined)?(!j.is(":visible")):(g);if(g){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var f=this;function g(){f.$el.children(".dataset-body").replaceWith(f._render_body());f.$el.children(".dataset-body").slideDown(f.fxSpeed,function(){f.expanded=true;f.trigger("body-expanded",f.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(h){f.urls=f.model.urls();g()})}else{g()}},collapseBody:function(){var f=this;this.$el.children(".dataset-body").slideUp(f.fxSpeed,function(){f.expanded=false;f.trigger("body-collapsed",f.model.get("id"))})},showSelector:function(){if(this.selected){this.select(null,true)}this.selectable=true;this.trigger("selectable",true,this);this.$(".dataset-primary-actions").hide();this.$(".dataset-selector").show()},hideSelector:function(){this.selectable=false;this.trigger("selectable",false,this);this.$(".dataset-selector").hide();this.$(".dataset-primary-actions").show()},toggleSelector:function(){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector()}else{this.hideSelector()}},select:function(f){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(f){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(f){if(this.selected){this.deselect(f)}else{this.select(f)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var f=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);f.addEventListener("dragstart",this.dragStartHandler,false);f.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var f=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);f.removeEventListener("dragstart",this.dragStartHandler,false);f.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(f){this.trigger("dragstart",this);f.dataTransfer.effectAllowed="move";f.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(f){this.trigger("dragend",this);return false},remove:function(g){var f=this;this.$el.fadeOut(f.fxSpeed,function(){f.$el.remove();f.off();if(g){g()}})},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+f+")"}});var a=['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',_l("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',_l("This dataset has been deleted and removed from disk."),"</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',_l("This dataset has been deleted."),"</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',_l("This dataset has been hidden."),"</strong></div>","<% } %>","</div>",'<div class="dataset-selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join("");var e=['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',_l("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',_l("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_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>","<% }); %>","<% _.each( hda.display_types, 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>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join("");c.templates={skeleton:function(f){return _.template(a,f,{variable:"hda"})},body:function(f){return _.template(e,f,{variable:"hda"})}};return{HDABaseView:c}});
\ No newline at end of file
https://bitbucket.org/galaxy/galaxy-central/commits/d79eccd2d0be/
Changeset: d79eccd2d0be
User: carlfeberhard
Date: 2014-04-08 20:14:58
Summary: merge next-stable
Affected #: 4 files
diff -r 121e69653f7728fddfadeb720f93e168a2fc8227 -r d79eccd2d0beae713abe1f44b6d2584c8528b03e static/scripts/galaxy.pages.js
--- a/static/scripts/galaxy.pages.js
+++ b/static/scripts/galaxy.pages.js
@@ -462,7 +462,6 @@
item_info.singular.toLowerCase(), " when it is displayed.]",
"</p>",
"</div>" ].join( '' );
- console.debug( item_embed_html );
// Insert embedded item into document.
//wym.insert(" "); // Needed to prevent insertion from occurring in child element in webkit browsers.
diff -r 121e69653f7728fddfadeb720f93e168a2fc8227 -r d79eccd2d0beae713abe1f44b6d2584c8528b03e static/scripts/mvc/dataset/hda-base.js
--- a/static/scripts/mvc/dataset/hda-base.js
+++ b/static/scripts/mvc/dataset/hda-base.js
@@ -194,7 +194,6 @@
// add frame manager option onclick event
var self = this;
displayBtnData.onclick = function( ev ){
- console.debug( 'displayBtn onclick', ev );
if( Galaxy.frame && Galaxy.frame.active ){
Galaxy.frame.add({
title : "Data Viewer: " + self.model.get('name'),
diff -r 121e69653f7728fddfadeb720f93e168a2fc8227 -r d79eccd2d0beae713abe1f44b6d2584c8528b03e static/scripts/packed/galaxy.pages.js
--- a/static/scripts/packed/galaxy.pages.js
+++ b/static/scripts/packed/galaxy.pages.js
@@ -1,1 +1,1 @@
-var Galaxy={ITEM_HISTORY:"item_history",ITEM_DATASET:"item_dataset",ITEM_WORKFLOW:"item_workflow",ITEM_PAGE:"item_page",ITEM_VISUALIZATION:"item_visualization",DIALOG_HISTORY_LINK:"link_history",DIALOG_DATASET_LINK:"link_dataset",DIALOG_WORKFLOW_LINK:"link_workflow",DIALOG_PAGE_LINK:"link_page",DIALOG_VISUALIZATION_LINK:"link_visualization",DIALOG_EMBED_HISTORY:"embed_history",DIALOG_EMBED_DATASET:"embed_dataset",DIALOG_EMBED_WORKFLOW:"embed_workflow",DIALOG_EMBED_PAGE:"embed_page",DIALOG_EMBED_VISUALIZATION:"embed_visualization",DIALOG_HISTORY_ANNOTATE:"history_annotate",};function init_galaxy_elts(a){$(".annotation",a._doc.body).each(function(){$(this).click(function(){var b=a._doc.createRange();b.selectNodeContents(this);var d=window.getSelection();d.removeAllRanges();d.addRange(b);var c=""})})}function get_item_info(d){var f,c,b;switch(d){case (Galaxy.ITEM_HISTORY):f="History";c="Histories";b="history";item_class="History";break;case (Galaxy.ITEM_DATASET):f="Dataset";c="Datasets";b="dataset";item_class="HistoryDatasetAssociation";break;case (Galaxy.ITEM_WORKFLOW):f="Workflow";c="Workflows";b="workflow";item_class="StoredWorkflow";break;case (Galaxy.ITEM_PAGE):f="Page";c="Pages";b="page";item_class="Page";break;case (Galaxy.ITEM_VISUALIZATION):f="Visualization";c="Visualizations";b="visualization";item_class="Visualization";break}var e="list_"+c.toLowerCase()+"_for_selection";var a=list_objects_url.replace("LIST_ACTION",e);return{singular:f,plural:c,controller:b,iclass:item_class,list_ajax_url:a}}function make_item_importable(a,c,b){ajax_url=set_accessible_url.replace("ITEM_CONTROLLER",a);$.ajax({type:"POST",url:ajax_url,data:{id:c,accessible:"True"},error:function(){alert("Making "+b+" accessible failed")}})}WYMeditor.editor.prototype.dialog=function(i,e,g){var a=this;var b=a.uniqueStamp();var f=a.selected();function h(){$("#set_link_id").click(function(){$("#link_attribute_label").text("ID/Name");var k=$(".wym_href");k.addClass("wym_id").removeClass("wym_href");if(f){k.val($(f).attr("id"))}$(this).remove()})}if(i==WYMeditor.DIALOG_LINK){if(f){$(a._options.hrefSelector).val($(f).attr(WYMeditor.HREF));$(a._options.srcSelector).val($(f).attr(WYMeditor.SRC));$(a._options.titleSelector).val($(f).attr(WYMeditor.TITLE));$(a._options.altSelector).val($(f).attr(WYMeditor.ALT))}var c,d;if(f){c=$(f).attr("href");if(c==undefined){c=""}d=$(f).attr("title");if(d==undefined){d=""}}show_modal("Create Link","<div><div><label id='link_attribute_label'>URL <span style='float: right; font-size: 90%'><a href='#' id='set_link_id'>Create in-page anchor</a></span></label><br><input type='text' class='wym_href' value='"+c+"' size='40' /></div><div><label>Title</label><br><input type='text' class='wym_title' value='"+d+"' size='40' /></div><div>",{"Make link":function(){var m=$(a._options.hrefSelector).val()||"",k=$(".wym_id").val()||"",n=$(a._options.titleSelector).val()||"";if(m||k){a._exec(WYMeditor.CREATE_LINK,b);var l=$("a[href="+b+"]",a._doc.body);l.attr(WYMeditor.HREF,m).attr(WYMeditor.TITLE,n).attr("id",k);if(l.text().indexOf("wym-")===0){l.text(n)}}hide_modal()},Cancel:function(){hide_modal()}},{},h)}if(i==WYMeditor.DIALOG_IMAGE){if(a._selected_image){$(a._options.dialogImageSelector+" "+a._options.srcSelector).val($(a._selected_image).attr(WYMeditor.SRC));$(a._options.dialogImageSelector+" "+a._options.titleSelector).val($(a._selected_image).attr(WYMeditor.TITLE));$(a._options.dialogImageSelector+" "+a._options.altSelector).val($(a._selected_image).attr(WYMeditor.ALT))}show_modal("Image","<div class='row'><label>URL</label><br><input type='text' class='wym_src' value='' size='40' /></div><div class='row'><label>Alt text</label><br><input type='text' class='wym_alt' value='' size='40' /></div><div class='row'><label>Title</label><br><input 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\ No newline at end of file
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page","progress");$.ajax({url:save_url,type:"POST",data:{id:page_id,content:d.xhtml(),annotations:JSON.stringify(new Object()),_:"true"},success:function(){g()}})};$("#save-button").click(function(){f(function(){hide_modal()})});$("#close-button").click(function(){var h=false;if(h){var g=function(){window.onbeforeunload=undefined;window.document.location=page_list_url};show_modal("Close editor","There are unsaved changes to your page which will be lost.",{Cancel:hide_modal,"Save Changes":function(){f(g)}},{"Don't Save":g})}else{window.document.location=page_list_url}});var a=$("<div class='galaxy-page-editor-button'><a id='insert-galaxy-link' class='action-button popup' href='#'>Paragraph type</a></div>");$(".wym_area_top").append(a);var b={};$.each(d._options.containersItems,function(h,g){var i=g.name;b[g.title.replace("_"," ")]=function(){d.container(i)}});make_popupmenu(a,b);var c=$("<div><a id='insert-galaxy-link' class='action-button popup' href='#'>Insert Link to Galaxy Object</a></div>").addClass("galaxy-page-editor-button");$(".wym_area_top").append(c);make_popupmenu(c,{"Insert History Link":function(){d.dialog(Galaxy.DIALOG_HISTORY_LINK)},"Insert Dataset Link":function(){d.dialog(Galaxy.DIALOG_DATASET_LINK)},"Insert Workflow Link":function(){d.dialog(Galaxy.DIALOG_WORKFLOW_LINK)},"Insert Page Link":function(){d.dialog(Galaxy.DIALOG_PAGE_LINK)},"Insert Visualization Link":function(){d.dialog(Galaxy.DIALOG_VISUALIZATION_LINK)},});var e=$("<div><a id='embed-galaxy-object' class='action-button popup' href='#'>Embed Galaxy Object</a></div>").addClass("galaxy-page-editor-button");$(".wym_area_top").append(e);make_popupmenu(e,{"Embed History":function(){d.dialog(Galaxy.DIALOG_EMBED_HISTORY)},"Embed Dataset":function(){d.dialog(Galaxy.DIALOG_EMBED_DATASET)},"Embed Workflow":function(){d.dialog(Galaxy.DIALOG_EMBED_WORKFLOW)},"Embed Visualization":function(){d.dialog(Galaxy.DIALOG_EMBED_VISUALIZATION)},})});
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diff -r 121e69653f7728fddfadeb720f93e168a2fc8227 -r d79eccd2d0beae713abe1f44b6d2584c8528b03e static/scripts/packed/mvc/dataset/hda-base.js
--- a/static/scripts/packed/mvc/dataset/hda-base.js
+++ b/static/scripts/packed/mvc/dataset/hda-base.js
@@ -1,1 +1,1 @@
-define(["mvc/dataset/hda-model","mvc/base-mvc"],function(d,b){var c=Backbone.View.extend(b.LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(f){if(f.logger){this.logger=this.model.logger=f.logger}this.log(this+".initialize:",f);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=f.linkTarget||"_blank";this.selectable=f.selectable||false;this.selected=f.selected||false;this.expanded=f.expanded||false;this.draggable=f.draggable||false;this._setUpListeners()},_setUpListeners:function(){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)},render:function(h){h=(h===undefined)?(true):(h);var f=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var g=this._buildNewRender();if(h){$(f).queue(function(i){this.$el.fadeOut(f.fxSpeed,i)})}$(f).queue(function(i){this.$el.empty().attr("class",f.className).addClass("state-"+f.model.get("state")).append(g.children());if(this.selectable){this.showSelector(0)}i()});if(h){$(f).queue(function(i){this.$el.fadeIn(f.fxSpeed,i)})}$(f).queue(function(i){this.trigger("rendered",f);if(this.model.inReadyState()){this.trigger("rendered:ready",f)}if(this.draggable){this.draggableOn()}i()});return this},_buildNewRender:function(){var f=$(c.templates.skeleton(this.model.toJSON()));f.find(".dataset-primary-actions").append(this._render_titleButtons());f.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(f);return f},_setUpBehaviors:function(f){f=f||this.$el;make_popup_menus(f);f.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var g={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){g.disabled=true;g.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){g.disabled=true;g.title=_l("This dataset must finish uploading before it can be viewed")}else{g.title=_l("View data");g.href=this.urls.display;var f=this;g.onclick=function(h){console.debug("displayBtn onclick",h);if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+f.model.get("name"),type:"url",content:f.urls.display});h.preventDefault()}}}}g.faIcon="fa-eye";return faIconButton(g)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var g=this.urls,h=this.model.get("meta_files");if(_.isEmpty(h)){return $(['<a href="'+g.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var i="dataset-"+this.model.get("id")+"-popup",f=['<div popupmenu="'+i+'">','<a href="'+g.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(h,function(j){return['<a class="action-button" href="',g.meta_download+j.file_type,'">',_l("Download")," ",j.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+g.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+i+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(f)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var g=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),f=this["_render_body_"+this.model.get("state")];if(_.isFunction(f)){g=f.call(this)}this._setUpBehaviors(g);if(this.expanded){g.show()}return g},_render_stateBodyHelper:function(f,i){i=i||[];var g=this,h=$(c.templates.body(_.extend(this.model.toJSON(),{body:f})));h.find(".dataset-actions .left").append(_.map(i,function(j){return j.call(g)}));return h},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var f=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){f="<div>"+this.model.get("misc_blurb")+"</div>"+f}return this._render_stateBodyHelper(f,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var f=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),g=this._render_body_ok();g.prepend(f);return g},_render_body_ok:function(){var f=this,h=$(c.templates.body(this.model.toJSON())),g=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);h.find(".dataset-actions .left").append(_.map(g,function(i){return i.call(f)}));if(this.model.isDeletedOrPurged()){return h}return h},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(i,g){var f=32,h=13;if(i&&(i.type==="keydown")&&!(i.keyCode===f||i.keyCode===h)){return true}var j=this.$el.find(".dataset-body");g=(g===undefined)?(!j.is(":visible")):(g);if(g){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var f=this;function g(){f.$el.children(".dataset-body").replaceWith(f._render_body());f.$el.children(".dataset-body").slideDown(f.fxSpeed,function(){f.expanded=true;f.trigger("body-expanded",f.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(h){f.urls=f.model.urls();g()})}else{g()}},collapseBody:function(){var f=this;this.$el.children(".dataset-body").slideUp(f.fxSpeed,function(){f.expanded=false;f.trigger("body-collapsed",f.model.get("id"))})},showSelector:function(){if(this.selected){this.select(null,true)}this.selectable=true;this.trigger("selectable",true,this);this.$(".dataset-primary-actions").hide();this.$(".dataset-selector").show()},hideSelector:function(){this.selectable=false;this.trigger("selectable",false,this);this.$(".dataset-selector").hide();this.$(".dataset-primary-actions").show()},toggleSelector:function(){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector()}else{this.hideSelector()}},select:function(f){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(f){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(f){if(this.selected){this.deselect(f)}else{this.select(f)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var f=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);f.addEventListener("dragstart",this.dragStartHandler,false);f.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var f=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);f.removeEventListener("dragstart",this.dragStartHandler,false);f.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(f){this.trigger("dragstart",this);f.dataTransfer.effectAllowed="move";f.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(f){this.trigger("dragend",this);return false},remove:function(g){var f=this;this.$el.fadeOut(f.fxSpeed,function(){f.$el.remove();f.off();if(g){g()}})},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+f+")"}});var a=['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',_l("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',_l("This dataset has been deleted and removed from disk."),"</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',_l("This dataset has been deleted."),"</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',_l("This dataset has been hidden."),"</strong></div>","<% } %>","</div>",'<div class="dataset-selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join("");var e=['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',_l("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',_l("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_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>","<% }); %>","<% _.each( hda.display_types, 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>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join("");c.templates={skeleton:function(f){return _.template(a,f,{variable:"hda"})},body:function(f){return _.template(e,f,{variable:"hda"})}};return{HDABaseView:c}});
\ No newline at end of file
+define(["mvc/dataset/hda-model","mvc/base-mvc"],function(d,b){var c=Backbone.View.extend(b.LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(f){if(f.logger){this.logger=this.model.logger=f.logger}this.log(this+".initialize:",f);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=f.linkTarget||"_blank";this.selectable=f.selectable||false;this.selected=f.selected||false;this.expanded=f.expanded||false;this.draggable=f.draggable||false;this._setUpListeners()},_setUpListeners:function(){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)},render:function(h){h=(h===undefined)?(true):(h);var f=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var g=this._buildNewRender();if(h){$(f).queue(function(i){this.$el.fadeOut(f.fxSpeed,i)})}$(f).queue(function(i){this.$el.empty().attr("class",f.className).addClass("state-"+f.model.get("state")).append(g.children());if(this.selectable){this.showSelector(0)}i()});if(h){$(f).queue(function(i){this.$el.fadeIn(f.fxSpeed,i)})}$(f).queue(function(i){this.trigger("rendered",f);if(this.model.inReadyState()){this.trigger("rendered:ready",f)}if(this.draggable){this.draggableOn()}i()});return this},_buildNewRender:function(){var f=$(c.templates.skeleton(this.model.toJSON()));f.find(".dataset-primary-actions").append(this._render_titleButtons());f.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(f);return f},_setUpBehaviors:function(f){f=f||this.$el;make_popup_menus(f);f.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var g={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){g.disabled=true;g.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){g.disabled=true;g.title=_l("This dataset must finish uploading before it can be viewed")}else{g.title=_l("View data");g.href=this.urls.display;var f=this;g.onclick=function(h){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+f.model.get("name"),type:"url",content:f.urls.display});h.preventDefault()}}}}g.faIcon="fa-eye";return faIconButton(g)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var g=this.urls,h=this.model.get("meta_files");if(_.isEmpty(h)){return $(['<a href="'+g.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var i="dataset-"+this.model.get("id")+"-popup",f=['<div popupmenu="'+i+'">','<a href="'+g.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(h,function(j){return['<a class="action-button" href="',g.meta_download+j.file_type,'">',_l("Download")," ",j.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+g.download+'" title="'+_l("Download")+'" ','class="icon-btn dataset-download-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+i+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(f)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),classes:"dataset-params-btn",href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var g=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),f=this["_render_body_"+this.model.get("state")];if(_.isFunction(f)){g=f.call(this)}this._setUpBehaviors(g);if(this.expanded){g.show()}return g},_render_stateBodyHelper:function(f,i){i=i||[];var g=this,h=$(c.templates.body(_.extend(this.model.toJSON(),{body:f})));h.find(".dataset-actions .left").append(_.map(i,function(j){return j.call(g)}));return h},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var f=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){f="<div>"+this.model.get("misc_blurb")+"</div>"+f}return this._render_stateBodyHelper(f,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var f=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),g=this._render_body_ok();g.prepend(f);return g},_render_body_ok:function(){var f=this,h=$(c.templates.body(this.model.toJSON())),g=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);h.find(".dataset-actions .left").append(_.map(g,function(i){return i.call(f)}));if(this.model.isDeletedOrPurged()){return h}return h},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect"},toggleBodyVisibility:function(i,g){var f=32,h=13;if(i&&(i.type==="keydown")&&!(i.keyCode===f||i.keyCode===h)){return true}var j=this.$el.find(".dataset-body");g=(g===undefined)?(!j.is(":visible")):(g);if(g){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var f=this;function g(){f.$el.children(".dataset-body").replaceWith(f._render_body());f.$el.children(".dataset-body").slideDown(f.fxSpeed,function(){f.expanded=true;f.trigger("body-expanded",f.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(h){f.urls=f.model.urls();g()})}else{g()}},collapseBody:function(){var f=this;this.$el.children(".dataset-body").slideUp(f.fxSpeed,function(){f.expanded=false;f.trigger("body-collapsed",f.model.get("id"))})},showSelector:function(){if(this.selected){this.select(null,true)}this.selectable=true;this.trigger("selectable",true,this);this.$(".dataset-primary-actions").hide();this.$(".dataset-selector").show()},hideSelector:function(){this.selectable=false;this.trigger("selectable",false,this);this.$(".dataset-selector").hide();this.$(".dataset-primary-actions").show()},toggleSelector:function(){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector()}else{this.hideSelector()}},select:function(f){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(f){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(f){if(this.selected){this.deselect(f)}else{this.select(f)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var f=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);f.addEventListener("dragstart",this.dragStartHandler,false);f.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var f=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);f.removeEventListener("dragstart",this.dragStartHandler,false);f.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(f){this.trigger("dragstart",this);f.dataTransfer.effectAllowed="move";f.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(f){this.trigger("dragend",this);return false},remove:function(g){var f=this;this.$el.fadeOut(f.fxSpeed,function(){f.$el.remove();f.off();if(g){g()}})},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+f+")"}});var a=['<div class="dataset hda">','<div class="dataset-warnings">',"<% if( hda.error ){ %>",'<div class="errormessagesmall">',_l("There was an error getting the data for this dataset"),":<%- hda.error %>","</div>","<% } %>","<% if( hda.deleted ){ %>","<% if( hda.purged ){ %>",'<div class="dataset-purged-msg warningmessagesmall"><strong>',_l("This dataset has been deleted and removed from disk."),"</strong></div>","<% } else { %>",'<div class="dataset-deleted-msg warningmessagesmall"><strong>',_l("This dataset has been deleted."),"</strong></div>","<% } %>","<% } %>","<% if( !hda.visible ){ %>",'<div class="dataset-hidden-msg warningmessagesmall"><strong>',_l("This dataset has been hidden."),"</strong></div>","<% } %>","</div>",'<div class="dataset-selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="dataset-primary-actions"></div>','<div class="dataset-title-bar clear" tabindex="0">','<span class="dataset-state-icon state-icon"></span>','<div class="dataset-title">','<span class="hda-hid"><%- hda.hid %></span> ','<span class="dataset-name"><%- hda.name %></span>',"</div>","</div>",'<div class="dataset-body"></div>',"</div>"].join("");var e=['<div class="dataset-body">',"<% if( hda.body ){ %>",'<div class="dataset-summary">',"<%= hda.body %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% } else { %>",'<div class="dataset-summary">',"<% if( hda.misc_blurb ){ %>",'<div class="dataset-blurb">','<span class="value"><%- hda.misc_blurb %></span>',"</div>","<% } %>","<% if( hda.data_type ){ %>",'<div class="dataset-datatype">','<label class="prompt">',_l("format"),"</label>",'<span class="value"><%- hda.data_type %></span>',"</div>","<% } %>","<% if( hda.metadata_dbkey ){ %>",'<div class="dataset-dbkey">','<label class="prompt">',_l("database"),"</label>",'<span class="value">',"<%- hda.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( hda.misc_info ){ %>",'<div class="dataset-info">','<span class="value"><%- hda.misc_info %></span>',"</div>","<% } %>","</div>",'<div class="dataset-actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !hda.deleted ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="dataset-display-applications">',"<% _.each( hda.display_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>","<% }); %>","<% _.each( hda.display_types, 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>","<% }); %>","</div>",'<div class="dataset-peek">',"<% if( hda.peek ){ %>",'<pre class="peek"><%= hda.peek %></pre>',"<% } %>","</div>","<% } %>","<% } %>","</div>"].join("");c.templates={skeleton:function(f){return _.template(a,f,{variable:"hda"})},body:function(f){return _.template(e,f,{variable:"hda"})}};return{HDABaseView:c}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: carlfeberhard: Metrics: allow time to be passed into fluent_log.py, log
by commits-noreplyï¼ bitbucket.org 08 Apr '14
by commits-noreplyï¼ bitbucket.org 08 Apr '14
08 Apr '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/121e69653f77/
Changeset: 121e69653f77
User: carlfeberhard
Date: 2014-04-08 18:55:30
Summary: Metrics: allow time to be passed into fluent_log.py, log
Affected #: 1 file
diff -r b231f3463565137c81dce701cd194095df873fed -r 121e69653f7728fddfadeb720f93e168a2fc8227 lib/galaxy/util/log/fluent_log.py
--- a/lib/galaxy/util/log/fluent_log.py
+++ b/lib/galaxy/util/log/fluent_log.py
@@ -39,9 +39,11 @@
del self.thread_local.context[key]
self.lock.release()
- def log( self, label, **kwargs ):
+ def log( self, label, time=None, **kwargs ):
self.lock.acquire()
if hasattr( self.thread_local, 'context' ):
kwargs.update( self.thread_local.context )
self.lock.release()
- self.sender.emit_with_time( label, int(time.time()), kwargs )
+ if time is None:
+ time = int( time.time() )
+ self.sender.emit_with_time( label, time, kwargs )
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/a4d225dbfc8f/
Changeset: a4d225dbfc8f
Branch: next-stable
User: Jeremy Goecks
Date: 2014-04-08 18:07:50
Summary: Trackster: update jQuery selector so that all tool inputs are updated on change rather only <input> elements. Pack script.
Affected #: 2 files
diff -r d05ef0e76e9f3040eb2996dfe22d8c5d2fce26fe -r a4d225dbfc8f2d3e7384ab206ecc30c4368b7c94 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/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).bind("dragstart",function(){$(this).addClass("dragging")}).bind("dragend",function(){$(this).removeClass("dragging")})};var D=20,z=100,G=12000,Q=400,I=5000,v=100,m="Cannot display dataset due to an error. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",O=10,F=20,A=["Histogram","Line","Filled","Intensity"];function U(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);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.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.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(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.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:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ae=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(af){aa.each(af,function(ag){ab.add_drawable(n(ag,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);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 ac=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}af.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ah,af){var ai=[],ag=$.map(ab.get_tracks(c),function(aj){return aj.data_manager.search_features(ah.term).success(function(ak){ai=ai.concat(ak)})});$.when.apply($,ag).done(function(){af($.map(ai,function(aj){return{label:aj[0],value:aj[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(af){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(af){ab.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ag)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=ab.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}).bind("mousewheel",function(ah,aj,ag,af){if(ag){ag*=50;var ai=Math.round(-ag/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX)-ab.container.offset().left,width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-ab.container.offset().left,af=Math.max(aj.pageX,ak.startX)-ab.container.offset().left,ai=(ab.high-ab.low),ah=ab.viewport_container.width();ab.update_location(Math.round(ag/ah*ai)+ab.low,Math.round(af/ah*ai)+ab.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(ab.high-ab.low),ah=ab.viewport_container.width(),aj=ab.low;ab.low=Math.round(ag/ah*ai)+aj;ab.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();ab.request_redraw()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.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(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){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(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ad,ai,ak,ac,af,ag,al,ab,ah,ae,aj){b.call(this,ad,ai,ak,ac,af);this.mode=ag;this.all_slotted=ab;this.feature_mapper=ah;this.has_icons=false;this.incomplete_features=ae;this.seq_data=aj};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.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=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get("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>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set_value("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},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 V){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 Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$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(af.mode){this.change_mode(af.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(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;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 ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(aa.find(ao,function(aC){return j.is_deferred(aC)})){ad.tile_cache.set_elt(al,undefined);$.when(ad.draw_helper(ak,am,an)).then(function(aC){ab.resolve(aC)});return}if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.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 V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:aa.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(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ab=this.visible_height_px;aa.each(this.drawables,function(ac){ac.visible_height_px=ab});f.prototype.on_resize.call(this)},change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.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 ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.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:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.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(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.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(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);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:aa.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(an,ae,ap,am){L.prototype.postdraw_actions.call(this,an,ae,ap,am);var ag=this,ah,al=aa.filter(an,function(aq){return(aq instanceof K)});if(al.length===0){var ab={};aa.each(aa.pluck(an,"incomplete_features"),function(aq){aa.each(aq,function(ar){ab[ar[0]]=ar})});var ao=this;aa.each(an,function(aq){ao.draw_tile({data:aa.values(ab)},aq.canvas.getContext("2d"),aq.mode,aq.region,ap,aq.seq_data,true)})}if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<an.length;ah++){if(an[ah].data.length){ak=an[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(an[0] instanceof M){var ac=true;for(ah=0;ah<an.length;ah++){if(!an[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.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(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(am,ar,ap,af,aj,ae,an){var aq=this,ad=ar.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,ar,ap,af,aj)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.config.to_key_value_dict(),ap,aB,az,ae,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.config.get_value("block_color");ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(am.data){var ab=aA.draw(ar,ad.width,ad.height,aj,ao);aw=ab.feature_mapper;incomplete_features=ab.incomplete_features;aw.translation=-ag}if(!an){return new M(aq,af,aj,ad,am.data,ap,am.message,all_slotted,aw,incomplete_features,ae)}}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.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(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color",default_value:"#DDDDDD"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:"#AAAAAA"},{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:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}});
\ No newline at end of file
+define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).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(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.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(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.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:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);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,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ae=$("<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":ab.dbkey},function(af){aa.each(af,function(ag){ab.add_drawable(n(ag,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<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=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}af.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ah,af){var ai=[],ag=$.map(ab.get_tracks(c),function(aj){return aj.data_manager.search_features(ah.term).success(function(ak){ai=ai.concat(ak)})});$.when.apply($,ag).done(function(){af($.map(ai,function(aj){return{label:aj[0],value:aj[1]}}))})}})});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(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(af){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(af){ab.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ag)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=ab.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}).bind("mousewheel",function(ah,aj,ag,af){if(ag){ag*=50;var ai=Math.round(-ag/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX)-ab.container.offset().left,width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-ab.container.offset().left,af=Math.max(aj.pageX,ak.startX)-ab.container.offset().left,ai=(ab.high-ab.low),ah=ab.viewport_container.width();ab.update_location(Math.round(ag/ah*ai)+ab.low,Math.round(af/ah*ai)+ab.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(ab.high-ab.low),ah=ab.viewport_container.width(),aj=ab.low;ab.low=Math.round(ag/ah*ai)+aj;ab.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();ab.request_redraw()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.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(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){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(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ad,ai,ak,ac,af,ag,al,ab,ah,ae,aj){b.call(this,ad,ai,ak,ac,af);this.mode=ag;this.all_slotted=ab;this.feature_mapper=ah;this.has_icons=false;this.incomplete_features=ae;this.seq_data=aj};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.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=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get("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>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set_value("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},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 V){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 Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$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(af.mode){this.change_mode(af.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(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;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 ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(aa.find(ao,function(aC){return j.is_deferred(aC)})){ad.tile_cache.set_elt(al,undefined);$.when(ad.draw_helper(ak,am,an)).then(function(aC){ab.resolve(aC)});return}if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.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 V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:aa.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(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ab=this.visible_height_px;aa.each(this.drawables,function(ac){ac.visible_height_px=ab});f.prototype.on_resize.call(this)},change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.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 ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.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:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.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(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.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(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);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:aa.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(an,ae,ap,am){L.prototype.postdraw_actions.call(this,an,ae,ap,am);var ag=this,ah,al=aa.filter(an,function(aq){return(aq instanceof K)});if(al.length===0){var ab={};aa.each(aa.pluck(an,"incomplete_features"),function(aq){aa.each(aq,function(ar){ab[ar[0]]=ar})});var ao=this;aa.each(an,function(aq){ao.draw_tile({data:aa.values(ab)},aq.canvas.getContext("2d"),aq.mode,aq.region,ap,aq.seq_data,true)})}if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<an.length;ah++){if(an[ah].data.length){ak=an[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(an[0] instanceof M){var ac=true;for(ah=0;ah<an.length;ah++){if(!an[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.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(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(am,ar,ap,af,aj,ae,an){var aq=this,ad=ar.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,ar,ap,af,aj)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.config.to_key_value_dict(),ap,aB,az,ae,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.config.get_value("block_color");ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(am.data){var ab=aA.draw(ar,ad.width,ad.height,aj,ao);aw=ab.feature_mapper;incomplete_features=ab.incomplete_features;aw.translation=-ag}if(!an){return new M(aq,af,aj,ad,am.data,ap,am.message,all_slotted,aw,incomplete_features,ae)}}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.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(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color",default_value:"#DDDDDD"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:"#AAAAAA"},{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:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}});
\ No newline at end of file
diff -r d05ef0e76e9f3040eb2996dfe22d8c5d2fce26fe -r a4d225dbfc8f2d3e7384ab206ecc30c4368b7c94 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -1661,7 +1661,7 @@
var ToolParameterView = Backbone.View.extend({
events: {
- 'change input': 'update_value'
+ 'change :input': 'update_value'
},
render: function() {
https://bitbucket.org/galaxy/galaxy-central/commits/b231f3463565/
Changeset: b231f3463565
User: Jeremy Goecks
Date: 2014-04-08 18:08:20
Summary: Automated merge of next-stable to default
Affected #: 2 files
diff -r 13c90b7197bf6e81aa630b6ccd1e128ea66eebbe -r b231f3463565137c81dce701cd194095df873fed 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/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).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(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.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(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.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:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);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,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ae=$("<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":ab.dbkey},function(af){aa.each(af,function(ag){ab.add_drawable(n(ag,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<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=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}af.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ah,af){var ai=[],ag=$.map(ab.get_tracks(c),function(aj){return aj.data_manager.search_features(ah.term).success(function(ak){ai=ai.concat(ak)})});$.when.apply($,ag).done(function(){af($.map(ai,function(aj){return{label:aj[0],value:aj[1]}}))})}})});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(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(af){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(af){ab.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ag)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=ab.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}).bind("mousewheel",function(ah,aj,ag,af){if(ag){ag*=50;var ai=Math.round(-ag/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX)-ab.container.offset().left,width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-ab.container.offset().left,af=Math.max(aj.pageX,ak.startX)-ab.container.offset().left,ai=(ab.high-ab.low),ah=ab.viewport_container.width();ab.update_location(Math.round(ag/ah*ai)+ab.low,Math.round(af/ah*ai)+ab.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(ab.high-ab.low),ah=ab.viewport_container.width(),aj=ab.low;ab.low=Math.round(ag/ah*ai)+aj;ab.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();ab.request_redraw()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.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(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){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(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ad,ai,ak,ac,af,ag,al,ab,ah,ae,aj){b.call(this,ad,ai,ak,ac,af);this.mode=ag;this.all_slotted=ab;this.feature_mapper=ah;this.has_icons=false;this.incomplete_features=ae;this.seq_data=aj};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.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=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get("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>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set_value("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},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 V){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 Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$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(af.mode){this.change_mode(af.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(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;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 ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(aa.find(ao,function(aC){return j.is_deferred(aC)})){ad.tile_cache.set_elt(al,undefined);$.when(ad.draw_helper(ak,am,an)).then(function(aC){ab.resolve(aC)});return}if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.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 V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:aa.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(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ab=this.visible_height_px;aa.each(this.drawables,function(ac){ac.visible_height_px=ab});f.prototype.on_resize.call(this)},change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.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 ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.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:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.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(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.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(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);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:aa.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(an,ae,ap,am){L.prototype.postdraw_actions.call(this,an,ae,ap,am);var ag=this,ah,al=aa.filter(an,function(aq){return(aq instanceof K)});if(al.length===0){var ab={};aa.each(aa.pluck(an,"incomplete_features"),function(aq){aa.each(aq,function(ar){ab[ar[0]]=ar})});var ao=this;aa.each(an,function(aq){ao.draw_tile({data:aa.values(ab)},aq.canvas.getContext("2d"),aq.mode,aq.region,ap,aq.seq_data,true)})}if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<an.length;ah++){if(an[ah].data.length){ak=an[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(an[0] instanceof M){var ac=true;for(ah=0;ah<an.length;ah++){if(!an[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.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(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(am,ar,ap,af,aj,ae,an){var aq=this,ad=ar.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,ar,ap,af,aj)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.config.to_key_value_dict(),ap,aB,az,ae,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.config.get_value("block_color");ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(am.data){var ab=aA.draw(ar,ad.width,ad.height,aj,ao);aw=ab.feature_mapper;incomplete_features=ab.incomplete_features;aw.translation=-ag}if(!an){return new M(aq,af,aj,ad,am.data,ap,am.message,all_slotted,aw,incomplete_features,ae)}}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.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(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color",default_value:"#DDDDDD"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:"#AAAAAA"},{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:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}});
\ No newline at end of file
+define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools","utils/config"],function(aa,w,j,s,J,h,W,P,R){var o=aa.extend;var l={};var i=function(ab,ac){l[ab.attr("id")]=ac};var k=function(ab,ac,ae,ad){ae=".group";l[ab.attr("id")]=ad;ab.bind("drag",{handle:"."+ac,relative:true},function(am,an){var al=$(this),aq=$(this).parent(),ai=aq.children(".track,.group"),ak=l[$(this).attr("id")],ah,ag,ao,af,aj;ag=$(this).parents(ae);if(ag.length!==0){ao=ag.position().top;af=ao+ag.outerHeight();var ap=l[ag.attr("id")];if(an.offsetY<ao){$(this).insertBefore(ag);ap.remove_drawable(ak);ap.container.add_drawable_before(ak,ap);return}else{if(an.offsetY>af){$(this).insertAfter(ag);ap.remove_drawable(ak);ap.container.add_drawable(ak);return}}}ag=null;for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));ao=ah.position().top;af=ao+ah.outerHeight();if(ah.is(ae)&&this!==ah.get(0)&&an.offsetY>=ao&&an.offsetY<=af){if(an.offsetY-ao<af-an.offsetY){ah.find(".content-div").prepend(this)}else{ah.find(".content-div").append(this)}if(ak.container){ak.container.remove_drawable(ak)}l[ah.attr("id")].add_drawable(ak);return}}for(aj=0;aj<ai.length;aj++){ah=$(ai.get(aj));if(an.offsetY<ah.position().top&&!(ah.hasClass("reference-track")||ah.hasClass("intro"))){break}}if(aj===ai.length){if(this!==ai.get(aj-1)){aq.append(this);l[aq.attr("id")].move_drawable(ak,aj)}}else{if(this!==ai.get(aj)){$(this).insertBefore(ai.get(aj));l[aq.attr("id")].move_drawable(ak,(an.deltaY>0?aj-1:aj))}}}).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(ac,ab){if(!ab){ab=0}var ad=Math.pow(10,ab);return Math.round(ac*ad)/ad}var p=function(ac,ab,ae){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.view=ac;this.container=ab;this.drag_handle_class=ae.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=R.ConfigSettingCollection.from_models_and_saved_values(this.config_params,ae.prefs);if(!this.config.get_value("name")){this.config.set_value("name",ae.name)}if(this.config_onchange){this.config.on("change",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").addClass("track-icons").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(af){af.stopPropagation()});var ad=this;this.container_div.hover(function(){ad.icons_div.show()},function(){ad.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ab){if(ab.config.get_value("content_visible")){ab.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ab.hide_contents();ab.config.set_value("content_visible",false)}else{ab.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ab.config.set_value("content_visible",true);ab.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"gear",on_click_fn:function(ac){var ab=new R.ConfigSettingCollectionView({collection:ac.config});ab.render_in_modal("Configure Track")}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ab){$(".tooltip").remove();ab.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(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ac,ah,ag,af,ab,ae){var ad=this;this.action_icons[ac]=$("<a/>").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(function(){af(ad)}).appendTo(this.icons_div);if(ae){this.action_icons[ac].hide()}},build_action_icons:function(ab){var ad;for(var ac=0;ac<ab.length;ac++){ad=ab[ac];this.add_action_icon(ad.name,ad.title,ad.css_class,ad.on_click_fn,ad.prepend,ad.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ac,ab,ad){p.call(this,ac,ab,ad);this.obj_type=ad.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(ad){this.drawables=[];var ac;for(var ab=0;ab<ad.length;ab++){ac=n(ad[ab],this.view,this);this.add_drawable(ac)}},init:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].init()}},_draw:function(ab){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw(ab)}},to_dict:function(){var ac=[];for(var ab=0;ab<this.drawables.length;ab++){ac.push(this.drawables[ab].to_dict())}return{prefs:this.config.to_key_value_dict(),obj_type:this.obj_type,drawables:ac}},add_drawable:function(ab){this.drawables.push(ab);ab.container=this;this.changed()},add_drawable_before:function(ad,ab){this.changed();var ac=this.drawables.indexOf(ab);if(ac!==-1){this.drawables.splice(ac,0,ad);return true}return false},replace_drawable:function(ad,ab,ac){var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables[ae]=ab;if(ac){ad.container_div.replaceWith(ab.container_div)}this.changed()}return ae},remove_drawable:function(ac){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);ac.container=null;this.changed();return true}return false},move_drawable:function(ac,ad){var ab=this.drawables.indexOf(ac);if(ab!==-1){this.drawables.splice(ab,1);this.drawables.splice(ad,0,ac);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ae){var ab=this.drawables.slice(0),ac=[],ad;while(ab.length!==0){ad=ab.shift();if(ad instanceof ae){ac.push(ad)}else{if(ad.drawables){ab=ab.concat(ad.drawables)}}}return ac}});var N=function(ac,ab,ae){o(ae,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ac,ab,ae);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ae){this.unpack_drawables(ae.drawables)}if("filters" in ae){var ad=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ae.filters);ad.parent_div.replaceWith(this.filters_manager.parent_div);if(ae.filters.visible){this.setup_multitrack_filtering()}}};o(N.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters();ab._restore_filter_managers()}else{ab.setup_multitrack_filtering();ab.request_draw({clear_tile_cache:true})}ab.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ab=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ab)}return ab},build_header_div:function(){var ab=$("<div/>").addClass("track-header");ab.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an&&this.drawables[0] instanceof g){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ab>1&&ab===this.drawables.length){var ao={},ac;ah=this.drawables[0];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];ao[ac.name]=[ac]}for(ak=1;ak<this.drawables.length;ak++){ah=this.drawables[ak];for(aj=0;aj<ah.filters_manager.filters.length;aj++){ac=ah.filters_manager.filters[aj];if(ac.name in ao){ao[ac.name].push(ac)}}}this.filters_manager.remove_all();var ae,ag,ai,al;for(var am in ao){ae=ao[am];if(ae.length===ab){ag=new h.NumberFilter({name:ae[0].name,index:ae[0].index});this.filters_manager.add_filter(ag)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ab=0;ab<this.drawables.length;ab++){this.drawables[ab].filters_manager=this.saved_filters_managers[ab]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ab=0;ab<this.drawables.length;ab++){drawable=this.drawables[ab];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ac=new e(this.view,this.view,{name:this.config.get_value("name"),drawables:this.drawables});var ab=this.container.replace_drawable(this,ac,true);ac.request_draw()},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);this.update_icons()},remove_drawable:function(ab){y.prototype.remove_drawable.call(this,ab);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ab=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ab},request_draw:function(ab){aa.each(this.drawables,function(ac){ac.request_draw(ab)})}});var X=Backbone.View.extend({initialize:function(ab){o(ab,{obj_type:"View"});y.call(this,"View",ab.container,ab);this.chrom=null;this.vis_id=ab.vis_id;this.dbkey=ab.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:ab.name})},render:function(){this.requested_redraw=false;var ad=this.container,ab=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ad);this.browser_content_div=$("<div/>").addClass("content").appendTo(ad);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ad);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,ab);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ae=$("<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":ab.dbkey},function(af){aa.each(af,function(ag){ab.add_drawable(n(ag,ab,ab))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<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=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(af){if(af.type==="focusout"||(af.keyCode||af.which)===13||(af.keyCode||af.which)===27){if((af.keyCode||af.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}af.stopPropagation()};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ac).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ab.location_span.hide();ab.chrom_select.hide();ab.nav_input.val(ab.chrom+":"+ab.low+"-"+ab.high);ab.nav_input.css("display","inline-block");ab.nav_input.select();ab.nav_input.focus();ab.nav_input.autocomplete({source:function(ah,af){var ai=[],ag=$.map(ab.get_tracks(c),function(aj){return aj.data_manager.search_features(ah.term).success(function(ak){ai=ai.concat(ak)})});$.when.apply($,ag).done(function(){af($.map(ai,function(aj){return{label:aj[0],value:aj[1]}}))})}})});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(){ab.zoom_out()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(af){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(af){ab.zoom_in(af.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(af,ag){this.current_x=ag.offsetX}).bind("drag",function(af,ah){var ai=ah.offsetX-this.current_x;this.current_x=ah.offsetX;var ag=Math.round(ai/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ag)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(af,ag){if(af.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(af,ag){ag.original_low=ab.low;ag.current_height=af.clientY;ag.current_x=ag.offsetX}).bind("drag",function(ah,aj){var af=$(this);var ak=aj.offsetX-aj.current_x;var ag=af.scrollTop()-(ah.clientY-aj.current_height);af.scrollTop(ag);aj.current_height=ah.clientY;aj.current_x=aj.offsetX;var ai=Math.round(ak/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}).bind("mousewheel",function(ah,aj,ag,af){if(ag){ag*=50;var ai=Math.round(-ag/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(ai)}});this.top_labeltrack.bind("dragstart",function(af,ag){return $("<div/>").addClass("zoom-area").css("height",ab.browser_content_div.height()+ab.top_labeltrack.height()+ab.nav_labeltrack.height()+1).appendTo($(this))}).bind("drag",function(aj,ak){$(ak.proxy).css({left:Math.min(aj.pageX,ak.startX)-ab.container.offset().left,width:Math.abs(aj.pageX-ak.startX)});var ag=Math.min(aj.pageX,ak.startX)-ab.container.offset().left,af=Math.max(aj.pageX,ak.startX)-ab.container.offset().left,ai=(ab.high-ab.low),ah=ab.viewport_container.width();ab.update_location(Math.round(ag/ah*ai)+ab.low,Math.round(af/ah*ai)+ab.low)}).bind("dragend",function(ak,al){var ag=Math.min(ak.pageX,al.startX),af=Math.max(ak.pageX,al.startX),ai=(ab.high-ab.low),ah=ab.viewport_container.width(),aj=ab.low;ab.low=Math.round(ag/ah*ai)+aj;ab.high=Math.round(af/ah*ai)+aj;$(al.proxy).remove();ab.request_redraw()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ab.resize_window()},500)});$(document).bind("redraw",function(){ab.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ab){return this.config.get_value(ab.toLowerCase()+"_color")||this.config.get_value("n_color")}});o(X.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ac,ae,ab,af){if(this.timer){clearTimeout(this.timer)}if(af){var ad=this;this.timer=setTimeout(function(){ad.trigger("navigate",ac+":"+ae+"-"+ab)},500)}else{view.trigger("navigate",ac+":"+ae+"-"+ab)}},update_location:function(ab,ad){this.location_span.text(commatize(ab)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ab)+"-"+commatize(ad));var ac=view.chrom_select.val();if(ac!==""){this.trigger_navigate(ac,view.low,view.high,true)}},load_chroms:function(ad){ad.num=v;var ab=this,ac=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ad,dataType:"json",success:function(af){if(af.chrom_info.length===0){return}if(af.reference){var ag=new B(ab);ab.add_label_track(ag);ab.reference_track=ag}ab.chrom_data=af.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,ae=ab.chrom_data.length;ai<ae;ai++){var ah=ab.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(af.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(af.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ab.chrom_select.html(aj);ab.chrom_start_index=af.start_index;ac.resolve(af.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ab.dbkey)}});return ac},change_chrom:function(ag,ac,ai){var ad=this;if(!ad.chrom_data){ad.load_chroms_deferred.then(function(){ad.change_chrom(ag,ac,ai)});return}if(!ag||ag==="None"){return}if(ag==="previous"){ad.load_chroms({low:this.chrom_start_index-v});return}if(ag==="next"){ad.load_chroms({low:this.chrom_start_index+v});return}var ah=$.grep(ad.chrom_data,function(aj,ak){return aj.chrom===ag})[0];if(ah===undefined){ad.load_chroms({chrom:ag},function(){ad.change_chrom(ag,ac,ai)});return}else{if(ag!==ad.chrom){ad.chrom=ag;ad.chrom_select.val(ad.chrom);ad.max_high=ah.len-1;ad.reset();for(var af=0,ab=ad.drawables.length;af<ab;af++){var ae=ad.drawables[af];if(ae.init){ae.init()}}if(ad.reference_track){ad.reference_track.init()}}if(ac===undefined&&ai===undefined){ad.low=0;ad.high=ad.max_high}else{ad.low=(ac!==undefined?Math.max(ac,0):0);if(ai===undefined){ad.low=Math.max(ad.low-15,0);ad.high=ad.low+30}else{ad.high=Math.min(ai,ad.max_high)}}ad.reset_overview();ad.request_redraw()}},go_to:function(af){af=af.replace(/,/g,"");af=af.replace(/:|\-/g," ");var ac=af.split(/\s+/),ae=ac[0],ad=(ac[1]?parseInt(ac[1],10):undefined),ab=(ac[2]?parseInt(ac[2],10):undefined);this.change_chrom(ae,ad,ab)},move_fraction:function(ad){var ab=this;var ac=ab.high-ab.low;this.move_delta(ad*ac)},move_delta:function(ae){var ab=this;var ad=ab.high-ab.low;if(ab.low-ae<ab.max_low){ab.low=ab.max_low;ab.high=ab.max_low+ad}else{if(ab.high-ae>ab.max_high){ab.high=ab.max_high;ab.low=ab.max_high-ad}else{ab.high-=ae;ab.low-=ae}}ab.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ab.request_redraw()},200);var ac=ab.chrom_select.val();this.trigger_navigate(ac,ab.low,ab.high,true)},add_drawable:function(ab){y.prototype.add_drawable.call(this,ab);ab.init();this.changed();this.update_intro_div()},add_label_track:function(ab){ab.view=this;ab.init();this.label_tracks.push(ab)},remove_drawable:function(ad,ac){y.prototype.remove_drawable.call(this,ad);if(ac){var ab=this;ad.container_div.hide(0,function(){$(this).remove();ab.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ac,ad){var ab=this,ae=(ad?[ad]:ab.drawables);aa.each(ae,function(af){var ag=aa.find(ab.tracks_to_be_redrawn,function(ah){return ah[0]===af});if(ag){ag[1]=ac}else{ab.tracks_to_be_redrawn.push([af,ac])}});if(!this.requested_redraw){requestAnimationFrame(function(){ab._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ab=this.low,af=this.high;if(ab<this.max_low){ab=this.max_low}if(af>this.max_high){af=this.max_high}var ac=this.high-this.low;if(this.high!==0&&ac<this.min_separation){af=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ag=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=13;this.overview_box.css({left:ae,width:Math.max(ad,ag)}).show();if(ag<ad){this.overview_box.css("left",ae-(ad-ag)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ag})}aa.each(this.tracks_to_be_redrawn,function(aj){var ah=aj[0],ai=aj[1];if(ah){ah._draw(ai)}});this.tracks_to_be_redrawn=[];aa.each(this.label_tracks,function(ah){ah._draw()})},zoom_in:function(ac,ad){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ae=this.high-this.low,af=ae/2+this.low,ab=(ae/this.zoom_factor)/2;if(ac){af=ac/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(af-ab);this.high=Math.round(af+ab);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ac=this.high-this.low,ad=ac/2+this.low,ab=(ac*this.zoom_factor)/2;this.low=Math.round(ad-ab);this.high=Math.round(ad+ab);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ad){if(this.overview_drawable){if(this.overview_drawable.dataset.id===ad.dataset.id){return}this.overview_viewport.find(".track").remove()}var ac=ad.copy({content_div:this.overview_viewport}),ab=this;ac.header_div.hide();ac.is_overview=true;ab.overview_drawable=ac;this.overview_drawable.postdraw_actions=function(){ab.overview_highlight.show().height(ab.overview_drawable.content_div.height());ab.overview_viewport.height(ab.overview_drawable.content_div.height()+ab.overview_box.outerHeight());ab.overview_close.show();ab.resize_window()};ab.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(ab){P.Tool.prototype.initialize.call(this,ab);var ac=true;if(ab.tool_state!==undefined&&ab.tool_state.hidden!==undefined){ac=ab.tool_state.hidden}this.set("hidden",ac);this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ab){return aa.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change :input":"update_value"},render:function(){var ad=this.$el.addClass("param-row"),ae=this.model;var ab=$("<div>").addClass("param-label").text(ae.get("label")).appendTo(ad);var ac=$("<div/>").addClass("param-input").html(ae.get("html")).appendTo(ad);ac.find(":input").val(ae.get("value"));$("<div style='clear: both;'/>").appendTo(ad)},update_value:function(ab){this.model.set_value($(ab.target).val())}});var Z=Backbone.View.extend({initialize:function(ab){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ac=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ag){ag.stopPropagation()}).click(function(ag){ag.stopPropagation()}).bind("dblclick",function(ag){ag.stopPropagation()}).keydown(function(ag){ag.stopPropagation()});var ad=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ah){var ag=new t({model:ah});ag.render();parent_div.append(ag.$el)});parent_div.find("input").click(function(){$(this).select()});var ae=$("<div>").addClass("param-row").appendTo(parent_div);var af=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ae);var ab=$("<input type='submit'>").attr("value","Run on visible region").appendTo(ae);ab.click(function(){ac.run_on_region()});af.click(function(){ac.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ab=0;ab<this.params.length;ab++){this.params[ab].update_value()}},run_on_dataset:function(){var ab=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ab.id},null,function(ac){Galaxy.modal.show({title:ab.get("name")+" is Running",body:ab.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ac=this.model.get("track"),af=this.model,ah=new w.GenomeRegion({chrom:ac.view.chrom,start:ac.view.low,end:ac.view.high}),ai={target_dataset_id:ac.dataset.id,action:"rerun",tool_id:af.id,regions:[ah.toJSON()]},ag=ac,ak=af.get("name")+ag.tool_region_and_parameters_str(ah),ab;if(ag.container===view){var aj=new N(view,view,{name:ac.config.get_value("name")});var ae=ag.container.replace_drawable(ag,aj,false);aj.container_div.insertBefore(ag.view.content_div.children()[ae]);aj.add_drawable(ag);ag.container_div.appendTo(aj.content_div);ab=aj}else{ab=ag.container}var ad=new ag.constructor(view,ab,{name:ak,hda_ldda:"hda"});ad.init_for_tool_data();ad.change_mode(ag.mode);ad.set_filters_manager(ag.filters_manager.copy(ad));ad.update_icons();ab.add_drawable(ad);ad.tiles_div.text("Starting job.");this.run(ai,ad,function(al){ad.set_dataset(new W.Dataset(al));ad.tiles_div.text("Running job.");ad.init()})},run:function(ab,ad,ae){ab.inputs=this.model.get_inputs_dict();var ac=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ab),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(af){return af!=="pending"}});$.when(ac.go()).then(function(af){if(af==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(af.error){ad.container_div.addClass("error");ad.content_div.text(x+af.message)}else{ae(af)}}})}});var C=function(ab,ac){J.Scaler.call(this,ac);this.filter=ab};C.prototype.gen_val=function(ab){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(ab[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var b=function(ab,ae,af,ac,ad){this.track=ab;this.region=ae;this.low=ae.get("start");this.high=ae.get("end");this.w_scale=af;this.canvas=ac;this.html_elt=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ad,ai,ak,ac,af,ag,al,ab,ah,ae,aj){b.call(this,ad,ai,ak,ac,af);this.mode=ag;this.all_slotted=ab;this.feature_mapper=ah;this.has_icons=false;this.incomplete_features=ae;this.seq_data=aj};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(an){if(!this.hovered){return}var ai=$(this).offset(),am=an.pageX-ai.left,al=an.pageY-ai.top,ar=ac.feature_mapper.get_feature_data(am,al),aj=(ar?ar[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!aj||$(this).attr("id")!==aj.toString()){$(this).remove()}});if(ar){var ae=ab[aj];if(!ae){var ao={name:ar[3],start:ar[1],end:ar[2],strand:ar[4]},ah=ac.track.filters_manager.filters,ag;for(var ak=0;ak<ah.length;ak++){ag=ah[ak];ao[ag.name]=ar[ag.index]}ae=$("<div/>").attr("id",aj).addClass("feature-popup");var at=$("<table/>"),aq,ap,au;for(aq in ao){ap=ao[aq];au=$("<tr/>").appendTo(at);$("<th/>").appendTo(au).text(aq);$("<td/>").attr("align","left").appendTo(au).text(typeof(ap)==="number"?U(ap,2):ap)}ae.append($("<div class='feature-popup-inner'>").append(at));ab[aj]=ae}ae.appendTo($(this).parents(".track-content").children(".overlay"));var af=am+parseInt(ac.html_elt.css("left"),10)-ae.width()/2,ad=al+parseInt(ac.html_elt.css("top"),10)+7;ae.css("left",af+"px").css("top",ad+"px")}else{if(!an.isPropagationStopped()){an.stopPropagation();$(this).siblings().each(function(){$(this).trigger(an)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ac,ab,ad){o(ad,{drag_handle_class:"draghandle"});p.call(this,ac,ab,ad);this.dataset=null;if(ad.dataset){this.dataset=(ad.dataset instanceof Backbone.Model?ad.dataset:new W.Dataset(ad.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ad?ad.data_query_wait:I);this.data_manager=("data_manager" in ad?ad.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ac.dbkey,chroms_info:{chrom_info:ac.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=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ad)||ad.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"application-dock-270",on_click_fn:function(ab){ab.view.set_overview(ab)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"ui-slider-050",on_click_fn:function(ab){if(ab.filters_manager.visible()){ab.filters_manager.clear_filters()}else{ab.filters_manager.init_filters()}ab.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ab){ab.tool.toggle();if(ab.tool.is_visible()){ab.set_name(ab.config.get_value("name")+ab.tool_region_and_parameters_str())}else{ab.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ab){var ae='<strong>Tool</strong>: <%= track.tool.get("name") %><br/><strong>Dataset</strong>: <%= track.config.get("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>',ad=aa.template(ae,{track:ab});var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ac=function(){var ai=$('select[name="regions"] option:selected').val(),ak,ah=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),aj=aa.map($(".bookmark"),function(al){return new w.GenomeRegion({from_str:$(al).children(".position").text()})});if(ai==="cur"){ak=[ah]}else{if(ai==="bookmarks"){ak=aj}else{ak=[ah].concat(aj)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ab.dataset.id,hda_ldda:ab.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(ak).toJSON())})},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ac()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ad,buttons:{No:ag,Yes:ac}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id)},build_header_div:function(){var ab=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ab)}this.name_div=$("<div/>").addClass("track-name").appendTo(ab).text(this.config.get_value("name")).attr("id",this.config.get_value("name").replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ab},set_dataset:function(ab){this.dataset=ab;this.data_manager.set("dataset",ab)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ab=this;var ae=false;var ad=false;var ac=$("<div class='track-resize'>");$(ab.container_div).hover(function(){if(ab.config.get_value("content_visible")){ae=true;ac.show()}},function(){ae=false;if(!ad){ac.hide()}});ac.hide().bind("dragstart",function(af,ag){ad=true;ag.original_height=$(ab.content_div).height()}).bind("drag",function(ag,ah){var af=Math.min(Math.max(ah.original_height+ah.deltaY,ab.min_height_px),ab.max_height_px);$(ab.tiles_div).css("height",af);ab.visible_height_px=(ab.max_height_px===af?0:af);ab.on_resize()}).bind("dragend",function(af,ag){ab.tile_cache.clear();ad=false;if(!ae){ac.hide()}ab.config.set_value("height",ab.visible_height_px);ab.changed()}).appendTo(ab.container_div)},set_display_modes:function(ae,ah){this.display_modes=ae;this.mode=(ah?ah:(this.config&&this.config.get_value("mode")?this.config.get_value("mode"):this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ac=this,af={};for(var ad=0,ab=ac.display_modes.length;ad<ab;ad++){var ag=ac.display_modes[ad];af[ag]=function(ai){return function(){ac.change_mode(ai);ac.icons_div.show();ac.container_div.mouseleave(function(){ac.icons_div.hide()})}}(ag)}make_popupmenu(this.action_icons.mode_icon,af)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},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 V){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 Y){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},show_message:function(ab){this.tiles_div.remove();return $("<span/>").addClass("message").html(ab).appendTo(this.content_div)},init:function(ad){var ac=this;ac.enabled=false;ac.tile_cache.clear();ac.data_manager.clear();ac.content_div.children().remove();ac.container_div.removeClass("nodata error pending");ac.tiles_div=$("<div/>").addClass("tiles").appendTo(ac.content_div);if(!ac.dataset.id){return}var ab=$.Deferred(),ae={hda_ldda:ac.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ac.view.chrom,retry:ad};$.getJSON(this.dataset.url(),ae,function(af){if(!af||af==="error"||af.kind==="error"){ac.container_div.addClass("error");var ag=ac.show_message(m);if(af.message){ag.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+af.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ag.append($("<span/>").text(" "));ag.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ac.init(true)}))}}else{if(af==="no converter"){ac.container_div.addClass("error");ac.show_message(H)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ac.container_div.addClass("nodata");ac.show_message(E)}else{if(af==="pending"){ac.container_div.addClass("pending");ac.show_message(u);setTimeout(function(){ac.init()},ac.data_query_wait)}else{if(af==="data"||af.status==="data"){if(af.valid_chroms){ac.valid_chroms=af.valid_chroms;ac.update_icons()}ac.tiles_div.text(T);if(ac.view.chrom){ac.tiles_div.text("");ac.tiles_div.css("height",ac.visible_height_px+"px");ac.enabled=true;$.when.apply($,ac.predraw_init()).done(function(){ab.resolve();ac.container_div.removeClass("nodata error pending");ac.request_draw()})}else{ab.resolve()}}}}}}});this.update_icons();return ab},predraw_init:function(){var ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(ae&&ae.min&&ae.max){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_default_value("min_value",ad);ab.config.set_default_value("max_value",af);ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},get_drawables:function(){return this}});var L=function(ad,ac,af){f.call(this,ad,ac,af);var ab=this;k(ab.container_div,ab.drag_handle_class,".group",ab);this.filters_manager=new h.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(af.tool?new q(aa.extend(af.tool,{track:this,tool_state:af.tool_state})):null);this.tile_cache=new w.Cache(O);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ae=new Z({model:this.tool});ae.render();this.dynamic_tool_div=ae.$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(af.mode){this.change_mode(af.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(ab){$(".tooltip").remove();ab.slotters[ab.view.resolution_px_b].max_rows*=2;ab.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ab){var ac=this.to_dict();o(ac,{data_manager:this.data_manager});var ad=new this.constructor(this.view,ab,ac);ad.change_mode(this.mode);ad.enabled=this.enabled;return ad},set_filters_manager:function(ab){this.filters_manager=ab;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 ab=this;return $.getJSON(ab.dataset.url(),{data_type:"data",stats:true,chrom:ab.view.chrom,low:0,high:ab.view.max_high,hda_ldda:ab.dataset.get("hda_ldda")},function(ac){var ae=ac.data;if(isNaN(parseFloat(ab.config.get_value("min_value")))||isNaN(parseFloat(ab.config.get_value("max_value")))){var ad=ae.min,af=ae.max;ad=Math.floor(Math.min(0,Math.max(ad,ae.mean-2*ae.sd)));af=Math.ceil(Math.max(0,Math.min(af,ae.mean+2*ae.sd)));ab.config.set_value("min_value",ad);ab.config.set_value("max_value",af)}})},change_mode:function(ac){var ab=this;ab.mode=ac;ab.config.set_value("mode",ac);if(ac==="Auto"){this.data_manager.clear()}ab.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ab.mode+")");return ab},update_icons:function(){var ab=this;if(ab.filters_available){ab.action_icons.filters_icon.show()}else{ab.action_icons.filters_icon.hide()}if(ab.tool){ab.action_icons.tools_icon.show();ab.action_icons.param_space_viz_icon.show()}else{ab.action_icons.tools_icon.hide();ab.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ac,ab){return ac+"_"+ab},request_draw:function(ab){if(ab&&ab.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ab,this)},before_draw:function(){this.max_height_px=0},_draw:function(ap){if(!this.can_draw()){return}var am=ap&&ap.clear_after,ak=this.view.low,af=this.view.high,ai=af-ak,ac=this.view.container.width(),ao=this.view.resolution_px_b,ae=1/ao;if(this.is_overview){ak=this.view.max_low;af=this.view.max_high;ao=ac/(view.max_high-view.max_low);ae=1/ao}this.before_draw();this.tiles_div.children().addClass("remove");var ab=Math.floor(ak/(ae*Q)),aj,al,ag,ah=[],an=[];while((ab*Q*ae)<af){aj=Math.floor(ab*Q*ae);al=new w.GenomeRegion({chrom:this.view.chrom,start:aj,end:Math.min(aj+Math.ceil(Q*ae),this.view.max_high)});ag=this.draw_helper(al,ao,ap);ah.push(ag);$.when(ag).then(function(aq){an.push(aq)});ab+=1}if(!am){this.tiles_div.children(".remove").removeClass("remove").remove()}var ad=this;$.when.apply($,ah).then(function(){ad.tiles_div.children(".remove").remove();an=aa.filter(an,function(aq){return aq!==null});if(an.length!==0){ad.postdraw_actions(an,ac,ao,am)}})},_add_yaxis_label:function(ae,ag){var ac=this,af=(ae==="max"?"top":"bottom"),ah=(ae==="max"?"max":"min"),ab=(ae==="max"?"max_value":"min_value"),ad=this.container_div.find(".yaxislabel."+af);ag=ag||function(){ac.request_draw({clear_tile_cache:true})};if(ad.length!==0){ad.text(ac.config.get_value(ab))}else{ad=$("<div/>").text(ac.config.get_value(ab)).make_text_editable({num_cols:12,on_finish:function(ai){$(".tooltip").remove();ac.config.set_value(ab,ai);ag()},help_text:"Set "+ah+" value"}).addClass("yaxislabel "+af).css("color",this.config.get_value("label_color"));this.container_div.prepend(ad)}},postdraw_actions:function(ae,af,ah,ab){var ad=aa.filter(ae,function(ai){return(ai instanceof K)});if(ad.length>0){this.max_height_px=0;var ac=this;aa.each(ae,function(ai){if(!(ai instanceof K)){ai.html_elt.remove();ac.draw_helper(ai.region,ah,{force:true,mode:"Coverage"})}});ac._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ag=aa.find(ae,function(ai){return ai.has_icons});if(ag){aa.each(ae,function(ai){if(!ai.has_icons){ai.html_elt.css("padding-top",D)}})}}},get_mode:function(ab){return this.mode},update_auto_mode:function(ab){},_get_drawables:function(){return[this]},draw_helper:function(ak,am,an){if(!an){an={}}var ac=an.force,ah=an.mode||this.mode,ae=1/am,ad=this,af=this._get_drawables(),al=this._gen_tile_cache_key(am,ak),ag=function(ao){return(ao&&"track" in ao)};var ai=(ac?undefined:ad.tile_cache.get_elt(al));if(ai){if(ag(ai)){ad.show_tile(ai,am)}return ai}if(an.data_fetch===false){return null}var aj=function(){var ao=(aa.find(A,function(aq){return aq===ah})?"Coverage":ah);var ap=aa.map(af,function(aq){return aq.data_manager.get_data(ak,ao,ae,ad.data_url_extra_params)});if(view.reference_track){ap.push(view.reference_track.data_manager.get_data(ak,ah,ae,view.reference_track.data_url_extra_params))}return ap};var ab=$.Deferred();ad.tile_cache.set_elt(al,ab);$.when.apply($,aj()).then(function(){var ao=aj(),au=ao,aA;if(aa.find(ao,function(aC){return j.is_deferred(aC)})){ad.tile_cache.set_elt(al,undefined);$.when(ad.draw_helper(ak,am,an)).then(function(aC){ab.resolve(aC)});return}if(view.reference_track){aA=view.reference_track.data_manager.subset_entry(ao.pop(),ak)}var av=[],ar=[];aa.each(af,function(aF,aC){var aE=aF.mode,aD=au[aC];if(aE==="Auto"){aE=aF.get_mode(aD);aF.update_auto_mode(aE)}av.push(aE);ar.push(aF.get_canvas_height(aD,aE,am,ap))});var at=ad.view.canvas_manager.new_canvas(),aw=ak.get("start"),aB=ak.get("end"),aq=0,ap=Math.ceil((aB-aw)*am)+ad.left_offset,ay=aa.max(ar),ax;at.width=ap;at.height=(an.height||ay);var az=at.getContext("2d");az.translate(ad.left_offset,0);if(af.length>1){az.globalAlpha=0.5;az.globalCompositeOperation="source-over"}aa.each(af,function(aD,aC){ax=aD.draw_tile(au[aC],az,av[aC],ak,am,aA)});if(ax!==undefined){ad.tile_cache.set_elt(al,ax);ad.show_tile(ax,am)}ab.resolve(ax)});return ab},get_canvas_height:function(ab,ad,ae,ac){return this.visible_height_px},_draw_line_track_tile:function(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.LinePainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new K(this,af,ah,ae,ab.data)},draw_tile:function(ab,ac,af,ae,ag,ad){},show_tile:function(ad,ag){var ac=this,ab=ad.html_elt;ad.predisplay_actions();var af=(ad.low-(this.is_overview?this.view.max_low:this.view.low))*ag;if(this.left_offset){af-=this.left_offset}ab.css("left",af);if(ab.hasClass("remove")){ab.removeClass("remove")}else{this.tiles_div.append(ab)}ab.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ab.height()-2);ab.parent().children().css("height",this.max_height_px+"px");var ae=this.max_height_px;if(this.visible_height_px!==0){ae=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ae+"px")},tool_region_and_parameters_str:function(ae){var ab=this,ad=(ae!==undefined?ae.toString():"all"),ac=aa.values(ab.tool.get_inputs_dict()).join(", ");return" - region=["+ad+"], parameters=["+ac+"]"},data_and_mode_compatible:function(ab,ac){if(ac==="Auto"){return true}else{if(ac==="Coverage"){return ab.dataset_type==="bigwig"}else{if(ab.dataset_type==="bigwig"||ab.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ab){if(ab.message||ab.extra_info==="no_detail"){return false}else{if(ab.dataset_type==="bigwig"){return(ab.data[1][0]-ab.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 V=function(ac,ab){var ad={resize:false};f.call(this,ac,ab,ad);this.container_div.addClass("label-track")};o(V.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(af){var ad=this.view,ae=ad.high-ad.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(ae)/Math.log(10)))),ab=Math.floor(ad.low/ai)*ai,ag=this.view.container.width(),ac=$("<div/>").addClass("label-container");while(ab<ad.high){var ah=(ab-ad.low)/ae*ag;ac.append($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,config_params:aa.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(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,config_onchange:function(){this.set_name(this.config.get_value("name"));this.request_draw({clear_tile_cache:true})},on_resize:function(){var ab=this.visible_height_px;aa.each(this.drawables,function(ac){ac.visible_height_px=ab});f.prototype.on_resize.call(this)},change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.when.apply($,ad).then(function(){ab.enabled=true;ab.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 ae=new N(this.view,this.container,{name:this.config.get_value("name")}),ab;for(var ad=0;ad<this.drawables.length;ad++){ab=this.drawables[ad];ab.update_icons();ae.add_drawable(ab);ab.container=ae;ae.content_div.append(ab.container_div)}var ac=this.container.replace_drawable(this,ae,true);ae.request_draw({clear_tile_cache:true})},before_draw:function(){var ac=aa.min(aa.map(this.drawables,function(ad){return ad.config.get_value("min_value")})),ab=aa.max(aa.map(this.drawables,function(ad){return ad.config.get_value("max_value")}));this.config.set_value("min_value",ac);this.config.set_value("max_value",ab);aa.each(this.drawables,function(ad){ad.config.set_value("min_value",ac);ad.config.set_value("max_value",ab)})},update_all_min_max:function(){var ac=this,ab=this.config.get_value("min_value"),ad=this.config.get_value("max_value");aa.each(this.drawables,function(ae){ae.config.set_value("min_value",ab);ae.config.set_value("max_value",ad)});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(ah,ab,ak,ag){var af=-1,ad;for(ad=0;ad<ah.length;ad++){var ai=ah[ad].html_elt.find("canvas").height();if(ai>af){af=ai}}for(ad=0;ad<ah.length;ad++){var ae=ah[ad];if(ae.html_elt.find("canvas").height()!==af){this.draw_helper(ae.region,ak,{force:true,height:af});ae.html_elt.remove()}}var ac=this,aj=function(){ac.update_all_min_max()};this._add_yaxis_label("min",aj);this._add_yaxis_label("max",aj)}});var B=function(ab){L.call(this,ab,{content_div:ab.top_labeltrack},{resize:false});this.left_offset=ab.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:aa.union(p.prototype.config_params,[{key:"height",type:"int",default_value:13,hidden:true}]),build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ac,ad,ab){if(ad>this.view.canvas_manager.char_width_px){this.tiles_div.show();return L.prototype.draw_helper.call(this,ac,ad,ab)}else{this.tiles_div.hide();return null}},can_subset:function(ab){return true},draw_tile:function(ad,aj,ae,ag,ak){var ac=this.data_manager.subset_entry(ad,ag),ai=ac.data;var ab=aj.canvas;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var af=0,ah=ai.length;af<ah;af++){aj.fillStyle=this.view.get_base_color(ai[af]);aj.fillText(ai[af],Math.floor(af*ak),10)}return new b(this,ag,ak,ab,ac)}});var g=function(ac,ab,ad){this.mode="Histogram";L.call(this,ac,ab,ad)};o(g.prototype,p.prototype,L.prototype,{display_modes:A,config_params:aa.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(ab,ac,ae,ad,af){return this._draw_line_track_tile(ab,ac,ae,ad,af)},can_subset:function(ab){return(ab.data[1][0]-ab.data[0][0]===1)},postdraw_actions:function(ac,ad,ae,ab){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(ac,ab,ad){this.mode="Heatmap";L.call(this,ac,ab,ad)};o(r.prototype,p.prototype,L.prototype,{display_modes:["Heatmap"],config_params:aa.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(ab,ad,ag,af,ah){var ae=ad.canvas,ac=new J.DiagonalHeatmapPainter(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag);ac.draw(ad,ae.width,ae.height,ah);return new b(this,af,ah,ae,ab.data)}});var c=function(ac,ab,ad){L.call(this,ac,ab,ad);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:aa.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(an,ae,ap,am){L.prototype.postdraw_actions.call(this,an,ae,ap,am);var ag=this,ah,al=aa.filter(an,function(aq){return(aq instanceof K)});if(al.length===0){var ab={};aa.each(aa.pluck(an,"incomplete_features"),function(aq){aa.each(aq,function(ar){ab[ar[0]]=ar})});var ao=this;aa.each(an,function(aq){ao.draw_tile({data:aa.values(ab)},aq.canvas.getContext("2d"),aq.mode,aq.region,ap,aq.seq_data,true)})}if(ag.filters_manager){var af=ag.filters_manager.filters,aj;for(aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<an.length;ah++){if(an[ah].data.length){ak=an[ah].data[0];for(aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(an[0] instanceof M){var ac=true;for(ah=0;ah<an.length;ah++){if(!an[ah].all_slotted){ac=false;break}}if(!ac){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ab){if(this.mode==="Auto"){if(ab==="no_detail"){ab="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ab+")")}},incremental_slots:function(af,ab,ae){var ac=this.view.canvas_manager.dummy_context,ad=this.slotters[af];if(!ad||(ad.mode!==ae)){ad=new (s.FeatureSlotter)(af,ae,z,function(ag){return ac.measureText(ag)});this.slotters[af]=ad}return ad.slot_features(ab)},get_mode:function(ab){if(ab.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(ab,af,ag,ac){if(af==="Coverage"||ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=this.incremental_slots(ag,ab.data,af);var ad=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return Math.max(this.min_height_px,ad.get_required_height(ae,ac))}},draw_tile:function(am,ar,ap,af,aj,ae,an){var aq=this,ad=ar.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,ar,ap,af,aj)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.config.to_key_value_dict(),ap,aB,az,ae,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.config.get_value("block_color");ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(am.data){var ab=aA.draw(ar,ad.width,ad.height,aj,ao);aw=ab.feature_mapper;incomplete_features=ab.incomplete_features;aw.translation=-ag}if(!an){return new M(aq,af,aj,ad,am.data,ap,am.message,all_slotted,aw,incomplete_features,ae)}}});var Y=function(ac,ab,ad){L.call(this,ac,ab,ad);this.painter=J.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Y.prototype,p.prototype,L.prototype,{display_modes:["Auto","Coverage","Dense","Squish","Pack"],config_params:aa.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(ab,ae,ag,af,ah){if(ab.dataset_type==="bigwig"){return this._draw_line_track_tile(ab,ae,"Histogram",af,ah)}else{var ad=this.view,ac=new (this.painter)(ab.data,af.get("start"),af.get("end"),this.config.to_key_value_dict(),ag,function(ai){return ad.get_base_color(ai)});ac.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new b(this,af,ah,ae.canvas,ab.data)}},get_canvas_height:function(ab,af,ag,ad){if(ab.dataset_type==="bigwig"){return this.summary_draw_height}else{var ac=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ac===0&&ab.data.length!==0){ac=ab.data[0][7].match(/,/g);if(ac===null){ac=1}else{ac=ac.length+1}}var ae=new (this.painter)(null,null,null,this.config.to_key_value_dict(),af);return ae.get_required_height(ac)}},predraw_init:function(){var ab=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ab.push(this.dataset.fetch())}return ab},postdraw_actions:function(af,ag,ai,ac){L.prototype.postdraw_actions.call(this,af,ag,ai,ac);var ae=aa.filter(af,function(aj){return(aj instanceof K)});var ad=this.dataset.get_metadata("sample_names");if(ae.length===0&&this.config.get_value("show_labels")&&ad&&ad.length>1){var ab;if(this.container_div.find(".yaxislabel.variant").length===0){ab=this.config.get_value("summary_height")/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ab+"px",top:(this.config.get_value("summary_height")-ab)/2+"px"}));if(this.config.get_value("show_sample_data")){var ah=ad.join("<br/>");this.tiles_div.prepend($("<div/>").html(ah).addClass("yaxislabel variant top sample").css({top:this.config.get_value("summary_height")}))}}ab=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ab,"line-height":ab});$(this.tiles_div).find(".yaxislabel").css("color",this.config.get_value("label_color"))}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ac,ab,ad){c.call(this,ac,ab,ad);this.painter=J.ReadPainter;this.update_icons()};o(S.prototype,p.prototype,L.prototype,c.prototype,{config_params:aa.union(p.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color",default_value:"#DDDDDD"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:"#AAAAAA"},{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:Y,VcfTrack:Y};var n=function(ad,ac,ab){if("copy" in ad){return ad.copy(ab)}else{var ae=ad.obj_type;if(!ae){ae=ad.track_type}return new d[ae](ac,ab,ad)}};return{TracksterView:X,DrawableGroup:N,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:S,VariantTrack:Y,CompositeTrack:e,object_from_template:n}});
\ No newline at end of file
diff -r 13c90b7197bf6e81aa630b6ccd1e128ea66eebbe -r b231f3463565137c81dce701cd194095df873fed static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -1661,7 +1661,7 @@
var ToolParameterView = Backbone.View.extend({
events: {
- 'change input': 'update_value'
+ 'change :input': 'update_value'
},
render: function() {
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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