commit/galaxy-central: guerler: Trackster: Fix trackster button in tabular data viewer
by commits-noreplyï¼ bitbucket.org 27 Mar '14
by commits-noreplyï¼ bitbucket.org 27 Mar '14
27 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/b6d04f39a37f/
Changeset: b6d04f39a37f
User: guerler
Date: 2014-03-27 04:00:42
Summary: Trackster: Fix trackster button in tabular data viewer
Affected #: 9 files
diff -r 8fe1141e032eb0ff70f72c3a438c80c125a97c71 -r b6d04f39a37fd73abd9c0c5e9695d74330786f47 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")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&(this.options.buttons.Pause||$(document).on("keyup",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-portlet",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find("#content"),this.$title=this.$el.find("#title-text"),this.options.height&&(this.$el.find("#body").css("height",this.options.height),this.$el.find("#content").css("overflow",this.options.overflow)),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var n=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),n.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var n=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),n.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="toolForm portlet-view no-highlight">';if(e.title||e.icon)t+='<div id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var n=this;this.options.onchange&&this.$select.on("change",function(){n.value(n.$select.val())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return"<label><b>"+e.title+"</b></label>"},value:function(){return options.title}}),r=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),i=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),s=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),o=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),u=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),f=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),c=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:r,Icon:i,ButtonIcon:s,Input:c,Anchor:o,Message:u,Searchbox:a,Title:f,Select:t,ButtonMenu:l}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},cleanup:function(t){var n=t.get("dataset_id_job");if(n!=""){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()}),t.set("dataset_id_job","")}},submit:function(t,n,r,i){var s=this,o=t.id,u=t.get("type"),a=this.app.types.get(u);data={tool_id:"rkit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:u,columns:r,settings:n}},t.state("submit","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response.");else{s._refreshHdas();var n=e.outputs[0];t.state("queued","Job has been queued..."),t.set("dataset_id_job",n.id),s._loop(n.id,function(e){switch(e.state){case"ok":return t.state("success","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),!0;case"running":return t.state("running","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the R-kit. Please make sure it is installed. "+n)})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/jobs/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/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})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","mvc/visualization/visualization-model"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state_info",t),this.set("state",e)},drawable:function(){return this.get("state")=="ok"||this.get("state")=="failed"||this.get("state")=="initialized"},editable:function(){return this.get("state")=="ok"||this.get("state")=="failed"}})}),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.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.state("ok","Loaded previously saved visualization."),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($(this._template()));var r=this;this.chart.on("redraw",function(){r._create_svg(),r._draw(r.chart)}),this.chart.on("change:state",function(){var e=r.$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":r.chart.trigger("drawable"),e.hide();break;case"failed":r.chart.trigger("drawable"),t.addClass("fa fa-warning");break;case"initialized":r.chart.trigger("drawable"),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_svg:function(){this.svg&&this.svg.remove(),this.$el.append($(this._template_svg())),this.svg=d3.select(this.$el.find("svg")[0])},_draw:function(e){var t=this;if(!e.drawable()){e.off("drawable"),e.on("drawable",function(){t.chart.off("drawable"),e.drawable()&&t._draw(e)});return}e.state("wait","Please wait...");var n=e.get("type"),r=this.app.types.get(n);if(!r.execute||r.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+n+"/"+n],function(n){var i=new n(t.app,{svg:t.svg});r.execute?e.get("dataset_id_job")==""?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){this.app.storage.save(),i.draw(e,t._defaultRequestDictionary(e))}):i.draw(e,t._defaultRequestDictionary(e)):i.draw(e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={groups:[]};t.execute?n.id=e.get("dataset_id_job"):n.id=e.get("dataset_id");var r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n},_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_svg:function(){return'<svg 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-gear",tooltip:"Customize 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)},_wait:function(e,t){if(e.editable())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=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<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.$el),this.table.append(o),s[o]=f}this.chart.state("wait","Loading metadata..."),this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show();r.chart.state("initialized","Metadata initialized...")})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll();for(var n in e)this._add(n,e[n],t)},_add:function(e,n,r){var i=null,s=n.type;switch(s){case"text":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"select":i=new t.Select.View({data:n.data,onchange:function(){r.set(e,i.value())}});break;case"slider":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"separator":i=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(s!="separator"){r.get(e)||r.set(e,n.init),i.value(r.get(e));var o=$("<div/>");o.append(i.$el),o.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(o)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(s,o){this.app=s,this.chart=this.app.chart,this.options=i.merge(o,this.optionsDefault),this.portlet=new r.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){u.app.go("viewer"),u._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){u.app.go("viewer"),u.app.storage.load()}})}});var u=this;this.table=new t.View({header:!1,onconfirm:function(e){u.chart.groups.length>0?u.app.modal.show({title:"Switching to another chart type?",body:"If you continue your settings and selections will be cleared.",buttons:{Cancel:function(){u.app.modal.hide()},Continue:function(){u.app.modal.hide(),u.table.value(e)}}}):u.table.value(e)},onchange:function(e){u.chart.groups.reset(),u.chart.settings.clear(),u.chart.set({type:e})},ondblclick:function(e){u.tabs.show("settings")},content:"No chart types available"});var f=0,l=s.types.attributes;for(var c in l){var h=l[c];this.table.add(++f+"."),h.execute?this.table.add(h.title+" (requires processing)"):this.table.add(h.title),this.table.append(c)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=u._addGroupModel();u.tabs.show(e.id)}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){u.app.config.set("title",u.title.value())}});var p=$("<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)),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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new o({id:i.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new u(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$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","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(),this.chart.trigger("redraw"),this.app.storage.save()}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:500}})}),define("plugin/charts/_nvd3/config",[],function(){return{title:"",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/bardiagram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/histogram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:!0,columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_tick:{init:".3"}}})}),define("plugin/charts/horizontal/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/line/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/linewithfocus/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/piechart/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Pie chart"})}),define("plugin/charts/scatterplot/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/stackedarea/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked area"})}),define("plugin/charts/types",["plugin/charts/bardiagram/config","plugin/charts/histogram/config","plugin/charts/horizontal/config","plugin/charts/line/config","plugin/charts/linewithfocus/config","plugin/charts/piechart/config","plugin/charts/scatterplot/config","plugin/charts/stackedarea/config"],function(e,t,n,r,i,s,o,u){return Backbone.Model.extend({defaults:{bardiagram:e,horizontal:n,histogram:t,line:r,linewithfocus:i,piechart:s,scatterplot:o,stackedarea:u}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new 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n=0;$.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:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),i=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),s=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),o=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),u=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),f=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),c=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:r,Icon:i,ButtonIcon:s,Input:c,Anchor:o,Message:u,Searchbox:a,Title:f,Select:t,ButtonMenu:l}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},cleanup:function(t){var n=t.get("dataset_id_job");if(n!=""){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()}),t.set("dataset_id_job","")}},submit:function(t,n,r,i){var s=this,o=t.id,u=t.get("type"),a=this.app.types.get(u);data={tool_id:"rkit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:u,columns:r,settings:n}},t.state("submit","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response.");else{s._refreshHdas();var n=e.outputs[0];t.state("queued","Job has been queued..."),t.set("dataset_id_job",n.id),s._loop(n.id,function(e){switch(e.state){case"ok":return t.state("success","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),!0;case"running":return t.state("running","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the R-kit. Please make sure it is installed. "+n)})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/jobs/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/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})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","mvc/visualization/visualization-model"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state_info",t),this.set("state",e)},drawable:function(){return this.get("state")=="ok"||this.get("state")=="failed"||this.get("state")=="initialized"},editable:function(){return this.get("state")=="ok"||this.get("state")=="failed"}})}),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.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.state("ok","Loaded previously saved visualization."),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()));var r=this;this.chart.on("redraw",function(){r._create_svg(),r._draw(r.chart)}),this.chart.on("change:state",function(){var e=r.$el.find("#info"),t=e.find("#icon");t.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var n=r.chart.get("state");switch(n){case"ok":r.chart.trigger("drawable"),e.hide();break;case"failed":r.chart.trigger("drawable"),t.addClass("fa fa-warning");break;case"initialized":r.chart.trigger("drawable");default:t.addClass("fa fa-spinner fa-spin")}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_create_svg:function(){this.svg&&this.svg.remove(),this.$el.append($(this._template_svg())),this.svg=d3.select(this.$el.find("svg")[0])},_draw:function(e){var t=this;if(!e.drawable()){e.off("drawable"),e.on("drawable",function(){t.chart.off("drawable"),e.drawable()&&t._draw(e)});return}e.state("wait","Please wait...");var n=e.get("type"),r=this.app.types.get(n);if(!r.execute||r.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+n+"/"+n],function(n){var i=new n(t.app,{svg:t.svg});r.execute?e.get("dataset_id_job")==""?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){this.app.storage.save(),i.draw(e,t._defaultRequestDictionary(e))}):i.draw(e,t._defaultRequestDictionary(e)):i.draw(e,t._defaultRequestDictionary(e))})},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={groups:[]};t.execute?n.id=e.get("dataset_id_job"):n.id=e.get("dataset_id");var r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n},_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_svg:function(){return'<svg 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-gear",tooltip:"Customize 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.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){if(e.editable())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait and try again.",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$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){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/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..."),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("initialized","Metadata initialized...")})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll();for(var n in e)this._add(n,e[n],t)},_add:function(e,n,r){var i=null,s=n.type;switch(s){case"text":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"select":i=new t.Select.View({data:n.data,onchange:function(){r.set(e,i.value())}});break;case"slider":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"separator":i=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(s!="separator"){r.get(e)||r.set(e,n.init),i.value(r.get(e));var o=$("<div/>");o.append(i.$el),o.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(o)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/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){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()}})}});var u=this;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"});var f=0,l=s.types.attributes;for(var c in l){var h=l[c];this.table.add(++f+"."),h.execute?this.table.add(h.title+" (requires processing)"):this.table.add(h.title),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.$el)),this.tabs.add({id:"main",title:"Start",$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","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(),this.chart.trigger("redraw"),this.app.storage.save()}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:500}})}),define("plugin/charts/_nvd3/config",[],function(){return{title:"",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/bardiagram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/histogram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:!0,columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_tick:{init:".3"}}})}),define("plugin/charts/horizontal/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/line/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/linewithfocus/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/piechart/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Pie chart"})}),define("plugin/charts/scatterplot/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/stackedarea/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked area"})}),define("plugin/charts/types",["plugin/charts/bardiagram/config","plugin/charts/histogram/config","plugin/charts/horizontal/config","plugin/charts/line/config","plugin/charts/linewithfocus/config","plugin/charts/piechart/config","plugin/charts/scatterplot/config","plugin/charts/stackedarea/config"],function(e,t,n,r,i,s,o,u){return Backbone.Model.extend({defaults:{bardiagram:e,horizontal:n,histogram:t,line:r,linewithfocus:i,piechart:s,scatterplot:o,stackedarea:u}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el),this.storage.load()?(this.go("viewer"),this.chart.trigger("redraw")):this.go("editor")},go:function(e){$(".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 8fe1141e032eb0ff70f72c3a438c80c125a97c71 -r b6d04f39a37fd73abd9c0c5e9695d74330786f47 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
@@ -135,7 +135,7 @@
this.title = new Ui.Input({
placeholder: 'Chart title',
onchange: function() {
- self.app.config.set('title', self.title.value());
+ self.chart.set('title', self.title.value());
}
});
@@ -223,6 +223,7 @@
_refreshTitle: function() {
var title = this.chart.get('title');
this.portlet.title(title);
+ this.title.value(title);
},
// update
diff -r 8fe1141e032eb0ff70f72c3a438c80c125a97c71 -r b6d04f39a37fd73abd9c0c5e9695d74330786f47 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
@@ -58,8 +58,6 @@
break;
case 'initialized':
self.chart.trigger('drawable');
- $icon.addClass('fa fa-warning');
- break;
default:
$icon.addClass('fa fa-spinner fa-spin');
break;
diff -r 8fe1141e032eb0ff70f72c3a438c80c125a97c71 -r b6d04f39a37fd73abd9c0c5e9695d74330786f47 lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -1242,7 +1242,7 @@
trans.sa_session.flush()
return imported_visualization
- def create_visualization( self, trans, type, title="Untitled Genome Vis", slug=None,
+ def create_visualization( self, trans, type, title="Untitled Visualization", slug=None,
dbkey=None, annotation=None, config={}, save=True ):
"""
Create visualiation and first revision.
diff -r 8fe1141e032eb0ff70f72c3a438c80c125a97c71 -r b6d04f39a37fd73abd9c0c5e9695d74330786f47 lib/galaxy/webapps/galaxy/api/visualizations.py
--- a/lib/galaxy/webapps/galaxy/api/visualizations.py
+++ b/lib/galaxy/webapps/galaxy/api/visualizations.py
@@ -178,9 +178,9 @@
revision = self.add_visualization_revision( trans, visualization, config, title, dbkey )
rval = { 'id' : id, 'revision' : revision.id }
- #TODO: allow updating vis title & slug
- #visualization.title = title
- #trans.sa_session.flush()
+ # allow updating vis title
+ visualization.title = title
+ trans.sa_session.flush()
except ( ItemAccessibilityException, ItemDeletionException ), exception:
trans.response.status = 403
diff -r 8fe1141e032eb0ff70f72c3a438c80c125a97c71 -r b6d04f39a37fd73abd9c0c5e9695d74330786f47 static/scripts/mvc/data.js
--- a/static/scripts/mvc/data.js
+++ b/static/scripts/mvc/data.js
@@ -1,5 +1,5 @@
// Additional dependencies: jQuery, underscore.
-define([], function() {
+define(['mvc/ui/ui-modal', 'mvc/ui/ui-frames'], function(Modal, Frames) {
/**
* Dataset metedata.
@@ -126,7 +126,10 @@
this.dark_row_color = '#DDD';
// load trackster button
- new TabularButtonTracksterView(options);
+ new TabularButtonTracksterView({
+ model : options.model,
+ $el : this.$el
+ });
},
render: function() {
@@ -301,8 +304,8 @@
});
// button for trackster visualization
-var TabularButtonTracksterView = Backbone.View.extend(
-{
+var TabularButtonTracksterView = Backbone.View.extend({
+
// gene region columns
col: {
chrom : null,
@@ -320,110 +323,137 @@
genome_build: null,
// data type
- data_type: null,
+ data_type : null,
// backbone initialize
- initialize: function (options)
- {
- // get options
- var attributes = options.model.attributes;
- var metadata = options.model.attributes.metadata.attributes;
+ initialize: function (options) {
+ // check if environment is available
+ var Galaxy = parent.Galaxy;
+
+ // link galaxy modal or create one
+ if (Galaxy && Galaxy.modal) {
+ this.modal = Galaxy.modal;
+ }
+
+ // link galaxy frames
+ if (Galaxy && Galaxy.frame) {
+ this.frame = Galaxy.frame;
+ }
+
+ // check
+ if (!this.modal || !this.frame) {
+ return;
+ }
+
+ // model/metadata
+ var model = options.model;
+ var metadata = model.get('metadata');
// check for datatype
- if (typeof attributes.data_type !== "undefined")
- this.data_type = attributes.data_type;
- else
- console.log("TabularButtonTrackster : Data type missing.");
-
+ if (!model.get('data_type')) {
+ return;
+ }
+
+ // get data type
+ this.data_type = model.get('data_type');
+
// check for bed-file format
- if (this.data_type == "bed")
+ if (this.data_type == 'bed')
{
// verify that metadata exists
- if (typeof metadata.chromCol !== "undefined" || typeof metadata.startCol !== "undefined" || typeof metadata.endCol !== "undefined")
+ if (metadata.get('chromCol') && metadata.get('startCol') && metadata.get('endCol'))
{
// read in columns
- this.col.chrom = metadata.chromCol - 1;
- this.col.start = metadata.startCol - 1;
- this.col.end = metadata.endCol - 1;
- } else
- console.log("TabularButtonTrackster : Bed-file metadata incomplete.");
+ this.col.chrom = metadata.get('chromCol') - 1;
+ this.col.start = metadata.get('startCol') - 1;
+ this.col.end = metadata.get('endCol') - 1;
+ } else {
+ console.log('TabularButtonTrackster : Bed-file metadata incomplete.');
+ return;
+ }
}
// check for vcf-file format
- if (this.data_type == "vcf")
+ if (this.data_type == 'vcf')
{
// search array
- function search (str, array)
- {
+ function search (str, array) {
for (var j = 0; j < array.length; j++)
if (array[j].match(str)) return j;
return -1;
};
// load
- this.col.chrom = search("Chrom", metadata.column_names);
- this.col.start = search("Pos", metadata.column_names);
+ this.col.chrom = search('Chrom', metadata.get('column_names'));
+ this.col.start = search('Pos', metadata.get('column_names'));
this.col.end = null;
// verify that metadata exists
- if (this.col.chrom == -1 || this.col.start == -1)
- console.log("TabularButtonTrackster : VCF-file metadata incomplete.");
+ if (this.col.chrom == -1 || this.col.start == -1) {
+ console.log('TabularButtonTrackster : VCF-file metadata incomplete.');
+ return;
+ }
}
-
+
// check
- if(this.col.chrom === null) {
+ if(this.col.chrom === undefined) {
return;
}
// get dataset id
- if (typeof options.model.attributes.id === "undefined") {
- console.log("TabularButtonTrackster : Dataset identification is missing.");
+ if (model.id) {
+ this.dataset_id = model.id;
} else {
- this.dataset_id = options.model.attributes.id;
+ console.log('TabularButtonTrackster : Dataset identification is missing.');
+ return;
}
// get url
- if (typeof options.model.attributes.url_viz === "undefined") {
- console.log("TabularButtonTrackster : Url for visualization controller is missing.");
+ if (model.get('url_viz')) {
+ this.url_viz = model.get('url_viz');
} else {
- this.url_viz = options.model.attributes.url_viz;
+ console.log('TabularButtonTrackster : Url for visualization controller is missing.');
+ return;
}
// get genome_build / database key
- if (typeof options.model.attributes.genome_build !== "undefined") {
- this.genome_build = options.model.attributes.genome_build;
+ if (model.get('genome_build')) {
+ this.genome_build = model.get('genome_build');
}
- // render the icon from template
- var btn_viz = new IconButtonView({ model : new IconButton({
- title : 'Visualize',
- icon_class : 'chart_curve',
- id : 'btn_viz'
- })});
+ // create the icon
+ var btn_viz = new IconButtonView({
+ model : new IconButton({
+ title : 'Visualize',
+ icon_class : 'chart_curve',
+ id : 'btn_viz'
+ })
+ });
- // add it to the screen
+ // set element
+ this.setElement(options.$el);
+
+ // add to element
this.$el.append(btn_viz.render().$el);
// hide the button
- $('#btn_viz').hide();
+ this.hide();
},
// backbone events
events:
{
- 'mouseover tr' : 'btn_viz_show',
- 'mouseleave' : 'btn_viz_hide'
+ 'mouseover tr' : 'show',
+ 'mouseleave' : 'hide'
},
// show button
- btn_viz_show: function (e)
- {
+ show: function (e) {
// is numeric
- function is_numeric(n)
- {
+ function is_numeric(n) {
return !isNaN(parseFloat(n)) && isFinite(n);
};
-
+
// check
if(this.col.chrom === null)
return;
@@ -439,8 +469,8 @@
var end = this.col.end ? row.children().eq(this.col.end).html() : start;
// double check location
- if (!chrom.match("^#") && chrom !== "" && is_numeric(start))
- {
+ if (!chrom.match("^#") && chrom !== "" && is_numeric(start)) {
+
// get target gene region
var btn_viz_pars = {
dataset_id : this.dataset_id,
@@ -450,7 +480,7 @@
// get button position
var offset = row.offset();
var left = offset.left - 10;
- var top = offset.top - $(window).scrollTop();
+ var top = offset.top - $(window).scrollTop() + 3;
// update css
$('#btn_viz').css({'position': 'fixed', 'top': top + 'px', 'left': left + 'px'});
@@ -466,72 +496,83 @@
},
// hide button
- btn_viz_hide: function ()
- {
- // hide button from screen
- $('#btn_viz').hide();
+ hide: function () {
+ this.$el.find('#btn_viz').hide();
},
// create action
create_trackster_action : function (vis_url, dataset_params, dbkey) {
+ // link this
+ var self = this;
+
+ // create function
return function() {
var listTracksParams = {};
- if (dbkey){
- // list_tracks seems to use 'f-dbkey' (??)
+ if (dbkey) {
listTracksParams[ 'f-dbkey' ] = dbkey;
}
$.ajax({
url: vis_url + '/list_tracks?' + $.param( listTracksParams ),
- dataType: "html",
- error: function() { alert( ( "Could not add this dataset to browser" ) + '.' ); },
+ dataType: 'html',
+ error: function() {
+ // show error message
+ self.modal.show({
+ title : 'Something went wrong!',
+ body : 'Unfortunately we could not add this dataset to the track browser. Please try again or contact us.',
+ buttons : {
+ 'Cancel': function(){
+ self.modal.hide();
+ }
+ }
+ });
+ },
success: function(table_html) {
- var parent = window.parent;
- parent.Galaxy.modal.show({
- title : "View Data in a New or Saved Visualization",
+ self.modal.show({
+ title : 'View Data in a New or Saved Visualization',
buttons :{
- "Cancel": function(){
- parent.Galaxy.modal.hide();
+ 'Cancel': function(){
+ self.modal.hide();
},
- "View in saved visualization": function(){
- // Show new modal with saved visualizations.
- parent.Galaxy.modal.show(
+ 'View in saved visualization': function(){
+ // show modal with saved visualizations
+ self.modal.show(
{
- title: "Add Data to Saved Visualization",
- body: table_html,
- buttons :{
- "Cancel": function(){
- parent.Galaxy.modal.hide();
+ title : 'Add Data to Saved Visualization',
+ body : table_html,
+ buttons : {
+ 'Cancel': function(){
+ self.modal.hide();
},
- "Add to visualization": function(){
- $(parent.document).find('input[name=id]:checked').each(function(){
- // hide
- parent.Galaxy.modal.hide();
+ 'Add to visualization': function(){
+ // hide
+ self.modal.hide();
+ // search selected fields
+ self.modal.$el.find('input[name=id]:checked').each(function(){
+ // get visualization id
var vis_id = $(this).val();
dataset_params.id = vis_id;
// add widget
- parent.Galaxy.frame.add({
- title : "Trackster",
- type : "url",
- content : vis_url + "/trackster?" + $.param(dataset_params)
+ self.frame.add({
+ title : 'Trackster',
+ type : 'url',
+ content : vis_url + '/trackster?' + $.param(dataset_params)
});
});
}
}
});
},
- "View in new visualization": function(){
+ 'View in new visualization': function(){
// hide
- parent.Galaxy.modal.hide();
+ self.modal.hide();
- var url = vis_url + "/trackster?" + $.param(dataset_params);
-
// add widget
- parent.Galaxy.frame.add({
- title : "Trackster",
- type : "url",
- content : url
+ self.frame.add({
+ title : 'Trackster',
+ type : 'url',
+ content : vis_url + '/trackster?' + $.param(dataset_params)
});
}
}
diff -r 8fe1141e032eb0ff70f72c3a438c80c125a97c71 -r b6d04f39a37fd73abd9c0c5e9695d74330786f47 static/scripts/mvc/grid/grid-template.js
--- a/static/scripts/mvc/grid/grid-template.js
+++ b/static/scripts/mvc/grid/grid-template.js
@@ -218,7 +218,7 @@
tmpl += '</div>';
}
} else {
- tmpl += '<div id="' + id + '" class="' + cls + '"><label id="' + column.label_id_prefix + encoded_id + '" for="' + encoded_id + '">' + value + '</label></div>';
+ tmpl += '<div id="' + id + '" class="' + cls + '"><label id="' + column.label_id_prefix + encoded_id + '" for="' + encoded_id + '">' + (value || '') + '</label></div>';
}
tmpl += '</td>';
}
diff -r 8fe1141e032eb0ff70f72c3a438c80c125a97c71 -r b6d04f39a37fd73abd9c0c5e9695d74330786f47 static/scripts/packed/mvc/data.js
--- a/static/scripts/packed/mvc/data.js
+++ b/static/scripts/packed/mvc/data.js
@@ -1,1 +1,1 @@
-define([],function(){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var k=new g();_.each(_.keys(this.attributes),function(l){if(l.indexOf("metadata_")===0){var m=l.split("metadata_")[1];k.set(m,this.attributes[l]);delete this.attributes[l]}},this);this.set("metadata",k,{silent:true})},get_metadata:function(k){return this.attributes.metadata.get(k)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(k){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var k=this,l=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:k.attributes.chunk_index++}).success(function(m){var n;if(m.ck_data!==""){n=m}else{k.attributes.at_eof=true;n=null}l.resolve(n)});return l}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(k){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new d(k)},render:function(){var o=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(o);var k=this.model.get_metadata("column_names"),p=$("<tr/>").css("background-color",this.header_color).appendTo(o);if(k){p.append("<th>"+k.join("</th><th>")+"</th>")}var m=this.model.get("first_data_chunk");if(m){this._renderChunk(m)}var l=this,n=false;this.scroll_elt.scroll(function(){if(!n&&l.scrolled_to_bottom()){n=true;$.when(l.model.get_next_chunk()).then(function(q){if(q){l._renderChunk(q);n=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},scrolled_to_bottom:function(){return false},_renderCell:function(n,k,o){var l=$("<td>").text(n);var m=this.model.get_metadata("column_types");if(o!==undefined){l.attr("colspan",o).addClass("stringalign")}else{if(m){if(k<m.length){if(m[k]==="str"||m==="list"){l.addClass("stringalign")}}}}return l},_renderRow:function(k){var l=k.split("\t"),n=$("<tr>"),m=this.model.get_metadata("columns");if(this.row_count%2!==0){n.css("background-color",this.dark_row_color)}if(l.length===m){_.each(l,function(p,o){n.append(this._renderCell(p,o))},this)}else{if(l.length>m){_.each(l.slice(0,m-1),function(p,o){n.append(this._renderCell(p,o))},this);n.append(this._renderCell(l.slice(m-1).join("\t"),m-1))}else{if(m>5&&l.length===m-1){_.each(l,function(p,o){n.append(this._renderCell(p,o))},this);n.append($("<td>"))}else{n.append(this._renderCell(k,0,m))}}}this.row_count++;return n},_renderChunk:function(k){var l=this.$el.find("table");_.each(k.ck_data.split("\n"),function(m,n){l.append(this._renderRow(m))},this)}});var f=a.extend({initialize:function(k){a.prototype.initialize.call(this,k);scroll_elt=_.find(this.$el.parents(),function(l){return $(l).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var j=a.extend({initialize:function(k){a.prototype.initialize.call(this,k);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(m){var l=m.model.attributes;var o=m.model.attributes.metadata.attributes;if(typeof l.data_type!=="undefined"){this.data_type=l.data_type}else{console.log("TabularButtonTrackster : Data type missing.")}if(this.data_type=="bed"){if(typeof o.chromCol!=="undefined"||typeof o.startCol!=="undefined"||typeof o.endCol!=="undefined"){this.col.chrom=o.chromCol-1;this.col.start=o.startCol-1;this.col.end=o.endCol-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.")}}if(this.data_type=="vcf"){function n(q,r){for(var p=0;p<r.length;p++){if(r[p].match(q)){return p}}return -1}this.col.chrom=n("Chrom",o.column_names);this.col.start=n("Pos",o.column_names);this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.")}}if(this.col.chrom===null){return}if(typeof m.model.attributes.id==="undefined"){console.log("TabularButtonTrackster : Dataset identification is missing.")}else{this.dataset_id=m.model.attributes.id}if(typeof m.model.attributes.url_viz==="undefined"){console.log("TabularButtonTrackster : Url for visualization controller is missing.")}else{this.url_viz=m.model.attributes.url_viz}if(typeof m.model.attributes.genome_build!=="undefined"){this.genome_build=m.model.attributes.genome_build}var k=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.$el.append(k.render().$el);$("#btn_viz").hide()},events:{"mouseover tr":"btn_viz_show",mouseleave:"btn_viz_hide"},btn_viz_show:function(p){function o(u){return !isNaN(parseFloat(u))&&isFinite(u)}if(this.col.chrom===null){return}var t=$(p.target).parent();var q=t.children().eq(this.col.chrom).html();var k=t.children().eq(this.col.start).html();var m=this.col.end?t.children().eq(this.col.end).html():k;if(!q.match("^#")&&q!==""&&o(k)){var s={dataset_id:this.dataset_id,gene_region:q+":"+k+"-"+m};var n=t.offset();var l=n.left-10;var r=n.top-$(window).scrollTop();$("#btn_viz").css({position:"fixed",top:r+"px",left:l+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,s,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},btn_viz_hide:function(){$("#btn_viz").hide()},create_trackster_action:function(k,m,l){return function(){var n={};if(l){n["f-dbkey"]=l}$.ajax({url:k+"/list_tracks?"+$.param(n),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(o){var p=window.parent;p.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){p.Galaxy.modal.hide()},"View in saved visualization":function(){p.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:o,buttons:{Cancel:function(){p.Galaxy.modal.hide()},"Add to visualization":function(){$(p.document).find("input[name=id]:checked").each(function(){p.Galaxy.modal.hide();var q=$(this).val();m.id=q;p.Galaxy.frame.add({title:"Trackster",type:"url",content:k+"/trackster?"+$.param(m)})})}}})},"View in new visualization":function(){p.Galaxy.modal.hide();var q=k+"/trackster?"+$.param(m);p.Galaxy.frame.add({title:"Trackster",type:"url",content:q})}}})}});return false}}});var i=function(n,l,o,k){var m=new l({model:new n(o)});m.render();if(k){k.append(m.$el)}return m};var c=function(m){m.model=new h(m.dataset_config);var l=m.parent_elt;var n=m.embedded;delete m.embedded;delete m.parent_elt;delete m.dataset_config;var k=(n?new j(m):new f(m));k.render();if(l){l.append(k.$el)}return k};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}});
\ No newline at end of file
+define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var m=new g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return n}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.header_color="#AAA";this.dark_row_color="#DDD";new d({model:m.model,$el:this.$el})},render:function(){var q=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(q);var m=this.model.get_metadata("column_names"),r=$("<tr/>").css("background-color",this.header_color).appendTo(q);if(m){r.append("<th>"+m.join("</th><th>")+"</th>")}var o=this.model.get("first_data_chunk");if(o){this._renderChunk(o)}var n=this,p=false;this.scroll_elt.scroll(function(){if(!p&&n.scrolled_to_bottom()){p=true;$.when(n.model.get_next_chunk()).then(function(s){if(s){n._renderChunk(s);p=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},scrolled_to_bottom:function(){return false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o==="list"){n.addClass("stringalign")}}}}return n},_renderRow:function(m){var n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return p},_renderChunk:function(m){var n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){n.append(this._renderRow(o))},this)}});var f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(o){var r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var n=o.model;var q=n.get("metadata");if(!n.get("data_type")){return}this.data_type=n.get("data_type");if(this.data_type=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.data_type=="vcf"){function p(t,u){for(var s=0;s<u.length;s++){if(u[s].match(t)){return s}}return -1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var m=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(r){function q(w){return !isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var m=v.children().eq(this.col.start).html();var o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var p=v.offset();var n=p.left-10;var t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var n=this;return function(){var q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View in new visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return false}}});var k=function(p,n,q,m){var o=new n({model:new p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){o.model=new h(o.dataset_config);var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new f(o));m.render();if(n){n.append(m.$el)}return m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}});
\ No newline at end of file
diff -r 8fe1141e032eb0ff70f72c3a438c80c125a97c71 -r b6d04f39a37fd73abd9c0c5e9695d74330786f47 static/scripts/packed/mvc/grid/grid-template.js
--- a/static/scripts/packed/mvc/grid/grid-template.js
+++ b/static/scripts/packed/mvc/grid/grid-template.js
@@ -1,1 +1,1 @@
-define([],function(){return{grid:function(b){var a="";if(b.embedded){a=this.grid_header(b)+this.grid_table(b)}else{a='<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(b)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(b)}if(b.info_text){a+='<br><div class="toolParamHelp" style="clear: both;">'+b.info_text+"</div>"}return a},grid_table:function(a){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(c){var b='<div class="grid-header">';if(!c.embedded){b+="<h2>"+c.title+"</h2>"}if(c.global_actions){b+='<ul class="manage-table-actions">';var d=(c.global_actions.length>=3);if(d){b+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">'}for(i in c.global_actions){var e=c.global_actions[i];var a="";if(e.inbound){a="use-inbound"}else{a="use-outbound"}b+='<li><a class="action-button '+a+'" href="'+e.url_args+'" onclick="return false;">'+e.label+"</a></li>"}if(d){b+="</div>"}b+="</ul>"}if(c.insert){b+=c.insert}b+=this.grid_filters(c);b+="</div>";return b},header:function(b){var a="<tr>";if(b.show_item_checkboxes){a+="<th>";if(b.items.length>0){a+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'}a+="</th>"}for(var c in b.columns){var d=b.columns[c];if(d.visible){a+='<th id="'+d.key+'-header">';if(d.href){a+='<a href="'+d.href+'" class="sort-link" sort_key="'+d.key+'">'+d.label+"</a>"}else{a+=d.label}a+='<span class="sort-arrow">'+d.extra+"</span></th>"}}a+="</tr>";return a},body:function(r){var k="";var s=0;var e=r.items.length;if(e==0){k+='<tr><td colspan="100"><em>No Items</em></td></tr>';s=1}for(var f in r.items){var p=r.items[f];var a=p.encode_id;var g="grid-"+f+"-popup";k+="<tr ";if(r.current_item_id==p.id){k+='class="current"'}k+=">";if(r.show_item_checkboxes){k+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+a+'" id="'+a+'" class="grid-row-select-checkbox" /></td>'}for(j in r.columns){var d=r.columns[j];if(d.visible){var c="";if(d.nowrap){c='style="white-space:nowrap;"'}var q=p.column_config[d.label];var h=q.link;var l=q.value;var o=q.inbound;if(jQuery.type(l)==="string"){l=l.replace(/\/\//g,"/")}var b="";var n="";if(d.attach_popup){b="grid-"+f+"-popup";n="menubutton";if(h!=""){n+=" split"}n+=" popup"}k+="<td "+c+">";if(h){if(r.operations.length!=0){k+='<div id="'+b+'" class="'+n+'" style="float: left;">'}var m="";if(o){m="use-inbound"}else{m="use-outbound"}k+='<a class="label '+m+'" href="'+h+'" onclick="return false;">'+l+"</a>";if(r.operations.length!=0){k+="</div>"}}else{k+='<div id="'+b+'" class="'+n+'"><label id="'+d.label_id_prefix+a+'" for="'+a+'">'+l+"</label></div>"}k+="</td>"}}k+="</tr>";s++}return k},footer:function(o){var k="";if(o.use_paging&&o.num_pages>1){var m=o.num_page_links;var a=o.cur_page_num;var n=o.num_pages;var h=m/2;var g=a-h;var e=0;if(g<=0){g=1;e=h-(a-g)}var d=h+e;var c=a+d;if(c<=n){max_offset=0}else{c=n;max_offset=d-(c+1-a)}if(max_offset!=0){g-=max_offset;if(g<1){g=1}}k+='<tr id="page-links-row">';if(o.show_item_checkboxes){k+="<td></td>"}k+='<td colspan="100"><span id="page-link-container">Page:';if(g>1){k+='<span class="page-link" id="page-link-1"><a href="javascript:void(0);" page_num="1" onclick="return false;">1</a></span> ...'}for(var l=g;l<c+1;l++){if(l==o.cur_page_num){k+='<span class="page-link inactive-link" id="page-link-'+l+'">'+l+"</span>"}else{k+='<span class="page-link" id="page-link-'+l+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+l+'">'+l+"</a></span>"}}if(c<n){k+='...<span class="page-link" id="page-link-'+n+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}k+="</span>";k+='<span class="page-link" id="show-all-link-span"> | <a href="javascript:void(0);" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(o.show_item_checkboxes){k+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+o.get_class_plural+": ";for(i in o.operations){var b=o.operations[i];if(b.allow_multiple){k+='<input type="button" value="'+b.label+'" class="operation-button action-button"> '}}k+="</td></tr>"}var f=false;for(i in o.operations){if(o.operations[i].global_operation){f=true;break}}if(f){k+='<tr><td colspan="100">';for(i in o.operations){var b=o.operations[i];if(b.global_operation){k+='<a class="action-button" href="'+b.global_operation+'">'+b.label+"</a>"}}k+="</td></tr>"}if(o.legend){k+='<tr><td colspan="100">'+o.legend+"</td></tr>"}return k},message:function(a){return'<p><div class="'+a.status+'message transient-message">'+a.message+'</div><div style="clear: both"></div></p>'},grid_filters:function(n){var a=n.default_filter_dict;var b=n.filters;var e="none";if(n.advanced_search){e="block"}var m=false;for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){var l=d.key;var c=b[l];var f=a[l];if(c&&f&&c!=f){e="block"}m=true}}var k="block";if(e=="block"){k="none"}var h='<div id="standard-search" style="display: '+k+';"><table><tr><td style="padding: 0;"><table>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="standard"){h+=this.grid_column_filter(n,d)}}h+="</table></td></tr><tr><td>";if(m){h+='<a href="" class="advanced-search-toggle">Advanced Search</a>'}h+="</td></tr></table></div>";h+='<div id="advanced-search" style="display: '+e+'; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){h+=this.grid_column_filter(n,d)}}h+="</table></div>";return h},grid_column_filter:function(e,c){var t=e.default_filter_dict;var l=e.filters;var a=c.label;var b=c.key;if(c.filterable=="advanced"){a=a.toLowerCase()}var k="<tr>";if(c.filterable=="advanced"){k+='<td align="left" style="padding-left: 10px">'+a+":</td>"}k+='<td style="padding-bottom: 1px;">';if(c.is_text){k+='<form class="text-filter-form" column_key="'+b+'" action="'+e.url+'" method="get" >';for(u in e.columns){var g=e.columns[u];var p=l[g.key];if(p){if(p!="All"){if(g.is_text){p=JSON.stringify(p)}k+='<input type="hidden" id="'+g.key+'" name="f-'+g.key+'" value="'+p+'"/>'}}}k+='<span id="'+b+'-filtering-criteria">';var h=l[b];if(h){var f=jQuery.type(h);if(f=="string"){if(h!="All"){k+=this.filter_element(b,h)}}if(f=="array"){for(var u in h){var n=h[u];var v=h;v=v.slice(u);k+=this.filter_element(b,n)}}}k+="</span>";var r="";if(c.filterable=="standard"){r=c.label.toLowerCase();var q=r.length;if(q<20){q=20}q=q+4}k+='<span class="search-box"><input class="search-box-input" id="input-'+b+'-filter" name="f-'+b+'" type="text" placeholder="'+r+'" size="'+q+'"/><button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;"><i class="fa fa-search"></i></button></span></form>'}else{k+='<span id="'+b+'-filtering-criteria">';var s=false;for(cf_label in e.categorical_filters[b]){var o=e.categorical_filters[b][cf_label];var d="";var m="";for(key in o){d=key;m=o[key]}if(s){k+=" | "}s=true;var n=l[b];if(n&&o[b]&&n==m){k+='<span class="categorical-filter '+b+'-filter current-filter">'+cf_label+"</span>"}else{k+='<span class="categorical-filter '+b+'-filter"><a href="javascript:void(0);" filter_key="'+d+'" filter_val="'+m+'">'+cf_label+"</a></span>"}}k+="</span>"}k+="</td></tr>";return k},filter_element:function(b,a){return'<span class="text-filter-val">'+a+'<a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+a+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}});
\ No newline at end of file
+define([],function(){return{grid:function(b){var a="";if(b.embedded){a=this.grid_header(b)+this.grid_table(b)}else{a='<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(b)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(b)}if(b.info_text){a+='<br><div class="toolParamHelp" style="clear: both;">'+b.info_text+"</div>"}return a},grid_table:function(a){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(c){var b='<div class="grid-header">';if(!c.embedded){b+="<h2>"+c.title+"</h2>"}if(c.global_actions){b+='<ul class="manage-table-actions">';var d=(c.global_actions.length>=3);if(d){b+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">'}for(i in c.global_actions){var e=c.global_actions[i];var a="";if(e.inbound){a="use-inbound"}else{a="use-outbound"}b+='<li><a class="action-button '+a+'" href="'+e.url_args+'" onclick="return false;">'+e.label+"</a></li>"}if(d){b+="</div>"}b+="</ul>"}if(c.insert){b+=c.insert}b+=this.grid_filters(c);b+="</div>";return b},header:function(b){var a="<tr>";if(b.show_item_checkboxes){a+="<th>";if(b.items.length>0){a+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'}a+="</th>"}for(var c in b.columns){var d=b.columns[c];if(d.visible){a+='<th id="'+d.key+'-header">';if(d.href){a+='<a href="'+d.href+'" class="sort-link" sort_key="'+d.key+'">'+d.label+"</a>"}else{a+=d.label}a+='<span class="sort-arrow">'+d.extra+"</span></th>"}}a+="</tr>";return a},body:function(r){var k="";var s=0;var e=r.items.length;if(e==0){k+='<tr><td colspan="100"><em>No Items</em></td></tr>';s=1}for(var f in r.items){var p=r.items[f];var a=p.encode_id;var g="grid-"+f+"-popup";k+="<tr ";if(r.current_item_id==p.id){k+='class="current"'}k+=">";if(r.show_item_checkboxes){k+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+a+'" id="'+a+'" class="grid-row-select-checkbox" /></td>'}for(j in r.columns){var d=r.columns[j];if(d.visible){var c="";if(d.nowrap){c='style="white-space:nowrap;"'}var q=p.column_config[d.label];var h=q.link;var l=q.value;var o=q.inbound;if(jQuery.type(l)==="string"){l=l.replace(/\/\//g,"/")}var b="";var n="";if(d.attach_popup){b="grid-"+f+"-popup";n="menubutton";if(h!=""){n+=" split"}n+=" popup"}k+="<td "+c+">";if(h){if(r.operations.length!=0){k+='<div id="'+b+'" class="'+n+'" style="float: left;">'}var m="";if(o){m="use-inbound"}else{m="use-outbound"}k+='<a class="label '+m+'" href="'+h+'" onclick="return false;">'+l+"</a>";if(r.operations.length!=0){k+="</div>"}}else{k+='<div id="'+b+'" class="'+n+'"><label id="'+d.label_id_prefix+a+'" for="'+a+'">'+(l||"")+"</label></div>"}k+="</td>"}}k+="</tr>";s++}return k},footer:function(o){var k="";if(o.use_paging&&o.num_pages>1){var m=o.num_page_links;var a=o.cur_page_num;var n=o.num_pages;var h=m/2;var g=a-h;var e=0;if(g<=0){g=1;e=h-(a-g)}var d=h+e;var c=a+d;if(c<=n){max_offset=0}else{c=n;max_offset=d-(c+1-a)}if(max_offset!=0){g-=max_offset;if(g<1){g=1}}k+='<tr id="page-links-row">';if(o.show_item_checkboxes){k+="<td></td>"}k+='<td colspan="100"><span id="page-link-container">Page:';if(g>1){k+='<span class="page-link" id="page-link-1"><a href="javascript:void(0);" page_num="1" onclick="return false;">1</a></span> ...'}for(var l=g;l<c+1;l++){if(l==o.cur_page_num){k+='<span class="page-link inactive-link" id="page-link-'+l+'">'+l+"</span>"}else{k+='<span class="page-link" id="page-link-'+l+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+l+'">'+l+"</a></span>"}}if(c<n){k+='...<span class="page-link" id="page-link-'+n+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}k+="</span>";k+='<span class="page-link" id="show-all-link-span"> | <a href="javascript:void(0);" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(o.show_item_checkboxes){k+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+o.get_class_plural+": ";for(i in o.operations){var b=o.operations[i];if(b.allow_multiple){k+='<input type="button" value="'+b.label+'" class="operation-button action-button"> '}}k+="</td></tr>"}var f=false;for(i in o.operations){if(o.operations[i].global_operation){f=true;break}}if(f){k+='<tr><td colspan="100">';for(i in o.operations){var b=o.operations[i];if(b.global_operation){k+='<a class="action-button" href="'+b.global_operation+'">'+b.label+"</a>"}}k+="</td></tr>"}if(o.legend){k+='<tr><td colspan="100">'+o.legend+"</td></tr>"}return k},message:function(a){return'<p><div class="'+a.status+'message transient-message">'+a.message+'</div><div style="clear: both"></div></p>'},grid_filters:function(n){var a=n.default_filter_dict;var b=n.filters;var e="none";if(n.advanced_search){e="block"}var m=false;for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){var l=d.key;var c=b[l];var f=a[l];if(c&&f&&c!=f){e="block"}m=true}}var k="block";if(e=="block"){k="none"}var h='<div id="standard-search" style="display: '+k+';"><table><tr><td style="padding: 0;"><table>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="standard"){h+=this.grid_column_filter(n,d)}}h+="</table></td></tr><tr><td>";if(m){h+='<a href="" class="advanced-search-toggle">Advanced Search</a>'}h+="</td></tr></table></div>";h+='<div id="advanced-search" style="display: '+e+'; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){h+=this.grid_column_filter(n,d)}}h+="</table></div>";return h},grid_column_filter:function(e,c){var t=e.default_filter_dict;var l=e.filters;var a=c.label;var b=c.key;if(c.filterable=="advanced"){a=a.toLowerCase()}var k="<tr>";if(c.filterable=="advanced"){k+='<td align="left" style="padding-left: 10px">'+a+":</td>"}k+='<td style="padding-bottom: 1px;">';if(c.is_text){k+='<form class="text-filter-form" column_key="'+b+'" action="'+e.url+'" method="get" >';for(u in e.columns){var g=e.columns[u];var p=l[g.key];if(p){if(p!="All"){if(g.is_text){p=JSON.stringify(p)}k+='<input type="hidden" id="'+g.key+'" name="f-'+g.key+'" value="'+p+'"/>'}}}k+='<span id="'+b+'-filtering-criteria">';var h=l[b];if(h){var f=jQuery.type(h);if(f=="string"){if(h!="All"){k+=this.filter_element(b,h)}}if(f=="array"){for(var u in h){var n=h[u];var v=h;v=v.slice(u);k+=this.filter_element(b,n)}}}k+="</span>";var r="";if(c.filterable=="standard"){r=c.label.toLowerCase();var q=r.length;if(q<20){q=20}q=q+4}k+='<span class="search-box"><input class="search-box-input" id="input-'+b+'-filter" name="f-'+b+'" type="text" placeholder="'+r+'" size="'+q+'"/><button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;"><i class="fa fa-search"></i></button></span></form>'}else{k+='<span id="'+b+'-filtering-criteria">';var s=false;for(cf_label in e.categorical_filters[b]){var o=e.categorical_filters[b][cf_label];var d="";var m="";for(key in o){d=key;m=o[key]}if(s){k+=" | "}s=true;var n=l[b];if(n&&o[b]&&n==m){k+='<span class="categorical-filter '+b+'-filter current-filter">'+cf_label+"</span>"}else{k+='<span class="categorical-filter '+b+'-filter"><a href="javascript:void(0);" filter_key="'+d+'" filter_val="'+m+'">'+cf_label+"</a></span>"}}k+="</span>"}k+="</td></tr>";return k},filter_element:function(b,a){return'<span class="text-filter-val">'+a+'<a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+a+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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27 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8fe1141e032e/
Changeset: 8fe1141e032e
User: Jeremy Goecks
Date: 2014-03-27 03:15:12
Summary: Pack script.
Affected #: 1 file
diff -r 6301e0c62a03b508f2a6fd218dd71ef5d6163511 -r 8fe1141e032eb0ff70f72c3a438c80c125a97c71 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(){this.track.set_name(this.track.config.get("values").name)},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||ab===1){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=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ae,al,an,ad,ag,ah,ao,ac,ak){b.call(this,ae,al,an,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ak;this.has_icons=false;if(ao){this.has_icons=true;var ai=this;ad=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D,width:ad.width}).prependTo(this.html_elt);var aj=new w.GenomeRegion({chrom:ae.view.chrom,start:this.low,end:this.high}),am=ag.length,af=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ab=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);af.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()});ab.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()})}};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("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_param_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,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.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(){L.prototype.before_draw.call(this);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){L.prototype.postdraw_actions.call(this,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(al,ad,am,ak){L.prototype.postdraw_actions.call(this,al,ad,am,ak);var af=this,ag;if(af.filters_manager){var ae=af.filters_manager.filters,ai;for(ai=0;ai<ae.length;ai++){ae[ai].update_ui_elt()}var ah=false,aj,ac;for(ag=0;ag<al.length;ag++){if(al[ag].data.length){aj=al[ag].data[0];for(ai=0;ai<ae.length;ai++){ac=ae[ai];if(ac.applies_to(aj)&&ac.min!==ac.max){ah=true;break}}}}if(af.filters_available!==ah){af.filters_available=ah;if(!af.filters_available){af.filters_manager.hide()}af.update_icons()}}if(al[0] instanceof M){var ab=true;for(ag=0;ag<al.length;ag++){if(!al[ag].all_slotted){ab=false;break}}if(!ab){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(al,ap,an,ae,ai,ad){var ao=this,ac=ap.canvas,aw=ae.get("start"),ab=ae.get("end"),af=this.left_offset;if(al.dataset_type==="bigwig"){return this._draw_line_track_tile(al,ap,an,ae,ai)}var ah=[],am=this.slotters[ai].slots;all_slotted=true;if(al.data){var aj=this.filters_manager.filters;for(var aq=0,at=al.data.length;aq<at;aq++){var ag=al.data[aq];var ar=false;var ak;for(var av=0,aA=aj.length;av<aA;av++){ak=aj[av];ak.update_attrs(ag);if(!ak.keep(ag)){ar=true;break}}if(!ar){ah.push(ag);if(!(ag[0] in am)){all_slotted=false}}}}var az=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),ax=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),ay=new (this.painter)(ah,aw,ab,this.config.to_key_value_dict(),an,az,ax,ad,function(aB){return ao.view.get_base_color(aB)});var au=null;ap.fillStyle=this.config.get_value("block_color");ap.font=ap.canvas.manager.default_font;ap.textAlign="right";if(al.data){au=ay.draw(ap,ac.width,ac.height,ai,am);au.translation=-af}return new M(ao,ae,ai,ac,al.data,an,al.message,all_slotted,au)}});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:32,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"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{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(){this.track.set_name(this.track.config.get("values").name)},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||ab===1){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=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ae,al,an,ad,ag,ah,ao,ac,ak){b.call(this,ae,al,an,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ak;this.has_icons=false;if(ao){this.has_icons=true;var ai=this;ad=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D,width:ad.width}).prependTo(this.html_elt);var aj=new w.GenomeRegion({chrom:ae.view.chrom,start:this.low,end:this.high}),am=ag.length,af=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ab=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);af.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()});ab.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()})}};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("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_param_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,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.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(){L.prototype.before_draw.call(this);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){L.prototype.postdraw_actions.call(this,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(al,ad,am,ak){L.prototype.postdraw_actions.call(this,al,ad,am,ak);var af=this,ag;if(af.filters_manager){var ae=af.filters_manager.filters,ai;for(ai=0;ai<ae.length;ai++){ae[ai].update_ui_elt()}var ah=false,aj,ac;for(ag=0;ag<al.length;ag++){if(al[ag].data.length){aj=al[ag].data[0];for(ai=0;ai<ae.length;ai++){ac=ae[ai];if(ac.applies_to(aj)&&ac.min!==ac.max){ah=true;break}}}}if(af.filters_available!==ah){af.filters_available=ah;if(!af.filters_available){af.filters_manager.hide()}af.update_icons()}}if(al[0] instanceof M){var ab=true;for(ag=0;ag<al.length;ag++){if(!al[ag].all_slotted){ab=false;break}}if(!ab){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(al,ap,an,ae,ai,ad){var ao=this,ac=ap.canvas,aw=ae.get("start"),ab=ae.get("end"),af=this.left_offset;if(al.dataset_type==="bigwig"){return this._draw_line_track_tile(al,ap,an,ae,ai)}var ah=[],am=this.slotters[ai].slots;all_slotted=true;if(al.data){var aj=this.filters_manager.filters;for(var aq=0,at=al.data.length;aq<at;aq++){var ag=al.data[aq];var ar=false;var ak;for(var av=0,aA=aj.length;av<aA;av++){ak=aj[av];ak.update_attrs(ag);if(!ak.keep(ag)){ar=true;break}}if(!ar){ah.push(ag);if(!(ag[0] in am)){all_slotted=false}}}}var az=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),ax=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),ay=new (this.painter)(ah,aw,ab,this.config.to_key_value_dict(),an,az,ax,ad,function(aB){return ao.view.get_base_color(aB)});var au=null;ap.fillStyle=this.config.get_value("block_color");ap.font=ap.canvas.manager.default_font;ap.textAlign="right";if(al.data){au=ay.draw(ap,ac.width,ac.height,ai,am);au.translation=-af}return new M(ao,ae,ai,ac,al.data,an,al.message,all_slotted,au)}});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
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: Jeremy Goecks: Trackster: (a) default read track block colors to gray in order to show variants; (b) do not set default height of variant track.
by commits-noreplyï¼ bitbucket.org 27 Mar '14
by commits-noreplyï¼ bitbucket.org 27 Mar '14
27 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/6301e0c62a03/
Changeset: 6301e0c62a03
User: Jeremy Goecks
Date: 2014-03-27 03:14:10
Summary: Trackster: (a) default read track block colors to gray in order to show variants; (b) do not set default height of variant track.
Affected #: 2 files
diff -r 8bb0825fe57b1592331ca685c1e3f74ffdb83ca9 -r 6301e0c62a03b508f2a6fd218dd71ef5d6163511 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -4031,7 +4031,7 @@
{ 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: 32, hidden: true }
+ { key: 'height', type: 'int', default_value: 0, hidden: true }
] ),
config_onchange: function() {
@@ -4169,8 +4169,8 @@
extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype, {
config_params: _.union( Drawable.prototype.config_params, [
- { key: 'block_color', label: 'Block and sense strand color', type: 'color' },
- { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color' },
+ { 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 },
diff -r 8bb0825fe57b1592331ca685c1e3f74ffdb83ca9 -r 6301e0c62a03b508f2a6fd218dd71ef5d6163511 static/scripts/viz/trackster_ui.js
--- a/static/scripts/viz/trackster_ui.js
+++ b/static/scripts/viz/trackster_ui.js
@@ -43,7 +43,7 @@
{ icon_class: 'plus-button', title: 'Add tracks', on_click: function() {
visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey }, function(tracks) {
_.each(tracks, function(track) {
- view.add_drawable( object_from_template(track, view, view) );
+ view.add_drawable( object_from_template(track, view, view) );
});
});
} },
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: Jeremy Goecks: Visualization JS: fix incorrect method call. Pack script.
by commits-noreplyï¼ bitbucket.org 26 Mar '14
by commits-noreplyï¼ bitbucket.org 26 Mar '14
26 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8bb0825fe57b/
Changeset: 8bb0825fe57b
User: Jeremy Goecks
Date: 2014-03-26 22:53:07
Summary: Visualization JS: fix incorrect method call. Pack script.
Affected #: 3 files
diff -r 231a61e88777bbf7e2db9ef1fdaa9d7fb757523f -r 8bb0825fe57b1592331ca685c1e3f74ffdb83ca9 static/scripts/packed/viz/visualization.js
--- a/static/scripts/packed/viz/visualization.js
+++ b/static/scripts/packed/viz/visualization.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(t,k,m,p){var f={toJSON:function(){var v=this,w={};t.each(v.constructor.to_json_keys,function(x){var y=v.get(x);if(x in v.constructor.to_json_mappers){y=v.constructor.to_json_mappers[x](y,v)}w[x]=y});return w}};var a=function(v,y,x,w){$.ajax({url:v,data:x,error:function(){alert("Grid failed")},success:function(z){Galaxy.modal.show({title:"Select datasets for new tracks",body:z,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var A=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var B={data_type:"track_config",hda_ldda:"hda"},C=$(this).val();if($(this).attr("name")!=="id"){B.hda_ldda="ldda"}A[A.length]=$.ajax({url:y+"/"+C,data:B,dataType:"json"})});$.when.apply($,A).then(function(){var B=(arguments[0] instanceof Array?$.map(arguments,function(C){return C[0]}):[arguments[0]]);w(B)});Galaxy.modal.hide()}}})}})};var g=function(v){this.default_font=v!==undefined?v:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};t.extend(g.prototype,{load_pattern:function(v,z){var w=this.patterns,x=this.dummy_context,y=new Image();y.src=galaxy_config.root+"static/images"+z;y.onload=function(){w[v]=x.createPattern(y,"repeat")}},get_pattern:function(v){return this.patterns[v]},new_canvas:function(){var v=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(v)}v.manager=this;return v}});var r=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(v){this.clear()},get_elt:function(x){var y=this.attributes.obj_cache,z=this.attributes.key_ary,w=x.toString(),v=t.indexOf(z,function(A){return A.toString()===w});if(v!==-1){if(y[w].stale){z.splice(v,1);delete y[w]}else{this.move_key_to_end(x,v)}}return y[w]},set_elt:function(x,z){var A=this.attributes.obj_cache,B=this.attributes.key_ary,w=x.toString(),y=this.attributes.num_elements;if(!A[w]){if(B.length>=y){var v=B.shift();delete A[v.toString()]}B.push(x)}A[w]=z;return z},move_key_to_end:function(w,v){this.attributes.key_ary.splice(v,1);this.attributes.key_ary.push(w)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=r.extend({defaults:t.extend({},r.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(v,w){return true},can_subset:function(v){return false}}),initialize:function(v){r.prototype.initialize.call(this);var w=this.get("init_data");if(w){this.add_data(w)}},add_data:function(v){if(this.get("num_elements")<v.length){this.set("num_elements",v.length)}var w=this;t.each(v,function(x){w.set_data(x.region,x)})},data_is_ready:function(){var y=this.get("dataset"),x=$.Deferred(),v=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),w=new m.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:y.get("hda_ldda"),data_type:v},dataType:"json"},interval:5000,success_fn:function(z){return z!=="pending"}});$.when(w.go()).then(function(z){x.resolve(z==="ok"||z==="data")});return x},search_features:function(v){var w=this.get("dataset"),x={query:v,hda_ldda:w.get("hda_ldda"),data_type:"features"};return $.getJSON(w.url(),x)},load_data:function(D,C,w,B){var z=this.get("dataset"),y={data_type:this.get("data_type"),chrom:D.get("chrom"),low:D.get("start"),high:D.get("end"),mode:C,resolution:w,hda_ldda:z.get("hda_ldda")};$.extend(y,B);var F=this.get("filters_manager");if(F){var G=[];var v=F.filters;for(var A=0;A<v.length;A++){G.push(v[A].name)}y.filter_cols=JSON.stringify(G)}var x=this,E=$.getJSON(z.url(),y,function(H){H.region=D;x.set_data(D,H)});this.set_data(D,E);return E},get_data:function(C,B,x,z){var D=this.get_elt(C);if(D&&(m.is_deferred(D)||this.get("data_mode_compatible")(D,B))){return D}var E=this.get("key_ary"),v=this.get("obj_cache"),w,A;for(var y=0;y<E.length;y++){w=E[y];if(w.contains(C)){A=true;D=v[w.toString()];if(m.is_deferred(D)||(this.get("data_mode_compatible")(D,B)&&this.get("can_subset")(D))){this.move_key_to_end(w,y);if(!m.is_deferred(D)){var G=this.subset_entry(D,C);this.set(C,G);D=G}return D}}}if(!A&&C.length()<this.attributes.min_region_size){C=C.copy();var F=this.most_recently_added();if(!F||(C.get("start")>F.get("start"))){C.set("end",C.get("start")+this.attributes.min_region_size)}else{C.set("start",C.get("end")-this.attributes.min_region_size)}C.set("genome",this.attributes.genome);C.trim()}return this.load_data(C,B,x,z)},set_data:function(w,v){this.set_elt(w,v)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(D,C,y,B,z){var F=this._mark_stale(D);if(!(F&&this.get("data_mode_compatible")(F,C))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var x=D.get("start");if(z===this.DEEP_DATA_REQ){$.extend(B,{start_val:F.data.length+1})}else{if(z===this.BROAD_DATA_REQ){x=(F.max_high?F.max_high:F.data[F.data.length-1][2])+1}}var E=D.copy().set("start",x);var w=this,A=this.load_data(E,C,y,B),v=$.Deferred();this.set_data(D,v);$.when(A).then(function(G){if(G.data){G.data=F.data.concat(G.data);if(G.max_low){G.max_low=F.max_low}if(G.message){G.message=G.message.replace(/[0-9]+/,G.data.length)}}w.set_data(D,G);v.resolve(G)});return v},can_get_more_detailed_data:function(w){var v=this.get_elt(w);return(v.dataset_type==="bigwig"&&v.data.length<8000)},get_more_detailed_data:function(y,A,w,z,x){var v=this._mark_stale(y);if(!v){console.log("ERROR getting more detailed data: no current data");return}if(!x){x={}}if(v.dataset_type==="bigwig"){x.num_samples=1000*z}return this.load_data(y,A,w,x)},_mark_stale:function(w){var v=this.get_elt(w);if(!v){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),w.toString())}v.stale=true;return v},get_genome_wide_data:function(v){var x=this,z=true,y=t.map(v.get("chroms_info").chrom_info,function(B){var A=x.get_elt(new h({chrom:B.chrom,start:0,end:B.len}));if(!A){z=false}return A});if(z){return y}var w=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(A){x.add_data(A.data);w.resolve(A.data)});return w},subset_entry:function(x,y){var v={bigwig:function(z,A){return t.filter(z,function(B){return B[0]>=A.get("start")&&B[0]<=A.get("end")})},refseq:function(A,B){var C=B.get("start")-x.region.get("start"),z=x.data.length-(x.region.get("end")-B.get("end"));return x.data.slice(C,z)}};var w=x.data;if(!x.region.same(y)&&x.dataset_type in v){w=v[x.dataset_type](x.data,y)}return{region:y,data:w,dataset_type:x.dataset_type}}});var q=d.extend({initialize:function(v){var w=new Backbone.Model();w.urlRoot=v.data_url;this.set("dataset",w)},load_data:function(x,y,v,w){return(x.length()<=100000?d.prototype.load_data.call(this,x,y,v,w):{data:null,region:x})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(v){this.id=v.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(v){var w=t.find(this.get_chroms_info(),function(x){return x.chrom===v});return new h({chrom:w.chrom,end:w.len})},get_chrom_len:function(v){return t.find(this.get_chroms_info(),function(w){return w.chrom===v}).len}});var h=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(v){return this.attributes.chrom===v.get("chrom")&&this.attributes.start===v.get("start")&&this.attributes.end===v.get("end")},initialize:function(w){if(w.from_str){var y=w.from_str.split(":"),x=y[0],v=y[1].split("-");this.set({chrom:x,start:parseInt(v[0],10),end:parseInt(v[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new h({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(C){var w=this.get("chrom"),B=C.get("chrom"),A=this.get("start"),y=C.get("start"),z=this.get("end"),x=C.get("end"),v;if(w&&B&&w!==B){return h.overlap_results.DIF_CHROMS}if(A<y){if(z<y){v=h.overlap_results.BEFORE}else{if(z<x){v=h.overlap_results.OVERLAP_START}else{v=h.overlap_results.CONTAINS}}}else{if(A>y){if(A>x){v=h.overlap_results.AFTER}else{if(z<=x){v=h.overlap_results.CONTAINED_BY}else{v=h.overlap_results.OVERLAP_END}}}else{v=(z>=x?h.overlap_results.CONTAINS:h.overlap_results.CONTAINED_BY)}}return v},trim:function(v){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var w=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>w){this.attributes.end=w-1}}return this},contains:function(v){return this.compute_overlap(v)===h.overlap_results.CONTAINS},overlaps:function(v){return t.intersection([this.compute_overlap(v)],[h.overlap_results.DIF_CHROMS,h.overlap_results.BEFORE,h.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var n=Backbone.Collection.extend({model:h});var e=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(v){this.set("region",new h(v.region))}});var s=Backbone.Collection.extend({model:e});var u=Backbone.Model.extend(f).extend({defaults:{mode:"Auto"},initialize:function(v){this.set("dataset",new k.Dataset(v.dataset));this.set("config",p.ConfigSettingCollection.from_config_dict(v.prefs));this.get("config").add([{key:"name",value:this.get("dataset").get("name")},{key:"color"}]);var w=this.get("preloaded_data");if(w){w=w.data}else{w=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:w}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(w,v){if(t.size(w)===0){w={name:v.get("config").get("name").get("value"),color:v.get("config").get("color").get("value")}}return w},dataset:function(v){return{id:v.id,hda_ldda:v.get("hda_ldda")}}}});var j=Backbone.Collection.extend({model:u});var o=Backbone.Model.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var l=o.extend(f).extend({defaults:t.extend({},o.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(v){this.set("drawables",new j(v.tracks));this.set("config",p.ConfigSettingCollection.from_config_dict(v.prefs||{}));this.unset("tracks");this.get("drawables").each(function(w){w.unset("preloaded_data")})},add_tracks:function(v){this.get("drawables").add(v)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(w,v){return{obj_type:"View",prefs:{name:v.get("title"),content_visible:true},drawables:v.get("drawables")}}}});var b=Backbone.Model.extend({});var i=Backbone.Router.extend({initialize:function(w){this.view=w.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var v=this;v.view.on("navigate",function(x){v.navigate(x)})},change_location:function(v){this.view.go_to(v)}});return{BackboneTrack:u,BrowserBookmark:e,BrowserBookmarkCollection:s,Cache:r,CanvasManager:g,Genome:c,GenomeDataManager:d,GenomeRegion:h,GenomeRegionCollection:n,GenomeVisualization:l,GenomeReferenceDataManager:q,TrackBrowserRouter:i,TrackConfig:b,Visualization:o,select_datasets:a}});
\ No newline at end of file
+define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(t,k,m,p){var f={toJSON:function(){var v=this,w={};t.each(v.constructor.to_json_keys,function(x){var y=v.get(x);if(x in v.constructor.to_json_mappers){y=v.constructor.to_json_mappers[x](y,v)}w[x]=y});return w}};var a=function(v,y,x,w){$.ajax({url:v,data:x,error:function(){alert("Grid failed")},success:function(z){Galaxy.modal.show({title:"Select datasets for new tracks",body:z,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var A=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var B={data_type:"track_config",hda_ldda:"hda"},C=$(this).val();if($(this).attr("name")!=="id"){B.hda_ldda="ldda"}A[A.length]=$.ajax({url:y+"/"+C,data:B,dataType:"json"})});$.when.apply($,A).then(function(){var B=(arguments[0] instanceof Array?$.map(arguments,function(C){return C[0]}):[arguments[0]]);w(B)});Galaxy.modal.hide()}}})}})};var g=function(v){this.default_font=v!==undefined?v:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};t.extend(g.prototype,{load_pattern:function(v,z){var w=this.patterns,x=this.dummy_context,y=new Image();y.src=galaxy_config.root+"static/images"+z;y.onload=function(){w[v]=x.createPattern(y,"repeat")}},get_pattern:function(v){return this.patterns[v]},new_canvas:function(){var v=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(v)}v.manager=this;return v}});var r=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(v){this.clear()},get_elt:function(x){var y=this.attributes.obj_cache,z=this.attributes.key_ary,w=x.toString(),v=t.indexOf(z,function(A){return A.toString()===w});if(v!==-1){if(y[w].stale){z.splice(v,1);delete y[w]}else{this.move_key_to_end(x,v)}}return y[w]},set_elt:function(x,z){var A=this.attributes.obj_cache,B=this.attributes.key_ary,w=x.toString(),y=this.attributes.num_elements;if(!A[w]){if(B.length>=y){var v=B.shift();delete A[v.toString()]}B.push(x)}A[w]=z;return z},move_key_to_end:function(w,v){this.attributes.key_ary.splice(v,1);this.attributes.key_ary.push(w)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=r.extend({defaults:t.extend({},r.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(v,w){return true},can_subset:function(v){return false}}),initialize:function(v){r.prototype.initialize.call(this);var w=this.get("init_data");if(w){this.add_data(w)}},add_data:function(v){if(this.get("num_elements")<v.length){this.set("num_elements",v.length)}var w=this;t.each(v,function(x){w.set_data(x.region,x)})},data_is_ready:function(){var y=this.get("dataset"),x=$.Deferred(),v=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),w=new m.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:y.get("hda_ldda"),data_type:v},dataType:"json"},interval:5000,success_fn:function(z){return z!=="pending"}});$.when(w.go()).then(function(z){x.resolve(z==="ok"||z==="data")});return x},search_features:function(v){var w=this.get("dataset"),x={query:v,hda_ldda:w.get("hda_ldda"),data_type:"features"};return $.getJSON(w.url(),x)},load_data:function(D,C,w,B){var z=this.get("dataset"),y={data_type:this.get("data_type"),chrom:D.get("chrom"),low:D.get("start"),high:D.get("end"),mode:C,resolution:w,hda_ldda:z.get("hda_ldda")};$.extend(y,B);var F=this.get("filters_manager");if(F){var G=[];var v=F.filters;for(var A=0;A<v.length;A++){G.push(v[A].name)}y.filter_cols=JSON.stringify(G)}var x=this,E=$.getJSON(z.url(),y,function(H){H.region=D;x.set_data(D,H)});this.set_data(D,E);return E},get_data:function(C,B,x,z){var D=this.get_elt(C);if(D&&(m.is_deferred(D)||this.get("data_mode_compatible")(D,B))){return D}var E=this.get("key_ary"),v=this.get("obj_cache"),w,A;for(var y=0;y<E.length;y++){w=E[y];if(w.contains(C)){A=true;D=v[w.toString()];if(m.is_deferred(D)||(this.get("data_mode_compatible")(D,B)&&this.get("can_subset")(D))){this.move_key_to_end(w,y);if(!m.is_deferred(D)){var G=this.subset_entry(D,C);this.set_data(C,G);D=G}return D}}}if(!A&&C.length()<this.attributes.min_region_size){C=C.copy();var F=this.most_recently_added();if(!F||(C.get("start")>F.get("start"))){C.set("end",C.get("start")+this.attributes.min_region_size)}else{C.set("start",C.get("end")-this.attributes.min_region_size)}C.set("genome",this.attributes.genome);C.trim()}return this.load_data(C,B,x,z)},set_data:function(w,v){this.set_elt(w,v)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(D,C,y,B,z){var F=this._mark_stale(D);if(!(F&&this.get("data_mode_compatible")(F,C))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var x=D.get("start");if(z===this.DEEP_DATA_REQ){$.extend(B,{start_val:F.data.length+1})}else{if(z===this.BROAD_DATA_REQ){x=(F.max_high?F.max_high:F.data[F.data.length-1][2])+1}}var E=D.copy().set("start",x);var w=this,A=this.load_data(E,C,y,B),v=$.Deferred();this.set_data(D,v);$.when(A).then(function(G){if(G.data){G.data=F.data.concat(G.data);if(G.max_low){G.max_low=F.max_low}if(G.message){G.message=G.message.replace(/[0-9]+/,G.data.length)}}w.set_data(D,G);v.resolve(G)});return v},can_get_more_detailed_data:function(w){var v=this.get_elt(w);return(v.dataset_type==="bigwig"&&v.data.length<8000)},get_more_detailed_data:function(y,A,w,z,x){var v=this._mark_stale(y);if(!v){console.log("ERROR getting more detailed data: no current data");return}if(!x){x={}}if(v.dataset_type==="bigwig"){x.num_samples=1000*z}return this.load_data(y,A,w,x)},_mark_stale:function(w){var v=this.get_elt(w);if(!v){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),w.toString())}v.stale=true;return v},get_genome_wide_data:function(v){var x=this,z=true,y=t.map(v.get("chroms_info").chrom_info,function(B){var A=x.get_elt(new h({chrom:B.chrom,start:0,end:B.len}));if(!A){z=false}return A});if(z){return y}var w=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(A){x.add_data(A.data);w.resolve(A.data)});return w},subset_entry:function(x,y){var v={bigwig:function(z,A){return t.filter(z,function(B){return B[0]>=A.get("start")&&B[0]<=A.get("end")})},refseq:function(A,B){var C=B.get("start")-x.region.get("start"),z=x.data.length-(x.region.get("end")-B.get("end"));return x.data.slice(C,z)}};var w=x.data;if(!x.region.same(y)&&x.dataset_type in v){w=v[x.dataset_type](x.data,y)}return{region:y,data:w,dataset_type:x.dataset_type}}});var q=d.extend({initialize:function(v){var w=new Backbone.Model();w.urlRoot=v.data_url;this.set("dataset",w)},load_data:function(x,y,v,w){return(x.length()<=100000?d.prototype.load_data.call(this,x,y,v,w):{data:null,region:x})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(v){this.id=v.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(v){var w=t.find(this.get_chroms_info(),function(x){return x.chrom===v});return new h({chrom:w.chrom,end:w.len})},get_chrom_len:function(v){return t.find(this.get_chroms_info(),function(w){return w.chrom===v}).len}});var h=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(v){return this.attributes.chrom===v.get("chrom")&&this.attributes.start===v.get("start")&&this.attributes.end===v.get("end")},initialize:function(w){if(w.from_str){var y=w.from_str.split(":"),x=y[0],v=y[1].split("-");this.set({chrom:x,start:parseInt(v[0],10),end:parseInt(v[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new h({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(C){var w=this.get("chrom"),B=C.get("chrom"),A=this.get("start"),y=C.get("start"),z=this.get("end"),x=C.get("end"),v;if(w&&B&&w!==B){return h.overlap_results.DIF_CHROMS}if(A<y){if(z<y){v=h.overlap_results.BEFORE}else{if(z<x){v=h.overlap_results.OVERLAP_START}else{v=h.overlap_results.CONTAINS}}}else{if(A>y){if(A>x){v=h.overlap_results.AFTER}else{if(z<=x){v=h.overlap_results.CONTAINED_BY}else{v=h.overlap_results.OVERLAP_END}}}else{v=(z>=x?h.overlap_results.CONTAINS:h.overlap_results.CONTAINED_BY)}}return v},trim:function(v){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var w=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>w){this.attributes.end=w-1}}return this},contains:function(v){return this.compute_overlap(v)===h.overlap_results.CONTAINS},overlaps:function(v){return t.intersection([this.compute_overlap(v)],[h.overlap_results.DIF_CHROMS,h.overlap_results.BEFORE,h.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var n=Backbone.Collection.extend({model:h});var e=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(v){this.set("region",new h(v.region))}});var s=Backbone.Collection.extend({model:e});var u=Backbone.Model.extend(f).extend({defaults:{mode:"Auto"},initialize:function(v){this.set("dataset",new k.Dataset(v.dataset));this.set("config",p.ConfigSettingCollection.from_config_dict(v.prefs));this.get("config").add([{key:"name",value:this.get("dataset").get("name")},{key:"color"}]);var w=this.get("preloaded_data");if(w){w=w.data}else{w=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:w}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(w,v){if(t.size(w)===0){w={name:v.get("config").get("name").get("value"),color:v.get("config").get("color").get("value")}}return w},dataset:function(v){return{id:v.id,hda_ldda:v.get("hda_ldda")}}}});var j=Backbone.Collection.extend({model:u});var o=Backbone.Model.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var l=o.extend(f).extend({defaults:t.extend({},o.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(v){this.set("drawables",new j(v.tracks));this.set("config",p.ConfigSettingCollection.from_config_dict(v.prefs||{}));this.unset("tracks");this.get("drawables").each(function(w){w.unset("preloaded_data")})},add_tracks:function(v){this.get("drawables").add(v)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(w,v){return{obj_type:"View",prefs:{name:v.get("title"),content_visible:true},drawables:v.get("drawables")}}}});var b=Backbone.Model.extend({});var i=Backbone.Router.extend({initialize:function(w){this.view=w.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var v=this;v.view.on("navigate",function(x){v.navigate(x)})},change_location:function(v){this.view.go_to(v)}});return{BackboneTrack:u,BrowserBookmark:e,BrowserBookmarkCollection:s,Cache:r,CanvasManager:g,Genome:c,GenomeDataManager:d,GenomeRegion:h,GenomeRegionCollection:n,GenomeVisualization:l,GenomeReferenceDataManager:q,TrackBrowserRouter:i,TrackConfig:b,Visualization:o,select_datasets:a}});
\ No newline at end of file
diff -r 231a61e88777bbf7e2db9ef1fdaa9d7fb757523f -r 8bb0825fe57b1592331ca685c1e3f74ffdb83ca9 static/scripts/viz/trackster/painters.js
--- a/static/scripts/viz/trackster/painters.js
+++ b/static/scripts/viz/trackster/painters.js
@@ -120,7 +120,7 @@
this.view_start = view_start;
this.view_end = view_end;
// Drawing prefs
- this.prefs = extend( {}, this.default_prefs, prefs );
+ this.prefs = extend({}, this.default_prefs, prefs);
this.mode = mode;
};
diff -r 231a61e88777bbf7e2db9ef1fdaa9d7fb757523f -r 8bb0825fe57b1592331ca685c1e3f74ffdb83ca9 static/scripts/viz/visualization.js
--- a/static/scripts/viz/visualization.js
+++ b/static/scripts/viz/visualization.js
@@ -403,7 +403,7 @@
// If there's data, subset it.
if ( !util_mod.is_deferred(entry) ) {
var subset_entry = this.subset_entry(entry, region);
- this.set(region, subset_entry);
+ this.set_data(region, subset_entry);
entry = subset_entry;
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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26 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/231a61e88777/
Changeset: 231a61e88777
User: Jeremy Goecks
Date: 2014-03-26 22:39:58
Summary: Pack scripts.
Affected #: 5 files
diff -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 -r 231a61e88777bbf7e2db9ef1fdaa9d7fb757523f static/scripts/packed/utils/config.js
--- a/static/scripts/packed/utils/config.js
+++ b/static/scripts/packed/utils/config.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","viz/trackster/util","utils/config"],function(c,f,b){var d=Backbone.Model.extend({initialize:function(g){var h=this.get("key");this.set("id",h);var i=c.find(d.known_settings_defaults,function(j){return j.key===h});if(i){this.set(c.extend({},i,g))}if(!this.get("value")){this.set_value(this.get("default_value"));if(!this.get("value")&&this.get("type")==="color"){this.set("value",f.get_random_color())}}},set_value:function(h){var g=this.get("type");if(g==="float"){h=parseFloat(h)}else{if(g==="int"){h=parseInt(h,10)}}this.set("value",h)}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var e=Backbone.Collection.extend({model:d,to_key_value_dict:function(){var g={};this.each(function(h){g[h.get("key")]=h.get("value")});return g},get_value:function(g){var h=this.get(g);if(h){return h.get("value")}return undefined},set_value:function(g,i){var h=this.get(g);if(h){return h.set_value(i)}return undefined},set_default_value:function(h,g){var i=this.get(h);if(i){return i.set("default_value",g)}return undefined}},{from_models_and_saved_values:function(h,g){if(g){h=c.map(h,function(i){return c.extend({},i,{value:g[i.key]})})}return new e(h)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var g=this.$el;this.collection.each(function(j,n){if(j.get("hidden")){return}var i="param_"+n,o=j.get("type"),s=j.get("value");var t=$("<div class='form-row' />").appendTo(g);t.append($("<label />").attr("for",i).text(j.get("label")+":"));if(o==="bool"){t.append($('<input type="checkbox" />').attr("id",i).attr("name",i).attr("checked",s))}else{if(o==="text"){t.append($('<input type="text"/>').attr("id",i).val(s).click(function(){$(this).select()}))}else{if(o==="select"){var q=$("<select />").attr("id",i);c.each(j.get("options"),function(v){$("<option/>").text(v.label).attr("value",v.value).appendTo(q)});q.val(s);t.append(q)}else{if(o==="color"){var u=$("<div/>").appendTo(t),p=$("<input />").attr("id",i).attr("name",i).val(s).css("float","left").appendTo(u).click(function(w){$(".tooltip").removeClass("in");var v=$(this).siblings(".tooltip").addClass("in");v.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(v).height()/2)+($(this).height()/2)}).show();v.click(function(x){x.stopPropagation()});$(document).bind("click.color-picker",function(){v.hide();$(document).unbind("click.color-picker")});w.stopPropagation()}),m=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(u).attr("title","Set new random color").tooltip(),r=$("<div class='tooltip right' style='position: absolute;' />").appendTo(u).hide(),k=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(r),h=$("<div class='tooltip-arrow'></div>").appendTo(r),l=$.farbtastic(k,{width:100,height:100,callback:p,color:s});u.append($("<div/>").css("clear","both"));(function(v){m.click(function(){v.setColor(f.get_random_color())})})(l)}else{t.append($("<input />").attr("id",i).attr("name",i).val(s))}}}}if(j.help){t.append($("<div class='help'/>").text(j.help))}});return this},render_in_modal:function(k){var g=this,j=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},h=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc");g.update_from_form()},i=function(l){if((l.keyCode||l.which)===27){j()}else{if((l.keyCode||l.which)===13){h()}}};$(window).bind("keypress.check_enter_esc",i);if(this.$el.children().length===0){this.render()}Galaxy.modal.show({title:k||"Configure",body:this.$el,buttons:{Cancel:j,OK:h}})},update_from_form:function(){var g=this;this.collection.each(function(i,h){if(!i.get("hidden")){var k="param_"+h;var j=g.$el.find("#"+k).val();if(i.get("type")==="bool"){j=g.$el.find("#"+k).is(":checked")}i.set_value(j)}})}});return{ConfigSettingCollection:e,ConfigSettingCollectionView:a}});
\ No newline at end of file
+define(["libs/underscore","viz/trackster/util","utils/config"],function(c,f,b){var d=Backbone.Model.extend({initialize:function(g){var h=this.get("key");this.set("id",h);var i=c.find(d.known_settings_defaults,function(j){return j.key===h});if(i){this.set(c.extend({},i,g))}if(this.get("value")===undefined){this.set_value(this.get("default_value"));if(!this.get("value")&&this.get("type")==="color"){this.set("value",f.get_random_color())}}},set_value:function(h){var g=this.get("type");if(g==="float"){h=parseFloat(h)}else{if(g==="int"){h=parseInt(h,10)}}this.set("value",h)}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var e=Backbone.Collection.extend({model:d,to_key_value_dict:function(){var g={};this.each(function(h){g[h.get("key")]=h.get("value")});return g},get_value:function(g){var h=this.get(g);if(h){return h.get("value")}return undefined},set_value:function(g,i){var h=this.get(g);if(h){return h.set_value(i)}return undefined},set_default_value:function(h,g){var i=this.get(h);if(i){return i.set("default_value",g)}return undefined}},{from_models_and_saved_values:function(h,g){if(g){h=c.map(h,function(i){return c.extend({},i,{value:g[i.key]})})}return new e(h)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var g=this.$el;this.collection.each(function(j,n){if(j.get("hidden")){return}var i="param_"+n,o=j.get("type"),s=j.get("value");var t=$("<div class='form-row' />").appendTo(g);t.append($("<label />").attr("for",i).text(j.get("label")+":"));if(o==="bool"){t.append($('<input type="checkbox" />').attr("id",i).attr("name",i).attr("checked",s))}else{if(o==="text"){t.append($('<input type="text"/>').attr("id",i).val(s).click(function(){$(this).select()}))}else{if(o==="select"){var q=$("<select />").attr("id",i);c.each(j.get("options"),function(v){$("<option/>").text(v.label).attr("value",v.value).appendTo(q)});q.val(s);t.append(q)}else{if(o==="color"){var u=$("<div/>").appendTo(t),p=$("<input />").attr("id",i).attr("name",i).val(s).css("float","left").appendTo(u).click(function(w){$(".tooltip").removeClass("in");var v=$(this).siblings(".tooltip").addClass("in");v.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(v).height()/2)+($(this).height()/2)}).show();v.click(function(x){x.stopPropagation()});$(document).bind("click.color-picker",function(){v.hide();$(document).unbind("click.color-picker")});w.stopPropagation()}),m=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(u).attr("title","Set new random color").tooltip(),r=$("<div class='tooltip right' style='position: absolute;' />").appendTo(u).hide(),k=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(r),h=$("<div class='tooltip-arrow'></div>").appendTo(r),l=$.farbtastic(k,{width:100,height:100,callback:p,color:s});u.append($("<div/>").css("clear","both"));(function(v){m.click(function(){v.setColor(f.get_random_color())})})(l)}else{t.append($("<input />").attr("id",i).attr("name",i).val(s))}}}}if(j.help){t.append($("<div class='help'/>").text(j.help))}});return this},render_in_modal:function(k){var g=this,j=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},h=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc");g.update_from_form()},i=function(l){if((l.keyCode||l.which)===27){j()}else{if((l.keyCode||l.which)===13){h()}}};$(window).bind("keypress.check_enter_esc",i);if(this.$el.children().length===0){this.render()}Galaxy.modal.show({title:k||"Configure",body:this.$el,buttons:{Cancel:j,OK:h}})},update_from_form:function(){var g=this;this.collection.each(function(i,h){if(!i.get("hidden")){var k="param_"+h;var j=g.$el.find("#"+k).val();if(i.get("type")==="bool"){j=g.$el.find("#"+k).is(":checked")}i.set_value(j)}})}});return{ConfigSettingCollection:e,ConfigSettingCollectionView:a}});
\ No newline at end of file
diff -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 -r 231a61e88777bbf7e2db9ef1fdaa9d7fb757523f static/scripts/packed/viz/trackster/painters.js
--- a/static/scripts/packed/viz/trackster/painters.js
+++ b/static/scripts/packed/viz/trackster/painters.js
@@ -1,1 +1,1 @@
-define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.round((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)},get_top_padding:function(width){return 0},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_start=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height)}}else{var cur_y_start,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_start=y_start+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_start=y_start;cur_height=thick_height}else{cur_y_start+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_start,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_start+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_start)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_start+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_start+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),paint_utils=new ReadPainterUtils(ctx,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),w_scale,mode);var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){if("MDN=X".indexOf(cig_op)!==-1){base_offset+=cig_len}continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":seq_offset+=cig_len;break;case"M":case"=":case"X":ctx.fillStyle=block_color;ctx.fillRect(s_start,y_start+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_start+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_start+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,y_start,1);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_start=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}var b1_end=Math.ceil(Math.min(width,Math.max(-0.5*w_scale,(feature[4][1]-tile_low-0.5)*w_scale))),b2_start=Math.floor(Math.max(-0.5*w_scale,(feature[5][0]-tile_low-0.5)*w_scale));if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_start+5,b2_start,y_start+5)}}else{this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8)}}return[0,0]}});var RefBasedReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){ReadPainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn)};extend(RefBasedReadPainter.prototype,ReadPainter.prototype,FeaturePainter,{draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),paint_utils=new ReadPainterUtils(ctx,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),w_scale,mode),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,y_start+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_start+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_start+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,y_start+(pack_mode?1:4),cig_len);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_start){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_start,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var ReadPainterUtils=function(ctx,row_height,px_per_base,mode){this.ctx=ctx;this.row_height=row_height;this.px_per_base=px_per_base;this.draw_details=(mode==="Pack"||mode==="Auto")&&(px_per_base>=ctx.canvas.manager.char_width_px);this.delete_details_thickness=0.2};extend(ReadPainterUtils.prototype,{draw_deletion:function(x,y,len){this.ctx.fillStyle="black";var thickness=(this.draw_details?this.delete_details_thickness:1)*this.row_height;y+=0.5*(this.row_height-thickness);this.ctx.fillRect(x,y,len*this.px_per_base,thickness)}});var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var get_deletion_info=function(ref,alt){var ref_len=ref.length,alt_len=alt.length,start=0,len=1,is_delete=false;if(alt==="-"){is_delete=true;len=ref.length}else{if(ref.indexOf(alt)===0&&ref_len>alt_len){is_delete=true;len=ref_len=alt_len;start+=alt_len}}return(is_delete?{start:start,len:len}:null)};var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,paint_utils=new ReadPainterUtils(ctx,row_height,w_scale,this.mode),j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];ref=locus_data[3];alt=[locus_data[4].split(",")];sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);alt=_.map(_.flatten(alt),function(a){var type,alt_info={},delete_info=get_deletion_info(ref,a);if(delete_info){type="deletion";_.extend(alt_info,delete_info)}else{type="snp"}return _.extend(alt_info,{type:type,value:a,})});if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=(alt[j].type==="deletion"?"black":this.base_color_fn(alt[j].value));allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){if(variant.type==="snp"){var snp=variant.value;ctx.fillStyle=this.base_color_fn(snp);if(paint_utils.draw_details){ctx.fillText(snp,char_x_start,draw_y_start+row_height)}else{ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}}else{if(variant.type==="deletion"){paint_utils.draw_deletion(draw_x_start+base_px*variant.start,draw_y_start+1,variant.len)}else{}}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,RefBasedReadPainter:RefBasedReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}});
\ No newline at end of file
+define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.round((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler());this.max_label_length=200};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)},get_top_padding:function(width){return 0},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_start=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_start+1,f_end-f_start,thick_height)}}else{var cur_y_start,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_start=y_start+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_start=y_start;cur_height=thick_height}else{cur_y_start+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_start,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_start+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_start+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_start)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_start+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_start+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8,this.max_label_length);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8,this.max_label_length);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,cigar,strand,read_seq){var update_base_offset=function(offset,cig_op,cig_len){if("M=NXD".indexOf(cig_op)!==-1){offset+=cig_len}return offset},update_seq_offset=function(offset,cig_op,cig_len){if("IX".indexOf(cig_op)!==-1){offset+=cig_len}return offset};ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),paint_utils=new ReadPainterUtils(ctx,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT),w_scale,mode),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,y_start+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(!is_overlap([seq_start,seq_start+cig_len],tile_region)){base_offset=update_base_offset(base_offset,cig_op,cig_len);seq_offset=update_seq_offset(seq_offset,cig_op,cig_len);continue}if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_start+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_start+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_start+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":paint_utils.draw_deletion(s_start,y_start+(pack_mode?1:4),cig_len);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_start-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_start+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_start)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_start+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_start+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_start=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}var b1_end=Math.ceil(Math.min(width,Math.max(-0.5*w_scale,(feature[4][1]-tile_low-0.5)*w_scale))),b2_start=Math.floor(Math.max(-0.5*w_scale,(feature[5][0]-tile_low-0.5)*w_scale));if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_start+5,b2_start,y_start+5)}}else{this.draw_read(ctx,mode,w_scale,y_start,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_start+8,this.max_label_length)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_start+8,this.max_label_length)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_start){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_start,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var ReadPainterUtils=function(ctx,row_height,px_per_base,mode){this.ctx=ctx;this.row_height=row_height;this.px_per_base=px_per_base;this.draw_details=(mode==="Pack"||mode==="Auto")&&(px_per_base>=ctx.canvas.manager.char_width_px);this.delete_details_thickness=0.2};extend(ReadPainterUtils.prototype,{draw_deletion:function(x,y,len){this.ctx.fillStyle="black";var thickness=(this.draw_details?this.delete_details_thickness:1)*this.row_height;y+=0.5*(this.row_height-thickness);this.ctx.fillRect(x,y,len*this.px_per_base,thickness)}});var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var get_deletion_info=function(ref,alt){var ref_len=ref.length,alt_len=alt.length,start=0,len=1,is_delete=false;if(alt==="-"){is_delete=true;len=ref.length}else{if(ref.indexOf(alt)===0&&ref_len>alt_len){is_delete=true;len=ref_len=alt_len;start+=alt_len}}return(is_delete?{start:start,len:len}:null)};var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,paint_utils=new ReadPainterUtils(ctx,row_height,w_scale,this.mode),j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];ref=locus_data[3];alt=[locus_data[4].split(",")];sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);alt=_.map(_.flatten(alt),function(a){var type,alt_info={},delete_info=get_deletion_info(ref,a);if(delete_info){type="deletion";_.extend(alt_info,delete_info)}else{type="snp"}return _.extend(alt_info,{type:type,value:a,})});if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=(alt[j].type==="deletion"?"black":this.base_color_fn(alt[j].value));allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){if(variant.type==="snp"){var snp=variant.value;ctx.fillStyle=this.base_color_fn(snp);if(paint_utils.draw_details){ctx.fillText(snp,char_x_start,draw_y_start+row_height)}else{ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}}else{if(variant.type==="deletion"){paint_utils.draw_deletion(draw_x_start+base_px*variant.start,draw_y_start+1,variant.len)}else{}}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}});
\ No newline at end of file
diff -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 -r 231a61e88777bbf7e2db9ef1fdaa9d7fb757523f 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(){this.track.set_name(this.track.config.get("values").name)},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||ab===1){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=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ab.dbkey},function(ag){aa.each(ag,function(ah){ab.add_drawable(n(ah,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=$("<select/>").attr({name:"chrom"}).addClass("chrom-nav").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ac=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ab.go_to($(this).val())}$(this).hide();$(this).val("");ab.location_span.show();ab.chrom_select.show()}ag.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(ai,ag){var aj=[],ah=$.map(ab.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});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=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ab.zoom_in()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ab.change_chrom(ab.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ab.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ab.viewport_container.width()*(ab.max_high-ab.max_low));ab.move_delta(-ah)});this.overview_close.click(function(){ab.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ab.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ab.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ab.viewport_container.width()*(ab.high-ab.low));ab.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){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(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ab.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ab.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ab.container.offset().left,aj=(ab.high-ab.low),ai=ab.viewport_container.width();ab.update_location(Math.round(ah/ai*aj)+ab.low,Math.round(ag/ai*aj)+ab.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ab.high-ab.low),ai=ab.viewport_container.width(),ak=ab.low;ab.low=Math.round(ah/ai*aj)+ak;ab.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ab.request_redraw()});var ae=$("<div/>").addClass("mouse-pos").appendTo(ad);ad.hover(function(){ae.show();ad.mousemove(function(ag){ae.css({left:ag.pageX-1})})},function(){ad.off("mousemove");ae.hide()});this.add_label_track(new V(this,{content_div:this.top_labeltrack}));this.add_label_track(new V(this,{content_div:this.nav_labeltrack}));$(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(ae,al,an,ad,ag,ah,ao,ac,ak){b.call(this,ae,al,an,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ak;this.has_icons=false;if(ao){this.has_icons=true;var ai=this;ad=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D,width:ad.width}).prependTo(this.html_elt);var aj=new w.GenomeRegion({chrom:ae.view.chrom,start:this.low,end:this.high}),am=ag.length,af=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ab=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);af.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()});ab.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()})}};o(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ac=this,ab={};if(ac.mode!=="Pack"){return}$(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("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_param_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(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($("<div/>").addClass("label").text(commatize(ab)).css({left:ah}));ab+=ai}this.content_div.children(":first").remove();this.content_div.append(ac)}});var e=function(ac,ab,af){L.call(this,ac,ab,af);this.drawables=[];if("drawables" in af){var ae;for(var ad=0;ad<af.drawables.length;ad++){ae=af.drawables[ad];this.drawables[ad]=n(ae,ac,null);if(ae.left_offset>this.left_offset){this.left_offset=ae.left_offset}}this.enabled=true}aa.each(this.drawables,function(ag){if(ag instanceof c||ag instanceof S){ag.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,L.prototype,{display_modes:A,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".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,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(){L.prototype.before_draw.call(this);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){L.prototype.postdraw_actions.call(this,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(al,ad,am,ak){L.prototype.postdraw_actions.call(this,al,ad,am,ak);var af=this,ag;if(af.filters_manager){var ae=af.filters_manager.filters,ai;for(ai=0;ai<ae.length;ai++){ae[ai].update_ui_elt()}var ah=false,aj,ac;for(ag=0;ag<al.length;ag++){if(al[ag].data.length){aj=al[ag].data[0];for(ai=0;ai<ae.length;ai++){ac=ae[ai];if(ac.applies_to(aj)&&ac.min!==ac.max){ah=true;break}}}}if(af.filters_available!==ah){af.filters_available=ah;if(!af.filters_available){af.filters_manager.hide()}af.update_icons()}}if(al[0] instanceof M){var ab=true;for(ag=0;ag<al.length;ag++){if(!al[ag].all_slotted){ab=false;break}}if(!ab){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(al,ap,an,ae,ai,ad){var ao=this,ac=ap.canvas,aw=ae.get("start"),ab=ae.get("end"),af=this.left_offset;if(al.dataset_type==="bigwig"){return this._draw_line_track_tile(al,ap,an,ae,ai)}var ah=[],am=this.slotters[ai].slots;all_slotted=true;if(al.data){var aj=this.filters_manager.filters;for(var aq=0,at=al.data.length;aq<at;aq++){var ag=al.data[aq];var ar=false;var ak;for(var av=0,aA=aj.length;av<aA;av++){ak=aj[av];ak.update_attrs(ag);if(!ak.keep(ag)){ar=true;break}}if(!ar){ah.push(ag);if(!(ag[0] in am)){all_slotted=false}}}}var az=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),ax=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),ay=new (this.painter)(ah,aw,ab,this.config.to_key_value_dict(),an,az,ax,ad,function(aB){return ao.view.get_base_color(aB)});var au=null;ap.fillStyle=this.config.get_value("block_color");ap.font=ap.canvas.manager.default_font;ap.textAlign="right";if(al.data){au=ay.draw(ap,ac.width,ac.height,ai,am);au.translation=-af}return new M(ao,ae,ai,ac,al.data,an,al.message,all_slotted,au)}});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:32,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=(ac.reference_track?J.RefBasedReadPainter: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"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{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){$(".tooltip").remove();ab.remove()}}];o(p.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.config.get_value("content_visible")){return true}return false},request_draw:function(){},_draw:function(ab){},to_dict:function(){},set_name:function(ab){this.old_name=this.config.get_value("name");this.config.set_value("name",ab);this.name_div.text(ab)},revert_name:function(){if(this.old_name){this.config.set_value("name",this.old_name);this.name_div.text(this.old_name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ab=this.view;this.container_div.hide(0,function(){$(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=$("<div/>").addClass("track-name").text(this.config.get_value("name")).appendTo(ab);return ab},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ad=this.drawables.length;if(ad===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ad===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ak,aj,ah,an=true,af=this.drawables[0].get_type(),ab=0;for(ak=0;ak<ad;ak++){ah=this.drawables[ak];if(ah.get_type()!==af){can_composite=false;break}if(ah instanceof c){ab++}}if(an||ab===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".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=$("<div class='track-tile'/>").append(ac);this.data=ad;this.stale=false};b.prototype.predisplay_actions=function(){};var K=function(ab,ae,af,ac,ad){b.call(this,ab,ae,af,ac,ad)};K.prototype.predisplay_actions=function(){};var M=function(ae,al,an,ad,ag,ah,ao,ac,ak){b.call(this,ae,al,an,ad,ag);this.mode=ah;this.all_slotted=ac;this.feature_mapper=ak;this.has_icons=false;if(ao){this.has_icons=true;var ai=this;ad=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D,width:ad.width}).prependTo(this.html_elt);var aj=new w.GenomeRegion({chrom:ae.view.chrom,start:this.low,end:this.high}),am=ag.length,af=$("<a/>").addClass("icon more-down").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ab=$("<a/>").addClass("icon more-across").attr("title","For speed, only the first "+am+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);af.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()});ab.click(function(){ai.stale=true;ae.data_manager.get_more_data(aj,ae.mode,1/ai.w_scale,{},ae.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ae.request_draw()}).dblclick(function(ap){ap.stopPropagation()})}};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("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_param_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,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ab){$(".tooltip").remove();ab.show_group()}}].concat(L.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ab){L.prototype.change_mode.call(this,ab);for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].change_mode(ab)}},init:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].init())}var ab=this;$.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(){L.prototype.before_draw.call(this);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){L.prototype.postdraw_actions.call(this,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(al,ad,am,ak){L.prototype.postdraw_actions.call(this,al,ad,am,ak);var af=this,ag;if(af.filters_manager){var ae=af.filters_manager.filters,ai;for(ai=0;ai<ae.length;ai++){ae[ai].update_ui_elt()}var ah=false,aj,ac;for(ag=0;ag<al.length;ag++){if(al[ag].data.length){aj=al[ag].data[0];for(ai=0;ai<ae.length;ai++){ac=ae[ai];if(ac.applies_to(aj)&&ac.min!==ac.max){ah=true;break}}}}if(af.filters_available!==ah){af.filters_available=ah;if(!af.filters_available){af.filters_manager.hide()}af.update_icons()}}if(al[0] instanceof M){var ab=true;for(ag=0;ag<al.length;ag++){if(!al[ag].all_slotted){ab=false;break}}if(!ab){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(al,ap,an,ae,ai,ad){var ao=this,ac=ap.canvas,aw=ae.get("start"),ab=ae.get("end"),af=this.left_offset;if(al.dataset_type==="bigwig"){return this._draw_line_track_tile(al,ap,an,ae,ai)}var ah=[],am=this.slotters[ai].slots;all_slotted=true;if(al.data){var aj=this.filters_manager.filters;for(var aq=0,at=al.data.length;aq<at;aq++){var ag=al.data[aq];var ar=false;var ak;for(var av=0,aA=aj.length;av<aA;av++){ak=aj[av];ak.update_attrs(ag);if(!ak.keep(ag)){ar=true;break}}if(!ar){ah.push(ag);if(!(ag[0] in am)){all_slotted=false}}}}var az=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),ax=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),ay=new (this.painter)(ah,aw,ab,this.config.to_key_value_dict(),an,az,ax,ad,function(aB){return ao.view.get_base_color(aB)});var au=null;ap.fillStyle=this.config.get_value("block_color");ap.font=ap.canvas.manager.default_font;ap.textAlign="right";if(al.data){au=ay.draw(ap,ac.width,ac.height,ai,am);au.translation=-af}return new M(ao,ae,ai,ac,al.data,an,al.message,all_slotted,au)}});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:32,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"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"},{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 bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 -r 231a61e88777bbf7e2db9ef1fdaa9d7fb757523f static/scripts/packed/viz/trackster/util.js
--- a/static/scripts/packed/viz/trackster/util.js
+++ b/static/scripts/packed/viz/trackster/util.js
@@ -1,1 +1,1 @@
-define(function(){var b=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(c){return true}},go:function(){var f=$.Deferred(),e=this,h=e.get("ajax_settings"),g=e.get("success_fn"),d=e.get("interval"),c=function(){$.ajax(h).success(function(i){if(g(i)){f.resolve(i)}else{setTimeout(c,d)}})};c();return f}});var a=function(c){if(!c){c="#ffffff"}if(typeof(c)==="string"){c=[c]}for(var l=0;l<c.length;l++){c[l]=parseInt(c[l].slice(1),16)}var p=function(v,u,i){return((v*299)+(u*587)+(i*114))/1000};var g=function(x,w,y,u,i,v){return(Math.max(x,u)-Math.min(x,u))+(Math.max(w,i)-Math.min(w,i))+(Math.max(y,v)-Math.min(y,v))};var j,q,h,m,s,k,t,e,f,d,r,o=false,n=0;do{j=Math.round(Math.random()*16777215);q=(j&16711680)>>16;h=(j&65280)>>8;m=j&255;f=p(q,h,m);o=true;for(l=0;l<c.length;l++){s=c[l];k=(s&16711680)>>16;t=(s&65280)>>8;e=s&255;d=p(k,t,e);r=g(q,h,m,k,t,e);if((Math.abs(f-d)<40)||(r<200)){o=false;break}}n++}while(!o&&n<=10);return"#"+(16777216+j).toString(16).substr(1,6)};return{ServerStateDeferred:b,get_random_color:a}});
\ No newline at end of file
+define(function(){var b=function(e){return("promise" in e)};var c=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(d){return true}},go:function(){var g=$.Deferred(),f=this,i=f.get("ajax_settings"),h=f.get("success_fn"),e=f.get("interval"),d=function(){$.ajax(i).success(function(j){if(h(j)){g.resolve(j)}else{setTimeout(d,e)}})};d();return g}});var a=function(d){if(!d){d="#ffffff"}if(typeof(d)==="string"){d=[d]}for(var m=0;m<d.length;m++){d[m]=parseInt(d[m].slice(1),16)}var q=function(w,v,i){return((w*299)+(v*587)+(i*114))/1000};var h=function(y,x,z,v,i,w){return(Math.max(y,v)-Math.min(y,v))+(Math.max(x,i)-Math.min(x,i))+(Math.max(z,w)-Math.min(z,w))};var k,r,j,n,t,l,u,f,g,e,s,p=false,o=0;do{k=Math.round(Math.random()*16777215);r=(k&16711680)>>16;j=(k&65280)>>8;n=k&255;g=q(r,j,n);p=true;for(m=0;m<d.length;m++){t=d[m];l=(t&16711680)>>16;u=(t&65280)>>8;f=t&255;e=q(l,u,f);s=h(r,j,n,l,u,f);if((Math.abs(g-e)<40)||(s<200)){p=false;break}}o++}while(!p&&o<=10);return"#"+(16777216+k).toString(16).substr(1,6)};return{is_deferred:b,ServerStateDeferred:c,get_random_color:a}});
\ No newline at end of file
diff -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 -r 231a61e88777bbf7e2db9ef1fdaa9d7fb757523f static/scripts/packed/viz/visualization.js
--- a/static/scripts/packed/viz/visualization.js
+++ b/static/scripts/packed/viz/visualization.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(u,k,n,q){var f={toJSON:function(){var w=this,x={};u.each(w.constructor.to_json_keys,function(y){var z=w.get(y);if(y in w.constructor.to_json_mappers){z=w.constructor.to_json_mappers[y](z,w)}x[y]=z});return x}};var a=function(w,z,y,x){$.ajax({url:w,data:y,error:function(){alert("Grid failed")},success:function(A){Galaxy.modal.show({title:"Select datasets for new tracks",body:A,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var B=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var C={data_type:"track_config",hda_ldda:"hda"},D=$(this).val();if($(this).attr("name")!=="id"){C.hda_ldda="ldda"}B[B.length]=$.ajax({url:z+"/"+D,data:C,dataType:"json"})});$.when.apply($,B).then(function(){var C=(arguments[0] instanceof Array?$.map(arguments,function(D){return D[0]}):[arguments[0]]);x(C)});Galaxy.modal.hide()}}})}})};var l=function(w){return("promise" in w)};var g=function(w){this.default_font=w!==undefined?w:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};u.extend(g.prototype,{load_pattern:function(w,A){var x=this.patterns,y=this.dummy_context,z=new Image();z.src=galaxy_config.root+"static/images"+A;z.onload=function(){x[w]=y.createPattern(z,"repeat")}},get_pattern:function(w){return this.patterns[w]},new_canvas:function(){var w=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(w)}w.manager=this;return w}});var s=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(w){this.clear()},get_elt:function(y){var z=this.attributes.obj_cache,A=this.attributes.key_ary,x=y.toString(),w=u.indexOf(A,function(B){return B.toString()===x});if(w!==-1){if(z[x].stale){A.splice(w,1);delete z[x]}else{this.move_key_to_end(y,w)}}return z[x]},set_elt:function(y,A){var B=this.attributes.obj_cache,C=this.attributes.key_ary,x=y.toString(),z=this.attributes.num_elements;if(!B[x]){if(C.length>=z){var w=C.shift();delete B[w.toString()]}C.push(y)}B[x]=A;return A},move_key_to_end:function(x,w){this.attributes.key_ary.splice(w,1);this.attributes.key_ary.push(x)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=s.extend({defaults:u.extend({},s.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(w,x){return true},can_subset:function(w){return false}}),initialize:function(w){s.prototype.initialize.call(this);var x=this.get("init_data");if(x){this.add_data(x)}},add_data:function(w){if(this.get("num_elements")<w.length){this.set("num_elements",w.length)}var x=this;u.each(w,function(y){x.set_data(y.region,y)})},data_is_ready:function(){var z=this.get("dataset"),y=$.Deferred(),w=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),x=new n.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:z.get("hda_ldda"),data_type:w},dataType:"json"},interval:5000,success_fn:function(A){return A!=="pending"}});$.when(x.go()).then(function(A){y.resolve(A==="ok"||A==="data")});return y},search_features:function(w){var x=this.get("dataset"),y={query:w,hda_ldda:x.get("hda_ldda"),data_type:"features"};return $.getJSON(x.url(),y)},load_data:function(E,D,x,C){var A=this.get("dataset"),z={data_type:this.get("data_type"),chrom:E.get("chrom"),low:E.get("start"),high:E.get("end"),mode:D,resolution:x,hda_ldda:A.get("hda_ldda")};$.extend(z,C);var G=this.get("filters_manager");if(G){var H=[];var w=G.filters;for(var B=0;B<w.length;B++){H.push(w[B].name)}z.filter_cols=JSON.stringify(H)}var y=this,F=$.getJSON(A.url(),z,function(I){I.region=E;y.set_data(E,I)});this.set_data(E,F);return F},get_data:function(D,C,y,A){var E=this.get_elt(D);if(E&&(l(E)||this.get("data_mode_compatible")(E,C))){return E}var F=this.get("key_ary"),w=this.get("obj_cache"),x,B;for(var z=0;z<F.length;z++){x=F[z];if(x.contains(D)){B=true;E=w[x.toString()];if(l(E)||(this.get("data_mode_compatible")(E,C)&&this.get("can_subset")(E))){this.move_key_to_end(x,z);if(!l(E)){var H=this.subset_entry(E,D);this.set(D,H);E=H}return E}}}if(!B&&D.length()<this.attributes.min_region_size){D=D.copy();var G=this.most_recently_added();if(!G||(D.get("start")>G.get("start"))){D.set("end",D.get("start")+this.attributes.min_region_size)}else{D.set("start",D.get("end")-this.attributes.min_region_size)}D.set("genome",this.attributes.genome);D.trim()}return this.load_data(D,C,y,A)},set_data:function(x,w){this.set_elt(x,w)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(E,D,z,C,A){var G=this._mark_stale(E);if(!(G&&this.get("data_mode_compatible")(G,D))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var y=E.get("start");if(A===this.DEEP_DATA_REQ){$.extend(C,{start_val:G.data.length+1})}else{if(A===this.BROAD_DATA_REQ){y=(G.max_high?G.max_high:G.data[G.data.length-1][2])+1}}var F=E.copy().set("start",y);var x=this,B=this.load_data(F,D,z,C),w=$.Deferred();this.set_data(E,w);$.when(B).then(function(H){if(H.data){H.data=G.data.concat(H.data);if(H.max_low){H.max_low=G.max_low}if(H.message){H.message=H.message.replace(/[0-9]+/,H.data.length)}}x.set_data(E,H);w.resolve(H)});return w},can_get_more_detailed_data:function(x){var w=this.get_elt(x);return(w.dataset_type==="bigwig"&&w.data.length<8000)},get_more_detailed_data:function(z,B,x,A,y){var w=this._mark_stale(z);if(!w){console.log("ERROR getting more detailed data: no current data");return}if(!y){y={}}if(w.dataset_type==="bigwig"){y.num_samples=1000*A}return this.load_data(z,B,x,y)},_mark_stale:function(x){var w=this.get_elt(x);if(!w){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),x.toString())}w.stale=true;return w},get_genome_wide_data:function(w){var y=this,A=true,z=u.map(w.get("chroms_info").chrom_info,function(C){var B=y.get_elt(new h({chrom:C.chrom,start:0,end:C.len}));if(!B){A=false}return B});if(A){return z}var x=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(B){y.add_data(B.data);x.resolve(B.data)});return x},subset_entry:function(y,z){var w={bigwig:function(A,B){return u.filter(A,function(C){return C[0]>=B.get("start")&&C[0]<=B.get("end")})},refseq:function(B,C){var D=C.get("start")-y.region.get("start"),A=y.data.length-(y.region.get("end")-C.get("end"));return y.data.slice(D,A)}};var x=y.data;if(!y.region.same(z)&&y.dataset_type in w){x=w[y.dataset_type](y.data,z)}return{region:z,data:x,dataset_type:y.dataset_type}}});var r=d.extend({initialize:function(w){var x=new Backbone.Model();x.urlRoot=w.data_url;this.set("dataset",x)},load_data:function(y,z,w,x){return(y.length()<=100000?d.prototype.load_data.call(this,y,z,w,x):{data:null,region:y})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(w){this.id=w.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(w){var x=u.find(this.get_chroms_info(),function(y){return y.chrom===w});return new h({chrom:x.chrom,end:x.len})},get_chrom_len:function(w){return u.find(this.get_chroms_info(),function(x){return x.chrom===w}).len}});var h=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(w){return this.attributes.chrom===w.get("chrom")&&this.attributes.start===w.get("start")&&this.attributes.end===w.get("end")},initialize:function(x){if(x.from_str){var z=x.from_str.split(":"),y=z[0],w=z[1].split("-");this.set({chrom:y,start:parseInt(w[0],10),end:parseInt(w[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new h({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(D){var x=this.get("chrom"),C=D.get("chrom"),B=this.get("start"),z=D.get("start"),A=this.get("end"),y=D.get("end"),w;if(x&&C&&x!==C){return h.overlap_results.DIF_CHROMS}if(B<z){if(A<z){w=h.overlap_results.BEFORE}else{if(A<y){w=h.overlap_results.OVERLAP_START}else{w=h.overlap_results.CONTAINS}}}else{if(B>z){if(B>y){w=h.overlap_results.AFTER}else{if(A<=y){w=h.overlap_results.CONTAINED_BY}else{w=h.overlap_results.OVERLAP_END}}}else{w=(A>=y?h.overlap_results.CONTAINS:h.overlap_results.CONTAINED_BY)}}return w},trim:function(w){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var x=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>x){this.attributes.end=x-1}}return this},contains:function(w){return this.compute_overlap(w)===h.overlap_results.CONTAINS},overlaps:function(w){return u.intersection([this.compute_overlap(w)],[h.overlap_results.DIF_CHROMS,h.overlap_results.BEFORE,h.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var o=Backbone.Collection.extend({model:h});var e=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(w){this.set("region",new h(w.region))}});var t=Backbone.Collection.extend({model:e});var v=Backbone.Model.extend(f).extend({defaults:{mode:"Auto"},initialize:function(w){this.set("dataset",new k.Dataset(w.dataset));this.set("config",q.ConfigSettingCollection.from_config_dict(w.prefs));this.get("config").add([{key:"name",value:this.get("dataset").get("name")},{key:"color"}]);var x=this.get("preloaded_data");if(x){x=x.data}else{x=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:x}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(x,w){if(u.size(x)===0){x={name:w.get("config").get("name").get("value"),color:w.get("config").get("color").get("value")}}return x},dataset:function(w){return{id:w.id,hda_ldda:w.get("hda_ldda")}}}});var j=Backbone.Collection.extend({model:v});var p=Backbone.Model.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var m=p.extend(f).extend({defaults:u.extend({},p.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(w){this.set("drawables",new j(w.tracks));this.set("config",q.ConfigSettingCollection.from_config_dict(w.prefs||{}));this.unset("tracks");this.get("drawables").each(function(x){x.unset("preloaded_data")})},add_tracks:function(w){this.get("drawables").add(w)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(x,w){return{obj_type:"View",prefs:{name:w.get("title"),content_visible:true},drawables:w.get("drawables")}}}});var b=Backbone.Model.extend({});var i=Backbone.Router.extend({initialize:function(x){this.view=x.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var w=this;w.view.on("navigate",function(y){w.navigate(y)})},change_location:function(w){this.view.go_to(w)}});return{BackboneTrack:v,BrowserBookmark:e,BrowserBookmarkCollection:t,Cache:s,CanvasManager:g,Genome:c,GenomeDataManager:d,GenomeRegion:h,GenomeRegionCollection:o,GenomeVisualization:m,GenomeReferenceDataManager:r,TrackBrowserRouter:i,TrackConfig:b,Visualization:p,select_datasets:a}});
\ No newline at end of file
+define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(t,k,m,p){var f={toJSON:function(){var v=this,w={};t.each(v.constructor.to_json_keys,function(x){var y=v.get(x);if(x in v.constructor.to_json_mappers){y=v.constructor.to_json_mappers[x](y,v)}w[x]=y});return w}};var a=function(v,y,x,w){$.ajax({url:v,data:x,error:function(){alert("Grid failed")},success:function(z){Galaxy.modal.show({title:"Select datasets for new tracks",body:z,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var A=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var B={data_type:"track_config",hda_ldda:"hda"},C=$(this).val();if($(this).attr("name")!=="id"){B.hda_ldda="ldda"}A[A.length]=$.ajax({url:y+"/"+C,data:B,dataType:"json"})});$.when.apply($,A).then(function(){var B=(arguments[0] instanceof Array?$.map(arguments,function(C){return C[0]}):[arguments[0]]);w(B)});Galaxy.modal.hide()}}})}})};var g=function(v){this.default_font=v!==undefined?v:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};t.extend(g.prototype,{load_pattern:function(v,z){var w=this.patterns,x=this.dummy_context,y=new Image();y.src=galaxy_config.root+"static/images"+z;y.onload=function(){w[v]=x.createPattern(y,"repeat")}},get_pattern:function(v){return this.patterns[v]},new_canvas:function(){var v=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(v)}v.manager=this;return v}});var r=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(v){this.clear()},get_elt:function(x){var y=this.attributes.obj_cache,z=this.attributes.key_ary,w=x.toString(),v=t.indexOf(z,function(A){return A.toString()===w});if(v!==-1){if(y[w].stale){z.splice(v,1);delete y[w]}else{this.move_key_to_end(x,v)}}return y[w]},set_elt:function(x,z){var A=this.attributes.obj_cache,B=this.attributes.key_ary,w=x.toString(),y=this.attributes.num_elements;if(!A[w]){if(B.length>=y){var v=B.shift();delete A[v.toString()]}B.push(x)}A[w]=z;return z},move_key_to_end:function(w,v){this.attributes.key_ary.splice(v,1);this.attributes.key_ary.push(w)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=r.extend({defaults:t.extend({},r.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(v,w){return true},can_subset:function(v){return false}}),initialize:function(v){r.prototype.initialize.call(this);var w=this.get("init_data");if(w){this.add_data(w)}},add_data:function(v){if(this.get("num_elements")<v.length){this.set("num_elements",v.length)}var w=this;t.each(v,function(x){w.set_data(x.region,x)})},data_is_ready:function(){var y=this.get("dataset"),x=$.Deferred(),v=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),w=new m.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:y.get("hda_ldda"),data_type:v},dataType:"json"},interval:5000,success_fn:function(z){return z!=="pending"}});$.when(w.go()).then(function(z){x.resolve(z==="ok"||z==="data")});return x},search_features:function(v){var w=this.get("dataset"),x={query:v,hda_ldda:w.get("hda_ldda"),data_type:"features"};return $.getJSON(w.url(),x)},load_data:function(D,C,w,B){var z=this.get("dataset"),y={data_type:this.get("data_type"),chrom:D.get("chrom"),low:D.get("start"),high:D.get("end"),mode:C,resolution:w,hda_ldda:z.get("hda_ldda")};$.extend(y,B);var F=this.get("filters_manager");if(F){var G=[];var v=F.filters;for(var A=0;A<v.length;A++){G.push(v[A].name)}y.filter_cols=JSON.stringify(G)}var x=this,E=$.getJSON(z.url(),y,function(H){H.region=D;x.set_data(D,H)});this.set_data(D,E);return E},get_data:function(C,B,x,z){var D=this.get_elt(C);if(D&&(m.is_deferred(D)||this.get("data_mode_compatible")(D,B))){return D}var E=this.get("key_ary"),v=this.get("obj_cache"),w,A;for(var y=0;y<E.length;y++){w=E[y];if(w.contains(C)){A=true;D=v[w.toString()];if(m.is_deferred(D)||(this.get("data_mode_compatible")(D,B)&&this.get("can_subset")(D))){this.move_key_to_end(w,y);if(!m.is_deferred(D)){var G=this.subset_entry(D,C);this.set(C,G);D=G}return D}}}if(!A&&C.length()<this.attributes.min_region_size){C=C.copy();var F=this.most_recently_added();if(!F||(C.get("start")>F.get("start"))){C.set("end",C.get("start")+this.attributes.min_region_size)}else{C.set("start",C.get("end")-this.attributes.min_region_size)}C.set("genome",this.attributes.genome);C.trim()}return this.load_data(C,B,x,z)},set_data:function(w,v){this.set_elt(w,v)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(D,C,y,B,z){var F=this._mark_stale(D);if(!(F&&this.get("data_mode_compatible")(F,C))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var x=D.get("start");if(z===this.DEEP_DATA_REQ){$.extend(B,{start_val:F.data.length+1})}else{if(z===this.BROAD_DATA_REQ){x=(F.max_high?F.max_high:F.data[F.data.length-1][2])+1}}var E=D.copy().set("start",x);var w=this,A=this.load_data(E,C,y,B),v=$.Deferred();this.set_data(D,v);$.when(A).then(function(G){if(G.data){G.data=F.data.concat(G.data);if(G.max_low){G.max_low=F.max_low}if(G.message){G.message=G.message.replace(/[0-9]+/,G.data.length)}}w.set_data(D,G);v.resolve(G)});return v},can_get_more_detailed_data:function(w){var v=this.get_elt(w);return(v.dataset_type==="bigwig"&&v.data.length<8000)},get_more_detailed_data:function(y,A,w,z,x){var v=this._mark_stale(y);if(!v){console.log("ERROR getting more detailed data: no current data");return}if(!x){x={}}if(v.dataset_type==="bigwig"){x.num_samples=1000*z}return this.load_data(y,A,w,x)},_mark_stale:function(w){var v=this.get_elt(w);if(!v){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),w.toString())}v.stale=true;return v},get_genome_wide_data:function(v){var x=this,z=true,y=t.map(v.get("chroms_info").chrom_info,function(B){var A=x.get_elt(new h({chrom:B.chrom,start:0,end:B.len}));if(!A){z=false}return A});if(z){return y}var w=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(A){x.add_data(A.data);w.resolve(A.data)});return w},subset_entry:function(x,y){var v={bigwig:function(z,A){return t.filter(z,function(B){return B[0]>=A.get("start")&&B[0]<=A.get("end")})},refseq:function(A,B){var C=B.get("start")-x.region.get("start"),z=x.data.length-(x.region.get("end")-B.get("end"));return x.data.slice(C,z)}};var w=x.data;if(!x.region.same(y)&&x.dataset_type in v){w=v[x.dataset_type](x.data,y)}return{region:y,data:w,dataset_type:x.dataset_type}}});var q=d.extend({initialize:function(v){var w=new Backbone.Model();w.urlRoot=v.data_url;this.set("dataset",w)},load_data:function(x,y,v,w){return(x.length()<=100000?d.prototype.load_data.call(this,x,y,v,w):{data:null,region:x})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(v){this.id=v.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(v){var w=t.find(this.get_chroms_info(),function(x){return x.chrom===v});return new h({chrom:w.chrom,end:w.len})},get_chrom_len:function(v){return t.find(this.get_chroms_info(),function(w){return w.chrom===v}).len}});var h=Backbone.Model.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(v){return this.attributes.chrom===v.get("chrom")&&this.attributes.start===v.get("start")&&this.attributes.end===v.get("end")},initialize:function(w){if(w.from_str){var y=w.from_str.split(":"),x=y[0],v=y[1].split("-");this.set({chrom:x,start:parseInt(v[0],10),end:parseInt(v[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new h({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(C){var w=this.get("chrom"),B=C.get("chrom"),A=this.get("start"),y=C.get("start"),z=this.get("end"),x=C.get("end"),v;if(w&&B&&w!==B){return h.overlap_results.DIF_CHROMS}if(A<y){if(z<y){v=h.overlap_results.BEFORE}else{if(z<x){v=h.overlap_results.OVERLAP_START}else{v=h.overlap_results.CONTAINS}}}else{if(A>y){if(A>x){v=h.overlap_results.AFTER}else{if(z<=x){v=h.overlap_results.CONTAINED_BY}else{v=h.overlap_results.OVERLAP_END}}}else{v=(z>=x?h.overlap_results.CONTAINS:h.overlap_results.CONTAINED_BY)}}return v},trim:function(v){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var w=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>w){this.attributes.end=w-1}}return this},contains:function(v){return this.compute_overlap(v)===h.overlap_results.CONTAINS},overlaps:function(v){return t.intersection([this.compute_overlap(v)],[h.overlap_results.DIF_CHROMS,h.overlap_results.BEFORE,h.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var n=Backbone.Collection.extend({model:h});var e=Backbone.Model.extend({defaults:{region:null,note:""},initialize:function(v){this.set("region",new h(v.region))}});var s=Backbone.Collection.extend({model:e});var u=Backbone.Model.extend(f).extend({defaults:{mode:"Auto"},initialize:function(v){this.set("dataset",new k.Dataset(v.dataset));this.set("config",p.ConfigSettingCollection.from_config_dict(v.prefs));this.get("config").add([{key:"name",value:this.get("dataset").get("name")},{key:"color"}]);var w=this.get("preloaded_data");if(w){w=w.data}else{w=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:w}))}},{to_json_keys:["track_type","dataset","prefs","mode","filters","tool_state"],to_json_mappers:{prefs:function(w,v){if(t.size(w)===0){w={name:v.get("config").get("name").get("value"),color:v.get("config").get("color").get("value")}}return w},dataset:function(v){return{id:v.id,hda_ldda:v.get("hda_ldda")}}}});var j=Backbone.Collection.extend({model:u});var o=Backbone.Model.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var l=o.extend(f).extend({defaults:t.extend({},o.prototype.defaults,{dbkey:"",drawables:null,bookmarks:null,viewport:null}),initialize:function(v){this.set("drawables",new j(v.tracks));this.set("config",p.ConfigSettingCollection.from_config_dict(v.prefs||{}));this.unset("tracks");this.get("drawables").each(function(w){w.unset("preloaded_data")})},add_tracks:function(v){this.get("drawables").add(v)}},{to_json_keys:["view","viewport","bookmarks"],to_json_mappers:{view:function(w,v){return{obj_type:"View",prefs:{name:v.get("title"),content_visible:true},drawables:v.get("drawables")}}}});var b=Backbone.Model.extend({});var i=Backbone.Router.extend({initialize:function(w){this.view=w.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var v=this;v.view.on("navigate",function(x){v.navigate(x)})},change_location:function(v){this.view.go_to(v)}});return{BackboneTrack:u,BrowserBookmark:e,BrowserBookmarkCollection:s,Cache:r,CanvasManager:g,Genome:c,GenomeDataManager:d,GenomeRegion:h,GenomeRegionCollection:n,GenomeVisualization:l,GenomeReferenceDataManager:q,TrackBrowserRouter:i,TrackConfig:b,Visualization:o,select_datasets:a}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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6 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/9e7f9282deba/
Changeset: 9e7f9282deba
User: Jeremy Goecks
Date: 2014-03-26 18:42:54
Summary: Trackster: consolidate read painters.
Affected #: 2 files
diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 9e7f9282deba9d383e708e210acea5dea8eb7673 static/scripts/viz/trackster/painters.js
--- a/static/scripts/viz/trackster/painters.js
+++ b/static/scripts/viz/trackster/painters.js
@@ -736,297 +736,6 @@
};
},
- // FIXME: extract common functionality from draw_read functions for ReadPainters.
-
- /**
- * Draw a single read.
- */
- draw_read: function(ctx, mode, w_scale, y_start, tile_low, tile_high, feature_start, cigar, strand, read_seq) {
- ctx.textAlign = "center";
- var tile_region = [tile_low, tile_high],
- base_offset = 0,
- seq_offset = 0,
- gap = Math.round(w_scale/2),
- char_width_px = ctx.canvas.manager.char_width_px,
- block_color = (strand === "+" ? this.prefs.block_color : this.prefs.reverse_strand_color),
- pack_mode = (mode === 'Pack'),
- paint_utils = new ReadPainterUtils(ctx, (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT), w_scale, mode);
-
- // Keep list of items that need to be drawn on top of initial drawing layer.
- var draw_last = [];
-
- // If no cigar string, then assume all matches.
- if (!cigar) {
- cigar = [ [0, read_seq.length] ];
- }
-
- // Draw read by processing cigar.
- for (var cig_id = 0, len = cigar.length; cig_id < len; cig_id++) {
- var cig = cigar[cig_id],
- cig_op = "MIDNSHP=X"[ cig[0] ],
- cig_len = cig[1];
-
- var seq_start = feature_start + base_offset,
- // -0.5 to offset sequence between bases.
- s_start = Math.floor( Math.max(-0.5 * w_scale, (seq_start - tile_low - 0.5) * w_scale) ),
- s_end = Math.floor( Math.max(0, (seq_start + cig_len - tile_low - 0.5) * w_scale) );
-
- if (!is_overlap([seq_start, seq_start + cig_len], tile_region)) {
- // Increment base offset only for certain operations.
- if ("MDN=X".indexOf(cig_op) !== -1) {
- base_offset += cig_len;
- }
- continue;
- }
-
- // Make sure that read is drawn even if it too small to be rendered officially; in this case,
- // read is drawn at 1px.
- // TODO: need to ensure that s_start, s_end are calcuated the same for both slotting
- // and drawing.
- if (s_start === s_end) {
- s_end += 1;
- }
-
- switch (cig_op) {
- case "H": // Hard clipping.
- // Sequence not present, so do not increment seq_offset.
- break;
- case "S": // Soft clipping.
- seq_offset += cig_len;
- break;
- case "M": // Loose match with reference; can be match or mismatch.
- case "=": // Strict match with reference.
- case "X": // Strict mismatch with reference.
- // Draw read base as rectangle.
- ctx.fillStyle = block_color;
- ctx.fillRect(s_start,
- y_start + (pack_mode ? 1 : 4 ),
- s_end - s_start,
- (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT));
-
- // Draw sequence and/or variants.
- var seq = read_seq.slice(seq_offset, seq_offset + cig_len),
- ref_char,
- read_char;
- for (var c = 0, str_len = seq.length; c < str_len; c++) {
- // Draw base if it's on tile:
- if (seq_start + c >= tile_low && seq_start + c <= tile_high) {
- // Get reference and read character.
- ref_char = (this.ref_seq ? this.ref_seq[seq_start - tile_low + c] : null);
- read_char = seq[c];
-
- // Draw base depending on (a) available reference data and (b) config options.
- if (
- // If there's reference data and (a) showing all (i.e. not showing
- // differences) or (b) if there is a variant.
- (ref_char &&
- (!this.prefs.show_differences ||
- (read_char.toLowerCase !== 'n' && (ref_char.toLowerCase() !== read_char.toLowerCase())))
- ) ||
- // If there's no reference data and showing all.
- (!ref_char && !this.prefs.show_differences)
- ) {
-
- // Draw base.
- var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) );
- ctx.fillStyle = this.base_color_fn(seq[c]);
- if (pack_mode && w_scale > char_width_px) {
- ctx.fillText(seq[c], c_start, y_start + 9);
- }
- // Require a minimum w_scale so that variants are only drawn when somewhat zoomed in.
- else if (w_scale > 0.05) {
- ctx.fillRect(c_start - gap,
- y_start + (pack_mode ? 1 : 4),
- Math.max( 1, Math.round(w_scale) ),
- (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT));
- }
- }
-
- }
- }
-
- seq_offset += cig_len;
- base_offset += cig_len;
- break;
- case "N": // Skipped bases.
- ctx.fillStyle = CONNECTOR_COLOR;
- ctx.fillRect(s_start, y_start + 5, s_end - s_start, 1);
- //ctx.dashedLine(s_start + this.left_offset, y_start + 5, this.left_offset + s_end, y_start + 5);
- base_offset += cig_len;
- break;
- case "D": // Deletion.
- paint_utils.draw_deletion(s_start, y_start, 1);
- base_offset += cig_len;
- break;
- case "P": // TODO: No good way to draw insertions/padding right now, so ignore
- // Sequences not present, so do not increment seq_offset.
- break;
- case "I": // Insertion.
- // Check to see if sequence should be drawn at all by looking at the overlap between
- // the sequence region and the tile region.
- var insert_x_coord = s_start - gap;
-
- if (is_overlap([seq_start, seq_start + cig_len], tile_region)) {
- var seq = read_seq.slice(seq_offset, seq_offset + cig_len);
- // Insertion point is between the sequence start and the previous base: (-gap) moves
- // back from sequence start to insertion point.
- if (this.prefs.show_insertions) {
- //
- // Show inserted sequence above, centered on insertion point.
- //
-
- // Draw sequence.
- // X center is offset + start - <half_sequence_length>
- var x_center = s_start - (s_end - s_start)/2;
- if ( (mode === "Pack" || this.mode === "Auto") && read_seq !== undefined && w_scale > char_width_px) {
- // Draw sequence container.
- ctx.fillStyle = "yellow";
- ctx.fillRect(x_center - gap, y_start - 9, s_end - s_start, 9);
- draw_last[draw_last.length] = {type: "triangle", data: [insert_x_coord, y_start + 4, 5]};
- ctx.fillStyle = CONNECTOR_COLOR;
- // Based on overlap b/t sequence and tile, get sequence to be drawn.
- switch( compute_overlap( [seq_start, seq_start + cig_len], tile_region ) ) {
- case(OVERLAP_START):
- seq = seq.slice(tile_low-seq_start);
- break;
- case(OVERLAP_END):
- seq = seq.slice(0, seq_start-tile_high);
- break;
- case(CONTAINED_BY):
- // All of sequence drawn.
- break;
- case(CONTAINS):
- seq = seq.slice(tile_low-seq_start, seq_start-tile_high);
- break;
- }
- // Draw sequence.
- for (var c = 0, str_len = seq.length; c < str_len; c++) {
- var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) );
- ctx.fillText(seq[c], c_start - (s_end - s_start)/2, y_start);
- }
- }
- else {
- // Draw block.
- ctx.fillStyle = "yellow";
- // TODO: This is a pretty hack-ish way to fill rectangle based on mode.
- ctx.fillRect(x_center, y_start + (this.mode !== "Dense" ? 2 : 5),
- s_end - s_start, (mode !== "Dense" ? SQUISH_FEATURE_HEIGHT : DENSE_FEATURE_HEIGHT));
- }
- }
- else {
- if ( (mode === "Pack" || this.mode === "Auto") && read_seq !== undefined && w_scale > char_width_px) {
- // Show insertions with a single number at the insertion point.
- draw_last.push( { type: "text", data: [seq.length, insert_x_coord, y_start + 9] } );
- }
- else {
- // TODO: probably can merge this case with code above.
- }
- }
- }
- seq_offset += cig_len;
- // No change to base offset because insertions are drawn above sequence/read.
- break;
- }
- }
-
- //
- // Draw last items.
- //
- ctx.fillStyle = "yellow";
- var item, type, data;
- for (var i = 0; i < draw_last.length; i++) {
- item = draw_last[i];
- type = item.type;
- data = item.data;
- if (type === "text") {
- ctx.save();
- ctx.font = "bold " + ctx.font;
- ctx.fillText(data[0], data[1], data[2]);
- ctx.restore();
- }
- else if (type === "triangle") {
- drawDownwardEquilateralTriangle(ctx, data[0], data[1], data[2]);
- }
- }
- },
-
- /**
- * Draw a complete read pair
- */
- draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width ) {
- // All features need a start, end, and vertical center.
- var feature_uid = feature[0],
- feature_start = feature[1],
- feature_end = feature[2],
- feature_name = feature[3],
- // -0.5 to put element between bases.
- f_start = Math.floor( Math.max(-0.5 * w_scale, (feature_start - tile_low - 0.5) * w_scale) ),
- f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low - 0.5) * w_scale)) ),
- y_start = (mode === "Dense" ? 0 : (0 + slot)) * y_scale,
- label_color = this.prefs.label_color;
-
- // Draw read.
- if (feature[5] instanceof Array) {
- // Read is paired.
- var connector = true;
-
- // Draw left/forward read.
- if (feature[4][1] >= tile_low && feature[4][0] <= tile_high && feature[4][2]) {
- this.draw_read(ctx, mode, w_scale, y_start, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], feature[4][4]);
- }
- else {
- connector = false;
- }
-
- // Draw right/reverse read.
- if (feature[5][1] >= tile_low && feature[5][0] <= tile_high && feature[5][2]) {
- this.draw_read(ctx, mode, w_scale, y_start, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], feature[5][4]);
- }
- else {
- connector = false;
- }
-
- // Draw connector if both reads were drawn.
- // TODO: currently, there is no way to connect reads drawn on different tiles; to connect reads on different tiles, data manager
- // code is needed to join mate pairs from different regions. Alternatively, requesting multiple regions of data at once would
- // make it possible to put together more easily.
- // -0.5 to position connector correctly between reads.
- var b1_end = Math.ceil( Math.min(width, Math.max(-0.5 * w_scale, (feature[4][1] - tile_low - 0.5) * w_scale)) ),
- b2_start = Math.floor( Math.max(-0.5 * w_scale, (feature[5][0] - tile_low - 0.5) * w_scale) );
- if (connector && b2_start > b1_end) {
- ctx.fillStyle = CONNECTOR_COLOR;
- dashedLine(ctx, b1_end, y_start + 5, b2_start, y_start + 5);
- }
- } else {
- // Read is single.
- this.draw_read(ctx, mode, w_scale, y_start, tile_low, tile_high, feature_start, feature[4], feature[5], feature[6]);
- }
- if (mode === "Pack" && feature_start >= tile_low && feature_name !== ".") {
- // Draw label.
- ctx.fillStyle = this.prefs.label_color;
- if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) {
- ctx.textAlign = "left";
- ctx.fillText(feature_name, f_end + LABEL_SPACING, y_start + 8);
- } else {
- ctx.textAlign = "right";
- ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 8);
- }
- }
-
- // FIXME: provide actual coordinates for drawn read.
- return [0,0];
- }
-});
-
-/**
- * Painter for reads encoded using reference-based compression.
- */
-var RefBasedReadPainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler, ref_seq, base_color_fn) {
- ReadPainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler, ref_seq, base_color_fn);
-};
-
-extend(RefBasedReadPainter.prototype, ReadPainter.prototype, FeaturePainter, {
-
/**
* Draw a single read from reference-based read sequence and cigar.
*/
@@ -1255,6 +964,73 @@
drawDownwardEquilateralTriangle(ctx, data[0], data[1], data[2]);
}
}
+ },
+
+ /**
+ * Draw a complete read pair
+ */
+ draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width ) {
+ // All features need a start, end, and vertical center.
+ var feature_uid = feature[0],
+ feature_start = feature[1],
+ feature_end = feature[2],
+ feature_name = feature[3],
+ // -0.5 to put element between bases.
+ f_start = Math.floor( Math.max(-0.5 * w_scale, (feature_start - tile_low - 0.5) * w_scale) ),
+ f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low - 0.5) * w_scale)) ),
+ y_start = (mode === "Dense" ? 0 : (0 + slot)) * y_scale,
+ label_color = this.prefs.label_color;
+
+ // Draw read.
+ if (feature[5] instanceof Array) {
+ // Read is paired.
+ var connector = true;
+
+ // Draw left/forward read.
+ if (feature[4][1] >= tile_low && feature[4][0] <= tile_high && feature[4][2]) {
+ this.draw_read(ctx, mode, w_scale, y_start, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], feature[4][4]);
+ }
+ else {
+ connector = false;
+ }
+
+ // Draw right/reverse read.
+ if (feature[5][1] >= tile_low && feature[5][0] <= tile_high && feature[5][2]) {
+ this.draw_read(ctx, mode, w_scale, y_start, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], feature[5][4]);
+ }
+ else {
+ connector = false;
+ }
+
+ // Draw connector if both reads were drawn.
+ // TODO: currently, there is no way to connect reads drawn on different tiles; to connect reads on different tiles, data manager
+ // code is needed to join mate pairs from different regions. Alternatively, requesting multiple regions of data at once would
+ // make it possible to put together more easily.
+ // -0.5 to position connector correctly between reads.
+ var b1_end = Math.ceil( Math.min(width, Math.max(-0.5 * w_scale, (feature[4][1] - tile_low - 0.5) * w_scale)) ),
+ b2_start = Math.floor( Math.max(-0.5 * w_scale, (feature[5][0] - tile_low - 0.5) * w_scale) );
+ if (connector && b2_start > b1_end) {
+ ctx.fillStyle = CONNECTOR_COLOR;
+ dashedLine(ctx, b1_end, y_start + 5, b2_start, y_start + 5);
+ }
+ } else {
+ // Read is single.
+ this.draw_read(ctx, mode, w_scale, y_start, tile_low, tile_high, feature_start, feature[4], feature[5], feature[6]);
+ }
+ if (mode === "Pack" && feature_start >= tile_low && feature_name !== ".") {
+ // Draw label.
+ ctx.fillStyle = this.prefs.label_color;
+ if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) {
+ ctx.textAlign = "left";
+ ctx.fillText(feature_name, f_end + LABEL_SPACING, y_start + 8);
+ } else {
+ ctx.textAlign = "right";
+ ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 8);
+ }
+ }
+
+ // FIXME: provide actual coordinates for drawn read.
+ return [0,0];
}
});
@@ -1775,7 +1551,6 @@
LinePainter: LinePainter,
LinkedFeaturePainter: LinkedFeaturePainter,
ReadPainter: ReadPainter,
- RefBasedReadPainter: RefBasedReadPainter,
ArcLinkedFeaturePainter: ArcLinkedFeaturePainter,
DiagonalHeatmapPainter: DiagonalHeatmapPainter,
VariantPainter: VariantPainter
diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 9e7f9282deba9d383e708e210acea5dea8eb7673 static/scripts/viz/trackster/tracks.js
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -4163,8 +4163,7 @@
*/
var ReadTrack = function (view, container, obj_dict) {
FeatureTrack.call(this, view, container, obj_dict);
- // Choose painter based on whether there is reference data.
- this.painter = (view.reference_track ? painters.RefBasedReadPainter : painters.ReadPainter);
+ this.painter = painters.ReadPainter;
this.update_icons();
};
https://bitbucket.org/galaxy/galaxy-central/commits/09676399640d/
Changeset: 09676399640d
User: Jeremy Goecks
Date: 2014-03-26 19:46:29
Summary: Trackster: remove reference to left_offset in painters because it is not needed.
Affected #: 1 file
diff -r 9e7f9282deba9d383e708e210acea5dea8eb7673 -r 09676399640d304d45dfeb81a32ed30d7314d855 static/scripts/viz/trackster/painters.js
--- a/static/scripts/viz/trackster/painters.js
+++ b/static/scripts/viz/trackster/painters.js
@@ -127,9 +127,7 @@
Painter.prototype.default_prefs = {};
/**
- * Draw on the context using a rectangle of width x height. w_scale is
- * needed because it cannot be computed from width and view size alone
- * as a left_offset may be present.
+ * Draw on the context using a rectangle of width x height using scale w_scale.
*/
Painter.prototype.draw = function(ctx, width, height, w_scale) {};
@@ -869,7 +867,6 @@
case "N": // Skipped bases.
ctx.fillStyle = CONNECTOR_COLOR;
ctx.fillRect(s_start, y_start + 5, s_end - s_start, 1);
- //ctx.dashedLine(s_start + this.left_offset, y_start + 5, this.left_offset + s_end, y_start + 5);
// No change in seq_offset because sequence not used when skipping.
base_offset += cig_len;
break;
@@ -1357,9 +1354,7 @@
},
/**
- * Draw on the context using a rectangle of width x height. w_scale is
- * needed because it cannot be computed from width and view size alone
- * as a left_offset may be present.
+ * Draw on the context using a rectangle of width x height with scale w_scale.
*/
draw: function(ctx, width, height, w_scale) {
ctx.save();
https://bitbucket.org/galaxy/galaxy-central/commits/ff91d665fb8e/
Changeset: ff91d665fb8e
User: Jeremy Goecks
Date: 2014-03-26 20:12:39
Summary: Trackster: set maximum label length.
Affected #: 1 file
diff -r 09676399640d304d45dfeb81a32ed30d7314d855 -r ff91d665fb8e211c0bea4c02d9c046f32be7005c static/scripts/viz/trackster/painters.js
--- a/static/scripts/viz/trackster/painters.js
+++ b/static/scripts/viz/trackster/painters.js
@@ -341,6 +341,7 @@
Painter.call(this, data, view_start, view_end, prefs, mode);
this.alpha_scaler = (alpha_scaler ? alpha_scaler : new Scaler());
this.height_scaler = (height_scaler ? height_scaler : new Scaler());
+ this.max_label_length = 200;
};
FeaturePainter.prototype.default_prefs = { block_color: "#FFF", connector_color: "#FFF" };
@@ -399,6 +400,7 @@
feature_mapper.y_translation = this.get_top_padding(width);
return feature_mapper;
},
+
/**
* Abstract function for drawing an individual feature.
*/
@@ -645,11 +647,11 @@
// FIXME: assumption here that the entire view starts at 0
if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) {
ctx.textAlign = "left";
- ctx.fillText(feature_name, f_end + LABEL_SPACING, y_start + 8);
+ ctx.fillText(feature_name, f_end + LABEL_SPACING, y_start + 8, this.max_label_length);
draw_end += ctx.measureText(feature_name).width + LABEL_SPACING;
} else {
ctx.textAlign = "right";
- ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 8);
+ ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 8, this.max_label_length);
draw_start -= ctx.measureText(feature_name).width + LABEL_SPACING;
}
//ctx.fillStyle = block_color;
@@ -1019,10 +1021,10 @@
ctx.fillStyle = this.prefs.label_color;
if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) {
ctx.textAlign = "left";
- ctx.fillText(feature_name, f_end + LABEL_SPACING, y_start + 8);
+ ctx.fillText(feature_name, f_end + LABEL_SPACING, y_start + 8, this.max_label_length);
} else {
ctx.textAlign = "right";
- ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 8);
+ ctx.fillText(feature_name, f_start - LABEL_SPACING, y_start + 8, this.max_label_length);
}
}
https://bitbucket.org/galaxy/galaxy-central/commits/cc7b0f0be551/
Changeset: cc7b0f0be551
User: Jeremy Goecks
Date: 2014-03-26 20:39:14
Summary: Fix initialization of boolean values in client-side config object.
Affected #: 1 file
diff -r ff91d665fb8e211c0bea4c02d9c046f32be7005c -r cc7b0f0be551dd1c0564c1fd7b95b6a2aaa7ee39 static/scripts/utils/config.js
--- a/static/scripts/utils/config.js
+++ b/static/scripts/utils/config.js
@@ -16,7 +16,7 @@
this.set(_.extend({}, defaults, options));
}
- if (!this.get('value')) {
+ if (this.get('value') === undefined) {
// Use default to set value.
this.set_value(this.get('default_value'));
https://bitbucket.org/galaxy/galaxy-central/commits/e298d0294721/
Changeset: e298d0294721
User: Jeremy Goecks
Date: 2014-03-26 22:37:03
Summary: Trackster: fix offset bug that was rendering bases incorrectly.
Affected #: 1 file
diff -r cc7b0f0be551dd1c0564c1fd7b95b6a2aaa7ee39 -r e298d029472150df08bfae9b6ec311c78cb63dfd static/scripts/viz/trackster/painters.js
--- a/static/scripts/viz/trackster/painters.js
+++ b/static/scripts/viz/trackster/painters.js
@@ -740,6 +740,20 @@
* Draw a single read from reference-based read sequence and cigar.
*/
draw_read: function(ctx, mode, w_scale, y_start, tile_low, tile_high, feature_start, cigar, strand, read_seq) {
+ // Helper function to update base and sequnence offsets.
+ var update_base_offset = function(offset, cig_op, cig_len) {
+ if ('M=NXD'.indexOf(cig_op) !== -1) {
+ offset += cig_len;
+ }
+ return offset;
+ },
+ update_seq_offset = function(offset, cig_op, cig_len) {
+ if ('IX'.indexOf(cig_op) !== -1) {
+ offset += cig_len;
+ }
+ return offset;
+ };
+
ctx.textAlign = "center";
var tile_region = [tile_low, tile_high],
base_offset = 0,
@@ -770,7 +784,7 @@
// Make sure that block is drawn even if it too small to be rendered officially; in this case,
// read is drawn at 1px.
- // TODO: need to ensure that s_start, s_end are calcuated the same for both slotting
+ // TODO: need to ensure that s_start, s_end are calculated the same for both slotting
// and drawing.
if (s_start === s_end) {
s_end += 1;
@@ -793,21 +807,26 @@
var seq_start = feature_start + base_offset,
// -0.5 to offset sequence between bases.
- s_start = Math.floor( Math.max(0, -0.5 * w_scale, (seq_start - tile_low - 0.5) * w_scale) ),
+ s_start = Math.floor( Math.max(-0.5 * w_scale, (seq_start - tile_low - 0.5) * w_scale) ),
s_end = Math.floor( Math.max(0, (seq_start + cig_len - tile_low - 0.5) * w_scale) );
+ // Skip feature if it's not in tile.
if (!is_overlap([seq_start, seq_start + cig_len], tile_region)) {
+ // Update offsets.
+ base_offset = update_base_offset(base_offset, cig_op, cig_len);
+ seq_offset = update_seq_offset(seq_offset, cig_op, cig_len);
continue;
}
// Make sure that read is drawn even if it too small to be rendered officially; in this case,
// read is drawn at 1px.
- // TODO: need to ensure that s_start, s_end are calcuated the same for both slotting
+ // TODO: need to ensure that s_start, s_end are calculated the same for both slotting
// and drawing.
if (s_start === s_end) {
s_end += 1;
}
-
+
+ // Draw read feature.
switch (cig_op) {
case "H": // Hard clipping.
case "S": // Soft clipping.
https://bitbucket.org/galaxy/galaxy-central/commits/bc739e4b5bdf/
Changeset: bc739e4b5bdf
User: Jeremy Goecks
Date: 2014-03-26 22:38:22
Summary: Automated merge of local changesets with -default
Affected #: 24 files
diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 eggs.ini
--- a/eggs.ini
+++ b/eggs.ini
@@ -56,6 +56,7 @@
python_openid = 2.2.5
python_daemon = 1.5.5
pytz = 2013.9
+requests = 2.2.1
Routes = 1.12.3
sqlalchemy_migrate = 0.7.2
ssh = 1.7.14
diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -41,6 +41,7 @@
from galaxy.tools.parameters.basic import DataToolParameter
from galaxy.util.json import to_json_string
from galaxy.workflow.modules import ToolModule
+from galaxy.workflow.steps import attach_ordered_steps
log = logging.getLogger( __name__ )
@@ -1676,7 +1677,6 @@
"""
Creates a workflow from a dict. Created workflow is stored in the database and returned.
"""
- from galaxy.webapps.galaxy.controllers.workflow import attach_ordered_steps
# Put parameters in workflow mode
trans.workflow_building_mode = True
diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 lib/galaxy/webapps/galaxy/api/workflows.py
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -11,8 +11,10 @@
from galaxy import web
from galaxy.web import _future_expose_api as expose_api
from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin
+from galaxy.web.base.controller import UsesHistoryMixin
from galaxy.workflow.modules import module_factory
from galaxy.workflow.run import invoke
+from galaxy.workflow.extract import extract_workflow
log = logging.getLogger(__name__)
@@ -51,7 +53,7 @@
step.state.inputs.update(param_dict)
-class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin):
+class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin):
@web.expose_api
def index(self, trans, **kwd):
@@ -141,9 +143,11 @@
"""
POST /api/workflows
- We're not creating workflows from the api. Just execute for now.
+ Run or create workflows from the api.
- However, we will import them if installed_repository_file is specified.
+ If installed_repository_file or from_history_id is specified a new
+ workflow will be created for this user. Otherwise, workflow_id must be
+ specified and this API method will cause a workflow to execute.
:param installed_repository_file The path of a workflow to import. Either workflow_id or installed_repository_file must be specified
:type installed_repository_file str
@@ -165,6 +169,15 @@
:param replacement_params: A dictionary used when renaming datasets
:type replacement_params: dict
+
+ :param from_history_id: Id of history to extract a workflow from. Should not be used with worfklow_id or installed_repository_file.
+ :type from_history_id: str
+
+ :param job_ids: If from_history_id is set - this should be a list of jobs to include when extracting workflow from history.
+ :type job_ids: str
+
+ :param dataset_ids: If from_history_id is set - this should be a list of HDA ids corresponding to workflow inputs when extracting workflow from history.
+ :type dataset_ids: str
"""
# Pull parameters out of payload.
@@ -183,6 +196,24 @@
cntrller='api',
**payload)
return result
+ if 'from_history_id' in payload:
+ from_history_id = payload.get( 'from_history_id' )
+ history = self.get_history( trans, from_history_id, check_ownership=False, check_accessible=True )
+ job_ids = map( trans.security.decode_id, payload.get( "job_ids", [] ) )
+ dataset_ids = map( trans.security.decode_id, payload.get( "dataset_ids", [] ) )
+ workflow_name = payload[ "workflow_name" ]
+ stored_workflow = extract_workflow(
+ trans=trans,
+ user=trans.get_user(),
+ history=history,
+ job_ids=job_ids,
+ dataset_ids=dataset_ids,
+ workflow_name=workflow_name,
+ )
+ item = stored_workflow.to_dict( value_mapper={ "id": trans.security.encode_id } )
+ item[ 'url' ] = url_for( 'workflow', id=item[ "id" ] )
+ return item
+
trans.response.status = 403
return "Either workflow_id or installed_repository_file must be specified"
if 'installed_repository_file' in payload:
diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 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
@@ -201,9 +201,13 @@
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 )
+ 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,
- 'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \
- ( web.url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) )
+ 'repository/check_for_updates%s' % params )
return trans.response.send_redirect( url )
@web.expose
@@ -367,9 +371,10 @@
@web.require_admin
def get_tool_dependencies( self, trans, repository_id, repository_name, repository_owner, changeset_revision ):
"""
- Send a request to the appropriate tool shed to retrieve the dictionary of tool dependencies defined for the received repository name,
- owner and changeset revision. The received repository_id is the encoded id of the installed tool shed repository in Galaxy. We need
- it so that we can derive the tool shed from which it was installed.
+ Send a request to the appropriate tool shed to retrieve the dictionary of tool dependencies defined for
+ the received repository name, owner and changeset revision. The received repository_id is the encoded id
+ of the installed tool shed repository in Galaxy. We need it so that we can derive the tool shed from which
+ 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 )
@@ -388,8 +393,8 @@
@web.require_admin
def get_updated_repository_information( self, trans, repository_id, repository_name, repository_owner, changeset_revision ):
"""
- Send a request to the appropriate tool shed to retrieve the dictionary of information required to reinstall an updated revision of an
- uninstalled tool shed repository.
+ Send a request to the appropriate tool shed to retrieve the dictionary of information required to reinstall
+ 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 )
@@ -436,13 +441,16 @@
@web.expose
@web.require_admin
- def initiate_tool_dependency_installation( self, trans, tool_dependencies ):
+ def initiate_tool_dependency_installation( self, trans, tool_dependencies, **kwd ):
"""Install specified dependencies for repository tools."""
# Get the tool_shed_repository from one of the tool_dependencies.
- message = ''
+ message = kwd.get( 'message', '' )
+ status = kwd.get( 'status', 'done' )
+ err_msg = ''
tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository
# Get the tool_dependencies.xml file from the repository.
- tool_dependencies_config = suc.get_config_from_disk( suc.TOOL_DEPENDENCY_DEFINITION_FILENAME, tool_shed_repository.repo_path( trans.app ) )
+ tool_dependencies_config = suc.get_config_from_disk( suc.TOOL_DEPENDENCY_DEFINITION_FILENAME,
+ tool_shed_repository.repo_path( trans.app ) )
installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=trans.app,
tool_shed_repository=tool_shed_repository,
tool_dependencies_config=tool_dependencies_config,
@@ -452,13 +460,12 @@
if installed_tool_dependency.status == trans.app.install_model.ToolDependency.installation_status.ERROR:
text = util.unicodify( installed_tool_dependency.error_message )
if text is not None:
- message += ' %s' % text
+ err_msg += ' %s' % text
tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in tool_dependencies ]
- if message:
+ if err_msg:
+ message += err_msg
status = 'error'
- else:
- message = "Installed tool dependencies: %s" % ','.join( td.name for td in installed_tool_dependencies )
- status = 'done'
+ message += "Installed tool dependencies: %s" % ','.join( td.name for td in installed_tool_dependencies )
td_ids = [ trans.security.encode_id( td.id ) for td in tool_shed_repository.tool_dependencies ]
return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
action='manage_tool_dependencies',
@@ -506,9 +513,10 @@
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?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \
- ( name, owner, latest_downloadable_revision, web.url_for( '/', qualified=True ) ) )
+ '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 )
@@ -521,43 +529,74 @@
message=message,
status=status ) )
-
@web.expose
@web.require_admin
- def install_tool_dependencies( self, trans, **kwd ):
+ def install_tool_dependencies_with_update( self, trans, **kwd ):
+ """
+ Updating an installed tool shed repository where new tool dependencies but no new repository
+ dependencies are included in the updated revision.
+ """
+ updating_repository_id = kwd.get( 'updating_repository_id', None )
+ repository = suc.get_installed_tool_shed_repository( trans, updating_repository_id )
+ # All received dependencies need to be installed - confirmed by the caller.
+ encoded_tool_dependencies_dict = kwd.get( 'encoded_tool_dependencies_dict', None )
+ if encoded_tool_dependencies_dict is not None:
+ tool_dependencies_dict = encoding_util.tool_shed_decode( encoded_tool_dependencies_dict )
+ else:
+ tool_dependencies_dict = {}
+ encoded_relative_install_dir = kwd.get( 'encoded_relative_install_dir', None )
+ if encoded_relative_install_dir is not None:
+ relative_install_dir = encoding_util.tool_shed_decode( encoded_relative_install_dir )
+ else:
+ relative_install_dir = ''
+ updating_to_changeset_revision = kwd.get( 'updating_to_changeset_revision', None )
+ updating_to_ctx_rev = kwd.get( 'updating_to_ctx_rev', None )
+ encoded_updated_metadata = kwd.get( 'encoded_updated_metadata', None )
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
- tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd )
- tool_dependencies = []
- for tool_dependency_id in tool_dependency_ids:
- tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id )
- tool_dependencies.append( tool_dependency )
- if kwd.get( 'install_tool_dependencies_button', False ):
- # Filter tool dependencies to only those that are installed.
- tool_dependencies_for_installation = []
- for tool_dependency in tool_dependencies:
- if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.UNINSTALLED,
- trans.install_model.ToolDependency.installation_status.ERROR ]:
- tool_dependencies_for_installation.append( tool_dependency )
- if tool_dependencies_for_installation:
- # Redirect back to the ToolDependencyGrid before initiating installation.
- encoded_tool_dependency_for_installation_ids = [ trans.security.encode_id( td.id ) for td in tool_dependencies_for_installation ]
- new_kwd = dict( action='manage_tool_dependencies',
- operation='initiate_tool_dependency_installation',
- tool_dependency_ids=encoded_tool_dependency_for_installation_ids,
- message=message,
- status=status )
- return self.tool_dependency_grid( trans, **new_kwd )
+ install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) )
+ if 'install_tool_dependencies_with_update_button' in kwd:
+ # Now that the user has chosen whether to install tool dependencies or not, we can
+ # update the repository record with the changes in the updated revision.
+ if encoded_updated_metadata:
+ updated_metadata = encoding_util.tool_shed_decode( encoded_updated_metadata )
else:
- message = 'All of the selected tool dependencies are already installed.'
- status = 'error'
- return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
- action='manage_repository_tool_dependencies',
- tool_dependency_ids=tool_dependency_ids,
- status=status,
- message=message ) )
- return trans.fill_template( '/admin/tool_shed_repository/install_tool_dependencies.mako',
- tool_dependencies=tool_dependencies,
+ updated_metadata = None
+ repository = repository_util.update_repository_record( trans,
+ repository=repository,
+ updated_metadata_dict=updated_metadata,
+ updated_changeset_revision=updating_to_changeset_revision,
+ updated_ctx_rev=updating_to_ctx_rev )
+ if install_tool_dependencies:
+ tool_dependencies = tool_dependency_util.create_tool_dependency_objects( trans.app,
+ repository,
+ relative_install_dir,
+ set_status=False )
+ message = "The installed repository named '%s' has been updated to change set revision '%s'. " % \
+ ( str( repository.name ), updating_to_changeset_revision )
+ self.initiate_tool_dependency_installation( trans, tool_dependencies, message=message, status=status )
+ # Handle tool dependencies check box.
+ if trans.app.config.tool_dependency_dir is None:
+ if includes_tool_dependencies:
+ message = "Tool dependencies defined in this repository can be automatically installed if you set "
+ message += "the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file "
+ message += "(universe_wsgi.ini) and restart your Galaxy server."
+ status = "warning"
+ install_tool_dependencies_check_box_checked = False
+ else:
+ install_tool_dependencies_check_box_checked = True
+ install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies',
+ checked=install_tool_dependencies_check_box_checked )
+ return trans.fill_template( '/admin/tool_shed_repository/install_tool_dependencies_with_update.mako',
+ repository=repository,
+ updating_repository_id=updating_repository_id,
+ updating_to_ctx_rev=updating_to_ctx_rev,
+ updating_to_changeset_revision=updating_to_changeset_revision,
+ encoded_updated_metadata=encoded_updated_metadata,
+ encoded_relative_install_dir=encoded_relative_install_dir,
+ encoded_tool_dependencies_dict=encoded_tool_dependencies_dict,
+ install_tool_dependencies_check_box=install_tool_dependencies_check_box,
+ tool_dependencies_dict=tool_dependencies_dict,
message=message,
status=status )
@@ -611,7 +650,8 @@
# TODO: I believe this block should be removed, but make sure..
repositories_for_uninstallation = []
for repository_id in tsridslist:
- repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( trans.security.decode_id( repository_id ) )
+ repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ) \
+ .get( trans.security.decode_id( repository_id ) )
if repository.status in [ trans.install_model.ToolShedRepository.installation_status.INSTALLED,
trans.install_model.ToolShedRepository.installation_status.ERROR ]:
repositories_for_uninstallation.append( repository )
@@ -632,28 +672,34 @@
filtered_repo_info_dicts = []
filtered_tool_panel_section_keys = []
repositories_for_installation = []
- # Some repositories may have repository dependencies that are required to be installed before the dependent repository, so we'll
- # order the list of tsr_ids to ensure all repositories install in the required order.
+ # Some repositories may have repository dependencies that are required to be installed before the
+ # dependent repository, so we'll order the list of tsr_ids to ensure all repositories install in the
+ # required order.
ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = \
repository_util.order_components_for_installation( trans,
tsr_ids,
repo_info_dicts,
tool_panel_section_keys=tool_panel_section_keys )
for tsr_id in ordered_tsr_ids:
- repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) )
+ repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ) \
+ .get( trans.security.decode_id( tsr_id ) )
if repository.status in [ trans.install_model.ToolShedRepository.installation_status.NEW,
trans.install_model.ToolShedRepository.installation_status.UNINSTALLED ]:
repositories_for_installation.append( repository )
- repo_info_dict, tool_panel_section_key = repository_util.get_repository_components_for_installation( tsr_id,
- ordered_tsr_ids,
- ordered_repo_info_dicts,
- ordered_tool_panel_section_keys )
+ repo_info_dict, tool_panel_section_key = \
+ repository_util.get_repository_components_for_installation( tsr_id,
+ ordered_tsr_ids,
+ ordered_repo_info_dicts,
+ ordered_tool_panel_section_keys )
filtered_repo_info_dicts.append( repo_info_dict )
filtered_tool_panel_section_keys.append( tool_panel_section_key )
if repositories_for_installation:
decoded_kwd[ 'repo_info_dicts' ] = filtered_repo_info_dicts
decoded_kwd[ 'tool_panel_section_keys' ] = filtered_tool_panel_section_keys
- self.install_tool_shed_repositories( trans, repositories_for_installation, reinstalling=reinstalling, **decoded_kwd )
+ self.install_tool_shed_repositories( trans,
+ repositories_for_installation,
+ reinstalling=reinstalling,
+ **decoded_kwd )
else:
kwd[ 'message' ] = 'All selected tool shed repositories are already installed.'
kwd[ 'status' ] = 'error'
@@ -772,7 +818,10 @@
trans.install_model.ToolDependency.installation_status.UNINSTALLED ]:
tool_dependencies_for_installation.append( tool_dependency )
if tool_dependencies_for_installation:
- self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation )
+ self.initiate_tool_dependency_installation( trans,
+ tool_dependencies_for_installation,
+ message=message,
+ status=status )
else:
message = 'All selected tool dependencies are already installed.'
status = 'error'
@@ -780,14 +829,16 @@
message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (universe_wsgi.ini) '
message += ' and restart your Galaxy server to install tool dependencies.'
status = 'error'
- installed_tool_dependencies_select_field = suc.build_tool_dependencies_select_field( trans,
- tool_shed_repository=tool_shed_repository,
- name='inst_td_ids',
- uninstalled_only=False )
- uninstalled_tool_dependencies_select_field = suc.build_tool_dependencies_select_field( trans,
- tool_shed_repository=tool_shed_repository,
- name='uninstalled_tool_dependency_ids',
- uninstalled_only=True )
+ installed_tool_dependencies_select_field = \
+ suc.build_tool_dependencies_select_field( trans,
+ tool_shed_repository=tool_shed_repository,
+ name='inst_td_ids',
+ uninstalled_only=False )
+ uninstalled_tool_dependencies_select_field = \
+ suc.build_tool_dependencies_select_field( trans,
+ tool_shed_repository=tool_shed_repository,
+ name='uninstalled_tool_dependency_ids',
+ uninstalled_only=True )
return trans.fill_template( '/admin/tool_shed_repository/manage_repository_tool_dependencies.mako',
repository=tool_shed_repository,
installed_tool_dependencies_select_field=installed_tool_dependencies_select_field,
@@ -836,7 +887,10 @@
trans.install_model.ToolDependency.installation_status.UNINSTALLED ]:
tool_dependencies_for_installation.append( tool_dependency )
if tool_dependencies_for_installation:
- self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation )
+ self.initiate_tool_dependency_installation( trans,
+ tool_dependencies_for_installation,
+ message=message,
+ status=status )
else:
kwd[ 'message' ] = 'All selected tool dependencies are already installed.'
kwd[ 'status' ] = 'error'
@@ -876,18 +930,21 @@
@web.require_admin
def prepare_for_install( self, trans, **kwd ):
if not suc.have_shed_tool_conf_for_install( trans ):
- message = 'The <b>tool_config_file</b> setting in <b>universe_wsgi.ini</b> must include at least one shed tool configuration file name with a '
- message += '<b><toolbox></b> tag that includes a <b>tool_path</b> attribute value which is a directory relative to the Galaxy installation '
- message += 'directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name <b>shed_tool_conf.xml</b> whose '
- message += '<b><toolbox></b> tag is <b><toolbox tool_path="../shed_tools"></b>).<p/>See the '
- message += '<a href="http://wiki.g2.bx.psu.edu/InstallingRepositoriesToGalaxy" target="_blank">Installation of Galaxy tool shed repository tools '
- message += 'into a local Galaxy instance</a> section of the Galaxy tool shed wiki for all of the details.'
+ message = 'The <b>tool_config_file</b> setting in <b>universe_wsgi.ini</b> must include at least one '
+ message += 'shed tool configuration file name with a <b><toolbox></b> tag that includes a <b>tool_path</b> '
+ message += 'attribute value which is a directory relative to the Galaxy installation directory in order '
+ message += 'to automatically install tools from a Galaxy Tool Shed (e.g., the file name <b>shed_tool_conf.xml</b> '
+ message += 'whose <b><toolbox></b> tag is <b><toolbox tool_path="../shed_tools"></b>).<p/>See the '
+ message += '<a href="http://wiki.g2.bx.psu.edu/InstallingRepositoriesToGalaxy" target="_blank">Installation '
+ message += 'of Galaxy Tool Shed repository tools into a local Galaxy instance</a> section of the Galaxy Tool '
+ message += 'Shed wiki for all of the details.'
return trans.show_error_message( message )
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 )
- # Handle repository dependencies, which do not include those that are required only for compiling a dependent repository's tool dependencies.
+ # 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 ) )
install_repository_dependencies = kwd.get( 'install_repository_dependencies', '' )
# Every repository will be installed into the same tool panel section or all will be installed outside of any sections.
@@ -900,13 +957,36 @@
includes_tools_for_display_in_tool_panel = util.string_as_bool( kwd.get( 'includes_tools_for_display_in_tool_panel', False ) )
includes_tool_dependencies = util.string_as_bool( kwd.get( 'includes_tool_dependencies', False ) )
install_tool_dependencies = kwd.get( 'install_tool_dependencies', '' )
+ # In addition to installing new repositories, this method is called when updating an installed repository
+ # to a new changeset_revision where the update includes newly defined repository dependencies.
+ updating = util.asbool( kwd.get( 'updating', False ) )
+ updating_repository_id = kwd.get( 'updating_repository_id', None )
+ updating_to_changeset_revision = kwd.get( 'updating_to_changeset_revision', None )
+ updating_to_ctx_rev = kwd.get( 'updating_to_ctx_rev', None )
+ encoded_updated_metadata = kwd.get( 'encoded_updated_metadata', None )
encoded_repo_info_dicts = kwd.get( 'encoded_repo_info_dicts', '' )
if encoded_repo_info_dicts:
encoded_repo_info_dicts = encoded_repo_info_dicts.split( encoding_util.encoding_sep )
if not encoded_repo_info_dicts:
- # The request originated in the tool shed via a tool search.
+ # The request originated in the tool shed via a tool search or from this controller's
+ # update_to_changeset_revision() method.
repository_ids = kwd.get( 'repository_ids', None )
- changeset_revisions = kwd.get( 'changeset_revisions', None )
+ if updating:
+ # We have updated an installed repository where the updates included newly defined repository
+ # and possibly tool dependencies. We will have arrived here only if the updates include newly
+ # defined repository dependencies. We're preparing to allow the user to elect to install these
+ # dependencies. At this point, the repository has been updated to the latest changeset revision,
+ # but the received repository id is from the Galaxy side (the caller is this controller's
+ # update_to_changeset_revision() method. We need to get the id of the same repository from the
+ # Tool Shed side.
+ repository = suc.get_tool_shed_repository_by_id( trans, updating_repository_id )
+ url = suc.url_join( tool_shed_url,
+ 'repository/get_repository_id?name=%s&owner=%s' % \
+ ( str( repository.name ), str( repository.owner ) ) )
+ repository_ids = common_util.tool_shed_get( trans.app, tool_shed_url, url )
+ changeset_revisions = updating_to_changeset_revision
+ 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' % \
@@ -918,7 +998,8 @@
if not includes_tools:
includes_tools = util.string_as_bool( decoded_repo_info_dict.get( 'includes_tools', False ) )
if not includes_tools_for_display_in_tool_panel:
- includes_tools_for_display_in_tool_panel = util.string_as_bool( decoded_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False ) )
+ includes_tools_for_display_in_tool_panel = \
+ util.string_as_bool( decoded_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False ) )
if not has_repository_dependencies:
has_repository_dependencies = util.string_as_bool( repo_information_dict.get( 'has_repository_dependencies', False ) )
if not includes_tool_dependencies:
@@ -927,6 +1008,19 @@
repo_info_dicts = [ encoding_util.tool_shed_decode( encoded_repo_info_dict ) for encoded_repo_info_dict in encoded_repo_info_dicts ]
if ( not includes_tools_for_display_in_tool_panel and kwd.get( 'select_shed_tool_panel_config_button', False ) ) or \
( includes_tools_for_display_in_tool_panel and kwd.get( 'select_tool_panel_section_button', False ) ):
+ if updating:
+ encoded_updated_metadata_dict = kwd.get( 'encoded_updated_metadata_dict', None )
+ updated_changeset_revision = kwd.get( 'updated_changeset_revision', None )
+ updated_ctx_rev = kwd.get( 'updated_ctx_rev', None )
+ repository = suc.get_tool_shed_repository_by_id( trans, updating_repository_id )
+ decoded_updated_metadata = encoding_util.tool_shed_decode( encoded_updated_metadata )
+ # Now that the user has decided whether they will handle dependencies, we can update
+ # the repository to the latest revision.
+ repository = repository_util.update_repository_record( trans,
+ repository=repository,
+ updated_metadata_dict=decoded_updated_metadata,
+ updated_changeset_revision=updating_to_changeset_revision,
+ updated_ctx_rev=updating_to_ctx_rev )
install_repository_dependencies = CheckboxField.is_checked( install_repository_dependencies )
if includes_tool_dependencies:
install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies )
@@ -959,7 +1053,8 @@
tool_panel_section_keys=tool_panel_section_keys,
tool_path=tool_path,
tool_shed_url=tool_shed_url )
- encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = repository_util.initiate_repository_installation( trans, installation_dict )
+ encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \
+ repository_util.initiate_repository_installation( trans, installation_dict )
return trans.fill_template( 'admin/tool_shed_repository/initiate_repository_installation.mako',
encoded_kwd=encoded_kwd,
query=query,
@@ -976,12 +1071,14 @@
tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf )
tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans )
if len( repo_info_dicts ) == 1:
- # If we're installing a single repository, see if it contains a readme or dependencies that we can display.
+ # If we're installing or updating a single repository, see if it contains a readme or
+ # dependencies that we can display.
repo_info_dict = repo_info_dicts[ 0 ]
dependencies_for_repository_dict = common_install_util.get_dependencies_for_repository( trans,
tool_shed_url,
repo_info_dict,
- includes_tool_dependencies )
+ includes_tool_dependencies,
+ updating=updating )
changeset_revision = dependencies_for_repository_dict.get( 'changeset_revision', None )
if not has_repository_dependencies:
has_repository_dependencies = dependencies_for_repository_dict.get( 'has_repository_dependencies', False )
@@ -990,7 +1087,8 @@
if not includes_tools:
includes_tools = dependencies_for_repository_dict.get( 'includes_tools', False )
if not includes_tools_for_display_in_tool_panel:
- includes_tools_for_display_in_tool_panel = dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False )
+ includes_tools_for_display_in_tool_panel = \
+ dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False )
installed_repository_dependencies = dependencies_for_repository_dict.get( 'installed_repository_dependencies', None )
installed_tool_dependencies = dependencies_for_repository_dict.get( 'installed_tool_dependencies', None )
missing_repository_dependencies = dependencies_for_repository_dict.get( 'missing_repository_dependencies', None )
@@ -998,19 +1096,25 @@
name = dependencies_for_repository_dict.get( 'name', None )
repository_owner = dependencies_for_repository_dict.get( 'repository_owner', None )
readme_files_dict = readme_util.get_readme_files_dict_for_display( trans, tool_shed_url, repo_info_dict )
- # We're handling 1 of 2 scenarios here: (1) we're installing a tool shed repository for the first time, so we've retrieved the list of installed
- # and missing repository dependencies from the database (2) we're handling the scenario where an error occurred during the installation process,
- # so we have a tool_shed_repository record in the database with associated repository dependency records. Since we have the repository
- # dependencies in either case, we'll merge the list of missing repository dependencies into the list of installed repository dependencies since
- # each displayed repository dependency will display a status, whether installed or missing.
- containers_dict = repository_util.populate_containers_dict_for_new_install( trans=trans,
- tool_shed_url=tool_shed_url,
- tool_path=tool_path,
- readme_files_dict=readme_files_dict,
- installed_repository_dependencies=installed_repository_dependencies,
- missing_repository_dependencies=missing_repository_dependencies,
- installed_tool_dependencies=installed_tool_dependencies,
- missing_tool_dependencies=missing_tool_dependencies )
+ # We're handling 1 of 3 scenarios here: (1) we're installing a tool shed repository for the first time, so we've
+ # retrieved the list of installed and missing repository dependencies from the database (2) we're handling the
+ # scenario where an error occurred during the installation process, so we have a tool_shed_repository record in
+ # the database with associated repository dependency records. Since we have the repository dependencies in both
+ # of the above 2 cases, we'll merge the list of missing repository dependencies into the list of installed
+ # repository dependencies since each displayed repository dependency will display a status, whether installed or
+ # missing. The 3rd scenario is where we're updating an installed repository and the updates include newly
+ # defined repository (and possibly tool) dependencies. In this case, merging will result in newly defined
+ # dependencies to be lost. We pass the updating parameter to make sure merging occurs only when appropriate.
+ containers_dict = \
+ repository_util.populate_containers_dict_for_new_install( trans=trans,
+ tool_shed_url=tool_shed_url,
+ tool_path=tool_path,
+ readme_files_dict=readme_files_dict,
+ installed_repository_dependencies=installed_repository_dependencies,
+ missing_repository_dependencies=missing_repository_dependencies,
+ installed_tool_dependencies=installed_tool_dependencies,
+ missing_tool_dependencies=missing_tool_dependencies,
+ updating=updating )
else:
# We're installing a list of repositories, each of which may have tool dependencies or repository dependencies.
containers_dicts = []
@@ -1018,7 +1122,8 @@
dependencies_for_repository_dict = common_install_util.get_dependencies_for_repository( trans,
tool_shed_url,
repo_info_dict,
- includes_tool_dependencies )
+ includes_tool_dependencies,
+ updating=updating )
changeset_revision = dependencies_for_repository_dict.get( 'changeset_revision', None )
if not has_repository_dependencies:
has_repository_dependencies = dependencies_for_repository_dict.get( 'has_repository_dependencies', False )
@@ -1027,34 +1132,39 @@
if not includes_tools:
includes_tools = dependencies_for_repository_dict.get( 'includes_tools', False )
if not includes_tools_for_display_in_tool_panel:
- includes_tools_for_display_in_tool_panel = dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False )
+ includes_tools_for_display_in_tool_panel = \
+ dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False )
installed_repository_dependencies = dependencies_for_repository_dict.get( 'installed_repository_dependencies', None )
installed_tool_dependencies = dependencies_for_repository_dict.get( 'installed_tool_dependencies', None )
missing_repository_dependencies = dependencies_for_repository_dict.get( 'missing_repository_dependencies', None )
missing_tool_dependencies = dependencies_for_repository_dict.get( 'missing_tool_dependencies', None )
name = dependencies_for_repository_dict.get( 'name', None )
repository_owner = dependencies_for_repository_dict.get( 'repository_owner', None )
- containers_dict = repository_util.populate_containers_dict_for_new_install( trans=trans,
- tool_shed_url=tool_shed_url,
- tool_path=tool_path,
- readme_files_dict=None,
- installed_repository_dependencies=installed_repository_dependencies,
- missing_repository_dependencies=missing_repository_dependencies,
- installed_tool_dependencies=installed_tool_dependencies,
- missing_tool_dependencies=missing_tool_dependencies )
+ containers_dict = \
+ repository_util.populate_containers_dict_for_new_install( trans=trans,
+ tool_shed_url=tool_shed_url,
+ tool_path=tool_path,
+ readme_files_dict=None,
+ installed_repository_dependencies=installed_repository_dependencies,
+ missing_repository_dependencies=missing_repository_dependencies,
+ installed_tool_dependencies=installed_tool_dependencies,
+ missing_tool_dependencies=missing_tool_dependencies,
+ updating=updating )
containers_dicts.append( containers_dict )
# Merge all containers into a single container.
containers_dict = repository_util.merge_containers_dicts_for_new_install( containers_dicts )
# Handle tool dependencies check box.
if trans.app.config.tool_dependency_dir is None:
if includes_tool_dependencies:
- message = "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> "
- message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository."
+ message = "Tool dependencies defined in this repository can be automatically installed if you set "
+ message += "the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file "
+ message += "(universe_wsgi.ini) and restart your Galaxy server before installing the repository."
status = "warning"
install_tool_dependencies_check_box_checked = False
else:
install_tool_dependencies_check_box_checked = True
- install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked )
+ install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies',
+ checked=install_tool_dependencies_check_box_checked )
# Handle repository dependencies check box.
install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True )
encoded_repo_info_dicts = encoding_util.encoding_sep.join( encoded_repo_info_dicts )
@@ -1062,6 +1172,11 @@
if includes_tools_for_display_in_tool_panel:
return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako',
encoded_repo_info_dicts=encoded_repo_info_dicts,
+ updating=updating,
+ updating_repository_id=updating_repository_id,
+ updating_to_ctx_rev=updating_to_ctx_rev,
+ updating_to_changeset_revision=updating_to_changeset_revision,
+ encoded_updated_metadata=encoded_updated_metadata,
includes_tools=includes_tools,
includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
includes_tool_dependencies=includes_tool_dependencies,
@@ -1077,10 +1192,16 @@
message=message,
status=status )
else:
- # If installing repositories that includes no tools and has no repository dependencies, display a page allowing the Galaxy administrator to
- # select a shed-related tool panel configuration file whose tool_path setting will be the location the repositories will be installed.
+ # If installing repositories that includes no tools and has no repository dependencies, display a page
+ # allowing the Galaxy administrator to select a shed-related tool panel configuration file whose tool_path
+ # setting will be the location the repositories will be installed.
return trans.fill_template( '/admin/tool_shed_repository/select_shed_tool_panel_config.mako',
encoded_repo_info_dicts=encoded_repo_info_dicts,
+ updating=updating,
+ updating_repository_id=updating_repository_id,
+ updating_to_ctx_rev=updating_to_ctx_rev,
+ updating_to_changeset_revision=updating_to_changeset_revision,
+ encoded_updated_metadata=encoded_updated_metadata,
includes_tools=includes_tools,
includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
includes_tool_dependencies=includes_tool_dependencies,
@@ -1400,7 +1521,8 @@
dependencies_for_repository_dict = common_install_util.get_dependencies_for_repository( trans,
tool_shed_url,
repo_info_dict,
- includes_tool_dependencies )
+ includes_tool_dependencies,
+ updating=False )
changeset_revision = dependencies_for_repository_dict.get( 'changeset_revision', None )
has_repository_dependencies = dependencies_for_repository_dict.get( 'has_repository_dependencies', False )
includes_tool_dependencies = dependencies_for_repository_dict.get( 'includes_tool_dependencies', False )
@@ -1449,14 +1571,16 @@
original_section_name = ''
tool_panel_section_select_field = None
shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans )
- containers_dict = repository_util.populate_containers_dict_for_new_install( trans=trans,
- tool_shed_url=tool_shed_url,
- tool_path=tool_path,
- readme_files_dict=readme_files_dict,
- installed_repository_dependencies=installed_repository_dependencies,
- missing_repository_dependencies=missing_repository_dependencies,
- installed_tool_dependencies=installed_tool_dependencies,
- missing_tool_dependencies=missing_tool_dependencies )
+ containers_dict = \
+ repository_util.populate_containers_dict_for_new_install( trans=trans,
+ tool_shed_url=tool_shed_url,
+ tool_path=tool_path,
+ readme_files_dict=readme_files_dict,
+ installed_repository_dependencies=installed_repository_dependencies,
+ missing_repository_dependencies=missing_repository_dependencies,
+ installed_tool_dependencies=installed_tool_dependencies,
+ missing_tool_dependencies=missing_tool_dependencies,
+ updating=False )
# Since we're reinstalling we'll merge the list of missing repository dependencies into the list of installed repository dependencies since each displayed
# repository dependency will display a status, whether installed or missing.
containers_dict = repository_dependency_util.merge_missing_repository_dependencies_to_installed_container( containers_dict )
@@ -1574,8 +1698,8 @@
@web.require_admin
def set_tool_versions( self, trans, **kwd ):
"""
- Get the tool_versions from the tool shed for each tool in the installed revision of a selected tool shed repository and update the
- metadata for the repository's revision in the Galaxy database.
+ Get the tool_versions from the tool shed for each tool in the installed revision of a selected tool shed
+ 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 )
@@ -1720,29 +1844,17 @@
resetting_all_metadata_on_repository=False,
updating_installed_repository=True,
persist=True )
- repository.metadata = metadata_dict
- # Update the repository.changeset_revision column in the database.
- repository.changeset_revision = latest_changeset_revision
- repository.ctx_rev = latest_ctx_rev
- # Update the repository.tool_shed_status column in the database.
- tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( trans.app, repository )
- if tool_shed_status_dict:
- repository.tool_shed_status = tool_shed_status_dict
- else:
- repository.tool_shed_status = None
- trans.install_model.context.add( repository )
- trans.install_model.context.flush()
if 'tools' in metadata_dict:
tool_panel_dict = metadata_dict.get( 'tool_panel_section', None )
if tool_panel_dict is None:
tool_panel_dict = suc.generate_tool_panel_dict_from_shed_tool_conf_entries( trans.app, repository )
repository_tools_tups = suc.get_repository_tools_tups( trans.app, metadata_dict )
tool_util.add_to_tool_panel( app=trans.app,
- repository_name=repository.name,
+ repository_name=str( repository.name ),
repository_clone_url=repository_clone_url,
- changeset_revision=repository.installed_changeset_revision,
+ changeset_revision=str( repository.installed_changeset_revision ),
repository_tools_tups=repository_tools_tups,
- owner=repository.owner,
+ owner=str( repository.owner ),
shed_tool_conf=shed_tool_conf,
tool_panel_dict=tool_panel_dict,
new_install=False )
@@ -1755,19 +1867,40 @@
os.path.join( relative_install_dir, name ),
repository,
repository_tools_tups )
- # Create tool_dependency records if necessary.
- if 'tool_dependencies' in metadata_dict:
- tool_dependencies = tool_dependency_util.create_tool_dependency_objects( trans.app,
- repository,
- relative_install_dir,
- set_status=False )
+ if 'repository_dependencies' in metadata_dict or 'tool_dependencies' in metadata_dict:
+ if 'repository_dependencies' in metadata_dict:
+ # Updates received include newly defined repository dependencies, so allow the user
+ # the option of installting them. We cannot update the repository with the changes
+ # until that happens, so we have to send them along.
+ new_kwd = dict( tool_shed_url=tool_shed_url,
+ updating_repository_id=trans.security.encode_id( repository.id ),
+ updating_to_ctx_rev=latest_ctx_rev,
+ updating_to_changeset_revision=latest_changeset_revision,
+ encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ),
+ updating=True )
+ return self.prepare_for_install( trans, **new_kwd )
+ # Updates received did not include any newly defined repository dependencies but did include
+ # newly defined tool dependencies.
+ encoded_tool_dependencies_dict = encoding_util.tool_shed_encode( metadata_dict.get( 'tool_dependencies', {} ) )
+ encoded_relative_install_dir = encoding_util.tool_shed_encode( relative_install_dir )
+ new_kwd = dict( updating_repository_id=trans.security.encode_id( repository.id ),
+ updating_to_ctx_rev=latest_ctx_rev,
+ updating_to_changeset_revision=latest_changeset_revision,
+ encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ),
+ encoded_relative_install_dir=encoded_relative_install_dir,
+ encoded_tool_dependencies_dict=encoded_tool_dependencies_dict,
+ message=message,
+ status = status )
+ return self.install_tool_dependencies_with_update( trans, **new_kwd )
+ # Updates received did not include any newly defined repository dependencies or newly defined
+ # tool dependencies.
+ repository = repository_util.update_repository_record( trans,
+ repository=repository,
+ updated_metadata_dict=metadata_dict,
+ updated_changeset_revision=latest_changeset_revision,
+ updated_ctx_rev=latest_ctx_rev )
message = "The installed repository named '%s' has been updated to change set revision '%s'. " % \
( name, latest_changeset_revision )
- # See if any tool dependencies can be installed.
- shed_tool_conf, tool_path, relative_install_dir = \
- suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository )
- if repository.missing_tool_dependencies:
- message += "Click the name of one of the missing tool dependencies listed below to install tool dependencies."
else:
message = "The directory containing the installed repository named '%s' cannot be found. " % name
status = 'error'
diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 lib/galaxy/webapps/galaxy/controllers/workflow.py
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -4,7 +4,6 @@
import base64
import httplib
import json
-import math
import os
import sgmllib
import svgfig
@@ -20,12 +19,9 @@
from galaxy.datatypes.data import Data
from galaxy.model.item_attrs import UsesItemRatings
from galaxy.model.mapping import desc
+from galaxy.tools.parameters.basic import DataToolParameter
from galaxy.tools.parameters import visit_input_values
-from galaxy.tools.parameters.basic import DataToolParameter, DrillDownSelectToolParameter, SelectToolParameter, UnvalidatedValue
-from galaxy.tools.parameters.grouping import Conditional, Repeat
-from galaxy.util.odict import odict
from galaxy.util.sanitize_html import sanitize_html
-from galaxy.util.topsort import CycleError, topsort, topsort_levels
from galaxy.web import error, url_for
from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin
from galaxy.web.framework import form
@@ -33,6 +29,14 @@
from galaxy.web.framework.helpers import to_unicode
from galaxy.workflow.modules import module_factory
from galaxy.workflow.run import invoke
+from galaxy.workflow.extract import summarize
+from galaxy.workflow.extract import extract_workflow
+from galaxy.workflow.steps import (
+ attach_ordered_steps,
+ order_workflow_steps,
+ edgelist_for_workflow_steps,
+ order_workflow_steps_with_levels,
+)
class StoredWorkflowListGrid( grids.Grid ):
@@ -1188,7 +1192,7 @@
if not user:
return trans.show_error_message( "Must be logged in to create workflows" )
if ( job_ids is None and dataset_ids is None ) or workflow_name is None:
- jobs, warnings = get_job_dict( trans )
+ jobs, warnings = summarize( trans )
# Render
return trans.fill_template(
"workflow/build_from_current_history.mako",
@@ -1197,82 +1201,13 @@
history=history
)
else:
- # Ensure job_ids and dataset_ids are lists (possibly empty)
- if job_ids is None:
- job_ids = []
- elif type( job_ids ) is not list:
- job_ids = [ job_ids ]
- if dataset_ids is None:
- dataset_ids = []
- elif type( dataset_ids ) is not list:
- dataset_ids = [ dataset_ids ]
- # Convert both sets of ids to integers
- job_ids = [ int( id ) for id in job_ids ]
- dataset_ids = [ int( id ) for id in dataset_ids ]
- # Find each job, for security we (implicately) check that they are
- # associated witha job in the current history.
- jobs, warnings = get_job_dict( trans )
- jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() )
- steps = []
- steps_by_job_id = {}
- hid_to_output_pair = {}
- # Input dataset steps
- for hid in dataset_ids:
- step = model.WorkflowStep()
- step.type = 'data_input'
- step.tool_inputs = dict( name="Input Dataset" )
- hid_to_output_pair[ hid ] = ( step, 'output' )
- steps.append( step )
- # Tool steps
- for job_id in job_ids:
- assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history"
- job = jobs_by_id[ job_id ]
- tool = trans.app.toolbox.get_tool( job.tool_id )
- param_values = job.get_param_values( trans.app, ignore_errors=True ) # If a tool was updated and e.g. had a text value changed to an integer, we don't want a traceback here
- associations = cleanup_param_values( tool.inputs, param_values )
- step = model.WorkflowStep()
- step.type = 'tool'
- step.tool_id = job.tool_id
- step.tool_inputs = tool.params_to_strings( param_values, trans.app )
- # NOTE: We shouldn't need to do two passes here since only
- # an earlier job can be used as an input to a later
- # job.
- for other_hid, input_name in associations:
- if other_hid in hid_to_output_pair:
- other_step, other_name = hid_to_output_pair[ other_hid ]
- conn = model.WorkflowStepConnection()
- conn.input_step = step
- conn.input_name = input_name
- # Should always be connected to an earlier step
- conn.output_step = other_step
- conn.output_name = other_name
- steps.append( step )
- steps_by_job_id[ job_id ] = step
- # Store created dataset hids
- for assoc in job.output_datasets:
- hid_to_output_pair[ assoc.dataset.hid ] = ( step, assoc.name )
- # Workflow to populate
- workflow = model.Workflow()
- workflow.name = workflow_name
- # Order the steps if possible
- attach_ordered_steps( workflow, steps )
- # And let's try to set up some reasonable locations on the canvas
- # (these are pretty arbitrary values)
- levorder = order_workflow_steps_with_levels( steps )
- base_pos = 10
- for i, steps_at_level in enumerate( levorder ):
- for j, index in enumerate( steps_at_level ):
- step = steps[ index ]
- step.position = dict( top=( base_pos + 120 * j ),
- left=( base_pos + 220 * i ) )
- # Store it
- stored = model.StoredWorkflow()
- stored.user = user
- stored.name = workflow_name
- workflow.stored_workflow = stored
- stored.latest_workflow = workflow
- trans.sa_session.add( stored )
- trans.sa_session.flush()
+ extract_workflow(
+ trans,
+ user=user,
+ job_ids=job_ids,
+ dataset_ids=dataset_ids,
+ workflow_name=workflow_name
+ )
# Index page with message
return trans.show_message( "Workflow '%s' created from current history." % workflow_name )
## return trans.show_ok_message( "<p>Workflow '%s' created.</p><p><a target='_top' href='%s'>Click to load in workflow editor</a></p>"
@@ -1692,148 +1627,6 @@
## ---- Utility methods -------------------------------------------------------
-def attach_ordered_steps( workflow, steps ):
- ordered_steps = order_workflow_steps( steps )
- if ordered_steps:
- workflow.has_cycles = False
- for i, step in enumerate( ordered_steps ):
- step.order_index = i
- workflow.steps.append( step )
- else:
- workflow.has_cycles = True
- workflow.steps = steps
-
-
-def edgelist_for_workflow_steps( steps ):
- """
- Create a list of tuples representing edges between ``WorkflowSteps`` based
- on associated ``WorkflowStepConnection``s
- """
- edges = []
- steps_to_index = dict( ( step, i ) for i, step in enumerate( steps ) )
- for step in steps:
- edges.append( ( steps_to_index[step], steps_to_index[step] ) )
- for conn in step.input_connections:
- edges.append( ( steps_to_index[conn.output_step], steps_to_index[conn.input_step] ) )
- return edges
-
-
-def order_workflow_steps( steps ):
- """
- Perform topological sort of the steps, return ordered or None
- """
- position_data_available = True
- for step in steps:
- if not step.position or not 'left' in step.position or not 'top' in step.position:
- position_data_available = False
- if position_data_available:
- steps.sort(cmp=lambda s1, s2: cmp( math.sqrt(s1.position['left'] ** 2 + s1.position['top'] ** 2), math.sqrt(s2.position['left'] ** 2 + s2.position['top'] ** 2)))
- try:
- edges = edgelist_for_workflow_steps( steps )
- node_order = topsort( edges )
- return [ steps[i] for i in node_order ]
- except CycleError:
- return None
-
-
-def order_workflow_steps_with_levels( steps ):
- try:
- return topsort_levels( edgelist_for_workflow_steps( steps ) )
- except CycleError:
- return None
-
-
-class FakeJob( object ):
- """
- Fake job object for datasets that have no creating_job_associations,
- they will be treated as "input" datasets.
- """
- def __init__( self, dataset ):
- self.is_fake = True
- self.id = "fake_%s" % dataset.id
-
-
-def get_job_dict( trans ):
- """
- Return a dictionary of Job -> [ Dataset ] mappings, for all finished
- active Datasets in the current history and the jobs that created them.
- """
- history = trans.get_history()
- # Get the jobs that created the datasets
- warnings = set()
- jobs = odict()
- for dataset in history.active_datasets:
- # FIXME: Create "Dataset.is_finished"
- if dataset.state in ( 'new', 'running', 'queued' ):
- warnings.add( "Some datasets still queued or running were ignored" )
- continue
-
- #if this hda was copied from another, we need to find the job that created the origial hda
- job_hda = dataset
- while job_hda.copied_from_history_dataset_association:
- job_hda = job_hda.copied_from_history_dataset_association
-
- if not job_hda.creating_job_associations:
- jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ]
-
- for assoc in job_hda.creating_job_associations:
- job = assoc.job
- if job in jobs:
- jobs[ job ].append( ( assoc.name, dataset ) )
- else:
- jobs[ job ] = [ ( assoc.name, dataset ) ]
- return jobs, warnings
-
-
-def cleanup_param_values( inputs, values ):
- """
- Remove 'Data' values from `param_values`, along with metadata cruft,
- but track the associations.
- """
- associations = []
- # dbkey is pushed in by the framework
- if 'dbkey' in values:
- del values['dbkey']
- root_values = values
-
- # Recursively clean data inputs and dynamic selects
- def cleanup( prefix, inputs, values ):
- for key, input in inputs.items():
- if isinstance( input, ( SelectToolParameter, DrillDownSelectToolParameter ) ):
- if input.is_dynamic and not isinstance( values[key], UnvalidatedValue ):
- values[key] = UnvalidatedValue( values[key] )
- if isinstance( input, DataToolParameter ):
- tmp = values[key]
- values[key] = None
- # HACK: Nested associations are not yet working, but we
- # still need to clean them up so we can serialize
- # if not( prefix ):
- if tmp: # this is false for a non-set optional dataset
- if not isinstance(tmp, list):
- associations.append( ( tmp.hid, prefix + key ) )
- else:
- associations.extend( [ (t.hid, prefix + key) for t in tmp] )
-
- # Cleanup the other deprecated crap associated with datasets
- # as well. Worse, for nested datasets all the metadata is
- # being pushed into the root. FIXME: MUST REMOVE SOON
- key = prefix + key + "_"
- for k in root_values.keys():
- if k.startswith( key ):
- del root_values[k]
- elif isinstance( input, Repeat ):
- group_values = values[key]
- for i, rep_values in enumerate( group_values ):
- rep_index = rep_values['__index__']
- cleanup( "%s%s_%d|" % (prefix, key, rep_index ), input.inputs, group_values[i] )
- elif isinstance( input, Conditional ):
- group_values = values[input.name]
- current_case = group_values['__current_case__']
- cleanup( "%s%s|" % ( prefix, key ), input.cases[current_case].inputs, group_values )
- cleanup( "", inputs, values )
- return associations
-
-
def _build_workflow_on_str(instance_ds_names):
# Returns suffix for new histories based on multi input iteration
num_multi_inputs = len(instance_ds_names)
diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 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
@@ -866,11 +866,13 @@
no_update = 'false'
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?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 ) )
+ 'admin_toolshed/update_to_changeset_revision%s' % params )
else:
- message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. You may need to enable third-party cookies in your browser. ' % galaxy_url
+ 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. '
return trans.show_error_message( message )
if changeset_revision == repository.tip( trans.app ):
# If changeset_revision is the repository tip, there are no additional updates.
@@ -883,15 +885,17 @@
trans.security.encode_id( repository.id ),
changeset_revision )
if repository_metadata:
- # If changeset_revision is in the repository_metadata table for this repository, there are no additional updates.
+ # If changeset_revision is in the repository_metadata table for this repository, there are no
+ # additional updates.
if from_update_manager:
return no_update
else:
# Return the same value for changeset_revision and latest_changeset_revision.
url += latest_changeset_revision
else:
- # The changeset_revision column in the repository_metadata table has been updated with a new changeset_revision value since the
- # repository was installed. We need to find the changeset_revision to which we need to update.
+ # The changeset_revision column in the repository_metadata table has been updated with a new
+ # changeset_revision value since the repository was installed. We need to find the changeset_revision
+ # to which we need to update.
update_to_changeset_hash = None
for changeset in repo.changelog:
changeset_hash = str( repo.changectx( changeset ) )
@@ -1680,6 +1684,16 @@
return encoding_util.tool_shed_encode( repository_dependencies )
return ''
+ @web.expose
+ def get_repository_id( self, trans, **kwd ):
+ """Given a repository name and owner, return the encoded repository id."""
+ repository_name = kwd[ 'name' ]
+ repository_owner = kwd[ 'owner' ]
+ repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
+ if repository:
+ return trans.security.encode_id( repository.id )
+ return ''
+
@web.json
def get_repository_information( self, trans, repository_ids, changeset_revisions, **kwd ):
"""
@@ -1824,7 +1838,9 @@
if not repository_metadata:
# The received changeset_revision is no longer associated with metadata, so get the next changeset_revision in the repository
# changelog that is associated with metadata.
- changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, after_changeset_revision=changeset_revision )
+ changeset_revision = suc.get_next_downloadable_changeset_revision( repository,
+ repo,
+ after_changeset_revision=changeset_revision )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
repo_info_dict = repository_util.create_repo_info_dict( trans=trans,
@@ -2039,11 +2055,12 @@
galaxy_url = suc.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?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 ) ) ) )
+ '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
@@ -2477,9 +2494,10 @@
@web.expose
def next_installable_changeset_revision( self, trans, **kwd ):
"""
- Handle a request from a Galaxy instance where the changeset_revision defined for a repository in a dependency definition file is older
- than the changeset_revision associated with the installed repository. This will occur with repository's of type tool_dependency_definition,
- and this scenario will occur while repository dependency hierarchies are bing installed.
+ Handle a request from a Galaxy instance where the changeset_revision defined for a repository
+ in a dependency definition file is older than the changeset_revision associated with the installed
+ repository. This will occur with repository's of type tool_dependency_definition, and this scenario
+ will occur while repository dependency hierarchies are bing installed.
"""
name = kwd.get( 'name', None )
owner = kwd.get( 'owner', None )
@@ -2981,12 +2999,13 @@
@web.expose
def updated_changeset_revisions( self, trans, **kwd ):
"""
- Handle a request from a local Galaxy instance to retrieve the list of changeset revisions to which an installed repository can be updated. This
- method will return a string of comma-separated changeset revision hashes for all available updates to the received changeset revision. Among
- other things , this method handles the scenario where an installed tool shed repository's tool_dependency definition file defines a changeset
- revision for a complex repository dependency that is outdated. In other words, a defined changeset revision is older than the current changeset
- revision for the required repository, making it impossible to discover the repository without knowledge of revisions to which it could have been
- updated.
+ Handle a request from a local Galaxy instance to retrieve the list of changeset revisions to which an
+ installed repository can be updated. This method will return a string of comma-separated changeset revision
+ hashes for all available updates to the received changeset revision. Among other things , this method
+ handles the scenario where an installed tool shed repository's tool_dependency definition file defines a
+ changeset revision for a complex repository dependency that is outdated. In other words, a defined changeset
+ revision is older than the current changeset revision for the required repository, making it impossible to
+ discover the repository without knowledge of revisions to which it could have been updated.
"""
name = kwd.get( 'name', None )
owner = kwd.get( 'owner', None )
diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 lib/galaxy/workflow/extract.py
--- /dev/null
+++ b/lib/galaxy/workflow/extract.py
@@ -0,0 +1,209 @@
+""" This module contains functionality to aid in extracting workflows from
+histories.
+"""
+from galaxy.util.odict import odict
+from galaxy import model
+from galaxy.tools.parameters.basic import (
+ DataToolParameter,
+ DrillDownSelectToolParameter,
+ SelectToolParameter,
+ UnvalidatedValue
+)
+from galaxy.tools.parameters.grouping import (
+ Conditional,
+ Repeat
+)
+from .steps import (
+ attach_ordered_steps,
+ order_workflow_steps_with_levels
+)
+
+WARNING_SOME_DATASETS_NOT_READY = "Some datasets still queued or running were ignored"
+
+
+def extract_workflow( trans, user, history=None, job_ids=None, dataset_ids=None, workflow_name=None ):
+ steps = extract_steps( trans, history=history, job_ids=job_ids, dataset_ids=dataset_ids )
+ # Workflow to populate
+ workflow = model.Workflow()
+ workflow.name = workflow_name
+ # Order the steps if possible
+ attach_ordered_steps( workflow, steps )
+ # And let's try to set up some reasonable locations on the canvas
+ # (these are pretty arbitrary values)
+ levorder = order_workflow_steps_with_levels( steps )
+ base_pos = 10
+ for i, steps_at_level in enumerate( levorder ):
+ for j, index in enumerate( steps_at_level ):
+ step = steps[ index ]
+ step.position = dict( top=( base_pos + 120 * j ),
+ left=( base_pos + 220 * i ) )
+ # Store it
+ stored = model.StoredWorkflow()
+ stored.user = user
+ stored.name = workflow_name
+ workflow.stored_workflow = stored
+ stored.latest_workflow = workflow
+ trans.sa_session.add( stored )
+ trans.sa_session.flush()
+ return stored
+
+
+def extract_steps( trans, history=None, job_ids=None, dataset_ids=None ):
+ # Ensure job_ids and dataset_ids are lists (possibly empty)
+ if job_ids is None:
+ job_ids = []
+ elif type( job_ids ) is not list:
+ job_ids = [ job_ids ]
+ if dataset_ids is None:
+ dataset_ids = []
+ elif type( dataset_ids ) is not list:
+ dataset_ids = [ dataset_ids ]
+ # Convert both sets of ids to integers
+ job_ids = [ int( id ) for id in job_ids ]
+ dataset_ids = [ int( id ) for id in dataset_ids ]
+ # Find each job, for security we (implicately) check that they are
+ # associated witha job in the current history.
+ jobs, warnings = summarize( trans, history=history )
+ jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() )
+ steps = []
+ steps_by_job_id = {}
+ hid_to_output_pair = {}
+ # Input dataset steps
+ for hid in dataset_ids:
+ step = model.WorkflowStep()
+ step.type = 'data_input'
+ step.tool_inputs = dict( name="Input Dataset" )
+ hid_to_output_pair[ hid ] = ( step, 'output' )
+ steps.append( step )
+ # Tool steps
+ for job_id in job_ids:
+ assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history"
+ job = jobs_by_id[ job_id ]
+ tool_inputs, associations = step_inputs( trans, job )
+ step = model.WorkflowStep()
+ step.type = 'tool'
+ step.tool_id = job.tool_id
+ step.tool_inputs = tool_inputs
+ # NOTE: We shouldn't need to do two passes here since only
+ # an earlier job can be used as an input to a later
+ # job.
+ for other_hid, input_name in associations:
+ if other_hid in hid_to_output_pair:
+ other_step, other_name = hid_to_output_pair[ other_hid ]
+ conn = model.WorkflowStepConnection()
+ conn.input_step = step
+ conn.input_name = input_name
+ # Should always be connected to an earlier step
+ conn.output_step = other_step
+ conn.output_name = other_name
+ steps.append( step )
+ steps_by_job_id[ job_id ] = step
+ # Store created dataset hids
+ for assoc in job.output_datasets:
+ hid_to_output_pair[ assoc.dataset.hid ] = ( step, assoc.name )
+ return steps
+
+
+class FakeJob( object ):
+ """
+ Fake job object for datasets that have no creating_job_associations,
+ they will be treated as "input" datasets.
+ """
+ def __init__( self, dataset ):
+ self.is_fake = True
+ self.id = "fake_%s" % dataset.id
+
+
+def summarize( trans, history=None ):
+ """ Return mapping of job description to datasets for active items in
+ supplied history - needed for building workflow from a history.
+
+ Formerly call get_job_dict in workflow web controller.
+ """
+ if not history:
+ history = trans.get_history()
+
+ # Get the jobs that created the datasets
+ warnings = set()
+ jobs = odict()
+ for dataset in history.active_datasets:
+ # FIXME: Create "Dataset.is_finished"
+ if dataset.state in ( 'new', 'running', 'queued' ):
+ warnings.add( WARNING_SOME_DATASETS_NOT_READY )
+ continue
+
+ #if this hda was copied from another, we need to find the job that created the origial hda
+ job_hda = dataset
+ while job_hda.copied_from_history_dataset_association:
+ job_hda = job_hda.copied_from_history_dataset_association
+
+ if not job_hda.creating_job_associations:
+ jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ]
+
+ for assoc in job_hda.creating_job_associations:
+ job = assoc.job
+ if job in jobs:
+ jobs[ job ].append( ( assoc.name, dataset ) )
+ else:
+ jobs[ job ] = [ ( assoc.name, dataset ) ]
+
+ return jobs, warnings
+
+
+def step_inputs( trans, job ):
+ tool = trans.app.toolbox.get_tool( job.tool_id )
+ param_values = job.get_param_values( trans.app, ignore_errors=True ) # If a tool was updated and e.g. had a text value changed to an integer, we don't want a traceback here
+ associations = __cleanup_param_values( tool.inputs, param_values )
+ tool_inputs = tool.params_to_strings( param_values, trans.app )
+ return tool_inputs, associations
+
+
+def __cleanup_param_values( inputs, values ):
+ """
+ Remove 'Data' values from `param_values`, along with metadata cruft,
+ but track the associations.
+ """
+ associations = []
+ # dbkey is pushed in by the framework
+ if 'dbkey' in values:
+ del values['dbkey']
+ root_values = values
+
+ # Recursively clean data inputs and dynamic selects
+ def cleanup( prefix, inputs, values ):
+ for key, input in inputs.items():
+ if isinstance( input, ( SelectToolParameter, DrillDownSelectToolParameter ) ):
+ if input.is_dynamic and not isinstance( values[key], UnvalidatedValue ):
+ values[key] = UnvalidatedValue( values[key] )
+ if isinstance( input, DataToolParameter ):
+ tmp = values[key]
+ values[key] = None
+ # HACK: Nested associations are not yet working, but we
+ # still need to clean them up so we can serialize
+ # if not( prefix ):
+ if tmp: # this is false for a non-set optional dataset
+ if not isinstance(tmp, list):
+ associations.append( ( tmp.hid, prefix + key ) )
+ else:
+ associations.extend( [ (t.hid, prefix + key) for t in tmp] )
+
+ # Cleanup the other deprecated crap associated with datasets
+ # as well. Worse, for nested datasets all the metadata is
+ # being pushed into the root. FIXME: MUST REMOVE SOON
+ key = prefix + key + "_"
+ for k in root_values.keys():
+ if k.startswith( key ):
+ del root_values[k]
+ elif isinstance( input, Repeat ):
+ group_values = values[key]
+ for i, rep_values in enumerate( group_values ):
+ rep_index = rep_values['__index__']
+ cleanup( "%s%s_%d|" % (prefix, key, rep_index ), input.inputs, group_values[i] )
+ elif isinstance( input, Conditional ):
+ group_values = values[input.name]
+ current_case = group_values['__current_case__']
+ cleanup( "%s%s|" % ( prefix, key ), input.cases[current_case].inputs, group_values )
+ cleanup( "", inputs, values )
+ return associations
+
+__all__ = [ summarize, extract_workflow ]
diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 lib/galaxy/workflow/steps.py
--- /dev/null
+++ b/lib/galaxy/workflow/steps.py
@@ -0,0 +1,63 @@
+""" This module contains utility methods for reasoning about and ordering
+workflow steps.
+"""
+import math
+from galaxy.util.topsort import (
+ CycleError,
+ topsort,
+ topsort_levels
+)
+
+
+def attach_ordered_steps( workflow, steps ):
+ """ Attempt to topologically order steps and attach to workflow. If this
+ fails - the workflow contains cycles so it mark it as such.
+ """
+ ordered_steps = order_workflow_steps( steps )
+ if ordered_steps:
+ workflow.has_cycles = False
+ for i, step in enumerate( ordered_steps ):
+ step.order_index = i
+ workflow.steps.append( step )
+ else:
+ workflow.has_cycles = True
+ workflow.steps = steps
+
+
+def order_workflow_steps( steps ):
+ """
+ Perform topological sort of the steps, return ordered or None
+ """
+ position_data_available = True
+ for step in steps:
+ if not step.position or not 'left' in step.position or not 'top' in step.position:
+ position_data_available = False
+ if position_data_available:
+ steps.sort(cmp=lambda s1, s2: cmp( math.sqrt(s1.position['left'] ** 2 + s1.position['top'] ** 2), math.sqrt(s2.position['left'] ** 2 + s2.position['top'] ** 2)))
+ try:
+ edges = edgelist_for_workflow_steps( steps )
+ node_order = topsort( edges )
+ return [ steps[i] for i in node_order ]
+ except CycleError:
+ return None
+
+
+def edgelist_for_workflow_steps( steps ):
+ """
+ Create a list of tuples representing edges between ``WorkflowSteps`` based
+ on associated ``WorkflowStepConnection``s
+ """
+ edges = []
+ steps_to_index = dict( ( step, i ) for i, step in enumerate( steps ) )
+ for step in steps:
+ edges.append( ( steps_to_index[step], steps_to_index[step] ) )
+ for conn in step.input_connections:
+ edges.append( ( steps_to_index[conn.output_step], steps_to_index[conn.input_step] ) )
+ return edges
+
+
+def order_workflow_steps_with_levels( steps ):
+ try:
+ return topsort_levels( edgelist_for_workflow_steps( steps ) )
+ except CycleError:
+ return None
diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 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
@@ -37,15 +37,19 @@
Galaxy instance. The dictionary will also contain the recursive list of repository dependencies defined
for the repository, as well as the defined tool dependencies.
- This method is called from Galaxy under three scenarios:
+ This method is called from Galaxy under four scenarios:
1. During the tool shed repository installation process via the tool shed's get_repository_information()
- method. In this case both the received repository and repository_metadata will be objects., but
+ method. In this case both the received repository and repository_metadata will be objects, but
tool_dependencies and repository_dependencies will be None.
- 2. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no
+ 2. When getting updates for an install repository where the updates include newly defined repository
+ dependency definitions. This scenario is similar to 1. above. The tool shed's get_repository_information()
+ method is the caller, and both the received repository and repository_metadata will be objects, but
+ tool_dependencies and repository_dependencies will be None.
+ 3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no
updates available. In this case, both repository and repository_metadata will be None, but tool_dependencies
and repository_dependencies will be objects previously retrieved from the tool shed if the repository includes
definitions for them.
- 3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates
+ 4. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates
available. In this case, this method is reached via the tool shed's get_updated_repository_information()
method, and both repository and repository_metadata will be objects but tool_dependencies and
repository_dependencies will be None.
@@ -184,16 +188,22 @@
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_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
+ repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans,
+ repository_id,
+ changeset_revision )
if not repository_metadata:
- # The received changeset_revision is no longer installable, so get the next changeset_revision in the repository's changelog.
- # This generally occurs only with repositories of type tool_dependency_definition.
- next_downloadable_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
+ # The received changeset_revision is no longer installable, so get the next changeset_revision
+ # in the repository's changelog. This generally occurs only with repositories of type
+ # tool_dependency_definition.
+ next_downloadable_changeset_revision = \
+ suc.get_next_downloadable_changeset_revision( repository,repo, changeset_revision )
if next_downloadable_changeset_revision:
- repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, next_downloadable_changeset_revision )
+ repository_metadata = \
+ suc.get_repository_metadata_by_changeset_revision( trans, repository_id, next_downloadable_changeset_revision )
if repository_metadata:
- # For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption is not valid we'll have to
- # enhance the callers to handle repository_metadata values of None in the returned repo_info_dict.
+ # For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption
+ # is not valid we'll have to enhance the callers to handle repository_metadata values of None in the
+ # returned repo_info_dict.
metadata = repository_metadata.metadata
if 'tools' in metadata:
includes_tools = True
@@ -743,9 +753,13 @@
ordered_tool_panel_section_keys.append( tool_panel_section_key )
return ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys
-def populate_containers_dict_for_new_install( trans, tool_shed_url, tool_path, readme_files_dict, installed_repository_dependencies, missing_repository_dependencies,
- installed_tool_dependencies, missing_tool_dependencies ):
- """Return the populated containers for a repository being installed for the first time."""
+def populate_containers_dict_for_new_install( trans, tool_shed_url, tool_path, readme_files_dict, installed_repository_dependencies,
+ missing_repository_dependencies, installed_tool_dependencies, missing_tool_dependencies,
+ updating=False ):
+ """
+ Return the populated containers for a repository being installed for the first time or for an installed repository
+ that is being updated and the updates include newly defined repository (and possibly tool) dependencies.
+ """
installed_tool_dependencies, missing_tool_dependencies = \
tool_dependency_util.populate_tool_dependencies_dicts( trans=trans,
tool_shed_url=tool_shed_url,
@@ -753,27 +767,32 @@
repository_installed_tool_dependencies=installed_tool_dependencies,
repository_missing_tool_dependencies=missing_tool_dependencies,
required_repo_info_dicts=None )
- # Since we are installing a new repository, most of the repository contents are set to None since we don't yet know what they are.
- containers_dict = container_util.build_repository_containers_for_galaxy( trans=trans,
- repository=None,
- datatypes=None,
- invalid_tools=None,
- missing_repository_dependencies=missing_repository_dependencies,
- missing_tool_dependencies=missing_tool_dependencies,
- readme_files_dict=readme_files_dict,
- repository_dependencies=installed_repository_dependencies,
- tool_dependencies=installed_tool_dependencies,
- valid_tools=None,
- workflows=None,
- valid_data_managers=None,
- invalid_data_managers=None,
- data_managers_errors=None,
- new_install=True,
- reinstalling=False )
- # Merge the missing_repository_dependencies container contents to the installed_repository_dependencies container.
- containers_dict = repository_dependency_util.merge_missing_repository_dependencies_to_installed_container( containers_dict )
- # Merge the missing_tool_dependencies container contents to the installed_tool_dependencies container.
- containers_dict = tool_dependency_util.merge_missing_tool_dependencies_to_installed_container( containers_dict )
+ # Most of the repository contents are set to None since we don't yet know what they are.
+ containers_dict = \
+ container_util.build_repository_containers_for_galaxy( trans=trans,
+ repository=None,
+ datatypes=None,
+ invalid_tools=None,
+ missing_repository_dependencies=missing_repository_dependencies,
+ missing_tool_dependencies=missing_tool_dependencies,
+ readme_files_dict=readme_files_dict,
+ repository_dependencies=installed_repository_dependencies,
+ tool_dependencies=installed_tool_dependencies,
+ valid_tools=None,
+ workflows=None,
+ valid_data_managers=None,
+ invalid_data_managers=None,
+ data_managers_errors=None,
+ new_install=True,
+ reinstalling=False )
+ if not updating:
+ # If we installing a new repository and not updaing an installed repository, we can merge
+ # the missing_repository_dependencies container contents to the installed_repository_dependencies
+ # container. When updating an installed repository, merging will result in losing newly defined
+ # dependencies included in the updates.
+ containers_dict = repository_dependency_util.merge_missing_repository_dependencies_to_installed_container( containers_dict )
+ # Merge the missing_tool_dependencies container contents to the installed_tool_dependencies container.
+ containers_dict = tool_dependency_util.merge_missing_tool_dependencies_to_installed_container( containers_dict )
return containers_dict
def pull_repository( repo, repository_clone_url, ctx_rev ):
@@ -875,3 +894,23 @@
repository.uninstalled = uninstalled
trans.install_model.context.add( repository )
trans.install_model.context.flush()
+
+def update_repository_record( trans, repository, updated_metadata_dict, updated_changeset_revision, updated_ctx_rev ):
+ """
+ Update a tool_shed_repository database record with new information retrieved from the
+ Tool Shed. This happens when updating an installed repository to a new changeset revision.
+ """
+ repository.metadata = updated_metadata_dict
+ # Update the repository.changeset_revision column in the database.
+ repository.changeset_revision = updated_changeset_revision
+ repository.ctx_rev = updated_ctx_rev
+ # Update the repository.tool_shed_status column in the database.
+ tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( trans.app, repository )
+ if tool_shed_status_dict:
+ repository.tool_shed_status = tool_shed_status_dict
+ else:
+ repository.tool_shed_status = None
+ trans.install_model.context.add( repository )
+ trans.install_model.context.flush()
+ trans.install_model.context.refresh( repository )
+ return repository
diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 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
@@ -359,13 +359,14 @@
can_install_tool_dependency = True
if can_install_tool_dependency:
package_install_version = package_elem.get( 'version', '1.0' )
- tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app,
- tool_shed_repository=tool_shed_repository,
- name=package_name,
- version=package_version,
- type='package',
- status=app.install_model.ToolDependency.installation_status.INSTALLING,
- set_status=True )
+ tool_dependency = \
+ tool_dependency_util.create_or_update_tool_dependency( app=app,
+ tool_shed_repository=tool_shed_repository,
+ name=package_name,
+ version=package_version,
+ type='package',
+ status=app.install_model.ToolDependency.installation_status.INSTALLING,
+ set_status=True )
# Get the information about the current platform in case the tool dependency definition includes tag sets
# for installing compiled binaries.
platform_info_dict = tool_dependency_util.get_platform_info_dict()
@@ -879,25 +880,28 @@
# Tool dependencies of type "set_environmnet" always have the version attribute set to None.
attr_tup = ( env_var_name, None, 'set_environment' )
if attr_tup in attr_tups_of_dependencies_for_install:
- install_dir = tool_dependency_util.get_tool_dependency_install_dir( app=app,
- repository_name=tool_shed_repository.name,
- repository_owner=tool_shed_repository.owner,
- repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
- tool_dependency_type='set_environment',
- tool_dependency_name=env_var_name,
- tool_dependency_version=None )
+ install_dir = \
+ tool_dependency_util.get_tool_dependency_install_dir( app=app,
+ repository_name=tool_shed_repository.name,
+ repository_owner=tool_shed_repository.owner,
+ repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
+ tool_dependency_type='set_environment',
+ tool_dependency_name=env_var_name,
+ tool_dependency_version=None )
tool_shed_repository_install_dir = get_tool_shed_repository_install_dir( app, tool_shed_repository )
env_var_dict = td_common_util.create_env_var_dict( env_var_elem, tool_shed_repository_install_dir=tool_shed_repository_install_dir )
if env_var_dict:
if not os.path.exists( install_dir ):
os.makedirs( install_dir )
- tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app,
- tool_shed_repository=tool_shed_repository,
- name=env_var_name,
- version=None,
- type='set_environment',
- status=app.install_model.ToolDependency.installation_status.INSTALLING,
- set_status=True )
+ status = app.install_model.ToolDependency.installation_status.INSTALLING
+ tool_dependency = \
+ tool_dependency_util.create_or_update_tool_dependency( app=app,
+ tool_shed_repository=tool_shed_repository,
+ name=env_var_name,
+ version=None,
+ type='set_environment',
+ status=status,
+ set_status=True )
if env_var_version == '1.0':
# Create this tool dependency's env.sh file.
env_file_builder = fabric_util.EnvFileBuilder( install_dir )
@@ -906,28 +910,34 @@
error_message = 'Error creating env.sh file for tool dependency %s, return_code: %s' % \
( str( tool_dependency.name ), str( return_code ) )
log.debug( error_message )
- tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
- tool_dependency=tool_dependency,
- status=app.install_model.ToolDependency.installation_status.ERROR,
- error_message=error_message,
- remove_from_disk=False )
+ status = app.install_model.ToolDependency.installation_status.ERROR
+ tool_dependency = \
+ tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency=tool_dependency,
+ status=status,
+ error_message=error_message,
+ remove_from_disk=False )
else:
if tool_dependency.status not in [ app.install_model.ToolDependency.installation_status.ERROR,
app.install_model.ToolDependency.installation_status.INSTALLED ]:
- tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
- tool_dependency=tool_dependency,
- status=app.install_model.ToolDependency.installation_status.INSTALLED,
- error_message=None,
- remove_from_disk=False )
+ status = app.install_model.ToolDependency.installation_status.INSTALLED
+ tool_dependency = \
+ tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency=tool_dependency,
+ status=status,
+ error_message=None,
+ remove_from_disk=False )
log.debug( 'Environment variable %s set in %s for tool dependency %s.' % \
( str( env_var_name ), str( install_dir ), str( tool_dependency.name ) ) )
else:
error_message = 'Only set_environment version 1.0 is currently supported (i.e., change your tag to be <set_environment version="1.0">).'
- tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
- tool_dependency=tool_dependency,
- status=app.install_model.ToolDependency.installation_status.ERROR,
- error_message=error_message,
- remove_from_disk=False )
+ status = app.install_model.ToolDependency.installation_status.ERROR
+ tool_dependency = \
+ tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency=tool_dependency,
+ status=status,
+ error_message=error_message,
+ remove_from_disk=False )
return tool_dependency
def strip_path( fpath ):
diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 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
@@ -70,7 +70,7 @@
if display_path is not None:
datatype_util.load_installed_display_applications( trans.app, installed_repository_dict, deactivate=False )
-def get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ):
+def get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies, updating=False ):
"""
Return dictionaries containing the sets of installed and missing tool dependencies and repository
dependencies associated with the repository defined by the received repo_info_dict.
@@ -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_installing_repository( trans, tool_shed_url, tool_dependencies )
+ get_installed_and_missing_tool_dependencies_for_repository( trans, tool_shed_url, 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:
@@ -101,10 +101,11 @@
name,
repository_owner,
changeset_revision )
- if repository and repository.metadata:
+ if not updating and repository and repository.metadata:
installed_rd, missing_rd = get_installed_and_missing_repository_dependencies( trans, repository )
else:
- installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple )
+ installed_rd, missing_rd = \
+ get_installed_and_missing_repository_dependencies_for_new_or_updated_install( trans, repo_info_tuple )
# Discover all repository dependencies and retrieve information for installing them.
all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) )
has_repository_dependencies = all_repo_info_dict.get( 'has_repository_dependencies', False )
@@ -119,7 +120,8 @@
required_tool_dependencies = {}
for rid in required_repo_info_dicts:
for name, repo_info_tuple in rid.items():
- description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, rid_repository_dependencies, rid_tool_dependencies = \
+ description, repository_clone_url, changeset_revision, ctx_rev, \
+ repository_owner, rid_repository_dependencies, rid_tool_dependencies = \
suc.get_repo_info_tuple_contents( repo_info_tuple )
if rid_tool_dependencies:
for td_key, td_dict in rid_tool_dependencies.items():
@@ -128,7 +130,9 @@
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_installing_repository( trans, tool_shed_url, required_tool_dependencies )
+ get_installed_and_missing_tool_dependencies_for_repository( trans,
+ tool_shed_url,
+ required_tool_dependencies )
if required_installed_td:
if not includes_tool_dependencies:
includes_tool_dependencies = True
@@ -168,11 +172,12 @@
def get_installed_and_missing_repository_dependencies( trans, repository ):
"""
- Return the installed and missing repository dependencies for a tool shed repository that has a record in the Galaxy database, but
- may or may not be installed. In this case, the repository dependencies are associated with the repository in the database. Do not
- include a repository dependency if it is required only to compile a tool dependency defined for the dependent repository since these
- special kinds of repository dependencies are really a dependency of the dependent repository's contained tool dependency, and only if
- that tool dependency requires compilation.
+ Return the installed and missing repository dependencies for a tool shed repository that has a record
+ in the Galaxy database, but may or may not be installed. In this case, the repository dependencies are
+ associated with the repository in the database. Do not include a repository dependency if it is required
+ only to compile a tool dependency defined for the dependent repository since these special kinds of repository
+ dependencies are really a dependency of the dependent repository's contained tool dependency, and only
+ if that tool dependency requires compilation.
"""
missing_repository_dependencies = {}
installed_repository_dependencies = {}
@@ -228,7 +233,7 @@
missing_repository_dependencies[ 'description' ] = description
return installed_repository_dependencies, missing_repository_dependencies
-def get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple ):
+def get_installed_and_missing_repository_dependencies_for_new_or_updated_install( trans, repo_info_tuple ):
"""
Parse the received repository_dependencies dictionary that is associated with a repository being
installed into Galaxy for the first time and attempt to determine repository dependencies that are
@@ -264,13 +269,13 @@
tmp_repo_info_tuple )
if repository:
new_rd_tup = [ tool_shed,
- name,
- owner,
- changeset_revision,
- prior_installation_required,
- only_if_compiling_contained_td,
- repository.id,
- repository.status ]
+ name,
+ owner,
+ changeset_revision,
+ prior_installation_required,
+ only_if_compiling_contained_td,
+ repository.id,
+ repository.status ]
if repository.status == trans.install_model.ToolShedRepository.installation_status.INSTALLED:
if new_rd_tup not in installed_rd_tups:
installed_rd_tups.append( new_rd_tup )
@@ -285,12 +290,12 @@
missing_rd_tups.append( new_rd_tup )
else:
new_rd_tup = [ tool_shed,
- name,
- owner,
- changeset_revision,
- prior_installation_required,
- only_if_compiling_contained_td,
- None,
+ name,
+ owner,
+ changeset_revision,
+ prior_installation_required,
+ only_if_compiling_contained_td,
+ None,
'Never installed' ]
if not util.asbool( only_if_compiling_contained_td ):
# A repository dependency that is not installed will not be considered missing if it's value for
@@ -307,11 +312,17 @@
missing_repository_dependencies[ 'description' ] = description
return installed_repository_dependencies, missing_repository_dependencies
-def get_installed_and_missing_tool_dependencies_for_installing_repository( trans, tool_shed_url, tool_dependencies_dict ):
+def get_installed_and_missing_tool_dependencies_for_repository( trans, tool_shed_url, tool_dependencies_dict ):
"""
Return the lists of installed tool dependencies and missing tool dependencies for a set of repositories
being installed into Galaxy.
"""
+ # FIXME: This implementation breaks when updates to a repository contain dependencies that result in
+ # multiple entries for a specific tool dependency. A scenario where this can happen is where 2 repositories
+ # define the same dependency internally (not using the complex repository dependency definition to a separate
+ # package repository approach). If 2 repositories contain the same tool_dependencies.xml file, one dependency
+ # will be lost since the values in these returned dictionaries are not lists. All tool dependency dictionaries
+ # should have lists as values. These scenarios are probably extreme corner cases, but still should be handled.
installed_tool_dependencies = {}
missing_tool_dependencies = {}
if tool_dependencies_dict:
diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 lib/tool_shed/util/container_util.py
--- a/lib/tool_shed/util/container_util.py
+++ b/lib/tool_shed/util/container_util.py
@@ -821,8 +821,8 @@
tool_dependencies = metadata[ 'tool_dependencies' ]
if trans.webapp.name == 'tool_shed':
if 'orphan_tool_dependencies' in metadata:
- # The use of the orphan_tool_dependencies category in metadata has been deprecated, but we still need to check in case
- # the metadata is out of date.
+ # The use of the orphan_tool_dependencies category in metadata has been deprecated,
+ # but we still need to check in case the metadata is out of date.
orphan_tool_dependencies = metadata[ 'orphan_tool_dependencies' ]
tool_dependencies.update( orphan_tool_dependencies )
# Tool dependencies can be categorized as orphans only if the repository contains tools.
diff -r e298d029472150df08bfae9b6ec311c78cb63dfd -r bc739e4b5bdf2a49a7c1a365b1e779df26d0f813 lib/tool_shed/util/encoding_util.py
--- a/lib/tool_shed/util/encoding_util.py
+++ b/lib/tool_shed/util/encoding_util.py
@@ -21,7 +21,6 @@
try:
values = json.loads( value )
except Exception, e:
- #log.debug( "Decoding json value from tool shed for value '%s' threw exception: %s" % ( str( value ), str( e ) ) )
pass
if values is not None:
try:
@@ -34,7 +33,7 @@
return values
def tool_shed_encode( val ):
- if isinstance( val, dict ):
+ if isinstance( val, dict ) or isinstance( val, list ):
value = json.dumps( val )
else:
value = val
This diff is so big that we needed to truncate the remainder.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jmchilton: Fix broken import with workflow PR.
by commits-noreplyï¼ bitbucket.org 26 Mar '14
by commits-noreplyï¼ bitbucket.org 26 Mar '14
26 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8af539a3006b/
Changeset: 8af539a3006b
User: jmchilton
Date: 2014-03-26 22:28:31
Summary: Fix broken import with workflow PR.
Affected #: 1 file
diff -r 46d4a48fcb7b6dd736f081f5d8b650b0a33a296c -r 8af539a3006b24e027215af4f270b5db0d07c5e6 lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -41,7 +41,7 @@
from galaxy.tools.parameters.basic import DataToolParameter
from galaxy.util.json import to_json_string
from galaxy.workflow.modules import ToolModule
-from galaxy.workflow.build_util import attach_ordered_steps
+from galaxy.workflow.steps import attach_ordered_steps
log = logging.getLogger( __name__ )
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/d5d2a3a7e244/
Changeset: d5d2a3a7e244
User: jmchilton
Date: 2014-03-20 16:43:24
Summary: Add dependency on requests 2.2.1.
Will improve and fix bugs in API testing and API driven tests of tools.
Affected #: 1 file
diff -r 215f23b27be962047909c7676fb8a42fa44ea053 -r d5d2a3a7e244a2ff91ca3392729ae7d58c4bb08b eggs.ini
--- a/eggs.ini
+++ b/eggs.ini
@@ -56,6 +56,7 @@
python_openid = 2.2.5
python_daemon = 1.5.5
pytz = 2013.9
+requests = 2.2.1
Routes = 1.12.3
sqlalchemy_migrate = 0.7.2
ssh = 1.7.14
https://bitbucket.org/galaxy/galaxy-central/commits/1996ad824139/
Changeset: 1996ad824139
User: jmchilton
Date: 2014-03-20 16:43:57
Summary: Force use of requests in API tests, eliminate hacked together compatibility layer.
Affected #: 1 file
diff -r d5d2a3a7e244a2ff91ca3392729ae7d58c4bb08b -r 1996ad824139dc5540a2844d90f0cd5cae0b0650 test/base/interactor.py
--- a/test/base/interactor.py
+++ b/test/base/interactor.py
@@ -1,6 +1,8 @@
import os
from StringIO import StringIO
from galaxy.tools.parameters import grouping
+from galaxy import eggs
+eggs.require( "requests" )
from galaxy.util import listify
from galaxy.util.odict import odict
import galaxy.model
@@ -424,104 +426,7 @@
}
-# Lets just try to use requests if it is available, but if not provide fallback
-# on custom implementations of limited requests get, put, etc... functionality.
-try:
- from requests import get as get_request
- from requests import post as post_request
- from requests import put as put_request
- from requests import delete as delete_request
-except ImportError:
- import urllib2
- import httplib
-
- class RequestsLikeResponse( object ):
-
- def __init__( self, content, status_code ):
- self.content = content
- self.status_code = status_code
-
- def json( self ):
- return loads( self.content )
-
- def get_request( url, params={} ):
- argsep = '&'
- if '?' not in url:
- argsep = '?'
- param_pairs = []
- for key, value in params.iteritems():
- # Handle single parameters or lists and tuples of them.
- if isinstance( value, tuple ):
- value = list( value )
- elif not isinstance( value, list ):
- value = [ value ]
- for val in value:
- param_pairs.append( "%s=%s" % ( key, val ) )
- url = url + argsep + '&'.join( param_pairs )
- #req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' } )
- try:
- response = urllib2.urlopen( url )
- return RequestsLikeResponse( response.read(), status_code=response.getcode() )
- except urllib2.HTTPError as e:
- return RequestsLikeResponse( e.read(), status_code=e.code )
-
- def post_request( url, data, files={} ):
- return __multipart_request( url, data, files, verb="POST" )
-
- def put_request( url, data=None ):
- if isinstance( data, dict ):
- assert False, "This test will fail, Galaxy's webob dependency does not parse out urlencoded PUT/PATCH entity data, API will receive empty payload."
- return __urllib_request( url, 'PUT', json_str=data )
-
- def delete_request( url ):
- return __urllib_request( url, 'DELETE' )
-
- def __urllib_request( url, verb, json_str=None ):
- opener = urllib2.build_opener(urllib2.HTTPHandler)
- request = urllib2.Request(url)
- request.get_method = lambda: verb
- if json_str:
- request.add_header( "content-type", "application/json" )
- request.add_data(json_str)
- try:
- response = opener.open(request)
- return RequestsLikeResponse( response.read(), status_code=response.getcode() )
- except urllib2.HTTPError as e:
- return RequestsLikeResponse( e.read(), status_code=e.code )
-
- def __multipart_request( url, data, files={}, verb="POST" ):
- parsed_url = urllib2.urlparse.urlparse( url )
- return __multipart( host=parsed_url.netloc, selector=parsed_url.path, fields=data.iteritems(), files=(files or {}).iteritems(), verb=verb )
-
- # http://stackoverflow.com/a/681182
- def __multipart(host, selector, fields, files, verb="POST"):
- h = httplib.HTTP(host)
- h.putrequest(verb, selector)
- content_type, body = __encode_multipart_formdata(fields, files)
- h.putheader('content-type', content_type)
- h.putheader('content-length', str(len(body)))
- h.endheaders()
- h.send(body)
- errcode, errmsg, headers = h.getreply()
- return RequestsLikeResponse(h.file.read(), status_code=errcode)
-
- def __encode_multipart_formdata(fields, files):
- LIMIT = '----------lImIt_of_THE_fIle_eW_$'
- CRLF = '\r\n'
- L = []
- for (key, value) in fields:
- L.append('--' + LIMIT)
- L.append('Content-Disposition: form-data; name="%s"' % key)
- L.append('')
- L.append(value)
- for (key, value) in files:
- L.append('--' + LIMIT)
- L.append('Content-Disposition: form-data; name="%s"; filename="%s";' % (key, key))
- L.append('Content-Type: application/octet-stream')
- L.append('')
- L.append(value.read())
- L.append('--' + LIMIT + '--')
- L.append('')
- body = CRLF.join(L)
- content_type = 'multipart/form-data; boundary=%s' % LIMIT
- return content_type, body
+from requests import get as get_request
+from requests import post as post_request
+from requests import put as put_request
+from requests import delete as delete_request
https://bitbucket.org/galaxy/galaxy-central/commits/46d4a48fcb7b/
Changeset: 46d4a48fcb7b
User: jmchilton
Date: 2014-03-26 22:22:34
Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #350)
Make requests dependency mandatory for testing
Affected #: 2 files
diff -r 6d0c89fc3558d7185daaa1dbda05e6d15879ff00 -r 46d4a48fcb7b6dd736f081f5d8b650b0a33a296c eggs.ini
--- a/eggs.ini
+++ b/eggs.ini
@@ -56,6 +56,7 @@
python_openid = 2.2.5
python_daemon = 1.5.5
pytz = 2013.9
+requests = 2.2.1
Routes = 1.12.3
sqlalchemy_migrate = 0.7.2
ssh = 1.7.14
diff -r 6d0c89fc3558d7185daaa1dbda05e6d15879ff00 -r 46d4a48fcb7b6dd736f081f5d8b650b0a33a296c test/base/interactor.py
--- a/test/base/interactor.py
+++ b/test/base/interactor.py
@@ -1,6 +1,8 @@
import os
from StringIO import StringIO
from galaxy.tools.parameters import grouping
+from galaxy import eggs
+eggs.require( "requests" )
from galaxy.util import listify
from galaxy.util.odict import odict
import galaxy.model
@@ -424,104 +426,7 @@
}
-# Lets just try to use requests if it is available, but if not provide fallback
-# on custom implementations of limited requests get, put, etc... functionality.
-try:
- from requests import get as get_request
- from requests import post as post_request
- from requests import put as put_request
- from requests import delete as delete_request
-except ImportError:
- import urllib2
- import httplib
-
- class RequestsLikeResponse( object ):
-
- def __init__( self, content, status_code ):
- self.content = content
- self.status_code = status_code
-
- def json( self ):
- return loads( self.content )
-
- def get_request( url, params={} ):
- argsep = '&'
- if '?' not in url:
- argsep = '?'
- param_pairs = []
- for key, value in params.iteritems():
- # Handle single parameters or lists and tuples of them.
- if isinstance( value, tuple ):
- value = list( value )
- elif not isinstance( value, list ):
- value = [ value ]
- for val in value:
- param_pairs.append( "%s=%s" % ( key, val ) )
- url = url + argsep + '&'.join( param_pairs )
- #req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' } )
- try:
- response = urllib2.urlopen( url )
- return RequestsLikeResponse( response.read(), status_code=response.getcode() )
- except urllib2.HTTPError as e:
- return RequestsLikeResponse( e.read(), status_code=e.code )
-
- def post_request( url, data, files={} ):
- return __multipart_request( url, data, files, verb="POST" )
-
- def put_request( url, data=None ):
- if isinstance( data, dict ):
- assert False, "This test will fail, Galaxy's webob dependency does not parse out urlencoded PUT/PATCH entity data, API will receive empty payload."
- return __urllib_request( url, 'PUT', json_str=data )
-
- def delete_request( url ):
- return __urllib_request( url, 'DELETE' )
-
- def __urllib_request( url, verb, json_str=None ):
- opener = urllib2.build_opener(urllib2.HTTPHandler)
- request = urllib2.Request(url)
- request.get_method = lambda: verb
- if json_str:
- request.add_header( "content-type", "application/json" )
- request.add_data(json_str)
- try:
- response = opener.open(request)
- return RequestsLikeResponse( response.read(), status_code=response.getcode() )
- except urllib2.HTTPError as e:
- return RequestsLikeResponse( e.read(), status_code=e.code )
-
- def __multipart_request( url, data, files={}, verb="POST" ):
- parsed_url = urllib2.urlparse.urlparse( url )
- return __multipart( host=parsed_url.netloc, selector=parsed_url.path, fields=data.iteritems(), files=(files or {}).iteritems(), verb=verb )
-
- # http://stackoverflow.com/a/681182
- def __multipart(host, selector, fields, files, verb="POST"):
- h = httplib.HTTP(host)
- h.putrequest(verb, selector)
- content_type, body = __encode_multipart_formdata(fields, files)
- h.putheader('content-type', content_type)
- h.putheader('content-length', str(len(body)))
- h.endheaders()
- h.send(body)
- errcode, errmsg, headers = h.getreply()
- return RequestsLikeResponse(h.file.read(), status_code=errcode)
-
- def __encode_multipart_formdata(fields, files):
- LIMIT = '----------lImIt_of_THE_fIle_eW_$'
- CRLF = '\r\n'
- L = []
- for (key, value) in fields:
- L.append('--' + LIMIT)
- L.append('Content-Disposition: form-data; name="%s"' % key)
- L.append('')
- L.append(value)
- for (key, value) in files:
- L.append('--' + LIMIT)
- L.append('Content-Disposition: form-data; name="%s"; filename="%s";' % (key, key))
- L.append('Content-Type: application/octet-stream')
- L.append('')
- L.append(value.read())
- L.append('--' + LIMIT + '--')
- L.append('')
- body = CRLF.join(L)
- content_type = 'multipart/form-data; boundary=%s' % LIMIT
- return content_type, body
+from requests import get as get_request
+from requests import post as post_request
+from requests import put as put_request
+from requests import delete as delete_request
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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5 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/6c786abce7e2/
Changeset: 6c786abce7e2
User: jmchilton
Date: 2014-03-17 16:44:09
Summary: Start work on stand-alone module for extracting workflows from histories.
In particular, this moves get_job_dict out of workflow controller. I am making big changes to this downstream in dataset collection work so I want unit tests - additionally get_job_dict isn't really a great name for what this becomes - so I am renaming it to summarize.
Affected #: 3 files
diff -r c53fbb2655e2756c8977782df2381d883c5aa8af -r 6c786abce7e2735e80f5f57482f72b57a98a74e7 lib/galaxy/webapps/galaxy/controllers/workflow.py
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -23,7 +23,6 @@
from galaxy.tools.parameters import visit_input_values
from galaxy.tools.parameters.basic import DataToolParameter, DrillDownSelectToolParameter, SelectToolParameter, UnvalidatedValue
from galaxy.tools.parameters.grouping import Conditional, Repeat
-from galaxy.util.odict import odict
from galaxy.util.sanitize_html import sanitize_html
from galaxy.util.topsort import CycleError, topsort, topsort_levels
from galaxy.web import error, url_for
@@ -33,6 +32,7 @@
from galaxy.web.framework.helpers import to_unicode
from galaxy.workflow.modules import module_factory
from galaxy.workflow.run import invoke
+from galaxy.workflow.extract import summarize
class StoredWorkflowListGrid( grids.Grid ):
@@ -1188,7 +1188,7 @@
if not user:
return trans.show_error_message( "Must be logged in to create workflows" )
if ( job_ids is None and dataset_ids is None ) or workflow_name is None:
- jobs, warnings = get_job_dict( trans )
+ jobs, warnings = summarize( trans )
# Render
return trans.fill_template(
"workflow/build_from_current_history.mako",
@@ -1211,7 +1211,7 @@
dataset_ids = [ int( id ) for id in dataset_ids ]
# Find each job, for security we (implicately) check that they are
# associated witha job in the current history.
- jobs, warnings = get_job_dict( trans )
+ jobs, warnings = summarize( trans )
jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() )
steps = []
steps_by_job_id = {}
@@ -1743,48 +1743,6 @@
return None
-class FakeJob( object ):
- """
- Fake job object for datasets that have no creating_job_associations,
- they will be treated as "input" datasets.
- """
- def __init__( self, dataset ):
- self.is_fake = True
- self.id = "fake_%s" % dataset.id
-
-
-def get_job_dict( trans ):
- """
- Return a dictionary of Job -> [ Dataset ] mappings, for all finished
- active Datasets in the current history and the jobs that created them.
- """
- history = trans.get_history()
- # Get the jobs that created the datasets
- warnings = set()
- jobs = odict()
- for dataset in history.active_datasets:
- # FIXME: Create "Dataset.is_finished"
- if dataset.state in ( 'new', 'running', 'queued' ):
- warnings.add( "Some datasets still queued or running were ignored" )
- continue
-
- #if this hda was copied from another, we need to find the job that created the origial hda
- job_hda = dataset
- while job_hda.copied_from_history_dataset_association:
- job_hda = job_hda.copied_from_history_dataset_association
-
- if not job_hda.creating_job_associations:
- jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ]
-
- for assoc in job_hda.creating_job_associations:
- job = assoc.job
- if job in jobs:
- jobs[ job ].append( ( assoc.name, dataset ) )
- else:
- jobs[ job ] = [ ( assoc.name, dataset ) ]
- return jobs, warnings
-
-
def cleanup_param_values( inputs, values ):
"""
Remove 'Data' values from `param_values`, along with metadata cruft,
diff -r c53fbb2655e2756c8977782df2381d883c5aa8af -r 6c786abce7e2735e80f5f57482f72b57a98a74e7 lib/galaxy/workflow/extract.py
--- /dev/null
+++ b/lib/galaxy/workflow/extract.py
@@ -0,0 +1,54 @@
+""" This module contains functionality to aid in extracting workflows from
+histories.
+"""
+from galaxy.util.odict import odict
+
+WARNING_SOME_DATASETS_NOT_READY = "Some datasets still queued or running were ignored"
+
+
+class FakeJob( object ):
+ """
+ Fake job object for datasets that have no creating_job_associations,
+ they will be treated as "input" datasets.
+ """
+ def __init__( self, dataset ):
+ self.is_fake = True
+ self.id = "fake_%s" % dataset.id
+
+
+def summarize( trans, history=None ):
+ """ Return mapping of job description to datasets for active items in
+ supplied history - needed for building workflow from a history.
+
+ Formerly call get_job_dict in workflow web controller.
+ """
+ if not history:
+ history = trans.get_history()
+
+ # Get the jobs that created the datasets
+ warnings = set()
+ jobs = odict()
+ for dataset in history.active_datasets:
+ # FIXME: Create "Dataset.is_finished"
+ if dataset.state in ( 'new', 'running', 'queued' ):
+ warnings.add( WARNING_SOME_DATASETS_NOT_READY )
+ continue
+
+ #if this hda was copied from another, we need to find the job that created the origial hda
+ job_hda = dataset
+ while job_hda.copied_from_history_dataset_association:
+ job_hda = job_hda.copied_from_history_dataset_association
+
+ if not job_hda.creating_job_associations:
+ jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ]
+
+ for assoc in job_hda.creating_job_associations:
+ job = assoc.job
+ if job in jobs:
+ jobs[ job ].append( ( assoc.name, dataset ) )
+ else:
+ jobs[ job ] = [ ( assoc.name, dataset ) ]
+
+ return jobs, warnings
+
+__all__ = [ summarize ]
diff -r c53fbb2655e2756c8977782df2381d883c5aa8af -r 6c786abce7e2735e80f5f57482f72b57a98a74e7 test/unit/workflows/test_extract_summary.py
--- /dev/null
+++ b/test/unit/workflows/test_extract_summary.py
@@ -0,0 +1,98 @@
+import unittest
+
+from galaxy import model
+from galaxy.workflow import extract
+
+UNDEFINED_JOB = object()
+
+
+class TestWorkflowExtractSummary( unittest.TestCase ):
+
+ def setUp( self ):
+ self.history = MockHistory()
+ self.trans = MockTrans( self.history )
+
+ def test_empty_history( self ):
+ job_dict, warnings = extract.summarize( trans=self.trans )
+ assert not warnings
+ assert not job_dict
+
+ def test_summarize_returns_name_and_dataset_list( self ):
+ # Create two jobs and three datasets, test they are groupped
+ # by job correctly with correct output names.
+ hda1 = MockHda()
+ self.history.active_datasets.append( hda1 )
+ hda2 = MockHda( job=hda1.job, output_name="out2" )
+ self.history.active_datasets.append( hda2 )
+ hda3 = MockHda( output_name="out3" )
+ self.history.active_datasets.append( hda3 )
+
+ job_dict, warnings = extract.summarize( trans=self.trans )
+ assert len( job_dict ) == 2
+ assert not warnings
+ self.assertEquals( job_dict[ hda1.job ], [ ( 'out1', hda1 ), ( 'out2', hda2 ) ] )
+ self.assertEquals( job_dict[ hda3.job ], [ ( 'out3', hda3 ) ] )
+
+ def test_finds_original_job_if_copied( self ):
+ hda = MockHda()
+ derived_hda_1 = MockHda()
+ derived_hda_1.copied_from_history_dataset_association = hda
+ derived_hda_2 = MockHda()
+ derived_hda_2.copied_from_history_dataset_association = derived_hda_1
+ self.history.active_datasets.append( derived_hda_2 )
+ job_dict, warnings = extract.summarize( trans=self.trans )
+ assert not warnings
+ assert len( job_dict ) == 1
+ self.assertEquals( job_dict[ hda.job ], [ ('out1', derived_hda_2 ) ] )
+
+ def test_fake_job( self ):
+ """ Fakes job if creating_job_associations is empty.
+ """
+ hda = MockHda( job=UNDEFINED_JOB )
+ self.history.active_datasets.append( hda )
+ job_dict, warnings = extract.summarize( trans=self.trans )
+ assert not warnings
+ assert len( job_dict ) == 1
+ fake_job = job_dict.keys()[ 0 ]
+ assert fake_job.id.startswith( "fake_" )
+ datasets = job_dict.values()[ 0 ]
+ assert datasets == [ ( None, hda ) ]
+
+ def test_warns_and_skips_datasets_if_not_finished( self ):
+ hda = MockHda( state='queued' )
+ self.history.active_datasets.append( hda )
+ job_dict, warnings = extract.summarize( trans=self.trans )
+ assert warnings
+ assert len( job_dict ) == 0
+
+
+class MockHistory( object ):
+
+ def __init__( self ):
+ self.active_datasets = []
+
+
+class MockTrans( object ):
+
+ def __init__( self, history ):
+ self.history = history
+
+ def get_history( self ):
+ return self.history
+
+
+class MockHda( object ):
+
+ def __init__( self, state='ok', output_name='out1', job=None ):
+ self.id = 123
+ self.state = state
+ self.copied_from_history_dataset_association = None
+ if job is not UNDEFINED_JOB:
+ if not job:
+ job = model.Job()
+ self.job = job
+ assoc = model.JobToOutputDatasetAssociation( output_name, self )
+ assoc.job = job
+ self.creating_job_associations = [ assoc ]
+ else:
+ self.creating_job_associations = []
https://bitbucket.org/galaxy/galaxy-central/commits/69e29134e64c/
Changeset: 69e29134e64c
User: jmchilton
Date: 2014-03-17 16:44:09
Summary: Refactor workflow controller step utilities into new module.
This will allow for cleaner reuse outside of web controller, clean up API import of attach_steps accordingly.
Affected #: 3 files
diff -r 6c786abce7e2735e80f5f57482f72b57a98a74e7 -r 69e29134e64c08c09e94a9f69d59329eb2f52107 lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -41,6 +41,7 @@
from galaxy.tools.parameters.basic import DataToolParameter
from galaxy.util.json import to_json_string
from galaxy.workflow.modules import ToolModule
+from galaxy.workflow.build_util import attach_ordered_steps
log = logging.getLogger( __name__ )
@@ -1626,7 +1627,6 @@
"""
Creates a workflow from a dict. Created workflow is stored in the database and returned.
"""
- from galaxy.webapps.galaxy.controllers.workflow import attach_ordered_steps
# Put parameters in workflow mode
trans.workflow_building_mode = True
diff -r 6c786abce7e2735e80f5f57482f72b57a98a74e7 -r 69e29134e64c08c09e94a9f69d59329eb2f52107 lib/galaxy/webapps/galaxy/controllers/workflow.py
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -4,7 +4,6 @@
import base64
import httplib
import json
-import math
import os
import sgmllib
import svgfig
@@ -24,7 +23,6 @@
from galaxy.tools.parameters.basic import DataToolParameter, DrillDownSelectToolParameter, SelectToolParameter, UnvalidatedValue
from galaxy.tools.parameters.grouping import Conditional, Repeat
from galaxy.util.sanitize_html import sanitize_html
-from galaxy.util.topsort import CycleError, topsort, topsort_levels
from galaxy.web import error, url_for
from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin
from galaxy.web.framework import form
@@ -33,6 +31,12 @@
from galaxy.workflow.modules import module_factory
from galaxy.workflow.run import invoke
from galaxy.workflow.extract import summarize
+from galaxy.workflow.steps import (
+ attach_ordered_steps,
+ order_workflow_steps,
+ edgelist_for_workflow_steps,
+ order_workflow_steps_with_levels,
+)
class StoredWorkflowListGrid( grids.Grid ):
@@ -1692,57 +1696,6 @@
## ---- Utility methods -------------------------------------------------------
-def attach_ordered_steps( workflow, steps ):
- ordered_steps = order_workflow_steps( steps )
- if ordered_steps:
- workflow.has_cycles = False
- for i, step in enumerate( ordered_steps ):
- step.order_index = i
- workflow.steps.append( step )
- else:
- workflow.has_cycles = True
- workflow.steps = steps
-
-
-def edgelist_for_workflow_steps( steps ):
- """
- Create a list of tuples representing edges between ``WorkflowSteps`` based
- on associated ``WorkflowStepConnection``s
- """
- edges = []
- steps_to_index = dict( ( step, i ) for i, step in enumerate( steps ) )
- for step in steps:
- edges.append( ( steps_to_index[step], steps_to_index[step] ) )
- for conn in step.input_connections:
- edges.append( ( steps_to_index[conn.output_step], steps_to_index[conn.input_step] ) )
- return edges
-
-
-def order_workflow_steps( steps ):
- """
- Perform topological sort of the steps, return ordered or None
- """
- position_data_available = True
- for step in steps:
- if not step.position or not 'left' in step.position or not 'top' in step.position:
- position_data_available = False
- if position_data_available:
- steps.sort(cmp=lambda s1, s2: cmp( math.sqrt(s1.position['left'] ** 2 + s1.position['top'] ** 2), math.sqrt(s2.position['left'] ** 2 + s2.position['top'] ** 2)))
- try:
- edges = edgelist_for_workflow_steps( steps )
- node_order = topsort( edges )
- return [ steps[i] for i in node_order ]
- except CycleError:
- return None
-
-
-def order_workflow_steps_with_levels( steps ):
- try:
- return topsort_levels( edgelist_for_workflow_steps( steps ) )
- except CycleError:
- return None
-
-
def cleanup_param_values( inputs, values ):
"""
Remove 'Data' values from `param_values`, along with metadata cruft,
diff -r 6c786abce7e2735e80f5f57482f72b57a98a74e7 -r 69e29134e64c08c09e94a9f69d59329eb2f52107 lib/galaxy/workflow/steps.py
--- /dev/null
+++ b/lib/galaxy/workflow/steps.py
@@ -0,0 +1,63 @@
+""" This module contains utility methods for reasoning about and ordering
+workflow steps.
+"""
+import math
+from galaxy.util.topsort import (
+ CycleError,
+ topsort,
+ topsort_levels
+)
+
+
+def attach_ordered_steps( workflow, steps ):
+ """ Attempt to topologically order steps and attach to workflow. If this
+ fails - the workflow contains cycles so it mark it as such.
+ """
+ ordered_steps = order_workflow_steps( steps )
+ if ordered_steps:
+ workflow.has_cycles = False
+ for i, step in enumerate( ordered_steps ):
+ step.order_index = i
+ workflow.steps.append( step )
+ else:
+ workflow.has_cycles = True
+ workflow.steps = steps
+
+
+def order_workflow_steps( steps ):
+ """
+ Perform topological sort of the steps, return ordered or None
+ """
+ position_data_available = True
+ for step in steps:
+ if not step.position or not 'left' in step.position or not 'top' in step.position:
+ position_data_available = False
+ if position_data_available:
+ steps.sort(cmp=lambda s1, s2: cmp( math.sqrt(s1.position['left'] ** 2 + s1.position['top'] ** 2), math.sqrt(s2.position['left'] ** 2 + s2.position['top'] ** 2)))
+ try:
+ edges = edgelist_for_workflow_steps( steps )
+ node_order = topsort( edges )
+ return [ steps[i] for i in node_order ]
+ except CycleError:
+ return None
+
+
+def edgelist_for_workflow_steps( steps ):
+ """
+ Create a list of tuples representing edges between ``WorkflowSteps`` based
+ on associated ``WorkflowStepConnection``s
+ """
+ edges = []
+ steps_to_index = dict( ( step, i ) for i, step in enumerate( steps ) )
+ for step in steps:
+ edges.append( ( steps_to_index[step], steps_to_index[step] ) )
+ for conn in step.input_connections:
+ edges.append( ( steps_to_index[conn.output_step], steps_to_index[conn.input_step] ) )
+ return edges
+
+
+def order_workflow_steps_with_levels( steps ):
+ try:
+ return topsort_levels( edgelist_for_workflow_steps( steps ) )
+ except CycleError:
+ return None
https://bitbucket.org/galaxy/galaxy-central/commits/0eb7631a6d67/
Changeset: 0eb7631a6d67
User: jmchilton
Date: 2014-03-17 16:44:09
Summary: Refactor code for extracting workflow from history into workflow extract module.
Will allow reuse with API controller.
Affected #: 2 files
diff -r 69e29134e64c08c09e94a9f69d59329eb2f52107 -r 0eb7631a6d67317a93b480794d9c4a33a3ceceda lib/galaxy/webapps/galaxy/controllers/workflow.py
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -19,9 +19,8 @@
from galaxy.datatypes.data import Data
from galaxy.model.item_attrs import UsesItemRatings
from galaxy.model.mapping import desc
+from galaxy.tools.parameters.basic import DataToolParameter
from galaxy.tools.parameters import visit_input_values
-from galaxy.tools.parameters.basic import DataToolParameter, DrillDownSelectToolParameter, SelectToolParameter, UnvalidatedValue
-from galaxy.tools.parameters.grouping import Conditional, Repeat
from galaxy.util.sanitize_html import sanitize_html
from galaxy.web import error, url_for
from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin
@@ -31,6 +30,7 @@
from galaxy.workflow.modules import module_factory
from galaxy.workflow.run import invoke
from galaxy.workflow.extract import summarize
+from galaxy.workflow.extract import extract_workflow
from galaxy.workflow.steps import (
attach_ordered_steps,
order_workflow_steps,
@@ -1201,82 +1201,13 @@
history=history
)
else:
- # Ensure job_ids and dataset_ids are lists (possibly empty)
- if job_ids is None:
- job_ids = []
- elif type( job_ids ) is not list:
- job_ids = [ job_ids ]
- if dataset_ids is None:
- dataset_ids = []
- elif type( dataset_ids ) is not list:
- dataset_ids = [ dataset_ids ]
- # Convert both sets of ids to integers
- job_ids = [ int( id ) for id in job_ids ]
- dataset_ids = [ int( id ) for id in dataset_ids ]
- # Find each job, for security we (implicately) check that they are
- # associated witha job in the current history.
- jobs, warnings = summarize( trans )
- jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() )
- steps = []
- steps_by_job_id = {}
- hid_to_output_pair = {}
- # Input dataset steps
- for hid in dataset_ids:
- step = model.WorkflowStep()
- step.type = 'data_input'
- step.tool_inputs = dict( name="Input Dataset" )
- hid_to_output_pair[ hid ] = ( step, 'output' )
- steps.append( step )
- # Tool steps
- for job_id in job_ids:
- assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history"
- job = jobs_by_id[ job_id ]
- tool = trans.app.toolbox.get_tool( job.tool_id )
- param_values = job.get_param_values( trans.app, ignore_errors=True ) # If a tool was updated and e.g. had a text value changed to an integer, we don't want a traceback here
- associations = cleanup_param_values( tool.inputs, param_values )
- step = model.WorkflowStep()
- step.type = 'tool'
- step.tool_id = job.tool_id
- step.tool_inputs = tool.params_to_strings( param_values, trans.app )
- # NOTE: We shouldn't need to do two passes here since only
- # an earlier job can be used as an input to a later
- # job.
- for other_hid, input_name in associations:
- if other_hid in hid_to_output_pair:
- other_step, other_name = hid_to_output_pair[ other_hid ]
- conn = model.WorkflowStepConnection()
- conn.input_step = step
- conn.input_name = input_name
- # Should always be connected to an earlier step
- conn.output_step = other_step
- conn.output_name = other_name
- steps.append( step )
- steps_by_job_id[ job_id ] = step
- # Store created dataset hids
- for assoc in job.output_datasets:
- hid_to_output_pair[ assoc.dataset.hid ] = ( step, assoc.name )
- # Workflow to populate
- workflow = model.Workflow()
- workflow.name = workflow_name
- # Order the steps if possible
- attach_ordered_steps( workflow, steps )
- # And let's try to set up some reasonable locations on the canvas
- # (these are pretty arbitrary values)
- levorder = order_workflow_steps_with_levels( steps )
- base_pos = 10
- for i, steps_at_level in enumerate( levorder ):
- for j, index in enumerate( steps_at_level ):
- step = steps[ index ]
- step.position = dict( top=( base_pos + 120 * j ),
- left=( base_pos + 220 * i ) )
- # Store it
- stored = model.StoredWorkflow()
- stored.user = user
- stored.name = workflow_name
- workflow.stored_workflow = stored
- stored.latest_workflow = workflow
- trans.sa_session.add( stored )
- trans.sa_session.flush()
+ extract_workflow(
+ trans,
+ user=user,
+ job_ids=job_ids,
+ dataset_ids=dataset_ids,
+ workflow_name=workflow_name
+ )
# Index page with message
return trans.show_message( "Workflow '%s' created from current history." % workflow_name )
## return trans.show_ok_message( "<p>Workflow '%s' created.</p><p><a target='_top' href='%s'>Click to load in workflow editor</a></p>"
@@ -1696,55 +1627,6 @@
## ---- Utility methods -------------------------------------------------------
-def cleanup_param_values( inputs, values ):
- """
- Remove 'Data' values from `param_values`, along with metadata cruft,
- but track the associations.
- """
- associations = []
- # dbkey is pushed in by the framework
- if 'dbkey' in values:
- del values['dbkey']
- root_values = values
-
- # Recursively clean data inputs and dynamic selects
- def cleanup( prefix, inputs, values ):
- for key, input in inputs.items():
- if isinstance( input, ( SelectToolParameter, DrillDownSelectToolParameter ) ):
- if input.is_dynamic and not isinstance( values[key], UnvalidatedValue ):
- values[key] = UnvalidatedValue( values[key] )
- if isinstance( input, DataToolParameter ):
- tmp = values[key]
- values[key] = None
- # HACK: Nested associations are not yet working, but we
- # still need to clean them up so we can serialize
- # if not( prefix ):
- if tmp: # this is false for a non-set optional dataset
- if not isinstance(tmp, list):
- associations.append( ( tmp.hid, prefix + key ) )
- else:
- associations.extend( [ (t.hid, prefix + key) for t in tmp] )
-
- # Cleanup the other deprecated crap associated with datasets
- # as well. Worse, for nested datasets all the metadata is
- # being pushed into the root. FIXME: MUST REMOVE SOON
- key = prefix + key + "_"
- for k in root_values.keys():
- if k.startswith( key ):
- del root_values[k]
- elif isinstance( input, Repeat ):
- group_values = values[key]
- for i, rep_values in enumerate( group_values ):
- rep_index = rep_values['__index__']
- cleanup( "%s%s_%d|" % (prefix, key, rep_index ), input.inputs, group_values[i] )
- elif isinstance( input, Conditional ):
- group_values = values[input.name]
- current_case = group_values['__current_case__']
- cleanup( "%s%s|" % ( prefix, key ), input.cases[current_case].inputs, group_values )
- cleanup( "", inputs, values )
- return associations
-
-
def _build_workflow_on_str(instance_ds_names):
# Returns suffix for new histories based on multi input iteration
num_multi_inputs = len(instance_ds_names)
diff -r 69e29134e64c08c09e94a9f69d59329eb2f52107 -r 0eb7631a6d67317a93b480794d9c4a33a3ceceda lib/galaxy/workflow/extract.py
--- a/lib/galaxy/workflow/extract.py
+++ b/lib/galaxy/workflow/extract.py
@@ -2,10 +2,108 @@
histories.
"""
from galaxy.util.odict import odict
+from galaxy import model
+from galaxy.tools.parameters.basic import (
+ DataToolParameter,
+ DrillDownSelectToolParameter,
+ SelectToolParameter,
+ UnvalidatedValue
+)
+from galaxy.tools.parameters.grouping import (
+ Conditional,
+ Repeat
+)
+from .steps import (
+ attach_ordered_steps,
+ order_workflow_steps_with_levels
+)
WARNING_SOME_DATASETS_NOT_READY = "Some datasets still queued or running were ignored"
+def extract_workflow( trans, user, history=None, job_ids=None, dataset_ids=None, workflow_name=None ):
+ steps = extract_steps( trans, history=history, job_ids=job_ids, dataset_ids=dataset_ids )
+ # Workflow to populate
+ workflow = model.Workflow()
+ workflow.name = workflow_name
+ # Order the steps if possible
+ attach_ordered_steps( workflow, steps )
+ # And let's try to set up some reasonable locations on the canvas
+ # (these are pretty arbitrary values)
+ levorder = order_workflow_steps_with_levels( steps )
+ base_pos = 10
+ for i, steps_at_level in enumerate( levorder ):
+ for j, index in enumerate( steps_at_level ):
+ step = steps[ index ]
+ step.position = dict( top=( base_pos + 120 * j ),
+ left=( base_pos + 220 * i ) )
+ # Store it
+ stored = model.StoredWorkflow()
+ stored.user = user
+ stored.name = workflow_name
+ workflow.stored_workflow = stored
+ stored.latest_workflow = workflow
+ trans.sa_session.add( stored )
+ trans.sa_session.flush()
+ return stored
+
+
+def extract_steps( trans, history=None, job_ids=None, dataset_ids=None ):
+ # Ensure job_ids and dataset_ids are lists (possibly empty)
+ if job_ids is None:
+ job_ids = []
+ elif type( job_ids ) is not list:
+ job_ids = [ job_ids ]
+ if dataset_ids is None:
+ dataset_ids = []
+ elif type( dataset_ids ) is not list:
+ dataset_ids = [ dataset_ids ]
+ # Convert both sets of ids to integers
+ job_ids = [ int( id ) for id in job_ids ]
+ dataset_ids = [ int( id ) for id in dataset_ids ]
+ # Find each job, for security we (implicately) check that they are
+ # associated witha job in the current history.
+ jobs, warnings = summarize( trans, history=history )
+ jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() )
+ steps = []
+ steps_by_job_id = {}
+ hid_to_output_pair = {}
+ # Input dataset steps
+ for hid in dataset_ids:
+ step = model.WorkflowStep()
+ step.type = 'data_input'
+ step.tool_inputs = dict( name="Input Dataset" )
+ hid_to_output_pair[ hid ] = ( step, 'output' )
+ steps.append( step )
+ # Tool steps
+ for job_id in job_ids:
+ assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history"
+ job = jobs_by_id[ job_id ]
+ tool_inputs, associations = step_inputs( trans, job )
+ step = model.WorkflowStep()
+ step.type = 'tool'
+ step.tool_id = job.tool_id
+ step.tool_inputs = tool_inputs
+ # NOTE: We shouldn't need to do two passes here since only
+ # an earlier job can be used as an input to a later
+ # job.
+ for other_hid, input_name in associations:
+ if other_hid in hid_to_output_pair:
+ other_step, other_name = hid_to_output_pair[ other_hid ]
+ conn = model.WorkflowStepConnection()
+ conn.input_step = step
+ conn.input_name = input_name
+ # Should always be connected to an earlier step
+ conn.output_step = other_step
+ conn.output_name = other_name
+ steps.append( step )
+ steps_by_job_id[ job_id ] = step
+ # Store created dataset hids
+ for assoc in job.output_datasets:
+ hid_to_output_pair[ assoc.dataset.hid ] = ( step, assoc.name )
+ return steps
+
+
class FakeJob( object ):
"""
Fake job object for datasets that have no creating_job_associations,
@@ -51,4 +149,61 @@
return jobs, warnings
-__all__ = [ summarize ]
+
+def step_inputs( trans, job ):
+ tool = trans.app.toolbox.get_tool( job.tool_id )
+ param_values = job.get_param_values( trans.app, ignore_errors=True ) # If a tool was updated and e.g. had a text value changed to an integer, we don't want a traceback here
+ associations = __cleanup_param_values( tool.inputs, param_values )
+ tool_inputs = tool.params_to_strings( param_values, trans.app )
+ return tool_inputs, associations
+
+
+def __cleanup_param_values( inputs, values ):
+ """
+ Remove 'Data' values from `param_values`, along with metadata cruft,
+ but track the associations.
+ """
+ associations = []
+ # dbkey is pushed in by the framework
+ if 'dbkey' in values:
+ del values['dbkey']
+ root_values = values
+
+ # Recursively clean data inputs and dynamic selects
+ def cleanup( prefix, inputs, values ):
+ for key, input in inputs.items():
+ if isinstance( input, ( SelectToolParameter, DrillDownSelectToolParameter ) ):
+ if input.is_dynamic and not isinstance( values[key], UnvalidatedValue ):
+ values[key] = UnvalidatedValue( values[key] )
+ if isinstance( input, DataToolParameter ):
+ tmp = values[key]
+ values[key] = None
+ # HACK: Nested associations are not yet working, but we
+ # still need to clean them up so we can serialize
+ # if not( prefix ):
+ if tmp: # this is false for a non-set optional dataset
+ if not isinstance(tmp, list):
+ associations.append( ( tmp.hid, prefix + key ) )
+ else:
+ associations.extend( [ (t.hid, prefix + key) for t in tmp] )
+
+ # Cleanup the other deprecated crap associated with datasets
+ # as well. Worse, for nested datasets all the metadata is
+ # being pushed into the root. FIXME: MUST REMOVE SOON
+ key = prefix + key + "_"
+ for k in root_values.keys():
+ if k.startswith( key ):
+ del root_values[k]
+ elif isinstance( input, Repeat ):
+ group_values = values[key]
+ for i, rep_values in enumerate( group_values ):
+ rep_index = rep_values['__index__']
+ cleanup( "%s%s_%d|" % (prefix, key, rep_index ), input.inputs, group_values[i] )
+ elif isinstance( input, Conditional ):
+ group_values = values[input.name]
+ current_case = group_values['__current_case__']
+ cleanup( "%s%s|" % ( prefix, key ), input.cases[current_case].inputs, group_values )
+ cleanup( "", inputs, values )
+ return associations
+
+__all__ = [ summarize, extract_workflow ]
https://bitbucket.org/galaxy/galaxy-central/commits/17a2dc7d3902/
Changeset: 17a2dc7d3902
User: jmchilton
Date: 2014-03-17 16:44:09
Summary: Add ability to extract workflow from a history to workflows API.
Affected #: 2 files
diff -r 0eb7631a6d67317a93b480794d9c4a33a3ceceda -r 17a2dc7d39027d97a4185adbd03944b4bb1642cf lib/galaxy/webapps/galaxy/api/workflows.py
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -11,8 +11,10 @@
from galaxy import web
from galaxy.web import _future_expose_api as expose_api
from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin
+from galaxy.web.base.controller import UsesHistoryMixin
from galaxy.workflow.modules import module_factory
from galaxy.workflow.run import invoke
+from galaxy.workflow.extract import extract_workflow
log = logging.getLogger(__name__)
@@ -51,7 +53,7 @@
step.state.inputs.update(param_dict)
-class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin):
+class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin):
@web.expose_api
def index(self, trans, **kwd):
@@ -141,9 +143,11 @@
"""
POST /api/workflows
- We're not creating workflows from the api. Just execute for now.
+ Run or create workflows from the api.
- However, we will import them if installed_repository_file is specified.
+ If installed_repository_file or from_history_id is specified a new
+ workflow will be created for this user. Otherwise, workflow_id must be
+ specified and this API method will cause a workflow to execute.
:param installed_repository_file The path of a workflow to import. Either workflow_id or installed_repository_file must be specified
:type installed_repository_file str
@@ -165,6 +169,15 @@
:param replacement_params: A dictionary used when renaming datasets
:type replacement_params: dict
+
+ :param from_history_id: Id of history to extract a workflow from. Should not be used with worfklow_id or installed_repository_file.
+ :type from_history_id: str
+
+ :param job_ids: If from_history_id is set - this should be a list of jobs to include when extracting workflow from history.
+ :type job_ids: str
+
+ :param dataset_ids: If from_history_id is set - this should be a list of HDA ids corresponding to workflow inputs when extracting workflow from history.
+ :type dataset_ids: str
"""
# Pull parameters out of payload.
@@ -183,6 +196,24 @@
cntrller='api',
**payload)
return result
+ if 'from_history_id' in payload:
+ from_history_id = payload.get( 'from_history_id' )
+ history = self.get_history( trans, from_history_id, check_ownership=False, check_accessible=True )
+ job_ids = map( trans.security.decode_id, payload.get( "job_ids", [] ) )
+ dataset_ids = map( trans.security.decode_id, payload.get( "dataset_ids", [] ) )
+ workflow_name = payload[ "workflow_name" ]
+ stored_workflow = extract_workflow(
+ trans=trans,
+ user=trans.get_user(),
+ history=history,
+ job_ids=job_ids,
+ dataset_ids=dataset_ids,
+ workflow_name=workflow_name,
+ )
+ item = stored_workflow.to_dict( value_mapper={ "id": trans.security.encode_id } )
+ item[ 'url' ] = url_for( 'workflow', id=item[ "id" ] )
+ return item
+
trans.response.status = 403
return "Either workflow_id or installed_repository_file must be specified"
if 'installed_repository_file' in payload:
diff -r 0eb7631a6d67317a93b480794d9c4a33a3ceceda -r 17a2dc7d39027d97a4185adbd03944b4bb1642cf test/functional/api/test_workflows.py
--- a/test/functional/api/test_workflows.py
+++ b/test/functional/api/test_workflows.py
@@ -67,6 +67,39 @@
self._assert_status_code_is( run_workflow_response, 200 )
self._wait_for_history( history_id, assert_ok=True )
+ def test_extract_from_history( self ):
+ workflow = self.workflow_populator.load_workflow( name="test_for_extract" )
+ workflow_request, history_id = self._setup_workflow_run( workflow )
+ contents_response = self._get( "histories/%s/contents" % history_id )
+ self._assert_status_code_is( contents_response, 200 )
+ hda_ids = map( lambda c: c[ "id" ], contents_response.json() )
+
+ run_workflow_response = self._post( "workflows", data=workflow_request )
+ self._assert_status_code_is( run_workflow_response, 200 )
+
+ self._wait_for_history( history_id, assert_ok=True )
+ data = dict( history_id=history_id, tool_id="cat1" )
+ jobs_response = self._get( "jobs", data=data )
+ self._assert_status_code_is( jobs_response, 200 )
+ cat1_job_id = jobs_response.json()[ 0 ][ "id" ]
+
+ contents_response = self._get( "history/%s/contents", data=data )
+ create_from_data = dict(
+ from_history_id=history_id,
+ dataset_ids=dumps( hda_ids ),
+ job_ids=dumps( [ cat1_job_id ] ),
+ workflow_name="test import from history",
+ )
+ run_workflow_response = self._post( "workflows", data=create_from_data )
+ self._assert_status_code_is( run_workflow_response, 200 )
+
+ new_workflow_id = run_workflow_response.json()[ "id" ]
+ download_response = self._get( "workflows/%s/download" % new_workflow_id )
+ self._assert_status_code_is( download_response, 200 )
+ downloaded_workflow = download_response.json()
+ self.assertEquals( downloaded_workflow[ "name" ], "test import from history" )
+ assert len( downloaded_workflow[ "steps" ] ) == 3
+
def test_run_replace_params_by_tool( self ):
workflow_request, history_id = self._setup_random_x2_workflow( "test_for_replace_tool_params" )
workflow_request[ "parameters" ] = dumps( dict( random_lines1=dict( num_lines=5 ) ) )
https://bitbucket.org/galaxy/galaxy-central/commits/6d0c89fc3558/
Changeset: 6d0c89fc3558
User: jmchilton
Date: 2014-03-26 22:21:15
Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #348)
Enhance workflows API to allow extracting workflow from history.
Affected #: 7 files
diff -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 -r 6d0c89fc3558d7185daaa1dbda05e6d15879ff00 lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -41,6 +41,7 @@
from galaxy.tools.parameters.basic import DataToolParameter
from galaxy.util.json import to_json_string
from galaxy.workflow.modules import ToolModule
+from galaxy.workflow.build_util import attach_ordered_steps
log = logging.getLogger( __name__ )
@@ -1676,7 +1677,6 @@
"""
Creates a workflow from a dict. Created workflow is stored in the database and returned.
"""
- from galaxy.webapps.galaxy.controllers.workflow import attach_ordered_steps
# Put parameters in workflow mode
trans.workflow_building_mode = True
diff -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 -r 6d0c89fc3558d7185daaa1dbda05e6d15879ff00 lib/galaxy/webapps/galaxy/api/workflows.py
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -11,8 +11,10 @@
from galaxy import web
from galaxy.web import _future_expose_api as expose_api
from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin
+from galaxy.web.base.controller import UsesHistoryMixin
from galaxy.workflow.modules import module_factory
from galaxy.workflow.run import invoke
+from galaxy.workflow.extract import extract_workflow
log = logging.getLogger(__name__)
@@ -51,7 +53,7 @@
step.state.inputs.update(param_dict)
-class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin):
+class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesHistoryMixin):
@web.expose_api
def index(self, trans, **kwd):
@@ -141,9 +143,11 @@
"""
POST /api/workflows
- We're not creating workflows from the api. Just execute for now.
+ Run or create workflows from the api.
- However, we will import them if installed_repository_file is specified.
+ If installed_repository_file or from_history_id is specified a new
+ workflow will be created for this user. Otherwise, workflow_id must be
+ specified and this API method will cause a workflow to execute.
:param installed_repository_file The path of a workflow to import. Either workflow_id or installed_repository_file must be specified
:type installed_repository_file str
@@ -165,6 +169,15 @@
:param replacement_params: A dictionary used when renaming datasets
:type replacement_params: dict
+
+ :param from_history_id: Id of history to extract a workflow from. Should not be used with worfklow_id or installed_repository_file.
+ :type from_history_id: str
+
+ :param job_ids: If from_history_id is set - this should be a list of jobs to include when extracting workflow from history.
+ :type job_ids: str
+
+ :param dataset_ids: If from_history_id is set - this should be a list of HDA ids corresponding to workflow inputs when extracting workflow from history.
+ :type dataset_ids: str
"""
# Pull parameters out of payload.
@@ -183,6 +196,24 @@
cntrller='api',
**payload)
return result
+ if 'from_history_id' in payload:
+ from_history_id = payload.get( 'from_history_id' )
+ history = self.get_history( trans, from_history_id, check_ownership=False, check_accessible=True )
+ job_ids = map( trans.security.decode_id, payload.get( "job_ids", [] ) )
+ dataset_ids = map( trans.security.decode_id, payload.get( "dataset_ids", [] ) )
+ workflow_name = payload[ "workflow_name" ]
+ stored_workflow = extract_workflow(
+ trans=trans,
+ user=trans.get_user(),
+ history=history,
+ job_ids=job_ids,
+ dataset_ids=dataset_ids,
+ workflow_name=workflow_name,
+ )
+ item = stored_workflow.to_dict( value_mapper={ "id": trans.security.encode_id } )
+ item[ 'url' ] = url_for( 'workflow', id=item[ "id" ] )
+ return item
+
trans.response.status = 403
return "Either workflow_id or installed_repository_file must be specified"
if 'installed_repository_file' in payload:
diff -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 -r 6d0c89fc3558d7185daaa1dbda05e6d15879ff00 lib/galaxy/webapps/galaxy/controllers/workflow.py
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -4,7 +4,6 @@
import base64
import httplib
import json
-import math
import os
import sgmllib
import svgfig
@@ -20,12 +19,9 @@
from galaxy.datatypes.data import Data
from galaxy.model.item_attrs import UsesItemRatings
from galaxy.model.mapping import desc
+from galaxy.tools.parameters.basic import DataToolParameter
from galaxy.tools.parameters import visit_input_values
-from galaxy.tools.parameters.basic import DataToolParameter, DrillDownSelectToolParameter, SelectToolParameter, UnvalidatedValue
-from galaxy.tools.parameters.grouping import Conditional, Repeat
-from galaxy.util.odict import odict
from galaxy.util.sanitize_html import sanitize_html
-from galaxy.util.topsort import CycleError, topsort, topsort_levels
from galaxy.web import error, url_for
from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin
from galaxy.web.framework import form
@@ -33,6 +29,14 @@
from galaxy.web.framework.helpers import to_unicode
from galaxy.workflow.modules import module_factory
from galaxy.workflow.run import invoke
+from galaxy.workflow.extract import summarize
+from galaxy.workflow.extract import extract_workflow
+from galaxy.workflow.steps import (
+ attach_ordered_steps,
+ order_workflow_steps,
+ edgelist_for_workflow_steps,
+ order_workflow_steps_with_levels,
+)
class StoredWorkflowListGrid( grids.Grid ):
@@ -1188,7 +1192,7 @@
if not user:
return trans.show_error_message( "Must be logged in to create workflows" )
if ( job_ids is None and dataset_ids is None ) or workflow_name is None:
- jobs, warnings = get_job_dict( trans )
+ jobs, warnings = summarize( trans )
# Render
return trans.fill_template(
"workflow/build_from_current_history.mako",
@@ -1197,82 +1201,13 @@
history=history
)
else:
- # Ensure job_ids and dataset_ids are lists (possibly empty)
- if job_ids is None:
- job_ids = []
- elif type( job_ids ) is not list:
- job_ids = [ job_ids ]
- if dataset_ids is None:
- dataset_ids = []
- elif type( dataset_ids ) is not list:
- dataset_ids = [ dataset_ids ]
- # Convert both sets of ids to integers
- job_ids = [ int( id ) for id in job_ids ]
- dataset_ids = [ int( id ) for id in dataset_ids ]
- # Find each job, for security we (implicately) check that they are
- # associated witha job in the current history.
- jobs, warnings = get_job_dict( trans )
- jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() )
- steps = []
- steps_by_job_id = {}
- hid_to_output_pair = {}
- # Input dataset steps
- for hid in dataset_ids:
- step = model.WorkflowStep()
- step.type = 'data_input'
- step.tool_inputs = dict( name="Input Dataset" )
- hid_to_output_pair[ hid ] = ( step, 'output' )
- steps.append( step )
- # Tool steps
- for job_id in job_ids:
- assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history"
- job = jobs_by_id[ job_id ]
- tool = trans.app.toolbox.get_tool( job.tool_id )
- param_values = job.get_param_values( trans.app, ignore_errors=True ) # If a tool was updated and e.g. had a text value changed to an integer, we don't want a traceback here
- associations = cleanup_param_values( tool.inputs, param_values )
- step = model.WorkflowStep()
- step.type = 'tool'
- step.tool_id = job.tool_id
- step.tool_inputs = tool.params_to_strings( param_values, trans.app )
- # NOTE: We shouldn't need to do two passes here since only
- # an earlier job can be used as an input to a later
- # job.
- for other_hid, input_name in associations:
- if other_hid in hid_to_output_pair:
- other_step, other_name = hid_to_output_pair[ other_hid ]
- conn = model.WorkflowStepConnection()
- conn.input_step = step
- conn.input_name = input_name
- # Should always be connected to an earlier step
- conn.output_step = other_step
- conn.output_name = other_name
- steps.append( step )
- steps_by_job_id[ job_id ] = step
- # Store created dataset hids
- for assoc in job.output_datasets:
- hid_to_output_pair[ assoc.dataset.hid ] = ( step, assoc.name )
- # Workflow to populate
- workflow = model.Workflow()
- workflow.name = workflow_name
- # Order the steps if possible
- attach_ordered_steps( workflow, steps )
- # And let's try to set up some reasonable locations on the canvas
- # (these are pretty arbitrary values)
- levorder = order_workflow_steps_with_levels( steps )
- base_pos = 10
- for i, steps_at_level in enumerate( levorder ):
- for j, index in enumerate( steps_at_level ):
- step = steps[ index ]
- step.position = dict( top=( base_pos + 120 * j ),
- left=( base_pos + 220 * i ) )
- # Store it
- stored = model.StoredWorkflow()
- stored.user = user
- stored.name = workflow_name
- workflow.stored_workflow = stored
- stored.latest_workflow = workflow
- trans.sa_session.add( stored )
- trans.sa_session.flush()
+ extract_workflow(
+ trans,
+ user=user,
+ job_ids=job_ids,
+ dataset_ids=dataset_ids,
+ workflow_name=workflow_name
+ )
# Index page with message
return trans.show_message( "Workflow '%s' created from current history." % workflow_name )
## return trans.show_ok_message( "<p>Workflow '%s' created.</p><p><a target='_top' href='%s'>Click to load in workflow editor</a></p>"
@@ -1692,148 +1627,6 @@
## ---- Utility methods -------------------------------------------------------
-def attach_ordered_steps( workflow, steps ):
- ordered_steps = order_workflow_steps( steps )
- if ordered_steps:
- workflow.has_cycles = False
- for i, step in enumerate( ordered_steps ):
- step.order_index = i
- workflow.steps.append( step )
- else:
- workflow.has_cycles = True
- workflow.steps = steps
-
-
-def edgelist_for_workflow_steps( steps ):
- """
- Create a list of tuples representing edges between ``WorkflowSteps`` based
- on associated ``WorkflowStepConnection``s
- """
- edges = []
- steps_to_index = dict( ( step, i ) for i, step in enumerate( steps ) )
- for step in steps:
- edges.append( ( steps_to_index[step], steps_to_index[step] ) )
- for conn in step.input_connections:
- edges.append( ( steps_to_index[conn.output_step], steps_to_index[conn.input_step] ) )
- return edges
-
-
-def order_workflow_steps( steps ):
- """
- Perform topological sort of the steps, return ordered or None
- """
- position_data_available = True
- for step in steps:
- if not step.position or not 'left' in step.position or not 'top' in step.position:
- position_data_available = False
- if position_data_available:
- steps.sort(cmp=lambda s1, s2: cmp( math.sqrt(s1.position['left'] ** 2 + s1.position['top'] ** 2), math.sqrt(s2.position['left'] ** 2 + s2.position['top'] ** 2)))
- try:
- edges = edgelist_for_workflow_steps( steps )
- node_order = topsort( edges )
- return [ steps[i] for i in node_order ]
- except CycleError:
- return None
-
-
-def order_workflow_steps_with_levels( steps ):
- try:
- return topsort_levels( edgelist_for_workflow_steps( steps ) )
- except CycleError:
- return None
-
-
-class FakeJob( object ):
- """
- Fake job object for datasets that have no creating_job_associations,
- they will be treated as "input" datasets.
- """
- def __init__( self, dataset ):
- self.is_fake = True
- self.id = "fake_%s" % dataset.id
-
-
-def get_job_dict( trans ):
- """
- Return a dictionary of Job -> [ Dataset ] mappings, for all finished
- active Datasets in the current history and the jobs that created them.
- """
- history = trans.get_history()
- # Get the jobs that created the datasets
- warnings = set()
- jobs = odict()
- for dataset in history.active_datasets:
- # FIXME: Create "Dataset.is_finished"
- if dataset.state in ( 'new', 'running', 'queued' ):
- warnings.add( "Some datasets still queued or running were ignored" )
- continue
-
- #if this hda was copied from another, we need to find the job that created the origial hda
- job_hda = dataset
- while job_hda.copied_from_history_dataset_association:
- job_hda = job_hda.copied_from_history_dataset_association
-
- if not job_hda.creating_job_associations:
- jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ]
-
- for assoc in job_hda.creating_job_associations:
- job = assoc.job
- if job in jobs:
- jobs[ job ].append( ( assoc.name, dataset ) )
- else:
- jobs[ job ] = [ ( assoc.name, dataset ) ]
- return jobs, warnings
-
-
-def cleanup_param_values( inputs, values ):
- """
- Remove 'Data' values from `param_values`, along with metadata cruft,
- but track the associations.
- """
- associations = []
- # dbkey is pushed in by the framework
- if 'dbkey' in values:
- del values['dbkey']
- root_values = values
-
- # Recursively clean data inputs and dynamic selects
- def cleanup( prefix, inputs, values ):
- for key, input in inputs.items():
- if isinstance( input, ( SelectToolParameter, DrillDownSelectToolParameter ) ):
- if input.is_dynamic and not isinstance( values[key], UnvalidatedValue ):
- values[key] = UnvalidatedValue( values[key] )
- if isinstance( input, DataToolParameter ):
- tmp = values[key]
- values[key] = None
- # HACK: Nested associations are not yet working, but we
- # still need to clean them up so we can serialize
- # if not( prefix ):
- if tmp: # this is false for a non-set optional dataset
- if not isinstance(tmp, list):
- associations.append( ( tmp.hid, prefix + key ) )
- else:
- associations.extend( [ (t.hid, prefix + key) for t in tmp] )
-
- # Cleanup the other deprecated crap associated with datasets
- # as well. Worse, for nested datasets all the metadata is
- # being pushed into the root. FIXME: MUST REMOVE SOON
- key = prefix + key + "_"
- for k in root_values.keys():
- if k.startswith( key ):
- del root_values[k]
- elif isinstance( input, Repeat ):
- group_values = values[key]
- for i, rep_values in enumerate( group_values ):
- rep_index = rep_values['__index__']
- cleanup( "%s%s_%d|" % (prefix, key, rep_index ), input.inputs, group_values[i] )
- elif isinstance( input, Conditional ):
- group_values = values[input.name]
- current_case = group_values['__current_case__']
- cleanup( "%s%s|" % ( prefix, key ), input.cases[current_case].inputs, group_values )
- cleanup( "", inputs, values )
- return associations
-
-
def _build_workflow_on_str(instance_ds_names):
# Returns suffix for new histories based on multi input iteration
num_multi_inputs = len(instance_ds_names)
diff -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 -r 6d0c89fc3558d7185daaa1dbda05e6d15879ff00 lib/galaxy/workflow/extract.py
--- /dev/null
+++ b/lib/galaxy/workflow/extract.py
@@ -0,0 +1,209 @@
+""" This module contains functionality to aid in extracting workflows from
+histories.
+"""
+from galaxy.util.odict import odict
+from galaxy import model
+from galaxy.tools.parameters.basic import (
+ DataToolParameter,
+ DrillDownSelectToolParameter,
+ SelectToolParameter,
+ UnvalidatedValue
+)
+from galaxy.tools.parameters.grouping import (
+ Conditional,
+ Repeat
+)
+from .steps import (
+ attach_ordered_steps,
+ order_workflow_steps_with_levels
+)
+
+WARNING_SOME_DATASETS_NOT_READY = "Some datasets still queued or running were ignored"
+
+
+def extract_workflow( trans, user, history=None, job_ids=None, dataset_ids=None, workflow_name=None ):
+ steps = extract_steps( trans, history=history, job_ids=job_ids, dataset_ids=dataset_ids )
+ # Workflow to populate
+ workflow = model.Workflow()
+ workflow.name = workflow_name
+ # Order the steps if possible
+ attach_ordered_steps( workflow, steps )
+ # And let's try to set up some reasonable locations on the canvas
+ # (these are pretty arbitrary values)
+ levorder = order_workflow_steps_with_levels( steps )
+ base_pos = 10
+ for i, steps_at_level in enumerate( levorder ):
+ for j, index in enumerate( steps_at_level ):
+ step = steps[ index ]
+ step.position = dict( top=( base_pos + 120 * j ),
+ left=( base_pos + 220 * i ) )
+ # Store it
+ stored = model.StoredWorkflow()
+ stored.user = user
+ stored.name = workflow_name
+ workflow.stored_workflow = stored
+ stored.latest_workflow = workflow
+ trans.sa_session.add( stored )
+ trans.sa_session.flush()
+ return stored
+
+
+def extract_steps( trans, history=None, job_ids=None, dataset_ids=None ):
+ # Ensure job_ids and dataset_ids are lists (possibly empty)
+ if job_ids is None:
+ job_ids = []
+ elif type( job_ids ) is not list:
+ job_ids = [ job_ids ]
+ if dataset_ids is None:
+ dataset_ids = []
+ elif type( dataset_ids ) is not list:
+ dataset_ids = [ dataset_ids ]
+ # Convert both sets of ids to integers
+ job_ids = [ int( id ) for id in job_ids ]
+ dataset_ids = [ int( id ) for id in dataset_ids ]
+ # Find each job, for security we (implicately) check that they are
+ # associated witha job in the current history.
+ jobs, warnings = summarize( trans, history=history )
+ jobs_by_id = dict( ( job.id, job ) for job in jobs.keys() )
+ steps = []
+ steps_by_job_id = {}
+ hid_to_output_pair = {}
+ # Input dataset steps
+ for hid in dataset_ids:
+ step = model.WorkflowStep()
+ step.type = 'data_input'
+ step.tool_inputs = dict( name="Input Dataset" )
+ hid_to_output_pair[ hid ] = ( step, 'output' )
+ steps.append( step )
+ # Tool steps
+ for job_id in job_ids:
+ assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history"
+ job = jobs_by_id[ job_id ]
+ tool_inputs, associations = step_inputs( trans, job )
+ step = model.WorkflowStep()
+ step.type = 'tool'
+ step.tool_id = job.tool_id
+ step.tool_inputs = tool_inputs
+ # NOTE: We shouldn't need to do two passes here since only
+ # an earlier job can be used as an input to a later
+ # job.
+ for other_hid, input_name in associations:
+ if other_hid in hid_to_output_pair:
+ other_step, other_name = hid_to_output_pair[ other_hid ]
+ conn = model.WorkflowStepConnection()
+ conn.input_step = step
+ conn.input_name = input_name
+ # Should always be connected to an earlier step
+ conn.output_step = other_step
+ conn.output_name = other_name
+ steps.append( step )
+ steps_by_job_id[ job_id ] = step
+ # Store created dataset hids
+ for assoc in job.output_datasets:
+ hid_to_output_pair[ assoc.dataset.hid ] = ( step, assoc.name )
+ return steps
+
+
+class FakeJob( object ):
+ """
+ Fake job object for datasets that have no creating_job_associations,
+ they will be treated as "input" datasets.
+ """
+ def __init__( self, dataset ):
+ self.is_fake = True
+ self.id = "fake_%s" % dataset.id
+
+
+def summarize( trans, history=None ):
+ """ Return mapping of job description to datasets for active items in
+ supplied history - needed for building workflow from a history.
+
+ Formerly call get_job_dict in workflow web controller.
+ """
+ if not history:
+ history = trans.get_history()
+
+ # Get the jobs that created the datasets
+ warnings = set()
+ jobs = odict()
+ for dataset in history.active_datasets:
+ # FIXME: Create "Dataset.is_finished"
+ if dataset.state in ( 'new', 'running', 'queued' ):
+ warnings.add( WARNING_SOME_DATASETS_NOT_READY )
+ continue
+
+ #if this hda was copied from another, we need to find the job that created the origial hda
+ job_hda = dataset
+ while job_hda.copied_from_history_dataset_association:
+ job_hda = job_hda.copied_from_history_dataset_association
+
+ if not job_hda.creating_job_associations:
+ jobs[ FakeJob( dataset ) ] = [ ( None, dataset ) ]
+
+ for assoc in job_hda.creating_job_associations:
+ job = assoc.job
+ if job in jobs:
+ jobs[ job ].append( ( assoc.name, dataset ) )
+ else:
+ jobs[ job ] = [ ( assoc.name, dataset ) ]
+
+ return jobs, warnings
+
+
+def step_inputs( trans, job ):
+ tool = trans.app.toolbox.get_tool( job.tool_id )
+ param_values = job.get_param_values( trans.app, ignore_errors=True ) # If a tool was updated and e.g. had a text value changed to an integer, we don't want a traceback here
+ associations = __cleanup_param_values( tool.inputs, param_values )
+ tool_inputs = tool.params_to_strings( param_values, trans.app )
+ return tool_inputs, associations
+
+
+def __cleanup_param_values( inputs, values ):
+ """
+ Remove 'Data' values from `param_values`, along with metadata cruft,
+ but track the associations.
+ """
+ associations = []
+ # dbkey is pushed in by the framework
+ if 'dbkey' in values:
+ del values['dbkey']
+ root_values = values
+
+ # Recursively clean data inputs and dynamic selects
+ def cleanup( prefix, inputs, values ):
+ for key, input in inputs.items():
+ if isinstance( input, ( SelectToolParameter, DrillDownSelectToolParameter ) ):
+ if input.is_dynamic and not isinstance( values[key], UnvalidatedValue ):
+ values[key] = UnvalidatedValue( values[key] )
+ if isinstance( input, DataToolParameter ):
+ tmp = values[key]
+ values[key] = None
+ # HACK: Nested associations are not yet working, but we
+ # still need to clean them up so we can serialize
+ # if not( prefix ):
+ if tmp: # this is false for a non-set optional dataset
+ if not isinstance(tmp, list):
+ associations.append( ( tmp.hid, prefix + key ) )
+ else:
+ associations.extend( [ (t.hid, prefix + key) for t in tmp] )
+
+ # Cleanup the other deprecated crap associated with datasets
+ # as well. Worse, for nested datasets all the metadata is
+ # being pushed into the root. FIXME: MUST REMOVE SOON
+ key = prefix + key + "_"
+ for k in root_values.keys():
+ if k.startswith( key ):
+ del root_values[k]
+ elif isinstance( input, Repeat ):
+ group_values = values[key]
+ for i, rep_values in enumerate( group_values ):
+ rep_index = rep_values['__index__']
+ cleanup( "%s%s_%d|" % (prefix, key, rep_index ), input.inputs, group_values[i] )
+ elif isinstance( input, Conditional ):
+ group_values = values[input.name]
+ current_case = group_values['__current_case__']
+ cleanup( "%s%s|" % ( prefix, key ), input.cases[current_case].inputs, group_values )
+ cleanup( "", inputs, values )
+ return associations
+
+__all__ = [ summarize, extract_workflow ]
diff -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 -r 6d0c89fc3558d7185daaa1dbda05e6d15879ff00 lib/galaxy/workflow/steps.py
--- /dev/null
+++ b/lib/galaxy/workflow/steps.py
@@ -0,0 +1,63 @@
+""" This module contains utility methods for reasoning about and ordering
+workflow steps.
+"""
+import math
+from galaxy.util.topsort import (
+ CycleError,
+ topsort,
+ topsort_levels
+)
+
+
+def attach_ordered_steps( workflow, steps ):
+ """ Attempt to topologically order steps and attach to workflow. If this
+ fails - the workflow contains cycles so it mark it as such.
+ """
+ ordered_steps = order_workflow_steps( steps )
+ if ordered_steps:
+ workflow.has_cycles = False
+ for i, step in enumerate( ordered_steps ):
+ step.order_index = i
+ workflow.steps.append( step )
+ else:
+ workflow.has_cycles = True
+ workflow.steps = steps
+
+
+def order_workflow_steps( steps ):
+ """
+ Perform topological sort of the steps, return ordered or None
+ """
+ position_data_available = True
+ for step in steps:
+ if not step.position or not 'left' in step.position or not 'top' in step.position:
+ position_data_available = False
+ if position_data_available:
+ steps.sort(cmp=lambda s1, s2: cmp( math.sqrt(s1.position['left'] ** 2 + s1.position['top'] ** 2), math.sqrt(s2.position['left'] ** 2 + s2.position['top'] ** 2)))
+ try:
+ edges = edgelist_for_workflow_steps( steps )
+ node_order = topsort( edges )
+ return [ steps[i] for i in node_order ]
+ except CycleError:
+ return None
+
+
+def edgelist_for_workflow_steps( steps ):
+ """
+ Create a list of tuples representing edges between ``WorkflowSteps`` based
+ on associated ``WorkflowStepConnection``s
+ """
+ edges = []
+ steps_to_index = dict( ( step, i ) for i, step in enumerate( steps ) )
+ for step in steps:
+ edges.append( ( steps_to_index[step], steps_to_index[step] ) )
+ for conn in step.input_connections:
+ edges.append( ( steps_to_index[conn.output_step], steps_to_index[conn.input_step] ) )
+ return edges
+
+
+def order_workflow_steps_with_levels( steps ):
+ try:
+ return topsort_levels( edgelist_for_workflow_steps( steps ) )
+ except CycleError:
+ return None
diff -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 -r 6d0c89fc3558d7185daaa1dbda05e6d15879ff00 test/functional/api/test_workflows.py
--- a/test/functional/api/test_workflows.py
+++ b/test/functional/api/test_workflows.py
@@ -67,6 +67,39 @@
self._assert_status_code_is( run_workflow_response, 200 )
self._wait_for_history( history_id, assert_ok=True )
+ def test_extract_from_history( self ):
+ workflow = self.workflow_populator.load_workflow( name="test_for_extract" )
+ workflow_request, history_id = self._setup_workflow_run( workflow )
+ contents_response = self._get( "histories/%s/contents" % history_id )
+ self._assert_status_code_is( contents_response, 200 )
+ hda_ids = map( lambda c: c[ "id" ], contents_response.json() )
+
+ run_workflow_response = self._post( "workflows", data=workflow_request )
+ self._assert_status_code_is( run_workflow_response, 200 )
+
+ self._wait_for_history( history_id, assert_ok=True )
+ data = dict( history_id=history_id, tool_id="cat1" )
+ jobs_response = self._get( "jobs", data=data )
+ self._assert_status_code_is( jobs_response, 200 )
+ cat1_job_id = jobs_response.json()[ 0 ][ "id" ]
+
+ contents_response = self._get( "history/%s/contents", data=data )
+ create_from_data = dict(
+ from_history_id=history_id,
+ dataset_ids=dumps( hda_ids ),
+ job_ids=dumps( [ cat1_job_id ] ),
+ workflow_name="test import from history",
+ )
+ run_workflow_response = self._post( "workflows", data=create_from_data )
+ self._assert_status_code_is( run_workflow_response, 200 )
+
+ new_workflow_id = run_workflow_response.json()[ "id" ]
+ download_response = self._get( "workflows/%s/download" % new_workflow_id )
+ self._assert_status_code_is( download_response, 200 )
+ downloaded_workflow = download_response.json()
+ self.assertEquals( downloaded_workflow[ "name" ], "test import from history" )
+ assert len( downloaded_workflow[ "steps" ] ) == 3
+
def test_run_replace_params_by_tool( self ):
workflow_request, history_id = self._setup_random_x2_workflow( "test_for_replace_tool_params" )
workflow_request[ "parameters" ] = dumps( dict( random_lines1=dict( num_lines=5 ) ) )
diff -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 -r 6d0c89fc3558d7185daaa1dbda05e6d15879ff00 test/unit/workflows/test_extract_summary.py
--- /dev/null
+++ b/test/unit/workflows/test_extract_summary.py
@@ -0,0 +1,98 @@
+import unittest
+
+from galaxy import model
+from galaxy.workflow import extract
+
+UNDEFINED_JOB = object()
+
+
+class TestWorkflowExtractSummary( unittest.TestCase ):
+
+ def setUp( self ):
+ self.history = MockHistory()
+ self.trans = MockTrans( self.history )
+
+ def test_empty_history( self ):
+ job_dict, warnings = extract.summarize( trans=self.trans )
+ assert not warnings
+ assert not job_dict
+
+ def test_summarize_returns_name_and_dataset_list( self ):
+ # Create two jobs and three datasets, test they are groupped
+ # by job correctly with correct output names.
+ hda1 = MockHda()
+ self.history.active_datasets.append( hda1 )
+ hda2 = MockHda( job=hda1.job, output_name="out2" )
+ self.history.active_datasets.append( hda2 )
+ hda3 = MockHda( output_name="out3" )
+ self.history.active_datasets.append( hda3 )
+
+ job_dict, warnings = extract.summarize( trans=self.trans )
+ assert len( job_dict ) == 2
+ assert not warnings
+ self.assertEquals( job_dict[ hda1.job ], [ ( 'out1', hda1 ), ( 'out2', hda2 ) ] )
+ self.assertEquals( job_dict[ hda3.job ], [ ( 'out3', hda3 ) ] )
+
+ def test_finds_original_job_if_copied( self ):
+ hda = MockHda()
+ derived_hda_1 = MockHda()
+ derived_hda_1.copied_from_history_dataset_association = hda
+ derived_hda_2 = MockHda()
+ derived_hda_2.copied_from_history_dataset_association = derived_hda_1
+ self.history.active_datasets.append( derived_hda_2 )
+ job_dict, warnings = extract.summarize( trans=self.trans )
+ assert not warnings
+ assert len( job_dict ) == 1
+ self.assertEquals( job_dict[ hda.job ], [ ('out1', derived_hda_2 ) ] )
+
+ def test_fake_job( self ):
+ """ Fakes job if creating_job_associations is empty.
+ """
+ hda = MockHda( job=UNDEFINED_JOB )
+ self.history.active_datasets.append( hda )
+ job_dict, warnings = extract.summarize( trans=self.trans )
+ assert not warnings
+ assert len( job_dict ) == 1
+ fake_job = job_dict.keys()[ 0 ]
+ assert fake_job.id.startswith( "fake_" )
+ datasets = job_dict.values()[ 0 ]
+ assert datasets == [ ( None, hda ) ]
+
+ def test_warns_and_skips_datasets_if_not_finished( self ):
+ hda = MockHda( state='queued' )
+ self.history.active_datasets.append( hda )
+ job_dict, warnings = extract.summarize( trans=self.trans )
+ assert warnings
+ assert len( job_dict ) == 0
+
+
+class MockHistory( object ):
+
+ def __init__( self ):
+ self.active_datasets = []
+
+
+class MockTrans( object ):
+
+ def __init__( self, history ):
+ self.history = history
+
+ def get_history( self ):
+ return self.history
+
+
+class MockHda( object ):
+
+ def __init__( self, state='ok', output_name='out1', job=None ):
+ self.id = 123
+ self.state = state
+ self.copied_from_history_dataset_association = None
+ if job is not UNDEFINED_JOB:
+ if not job:
+ job = model.Job()
+ self.job = job
+ assoc = model.JobToOutputDatasetAssociation( output_name, self )
+ assoc.job = job
+ self.creating_job_associations = [ assoc ]
+ else:
+ self.creating_job_associations = []
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: Handle combinations of newly defined tool dependencies and repository dependencies that are included in updates being pulled to tool shed repositories installed into Galaxy.
by commits-noreplyï¼ bitbucket.org 26 Mar '14
by commits-noreplyï¼ bitbucket.org 26 Mar '14
26 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/90b4baa5c2b1/
Changeset: 90b4baa5c2b1
User: greg
Date: 2014-03-26 19:58:08
Summary: Handle combinations of newly defined tool dependencies and repository dependencies that are included in updates being pulled to tool shed repositories installed into Galaxy.
Affected #: 15 files
diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 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
@@ -201,9 +201,13 @@
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 )
+ 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,
- 'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \
- ( web.url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) )
+ 'repository/check_for_updates%s' % params )
return trans.response.send_redirect( url )
@web.expose
@@ -367,9 +371,10 @@
@web.require_admin
def get_tool_dependencies( self, trans, repository_id, repository_name, repository_owner, changeset_revision ):
"""
- Send a request to the appropriate tool shed to retrieve the dictionary of tool dependencies defined for the received repository name,
- owner and changeset revision. The received repository_id is the encoded id of the installed tool shed repository in Galaxy. We need
- it so that we can derive the tool shed from which it was installed.
+ Send a request to the appropriate tool shed to retrieve the dictionary of tool dependencies defined for
+ the received repository name, owner and changeset revision. The received repository_id is the encoded id
+ of the installed tool shed repository in Galaxy. We need it so that we can derive the tool shed from which
+ 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 )
@@ -388,8 +393,8 @@
@web.require_admin
def get_updated_repository_information( self, trans, repository_id, repository_name, repository_owner, changeset_revision ):
"""
- Send a request to the appropriate tool shed to retrieve the dictionary of information required to reinstall an updated revision of an
- uninstalled tool shed repository.
+ Send a request to the appropriate tool shed to retrieve the dictionary of information required to reinstall
+ 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 )
@@ -436,13 +441,16 @@
@web.expose
@web.require_admin
- def initiate_tool_dependency_installation( self, trans, tool_dependencies ):
+ def initiate_tool_dependency_installation( self, trans, tool_dependencies, **kwd ):
"""Install specified dependencies for repository tools."""
# Get the tool_shed_repository from one of the tool_dependencies.
- message = ''
+ message = kwd.get( 'message', '' )
+ status = kwd.get( 'status', 'done' )
+ err_msg = ''
tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository
# Get the tool_dependencies.xml file from the repository.
- tool_dependencies_config = suc.get_config_from_disk( suc.TOOL_DEPENDENCY_DEFINITION_FILENAME, tool_shed_repository.repo_path( trans.app ) )
+ tool_dependencies_config = suc.get_config_from_disk( suc.TOOL_DEPENDENCY_DEFINITION_FILENAME,
+ tool_shed_repository.repo_path( trans.app ) )
installed_tool_dependencies = common_install_util.handle_tool_dependencies( app=trans.app,
tool_shed_repository=tool_shed_repository,
tool_dependencies_config=tool_dependencies_config,
@@ -452,13 +460,12 @@
if installed_tool_dependency.status == trans.app.install_model.ToolDependency.installation_status.ERROR:
text = util.unicodify( installed_tool_dependency.error_message )
if text is not None:
- message += ' %s' % text
+ err_msg += ' %s' % text
tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in tool_dependencies ]
- if message:
+ if err_msg:
+ message += err_msg
status = 'error'
- else:
- message = "Installed tool dependencies: %s" % ','.join( td.name for td in installed_tool_dependencies )
- status = 'done'
+ message += "Installed tool dependencies: %s" % ','.join( td.name for td in installed_tool_dependencies )
td_ids = [ trans.security.encode_id( td.id ) for td in tool_shed_repository.tool_dependencies ]
return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
action='manage_tool_dependencies',
@@ -506,9 +513,10 @@
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?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \
- ( name, owner, latest_downloadable_revision, web.url_for( '/', qualified=True ) ) )
+ '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 )
@@ -521,43 +529,74 @@
message=message,
status=status ) )
-
@web.expose
@web.require_admin
- def install_tool_dependencies( self, trans, **kwd ):
+ def install_tool_dependencies_with_update( self, trans, **kwd ):
+ """
+ Updating an installed tool shed repository where new tool dependencies but no new repository
+ dependencies are included in the updated revision.
+ """
+ updating_repository_id = kwd.get( 'updating_repository_id', None )
+ repository = suc.get_installed_tool_shed_repository( trans, updating_repository_id )
+ # All received dependencies need to be installed - confirmed by the caller.
+ encoded_tool_dependencies_dict = kwd.get( 'encoded_tool_dependencies_dict', None )
+ if encoded_tool_dependencies_dict is not None:
+ tool_dependencies_dict = encoding_util.tool_shed_decode( encoded_tool_dependencies_dict )
+ else:
+ tool_dependencies_dict = {}
+ encoded_relative_install_dir = kwd.get( 'encoded_relative_install_dir', None )
+ if encoded_relative_install_dir is not None:
+ relative_install_dir = encoding_util.tool_shed_decode( encoded_relative_install_dir )
+ else:
+ relative_install_dir = ''
+ updating_to_changeset_revision = kwd.get( 'updating_to_changeset_revision', None )
+ updating_to_ctx_rev = kwd.get( 'updating_to_ctx_rev', None )
+ encoded_updated_metadata = kwd.get( 'encoded_updated_metadata', None )
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
- tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd )
- tool_dependencies = []
- for tool_dependency_id in tool_dependency_ids:
- tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id )
- tool_dependencies.append( tool_dependency )
- if kwd.get( 'install_tool_dependencies_button', False ):
- # Filter tool dependencies to only those that are installed.
- tool_dependencies_for_installation = []
- for tool_dependency in tool_dependencies:
- if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.UNINSTALLED,
- trans.install_model.ToolDependency.installation_status.ERROR ]:
- tool_dependencies_for_installation.append( tool_dependency )
- if tool_dependencies_for_installation:
- # Redirect back to the ToolDependencyGrid before initiating installation.
- encoded_tool_dependency_for_installation_ids = [ trans.security.encode_id( td.id ) for td in tool_dependencies_for_installation ]
- new_kwd = dict( action='manage_tool_dependencies',
- operation='initiate_tool_dependency_installation',
- tool_dependency_ids=encoded_tool_dependency_for_installation_ids,
- message=message,
- status=status )
- return self.tool_dependency_grid( trans, **new_kwd )
+ install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) )
+ if 'install_tool_dependencies_with_update_button' in kwd:
+ # Now that the user has chosen whether to install tool dependencies or not, we can
+ # update the repository record with the changes in the updated revision.
+ if encoded_updated_metadata:
+ updated_metadata = encoding_util.tool_shed_decode( encoded_updated_metadata )
else:
- message = 'All of the selected tool dependencies are already installed.'
- status = 'error'
- return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
- action='manage_repository_tool_dependencies',
- tool_dependency_ids=tool_dependency_ids,
- status=status,
- message=message ) )
- return trans.fill_template( '/admin/tool_shed_repository/install_tool_dependencies.mako',
- tool_dependencies=tool_dependencies,
+ updated_metadata = None
+ repository = repository_util.update_repository_record( trans,
+ repository=repository,
+ updated_metadata_dict=updated_metadata,
+ updated_changeset_revision=updating_to_changeset_revision,
+ updated_ctx_rev=updating_to_ctx_rev )
+ if install_tool_dependencies:
+ tool_dependencies = tool_dependency_util.create_tool_dependency_objects( trans.app,
+ repository,
+ relative_install_dir,
+ set_status=False )
+ message = "The installed repository named '%s' has been updated to change set revision '%s'. " % \
+ ( str( repository.name ), updating_to_changeset_revision )
+ self.initiate_tool_dependency_installation( trans, tool_dependencies, message=message, status=status )
+ # Handle tool dependencies check box.
+ if trans.app.config.tool_dependency_dir is None:
+ if includes_tool_dependencies:
+ message = "Tool dependencies defined in this repository can be automatically installed if you set "
+ message += "the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file "
+ message += "(universe_wsgi.ini) and restart your Galaxy server."
+ status = "warning"
+ install_tool_dependencies_check_box_checked = False
+ else:
+ install_tool_dependencies_check_box_checked = True
+ install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies',
+ checked=install_tool_dependencies_check_box_checked )
+ return trans.fill_template( '/admin/tool_shed_repository/install_tool_dependencies_with_update.mako',
+ repository=repository,
+ updating_repository_id=updating_repository_id,
+ updating_to_ctx_rev=updating_to_ctx_rev,
+ updating_to_changeset_revision=updating_to_changeset_revision,
+ encoded_updated_metadata=encoded_updated_metadata,
+ encoded_relative_install_dir=encoded_relative_install_dir,
+ encoded_tool_dependencies_dict=encoded_tool_dependencies_dict,
+ install_tool_dependencies_check_box=install_tool_dependencies_check_box,
+ tool_dependencies_dict=tool_dependencies_dict,
message=message,
status=status )
@@ -611,7 +650,8 @@
# TODO: I believe this block should be removed, but make sure..
repositories_for_uninstallation = []
for repository_id in tsridslist:
- repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( trans.security.decode_id( repository_id ) )
+ repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ) \
+ .get( trans.security.decode_id( repository_id ) )
if repository.status in [ trans.install_model.ToolShedRepository.installation_status.INSTALLED,
trans.install_model.ToolShedRepository.installation_status.ERROR ]:
repositories_for_uninstallation.append( repository )
@@ -632,28 +672,34 @@
filtered_repo_info_dicts = []
filtered_tool_panel_section_keys = []
repositories_for_installation = []
- # Some repositories may have repository dependencies that are required to be installed before the dependent repository, so we'll
- # order the list of tsr_ids to ensure all repositories install in the required order.
+ # Some repositories may have repository dependencies that are required to be installed before the
+ # dependent repository, so we'll order the list of tsr_ids to ensure all repositories install in the
+ # required order.
ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = \
repository_util.order_components_for_installation( trans,
tsr_ids,
repo_info_dicts,
tool_panel_section_keys=tool_panel_section_keys )
for tsr_id in ordered_tsr_ids:
- repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) )
+ repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ) \
+ .get( trans.security.decode_id( tsr_id ) )
if repository.status in [ trans.install_model.ToolShedRepository.installation_status.NEW,
trans.install_model.ToolShedRepository.installation_status.UNINSTALLED ]:
repositories_for_installation.append( repository )
- repo_info_dict, tool_panel_section_key = repository_util.get_repository_components_for_installation( tsr_id,
- ordered_tsr_ids,
- ordered_repo_info_dicts,
- ordered_tool_panel_section_keys )
+ repo_info_dict, tool_panel_section_key = \
+ repository_util.get_repository_components_for_installation( tsr_id,
+ ordered_tsr_ids,
+ ordered_repo_info_dicts,
+ ordered_tool_panel_section_keys )
filtered_repo_info_dicts.append( repo_info_dict )
filtered_tool_panel_section_keys.append( tool_panel_section_key )
if repositories_for_installation:
decoded_kwd[ 'repo_info_dicts' ] = filtered_repo_info_dicts
decoded_kwd[ 'tool_panel_section_keys' ] = filtered_tool_panel_section_keys
- self.install_tool_shed_repositories( trans, repositories_for_installation, reinstalling=reinstalling, **decoded_kwd )
+ self.install_tool_shed_repositories( trans,
+ repositories_for_installation,
+ reinstalling=reinstalling,
+ **decoded_kwd )
else:
kwd[ 'message' ] = 'All selected tool shed repositories are already installed.'
kwd[ 'status' ] = 'error'
@@ -772,7 +818,10 @@
trans.install_model.ToolDependency.installation_status.UNINSTALLED ]:
tool_dependencies_for_installation.append( tool_dependency )
if tool_dependencies_for_installation:
- self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation )
+ self.initiate_tool_dependency_installation( trans,
+ tool_dependencies_for_installation,
+ message=message,
+ status=status )
else:
message = 'All selected tool dependencies are already installed.'
status = 'error'
@@ -780,14 +829,16 @@
message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (universe_wsgi.ini) '
message += ' and restart your Galaxy server to install tool dependencies.'
status = 'error'
- installed_tool_dependencies_select_field = suc.build_tool_dependencies_select_field( trans,
- tool_shed_repository=tool_shed_repository,
- name='inst_td_ids',
- uninstalled_only=False )
- uninstalled_tool_dependencies_select_field = suc.build_tool_dependencies_select_field( trans,
- tool_shed_repository=tool_shed_repository,
- name='uninstalled_tool_dependency_ids',
- uninstalled_only=True )
+ installed_tool_dependencies_select_field = \
+ suc.build_tool_dependencies_select_field( trans,
+ tool_shed_repository=tool_shed_repository,
+ name='inst_td_ids',
+ uninstalled_only=False )
+ uninstalled_tool_dependencies_select_field = \
+ suc.build_tool_dependencies_select_field( trans,
+ tool_shed_repository=tool_shed_repository,
+ name='uninstalled_tool_dependency_ids',
+ uninstalled_only=True )
return trans.fill_template( '/admin/tool_shed_repository/manage_repository_tool_dependencies.mako',
repository=tool_shed_repository,
installed_tool_dependencies_select_field=installed_tool_dependencies_select_field,
@@ -836,7 +887,10 @@
trans.install_model.ToolDependency.installation_status.UNINSTALLED ]:
tool_dependencies_for_installation.append( tool_dependency )
if tool_dependencies_for_installation:
- self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation )
+ self.initiate_tool_dependency_installation( trans,
+ tool_dependencies_for_installation,
+ message=message,
+ status=status )
else:
kwd[ 'message' ] = 'All selected tool dependencies are already installed.'
kwd[ 'status' ] = 'error'
@@ -876,18 +930,21 @@
@web.require_admin
def prepare_for_install( self, trans, **kwd ):
if not suc.have_shed_tool_conf_for_install( trans ):
- message = 'The <b>tool_config_file</b> setting in <b>universe_wsgi.ini</b> must include at least one shed tool configuration file name with a '
- message += '<b><toolbox></b> tag that includes a <b>tool_path</b> attribute value which is a directory relative to the Galaxy installation '
- message += 'directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name <b>shed_tool_conf.xml</b> whose '
- message += '<b><toolbox></b> tag is <b><toolbox tool_path="../shed_tools"></b>).<p/>See the '
- message += '<a href="http://wiki.g2.bx.psu.edu/InstallingRepositoriesToGalaxy" target="_blank">Installation of Galaxy tool shed repository tools '
- message += 'into a local Galaxy instance</a> section of the Galaxy tool shed wiki for all of the details.'
+ message = 'The <b>tool_config_file</b> setting in <b>universe_wsgi.ini</b> must include at least one '
+ message += 'shed tool configuration file name with a <b><toolbox></b> tag that includes a <b>tool_path</b> '
+ message += 'attribute value which is a directory relative to the Galaxy installation directory in order '
+ message += 'to automatically install tools from a Galaxy Tool Shed (e.g., the file name <b>shed_tool_conf.xml</b> '
+ message += 'whose <b><toolbox></b> tag is <b><toolbox tool_path="../shed_tools"></b>).<p/>See the '
+ message += '<a href="http://wiki.g2.bx.psu.edu/InstallingRepositoriesToGalaxy" target="_blank">Installation '
+ message += 'of Galaxy Tool Shed repository tools into a local Galaxy instance</a> section of the Galaxy Tool '
+ message += 'Shed wiki for all of the details.'
return trans.show_error_message( message )
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 )
- # Handle repository dependencies, which do not include those that are required only for compiling a dependent repository's tool dependencies.
+ # 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 ) )
install_repository_dependencies = kwd.get( 'install_repository_dependencies', '' )
# Every repository will be installed into the same tool panel section or all will be installed outside of any sections.
@@ -900,13 +957,36 @@
includes_tools_for_display_in_tool_panel = util.string_as_bool( kwd.get( 'includes_tools_for_display_in_tool_panel', False ) )
includes_tool_dependencies = util.string_as_bool( kwd.get( 'includes_tool_dependencies', False ) )
install_tool_dependencies = kwd.get( 'install_tool_dependencies', '' )
+ # In addition to installing new repositories, this method is called when updating an installed repository
+ # to a new changeset_revision where the update includes newly defined repository dependencies.
+ updating = util.asbool( kwd.get( 'updating', False ) )
+ updating_repository_id = kwd.get( 'updating_repository_id', None )
+ updating_to_changeset_revision = kwd.get( 'updating_to_changeset_revision', None )
+ updating_to_ctx_rev = kwd.get( 'updating_to_ctx_rev', None )
+ encoded_updated_metadata = kwd.get( 'encoded_updated_metadata', None )
encoded_repo_info_dicts = kwd.get( 'encoded_repo_info_dicts', '' )
if encoded_repo_info_dicts:
encoded_repo_info_dicts = encoded_repo_info_dicts.split( encoding_util.encoding_sep )
if not encoded_repo_info_dicts:
- # The request originated in the tool shed via a tool search.
+ # The request originated in the tool shed via a tool search or from this controller's
+ # update_to_changeset_revision() method.
repository_ids = kwd.get( 'repository_ids', None )
- changeset_revisions = kwd.get( 'changeset_revisions', None )
+ if updating:
+ # We have updated an installed repository where the updates included newly defined repository
+ # and possibly tool dependencies. We will have arrived here only if the updates include newly
+ # defined repository dependencies. We're preparing to allow the user to elect to install these
+ # dependencies. At this point, the repository has been updated to the latest changeset revision,
+ # but the received repository id is from the Galaxy side (the caller is this controller's
+ # update_to_changeset_revision() method. We need to get the id of the same repository from the
+ # Tool Shed side.
+ repository = suc.get_tool_shed_repository_by_id( trans, updating_repository_id )
+ url = suc.url_join( tool_shed_url,
+ 'repository/get_repository_id?name=%s&owner=%s' % \
+ ( str( repository.name ), str( repository.owner ) ) )
+ repository_ids = common_util.tool_shed_get( trans.app, tool_shed_url, url )
+ changeset_revisions = updating_to_changeset_revision
+ 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' % \
@@ -918,7 +998,8 @@
if not includes_tools:
includes_tools = util.string_as_bool( decoded_repo_info_dict.get( 'includes_tools', False ) )
if not includes_tools_for_display_in_tool_panel:
- includes_tools_for_display_in_tool_panel = util.string_as_bool( decoded_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False ) )
+ includes_tools_for_display_in_tool_panel = \
+ util.string_as_bool( decoded_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False ) )
if not has_repository_dependencies:
has_repository_dependencies = util.string_as_bool( repo_information_dict.get( 'has_repository_dependencies', False ) )
if not includes_tool_dependencies:
@@ -927,6 +1008,19 @@
repo_info_dicts = [ encoding_util.tool_shed_decode( encoded_repo_info_dict ) for encoded_repo_info_dict in encoded_repo_info_dicts ]
if ( not includes_tools_for_display_in_tool_panel and kwd.get( 'select_shed_tool_panel_config_button', False ) ) or \
( includes_tools_for_display_in_tool_panel and kwd.get( 'select_tool_panel_section_button', False ) ):
+ if updating:
+ encoded_updated_metadata_dict = kwd.get( 'encoded_updated_metadata_dict', None )
+ updated_changeset_revision = kwd.get( 'updated_changeset_revision', None )
+ updated_ctx_rev = kwd.get( 'updated_ctx_rev', None )
+ repository = suc.get_tool_shed_repository_by_id( trans, updating_repository_id )
+ decoded_updated_metadata = encoding_util.tool_shed_decode( encoded_updated_metadata )
+ # Now that the user has decided whether they will handle dependencies, we can update
+ # the repository to the latest revision.
+ repository = repository_util.update_repository_record( trans,
+ repository=repository,
+ updated_metadata_dict=decoded_updated_metadata,
+ updated_changeset_revision=updating_to_changeset_revision,
+ updated_ctx_rev=updating_to_ctx_rev )
install_repository_dependencies = CheckboxField.is_checked( install_repository_dependencies )
if includes_tool_dependencies:
install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies )
@@ -959,7 +1053,8 @@
tool_panel_section_keys=tool_panel_section_keys,
tool_path=tool_path,
tool_shed_url=tool_shed_url )
- encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = repository_util.initiate_repository_installation( trans, installation_dict )
+ encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \
+ repository_util.initiate_repository_installation( trans, installation_dict )
return trans.fill_template( 'admin/tool_shed_repository/initiate_repository_installation.mako',
encoded_kwd=encoded_kwd,
query=query,
@@ -976,12 +1071,14 @@
tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf )
tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans )
if len( repo_info_dicts ) == 1:
- # If we're installing a single repository, see if it contains a readme or dependencies that we can display.
+ # If we're installing or updating a single repository, see if it contains a readme or
+ # dependencies that we can display.
repo_info_dict = repo_info_dicts[ 0 ]
dependencies_for_repository_dict = common_install_util.get_dependencies_for_repository( trans,
tool_shed_url,
repo_info_dict,
- includes_tool_dependencies )
+ includes_tool_dependencies,
+ updating=updating )
changeset_revision = dependencies_for_repository_dict.get( 'changeset_revision', None )
if not has_repository_dependencies:
has_repository_dependencies = dependencies_for_repository_dict.get( 'has_repository_dependencies', False )
@@ -990,7 +1087,8 @@
if not includes_tools:
includes_tools = dependencies_for_repository_dict.get( 'includes_tools', False )
if not includes_tools_for_display_in_tool_panel:
- includes_tools_for_display_in_tool_panel = dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False )
+ includes_tools_for_display_in_tool_panel = \
+ dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False )
installed_repository_dependencies = dependencies_for_repository_dict.get( 'installed_repository_dependencies', None )
installed_tool_dependencies = dependencies_for_repository_dict.get( 'installed_tool_dependencies', None )
missing_repository_dependencies = dependencies_for_repository_dict.get( 'missing_repository_dependencies', None )
@@ -998,19 +1096,25 @@
name = dependencies_for_repository_dict.get( 'name', None )
repository_owner = dependencies_for_repository_dict.get( 'repository_owner', None )
readme_files_dict = readme_util.get_readme_files_dict_for_display( trans, tool_shed_url, repo_info_dict )
- # We're handling 1 of 2 scenarios here: (1) we're installing a tool shed repository for the first time, so we've retrieved the list of installed
- # and missing repository dependencies from the database (2) we're handling the scenario where an error occurred during the installation process,
- # so we have a tool_shed_repository record in the database with associated repository dependency records. Since we have the repository
- # dependencies in either case, we'll merge the list of missing repository dependencies into the list of installed repository dependencies since
- # each displayed repository dependency will display a status, whether installed or missing.
- containers_dict = repository_util.populate_containers_dict_for_new_install( trans=trans,
- tool_shed_url=tool_shed_url,
- tool_path=tool_path,
- readme_files_dict=readme_files_dict,
- installed_repository_dependencies=installed_repository_dependencies,
- missing_repository_dependencies=missing_repository_dependencies,
- installed_tool_dependencies=installed_tool_dependencies,
- missing_tool_dependencies=missing_tool_dependencies )
+ # We're handling 1 of 3 scenarios here: (1) we're installing a tool shed repository for the first time, so we've
+ # retrieved the list of installed and missing repository dependencies from the database (2) we're handling the
+ # scenario where an error occurred during the installation process, so we have a tool_shed_repository record in
+ # the database with associated repository dependency records. Since we have the repository dependencies in both
+ # of the above 2 cases, we'll merge the list of missing repository dependencies into the list of installed
+ # repository dependencies since each displayed repository dependency will display a status, whether installed or
+ # missing. The 3rd scenario is where we're updating an installed repository and the updates include newly
+ # defined repository (and possibly tool) dependencies. In this case, merging will result in newly defined
+ # dependencies to be lost. We pass the updating parameter to make sure merging occurs only when appropriate.
+ containers_dict = \
+ repository_util.populate_containers_dict_for_new_install( trans=trans,
+ tool_shed_url=tool_shed_url,
+ tool_path=tool_path,
+ readme_files_dict=readme_files_dict,
+ installed_repository_dependencies=installed_repository_dependencies,
+ missing_repository_dependencies=missing_repository_dependencies,
+ installed_tool_dependencies=installed_tool_dependencies,
+ missing_tool_dependencies=missing_tool_dependencies,
+ updating=updating )
else:
# We're installing a list of repositories, each of which may have tool dependencies or repository dependencies.
containers_dicts = []
@@ -1018,7 +1122,8 @@
dependencies_for_repository_dict = common_install_util.get_dependencies_for_repository( trans,
tool_shed_url,
repo_info_dict,
- includes_tool_dependencies )
+ includes_tool_dependencies,
+ updating=updating )
changeset_revision = dependencies_for_repository_dict.get( 'changeset_revision', None )
if not has_repository_dependencies:
has_repository_dependencies = dependencies_for_repository_dict.get( 'has_repository_dependencies', False )
@@ -1027,34 +1132,39 @@
if not includes_tools:
includes_tools = dependencies_for_repository_dict.get( 'includes_tools', False )
if not includes_tools_for_display_in_tool_panel:
- includes_tools_for_display_in_tool_panel = dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False )
+ includes_tools_for_display_in_tool_panel = \
+ dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False )
installed_repository_dependencies = dependencies_for_repository_dict.get( 'installed_repository_dependencies', None )
installed_tool_dependencies = dependencies_for_repository_dict.get( 'installed_tool_dependencies', None )
missing_repository_dependencies = dependencies_for_repository_dict.get( 'missing_repository_dependencies', None )
missing_tool_dependencies = dependencies_for_repository_dict.get( 'missing_tool_dependencies', None )
name = dependencies_for_repository_dict.get( 'name', None )
repository_owner = dependencies_for_repository_dict.get( 'repository_owner', None )
- containers_dict = repository_util.populate_containers_dict_for_new_install( trans=trans,
- tool_shed_url=tool_shed_url,
- tool_path=tool_path,
- readme_files_dict=None,
- installed_repository_dependencies=installed_repository_dependencies,
- missing_repository_dependencies=missing_repository_dependencies,
- installed_tool_dependencies=installed_tool_dependencies,
- missing_tool_dependencies=missing_tool_dependencies )
+ containers_dict = \
+ repository_util.populate_containers_dict_for_new_install( trans=trans,
+ tool_shed_url=tool_shed_url,
+ tool_path=tool_path,
+ readme_files_dict=None,
+ installed_repository_dependencies=installed_repository_dependencies,
+ missing_repository_dependencies=missing_repository_dependencies,
+ installed_tool_dependencies=installed_tool_dependencies,
+ missing_tool_dependencies=missing_tool_dependencies,
+ updating=updating )
containers_dicts.append( containers_dict )
# Merge all containers into a single container.
containers_dict = repository_util.merge_containers_dicts_for_new_install( containers_dicts )
# Handle tool dependencies check box.
if trans.app.config.tool_dependency_dir is None:
if includes_tool_dependencies:
- message = "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> "
- message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository."
+ message = "Tool dependencies defined in this repository can be automatically installed if you set "
+ message += "the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file "
+ message += "(universe_wsgi.ini) and restart your Galaxy server before installing the repository."
status = "warning"
install_tool_dependencies_check_box_checked = False
else:
install_tool_dependencies_check_box_checked = True
- install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked )
+ install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies',
+ checked=install_tool_dependencies_check_box_checked )
# Handle repository dependencies check box.
install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True )
encoded_repo_info_dicts = encoding_util.encoding_sep.join( encoded_repo_info_dicts )
@@ -1062,6 +1172,11 @@
if includes_tools_for_display_in_tool_panel:
return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako',
encoded_repo_info_dicts=encoded_repo_info_dicts,
+ updating=updating,
+ updating_repository_id=updating_repository_id,
+ updating_to_ctx_rev=updating_to_ctx_rev,
+ updating_to_changeset_revision=updating_to_changeset_revision,
+ encoded_updated_metadata=encoded_updated_metadata,
includes_tools=includes_tools,
includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
includes_tool_dependencies=includes_tool_dependencies,
@@ -1077,10 +1192,16 @@
message=message,
status=status )
else:
- # If installing repositories that includes no tools and has no repository dependencies, display a page allowing the Galaxy administrator to
- # select a shed-related tool panel configuration file whose tool_path setting will be the location the repositories will be installed.
+ # If installing repositories that includes no tools and has no repository dependencies, display a page
+ # allowing the Galaxy administrator to select a shed-related tool panel configuration file whose tool_path
+ # setting will be the location the repositories will be installed.
return trans.fill_template( '/admin/tool_shed_repository/select_shed_tool_panel_config.mako',
encoded_repo_info_dicts=encoded_repo_info_dicts,
+ updating=updating,
+ updating_repository_id=updating_repository_id,
+ updating_to_ctx_rev=updating_to_ctx_rev,
+ updating_to_changeset_revision=updating_to_changeset_revision,
+ encoded_updated_metadata=encoded_updated_metadata,
includes_tools=includes_tools,
includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel,
includes_tool_dependencies=includes_tool_dependencies,
@@ -1400,7 +1521,8 @@
dependencies_for_repository_dict = common_install_util.get_dependencies_for_repository( trans,
tool_shed_url,
repo_info_dict,
- includes_tool_dependencies )
+ includes_tool_dependencies,
+ updating=False )
changeset_revision = dependencies_for_repository_dict.get( 'changeset_revision', None )
has_repository_dependencies = dependencies_for_repository_dict.get( 'has_repository_dependencies', False )
includes_tool_dependencies = dependencies_for_repository_dict.get( 'includes_tool_dependencies', False )
@@ -1449,14 +1571,16 @@
original_section_name = ''
tool_panel_section_select_field = None
shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans )
- containers_dict = repository_util.populate_containers_dict_for_new_install( trans=trans,
- tool_shed_url=tool_shed_url,
- tool_path=tool_path,
- readme_files_dict=readme_files_dict,
- installed_repository_dependencies=installed_repository_dependencies,
- missing_repository_dependencies=missing_repository_dependencies,
- installed_tool_dependencies=installed_tool_dependencies,
- missing_tool_dependencies=missing_tool_dependencies )
+ containers_dict = \
+ repository_util.populate_containers_dict_for_new_install( trans=trans,
+ tool_shed_url=tool_shed_url,
+ tool_path=tool_path,
+ readme_files_dict=readme_files_dict,
+ installed_repository_dependencies=installed_repository_dependencies,
+ missing_repository_dependencies=missing_repository_dependencies,
+ installed_tool_dependencies=installed_tool_dependencies,
+ missing_tool_dependencies=missing_tool_dependencies,
+ updating=False )
# Since we're reinstalling we'll merge the list of missing repository dependencies into the list of installed repository dependencies since each displayed
# repository dependency will display a status, whether installed or missing.
containers_dict = repository_dependency_util.merge_missing_repository_dependencies_to_installed_container( containers_dict )
@@ -1574,8 +1698,8 @@
@web.require_admin
def set_tool_versions( self, trans, **kwd ):
"""
- Get the tool_versions from the tool shed for each tool in the installed revision of a selected tool shed repository and update the
- metadata for the repository's revision in the Galaxy database.
+ Get the tool_versions from the tool shed for each tool in the installed revision of a selected tool shed
+ 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 )
@@ -1720,29 +1844,17 @@
resetting_all_metadata_on_repository=False,
updating_installed_repository=True,
persist=True )
- repository.metadata = metadata_dict
- # Update the repository.changeset_revision column in the database.
- repository.changeset_revision = latest_changeset_revision
- repository.ctx_rev = latest_ctx_rev
- # Update the repository.tool_shed_status column in the database.
- tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( trans.app, repository )
- if tool_shed_status_dict:
- repository.tool_shed_status = tool_shed_status_dict
- else:
- repository.tool_shed_status = None
- trans.install_model.context.add( repository )
- trans.install_model.context.flush()
if 'tools' in metadata_dict:
tool_panel_dict = metadata_dict.get( 'tool_panel_section', None )
if tool_panel_dict is None:
tool_panel_dict = suc.generate_tool_panel_dict_from_shed_tool_conf_entries( trans.app, repository )
repository_tools_tups = suc.get_repository_tools_tups( trans.app, metadata_dict )
tool_util.add_to_tool_panel( app=trans.app,
- repository_name=repository.name,
+ repository_name=str( repository.name ),
repository_clone_url=repository_clone_url,
- changeset_revision=repository.installed_changeset_revision,
+ changeset_revision=str( repository.installed_changeset_revision ),
repository_tools_tups=repository_tools_tups,
- owner=repository.owner,
+ owner=str( repository.owner ),
shed_tool_conf=shed_tool_conf,
tool_panel_dict=tool_panel_dict,
new_install=False )
@@ -1755,19 +1867,40 @@
os.path.join( relative_install_dir, name ),
repository,
repository_tools_tups )
- # Create tool_dependency records if necessary.
- if 'tool_dependencies' in metadata_dict:
- tool_dependencies = tool_dependency_util.create_tool_dependency_objects( trans.app,
- repository,
- relative_install_dir,
- set_status=False )
+ if 'repository_dependencies' in metadata_dict or 'tool_dependencies' in metadata_dict:
+ if 'repository_dependencies' in metadata_dict:
+ # Updates received include newly defined repository dependencies, so allow the user
+ # the option of installting them. We cannot update the repository with the changes
+ # until that happens, so we have to send them along.
+ new_kwd = dict( tool_shed_url=tool_shed_url,
+ updating_repository_id=trans.security.encode_id( repository.id ),
+ updating_to_ctx_rev=latest_ctx_rev,
+ updating_to_changeset_revision=latest_changeset_revision,
+ encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ),
+ updating=True )
+ return self.prepare_for_install( trans, **new_kwd )
+ # Updates received did not include any newly defined repository dependencies but did include
+ # newly defined tool dependencies.
+ encoded_tool_dependencies_dict = encoding_util.tool_shed_encode( metadata_dict.get( 'tool_dependencies', {} ) )
+ encoded_relative_install_dir = encoding_util.tool_shed_encode( relative_install_dir )
+ new_kwd = dict( updating_repository_id=trans.security.encode_id( repository.id ),
+ updating_to_ctx_rev=latest_ctx_rev,
+ updating_to_changeset_revision=latest_changeset_revision,
+ encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ),
+ encoded_relative_install_dir=encoded_relative_install_dir,
+ encoded_tool_dependencies_dict=encoded_tool_dependencies_dict,
+ message=message,
+ status = status )
+ return self.install_tool_dependencies_with_update( trans, **new_kwd )
+ # Updates received did not include any newly defined repository dependencies or newly defined
+ # tool dependencies.
+ repository = repository_util.update_repository_record( trans,
+ repository=repository,
+ updated_metadata_dict=metadata_dict,
+ updated_changeset_revision=latest_changeset_revision,
+ updated_ctx_rev=latest_ctx_rev )
message = "The installed repository named '%s' has been updated to change set revision '%s'. " % \
( name, latest_changeset_revision )
- # See if any tool dependencies can be installed.
- shed_tool_conf, tool_path, relative_install_dir = \
- suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository )
- if repository.missing_tool_dependencies:
- message += "Click the name of one of the missing tool dependencies listed below to install tool dependencies."
else:
message = "The directory containing the installed repository named '%s' cannot be found. " % name
status = 'error'
diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 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
@@ -866,11 +866,13 @@
no_update = 'false'
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?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 ) )
+ 'admin_toolshed/update_to_changeset_revision%s' % params )
else:
- message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. You may need to enable third-party cookies in your browser. ' % galaxy_url
+ 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. '
return trans.show_error_message( message )
if changeset_revision == repository.tip( trans.app ):
# If changeset_revision is the repository tip, there are no additional updates.
@@ -883,15 +885,17 @@
trans.security.encode_id( repository.id ),
changeset_revision )
if repository_metadata:
- # If changeset_revision is in the repository_metadata table for this repository, there are no additional updates.
+ # If changeset_revision is in the repository_metadata table for this repository, there are no
+ # additional updates.
if from_update_manager:
return no_update
else:
# Return the same value for changeset_revision and latest_changeset_revision.
url += latest_changeset_revision
else:
- # The changeset_revision column in the repository_metadata table has been updated with a new changeset_revision value since the
- # repository was installed. We need to find the changeset_revision to which we need to update.
+ # The changeset_revision column in the repository_metadata table has been updated with a new
+ # changeset_revision value since the repository was installed. We need to find the changeset_revision
+ # to which we need to update.
update_to_changeset_hash = None
for changeset in repo.changelog:
changeset_hash = str( repo.changectx( changeset ) )
@@ -1680,6 +1684,16 @@
return encoding_util.tool_shed_encode( repository_dependencies )
return ''
+ @web.expose
+ def get_repository_id( self, trans, **kwd ):
+ """Given a repository name and owner, return the encoded repository id."""
+ repository_name = kwd[ 'name' ]
+ repository_owner = kwd[ 'owner' ]
+ repository = suc.get_repository_by_name_and_owner( trans.app, repository_name, repository_owner )
+ if repository:
+ return trans.security.encode_id( repository.id )
+ return ''
+
@web.json
def get_repository_information( self, trans, repository_ids, changeset_revisions, **kwd ):
"""
@@ -1824,7 +1838,9 @@
if not repository_metadata:
# The received changeset_revision is no longer associated with metadata, so get the next changeset_revision in the repository
# changelog that is associated with metadata.
- changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, after_changeset_revision=changeset_revision )
+ changeset_revision = suc.get_next_downloadable_changeset_revision( repository,
+ repo,
+ after_changeset_revision=changeset_revision )
repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
repo_info_dict = repository_util.create_repo_info_dict( trans=trans,
@@ -2039,11 +2055,12 @@
galaxy_url = suc.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?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 ) ) ) )
+ '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
@@ -2477,9 +2494,10 @@
@web.expose
def next_installable_changeset_revision( self, trans, **kwd ):
"""
- Handle a request from a Galaxy instance where the changeset_revision defined for a repository in a dependency definition file is older
- than the changeset_revision associated with the installed repository. This will occur with repository's of type tool_dependency_definition,
- and this scenario will occur while repository dependency hierarchies are bing installed.
+ Handle a request from a Galaxy instance where the changeset_revision defined for a repository
+ in a dependency definition file is older than the changeset_revision associated with the installed
+ repository. This will occur with repository's of type tool_dependency_definition, and this scenario
+ will occur while repository dependency hierarchies are bing installed.
"""
name = kwd.get( 'name', None )
owner = kwd.get( 'owner', None )
@@ -2981,12 +2999,13 @@
@web.expose
def updated_changeset_revisions( self, trans, **kwd ):
"""
- Handle a request from a local Galaxy instance to retrieve the list of changeset revisions to which an installed repository can be updated. This
- method will return a string of comma-separated changeset revision hashes for all available updates to the received changeset revision. Among
- other things , this method handles the scenario where an installed tool shed repository's tool_dependency definition file defines a changeset
- revision for a complex repository dependency that is outdated. In other words, a defined changeset revision is older than the current changeset
- revision for the required repository, making it impossible to discover the repository without knowledge of revisions to which it could have been
- updated.
+ Handle a request from a local Galaxy instance to retrieve the list of changeset revisions to which an
+ installed repository can be updated. This method will return a string of comma-separated changeset revision
+ hashes for all available updates to the received changeset revision. Among other things , this method
+ handles the scenario where an installed tool shed repository's tool_dependency definition file defines a
+ changeset revision for a complex repository dependency that is outdated. In other words, a defined changeset
+ revision is older than the current changeset revision for the required repository, making it impossible to
+ discover the repository without knowledge of revisions to which it could have been updated.
"""
name = kwd.get( 'name', None )
owner = kwd.get( 'owner', None )
diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 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
@@ -37,15 +37,19 @@
Galaxy instance. The dictionary will also contain the recursive list of repository dependencies defined
for the repository, as well as the defined tool dependencies.
- This method is called from Galaxy under three scenarios:
+ This method is called from Galaxy under four scenarios:
1. During the tool shed repository installation process via the tool shed's get_repository_information()
- method. In this case both the received repository and repository_metadata will be objects., but
+ method. In this case both the received repository and repository_metadata will be objects, but
tool_dependencies and repository_dependencies will be None.
- 2. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no
+ 2. When getting updates for an install repository where the updates include newly defined repository
+ dependency definitions. This scenario is similar to 1. above. The tool shed's get_repository_information()
+ method is the caller, and both the received repository and repository_metadata will be objects, but
+ tool_dependencies and repository_dependencies will be None.
+ 3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no
updates available. In this case, both repository and repository_metadata will be None, but tool_dependencies
and repository_dependencies will be objects previously retrieved from the tool shed if the repository includes
definitions for them.
- 3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates
+ 4. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates
available. In this case, this method is reached via the tool shed's get_updated_repository_information()
method, and both repository and repository_metadata will be objects but tool_dependencies and
repository_dependencies will be None.
@@ -184,16 +188,22 @@
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_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
+ repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans,
+ repository_id,
+ changeset_revision )
if not repository_metadata:
- # The received changeset_revision is no longer installable, so get the next changeset_revision in the repository's changelog.
- # This generally occurs only with repositories of type tool_dependency_definition.
- next_downloadable_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
+ # The received changeset_revision is no longer installable, so get the next changeset_revision
+ # in the repository's changelog. This generally occurs only with repositories of type
+ # tool_dependency_definition.
+ next_downloadable_changeset_revision = \
+ suc.get_next_downloadable_changeset_revision( repository,repo, changeset_revision )
if next_downloadable_changeset_revision:
- repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, next_downloadable_changeset_revision )
+ repository_metadata = \
+ suc.get_repository_metadata_by_changeset_revision( trans, repository_id, next_downloadable_changeset_revision )
if repository_metadata:
- # For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption is not valid we'll have to
- # enhance the callers to handle repository_metadata values of None in the returned repo_info_dict.
+ # For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption
+ # is not valid we'll have to enhance the callers to handle repository_metadata values of None in the
+ # returned repo_info_dict.
metadata = repository_metadata.metadata
if 'tools' in metadata:
includes_tools = True
@@ -743,9 +753,13 @@
ordered_tool_panel_section_keys.append( tool_panel_section_key )
return ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys
-def populate_containers_dict_for_new_install( trans, tool_shed_url, tool_path, readme_files_dict, installed_repository_dependencies, missing_repository_dependencies,
- installed_tool_dependencies, missing_tool_dependencies ):
- """Return the populated containers for a repository being installed for the first time."""
+def populate_containers_dict_for_new_install( trans, tool_shed_url, tool_path, readme_files_dict, installed_repository_dependencies,
+ missing_repository_dependencies, installed_tool_dependencies, missing_tool_dependencies,
+ updating=False ):
+ """
+ Return the populated containers for a repository being installed for the first time or for an installed repository
+ that is being updated and the updates include newly defined repository (and possibly tool) dependencies.
+ """
installed_tool_dependencies, missing_tool_dependencies = \
tool_dependency_util.populate_tool_dependencies_dicts( trans=trans,
tool_shed_url=tool_shed_url,
@@ -753,27 +767,32 @@
repository_installed_tool_dependencies=installed_tool_dependencies,
repository_missing_tool_dependencies=missing_tool_dependencies,
required_repo_info_dicts=None )
- # Since we are installing a new repository, most of the repository contents are set to None since we don't yet know what they are.
- containers_dict = container_util.build_repository_containers_for_galaxy( trans=trans,
- repository=None,
- datatypes=None,
- invalid_tools=None,
- missing_repository_dependencies=missing_repository_dependencies,
- missing_tool_dependencies=missing_tool_dependencies,
- readme_files_dict=readme_files_dict,
- repository_dependencies=installed_repository_dependencies,
- tool_dependencies=installed_tool_dependencies,
- valid_tools=None,
- workflows=None,
- valid_data_managers=None,
- invalid_data_managers=None,
- data_managers_errors=None,
- new_install=True,
- reinstalling=False )
- # Merge the missing_repository_dependencies container contents to the installed_repository_dependencies container.
- containers_dict = repository_dependency_util.merge_missing_repository_dependencies_to_installed_container( containers_dict )
- # Merge the missing_tool_dependencies container contents to the installed_tool_dependencies container.
- containers_dict = tool_dependency_util.merge_missing_tool_dependencies_to_installed_container( containers_dict )
+ # Most of the repository contents are set to None since we don't yet know what they are.
+ containers_dict = \
+ container_util.build_repository_containers_for_galaxy( trans=trans,
+ repository=None,
+ datatypes=None,
+ invalid_tools=None,
+ missing_repository_dependencies=missing_repository_dependencies,
+ missing_tool_dependencies=missing_tool_dependencies,
+ readme_files_dict=readme_files_dict,
+ repository_dependencies=installed_repository_dependencies,
+ tool_dependencies=installed_tool_dependencies,
+ valid_tools=None,
+ workflows=None,
+ valid_data_managers=None,
+ invalid_data_managers=None,
+ data_managers_errors=None,
+ new_install=True,
+ reinstalling=False )
+ if not updating:
+ # If we installing a new repository and not updaing an installed repository, we can merge
+ # the missing_repository_dependencies container contents to the installed_repository_dependencies
+ # container. When updating an installed repository, merging will result in losing newly defined
+ # dependencies included in the updates.
+ containers_dict = repository_dependency_util.merge_missing_repository_dependencies_to_installed_container( containers_dict )
+ # Merge the missing_tool_dependencies container contents to the installed_tool_dependencies container.
+ containers_dict = tool_dependency_util.merge_missing_tool_dependencies_to_installed_container( containers_dict )
return containers_dict
def pull_repository( repo, repository_clone_url, ctx_rev ):
@@ -875,3 +894,23 @@
repository.uninstalled = uninstalled
trans.install_model.context.add( repository )
trans.install_model.context.flush()
+
+def update_repository_record( trans, repository, updated_metadata_dict, updated_changeset_revision, updated_ctx_rev ):
+ """
+ Update a tool_shed_repository database record with new information retrieved from the
+ Tool Shed. This happens when updating an installed repository to a new changeset revision.
+ """
+ repository.metadata = updated_metadata_dict
+ # Update the repository.changeset_revision column in the database.
+ repository.changeset_revision = updated_changeset_revision
+ repository.ctx_rev = updated_ctx_rev
+ # Update the repository.tool_shed_status column in the database.
+ tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( trans.app, repository )
+ if tool_shed_status_dict:
+ repository.tool_shed_status = tool_shed_status_dict
+ else:
+ repository.tool_shed_status = None
+ trans.install_model.context.add( repository )
+ trans.install_model.context.flush()
+ trans.install_model.context.refresh( repository )
+ return repository
diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 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
@@ -359,13 +359,14 @@
can_install_tool_dependency = True
if can_install_tool_dependency:
package_install_version = package_elem.get( 'version', '1.0' )
- tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app,
- tool_shed_repository=tool_shed_repository,
- name=package_name,
- version=package_version,
- type='package',
- status=app.install_model.ToolDependency.installation_status.INSTALLING,
- set_status=True )
+ tool_dependency = \
+ tool_dependency_util.create_or_update_tool_dependency( app=app,
+ tool_shed_repository=tool_shed_repository,
+ name=package_name,
+ version=package_version,
+ type='package',
+ status=app.install_model.ToolDependency.installation_status.INSTALLING,
+ set_status=True )
# Get the information about the current platform in case the tool dependency definition includes tag sets
# for installing compiled binaries.
platform_info_dict = tool_dependency_util.get_platform_info_dict()
@@ -879,25 +880,28 @@
# Tool dependencies of type "set_environmnet" always have the version attribute set to None.
attr_tup = ( env_var_name, None, 'set_environment' )
if attr_tup in attr_tups_of_dependencies_for_install:
- install_dir = tool_dependency_util.get_tool_dependency_install_dir( app=app,
- repository_name=tool_shed_repository.name,
- repository_owner=tool_shed_repository.owner,
- repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
- tool_dependency_type='set_environment',
- tool_dependency_name=env_var_name,
- tool_dependency_version=None )
+ install_dir = \
+ tool_dependency_util.get_tool_dependency_install_dir( app=app,
+ repository_name=tool_shed_repository.name,
+ repository_owner=tool_shed_repository.owner,
+ repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
+ tool_dependency_type='set_environment',
+ tool_dependency_name=env_var_name,
+ tool_dependency_version=None )
tool_shed_repository_install_dir = get_tool_shed_repository_install_dir( app, tool_shed_repository )
env_var_dict = td_common_util.create_env_var_dict( env_var_elem, tool_shed_repository_install_dir=tool_shed_repository_install_dir )
if env_var_dict:
if not os.path.exists( install_dir ):
os.makedirs( install_dir )
- tool_dependency = tool_dependency_util.create_or_update_tool_dependency( app=app,
- tool_shed_repository=tool_shed_repository,
- name=env_var_name,
- version=None,
- type='set_environment',
- status=app.install_model.ToolDependency.installation_status.INSTALLING,
- set_status=True )
+ status = app.install_model.ToolDependency.installation_status.INSTALLING
+ tool_dependency = \
+ tool_dependency_util.create_or_update_tool_dependency( app=app,
+ tool_shed_repository=tool_shed_repository,
+ name=env_var_name,
+ version=None,
+ type='set_environment',
+ status=status,
+ set_status=True )
if env_var_version == '1.0':
# Create this tool dependency's env.sh file.
env_file_builder = fabric_util.EnvFileBuilder( install_dir )
@@ -906,28 +910,34 @@
error_message = 'Error creating env.sh file for tool dependency %s, return_code: %s' % \
( str( tool_dependency.name ), str( return_code ) )
log.debug( error_message )
- tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
- tool_dependency=tool_dependency,
- status=app.install_model.ToolDependency.installation_status.ERROR,
- error_message=error_message,
- remove_from_disk=False )
+ status = app.install_model.ToolDependency.installation_status.ERROR
+ tool_dependency = \
+ tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency=tool_dependency,
+ status=status,
+ error_message=error_message,
+ remove_from_disk=False )
else:
if tool_dependency.status not in [ app.install_model.ToolDependency.installation_status.ERROR,
app.install_model.ToolDependency.installation_status.INSTALLED ]:
- tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
- tool_dependency=tool_dependency,
- status=app.install_model.ToolDependency.installation_status.INSTALLED,
- error_message=None,
- remove_from_disk=False )
+ status = app.install_model.ToolDependency.installation_status.INSTALLED
+ tool_dependency = \
+ tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency=tool_dependency,
+ status=status,
+ error_message=None,
+ remove_from_disk=False )
log.debug( 'Environment variable %s set in %s for tool dependency %s.' % \
( str( env_var_name ), str( install_dir ), str( tool_dependency.name ) ) )
else:
error_message = 'Only set_environment version 1.0 is currently supported (i.e., change your tag to be <set_environment version="1.0">).'
- tool_dependency = tool_dependency_util.set_tool_dependency_attributes( app,
- tool_dependency=tool_dependency,
- status=app.install_model.ToolDependency.installation_status.ERROR,
- error_message=error_message,
- remove_from_disk=False )
+ status = app.install_model.ToolDependency.installation_status.ERROR
+ tool_dependency = \
+ tool_dependency_util.set_tool_dependency_attributes( app,
+ tool_dependency=tool_dependency,
+ status=status,
+ error_message=error_message,
+ remove_from_disk=False )
return tool_dependency
def strip_path( fpath ):
diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 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
@@ -70,7 +70,7 @@
if display_path is not None:
datatype_util.load_installed_display_applications( trans.app, installed_repository_dict, deactivate=False )
-def get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ):
+def get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies, updating=False ):
"""
Return dictionaries containing the sets of installed and missing tool dependencies and repository
dependencies associated with the repository defined by the received repo_info_dict.
@@ -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_installing_repository( trans, tool_shed_url, tool_dependencies )
+ get_installed_and_missing_tool_dependencies_for_repository( trans, tool_shed_url, 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:
@@ -101,10 +101,11 @@
name,
repository_owner,
changeset_revision )
- if repository and repository.metadata:
+ if not updating and repository and repository.metadata:
installed_rd, missing_rd = get_installed_and_missing_repository_dependencies( trans, repository )
else:
- installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple )
+ installed_rd, missing_rd = \
+ get_installed_and_missing_repository_dependencies_for_new_or_updated_install( trans, repo_info_tuple )
# Discover all repository dependencies and retrieve information for installing them.
all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) )
has_repository_dependencies = all_repo_info_dict.get( 'has_repository_dependencies', False )
@@ -119,7 +120,8 @@
required_tool_dependencies = {}
for rid in required_repo_info_dicts:
for name, repo_info_tuple in rid.items():
- description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, rid_repository_dependencies, rid_tool_dependencies = \
+ description, repository_clone_url, changeset_revision, ctx_rev, \
+ repository_owner, rid_repository_dependencies, rid_tool_dependencies = \
suc.get_repo_info_tuple_contents( repo_info_tuple )
if rid_tool_dependencies:
for td_key, td_dict in rid_tool_dependencies.items():
@@ -128,7 +130,9 @@
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_installing_repository( trans, tool_shed_url, required_tool_dependencies )
+ get_installed_and_missing_tool_dependencies_for_repository( trans,
+ tool_shed_url,
+ required_tool_dependencies )
if required_installed_td:
if not includes_tool_dependencies:
includes_tool_dependencies = True
@@ -168,11 +172,12 @@
def get_installed_and_missing_repository_dependencies( trans, repository ):
"""
- Return the installed and missing repository dependencies for a tool shed repository that has a record in the Galaxy database, but
- may or may not be installed. In this case, the repository dependencies are associated with the repository in the database. Do not
- include a repository dependency if it is required only to compile a tool dependency defined for the dependent repository since these
- special kinds of repository dependencies are really a dependency of the dependent repository's contained tool dependency, and only if
- that tool dependency requires compilation.
+ Return the installed and missing repository dependencies for a tool shed repository that has a record
+ in the Galaxy database, but may or may not be installed. In this case, the repository dependencies are
+ associated with the repository in the database. Do not include a repository dependency if it is required
+ only to compile a tool dependency defined for the dependent repository since these special kinds of repository
+ dependencies are really a dependency of the dependent repository's contained tool dependency, and only
+ if that tool dependency requires compilation.
"""
missing_repository_dependencies = {}
installed_repository_dependencies = {}
@@ -228,7 +233,7 @@
missing_repository_dependencies[ 'description' ] = description
return installed_repository_dependencies, missing_repository_dependencies
-def get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple ):
+def get_installed_and_missing_repository_dependencies_for_new_or_updated_install( trans, repo_info_tuple ):
"""
Parse the received repository_dependencies dictionary that is associated with a repository being
installed into Galaxy for the first time and attempt to determine repository dependencies that are
@@ -264,13 +269,13 @@
tmp_repo_info_tuple )
if repository:
new_rd_tup = [ tool_shed,
- name,
- owner,
- changeset_revision,
- prior_installation_required,
- only_if_compiling_contained_td,
- repository.id,
- repository.status ]
+ name,
+ owner,
+ changeset_revision,
+ prior_installation_required,
+ only_if_compiling_contained_td,
+ repository.id,
+ repository.status ]
if repository.status == trans.install_model.ToolShedRepository.installation_status.INSTALLED:
if new_rd_tup not in installed_rd_tups:
installed_rd_tups.append( new_rd_tup )
@@ -285,12 +290,12 @@
missing_rd_tups.append( new_rd_tup )
else:
new_rd_tup = [ tool_shed,
- name,
- owner,
- changeset_revision,
- prior_installation_required,
- only_if_compiling_contained_td,
- None,
+ name,
+ owner,
+ changeset_revision,
+ prior_installation_required,
+ only_if_compiling_contained_td,
+ None,
'Never installed' ]
if not util.asbool( only_if_compiling_contained_td ):
# A repository dependency that is not installed will not be considered missing if it's value for
@@ -307,11 +312,17 @@
missing_repository_dependencies[ 'description' ] = description
return installed_repository_dependencies, missing_repository_dependencies
-def get_installed_and_missing_tool_dependencies_for_installing_repository( trans, tool_shed_url, tool_dependencies_dict ):
+def get_installed_and_missing_tool_dependencies_for_repository( trans, tool_shed_url, tool_dependencies_dict ):
"""
Return the lists of installed tool dependencies and missing tool dependencies for a set of repositories
being installed into Galaxy.
"""
+ # FIXME: This implementation breaks when updates to a repository contain dependencies that result in
+ # multiple entries for a specific tool dependency. A scenario where this can happen is where 2 repositories
+ # define the same dependency internally (not using the complex repository dependency definition to a separate
+ # package repository approach). If 2 repositories contain the same tool_dependencies.xml file, one dependency
+ # will be lost since the values in these returned dictionaries are not lists. All tool dependency dictionaries
+ # should have lists as values. These scenarios are probably extreme corner cases, but still should be handled.
installed_tool_dependencies = {}
missing_tool_dependencies = {}
if tool_dependencies_dict:
diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 lib/tool_shed/util/container_util.py
--- a/lib/tool_shed/util/container_util.py
+++ b/lib/tool_shed/util/container_util.py
@@ -821,8 +821,8 @@
tool_dependencies = metadata[ 'tool_dependencies' ]
if trans.webapp.name == 'tool_shed':
if 'orphan_tool_dependencies' in metadata:
- # The use of the orphan_tool_dependencies category in metadata has been deprecated, but we still need to check in case
- # the metadata is out of date.
+ # The use of the orphan_tool_dependencies category in metadata has been deprecated,
+ # but we still need to check in case the metadata is out of date.
orphan_tool_dependencies = metadata[ 'orphan_tool_dependencies' ]
tool_dependencies.update( orphan_tool_dependencies )
# Tool dependencies can be categorized as orphans only if the repository contains tools.
diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 lib/tool_shed/util/encoding_util.py
--- a/lib/tool_shed/util/encoding_util.py
+++ b/lib/tool_shed/util/encoding_util.py
@@ -21,7 +21,6 @@
try:
values = json.loads( value )
except Exception, e:
- #log.debug( "Decoding json value from tool shed for value '%s' threw exception: %s" % ( str( value ), str( e ) ) )
pass
if values is not None:
try:
@@ -34,7 +33,7 @@
return values
def tool_shed_encode( val ):
- if isinstance( val, dict ):
+ if isinstance( val, dict ) or isinstance( val, list ):
value = json.dumps( val )
else:
value = val
diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 lib/tool_shed/util/metadata_util.py
--- a/lib/tool_shed/util/metadata_util.py
+++ b/lib/tool_shed/util/metadata_util.py
@@ -662,9 +662,11 @@
# See if we have a repository dependencies defined.
if name == suc.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME:
path_to_repository_dependencies_config = os.path.join( root, name )
- metadata_dict, error_message = generate_repository_dependency_metadata( app,
- path_to_repository_dependencies_config,
- metadata_dict )
+ metadata_dict, error_message = \
+ generate_repository_dependency_metadata( app,
+ path_to_repository_dependencies_config,
+ metadata_dict,
+ updating_installed_repository=updating_installed_repository )
if error_message:
invalid_file_tups.append( ( name, error_message ) )
# See if we have one or more READ_ME files.
@@ -795,7 +797,10 @@
# is True, the tool dependency definition will be set as invalid. This is currently the only case
# where a tool dependency definition is considered invalid.
repository_dependency_tup, repository_dependency_is_valid, error_message = \
- handle_repository_elem( app=app, repository_elem=sub_elem, only_if_compiling_contained_td=False )
+ handle_repository_elem( app=app,
+ repository_elem=sub_elem,
+ only_if_compiling_contained_td=False,
+ updating_installed_repository=False )
elif sub_elem.tag == 'install':
package_install_version = sub_elem.get( 'version', '1.0' )
if package_install_version == '1.0':
@@ -829,7 +834,8 @@
repository_dependency_tup, repository_dependency_is_valid, error_message = \
handle_repository_elem( app=app,
repository_elem=sub_action_elem,
- only_if_compiling_contained_td=True )
+ only_if_compiling_contained_td=True,
+ updating_installed_repository=False )
if requirements_dict:
dependency_key = '%s/%s' % ( package_name, package_version )
if repository_dependency_is_valid:
@@ -841,10 +847,10 @@
return valid_tool_dependencies_dict, invalid_tool_dependencies_dict, repository_dependency_tup, \
repository_dependency_is_valid, error_message
-def generate_repository_dependency_metadata( app, repository_dependencies_config, metadata_dict ):
+def generate_repository_dependency_metadata( app, repository_dependencies_config, metadata_dict, updating_installed_repository=False ):
"""
- Generate a repository dependencies dictionary based on valid information defined in the received repository_dependencies_config. This method
- is called from the tool shed as well as from Galaxy.
+ Generate a repository dependencies dictionary based on valid information defined in the received
+ repository_dependencies_config. This method is called from the tool shed as well as from Galaxy.
"""
error_message = ''
# Make sure we're looking at a valid repository_dependencies.xml file.
@@ -861,7 +867,10 @@
valid_repository_dependency_tups = []
for repository_elem in root.findall( 'repository' ):
repository_dependency_tup, repository_dependency_is_valid, err_msg = \
- handle_repository_elem( app, repository_elem, only_if_compiling_contained_td=False )
+ handle_repository_elem( app,
+ repository_elem,
+ only_if_compiling_contained_td=False,
+ updating_installed_repository=updating_installed_repository )
if repository_dependency_is_valid:
valid_repository_dependency_tups.append( repository_dependency_tup )
else:
@@ -885,11 +894,12 @@
metadata_dict[ 'repository_dependencies' ] = valid_repository_dependencies_dict
return metadata_dict, error_message
-def generate_tool_dependency_metadata( app, repository, changeset_revision, repository_clone_url, tool_dependencies_config, metadata_dict,
- original_repository_metadata=None ):
+def generate_tool_dependency_metadata( app, repository, changeset_revision, repository_clone_url, tool_dependencies_config,
+ metadata_dict, original_repository_metadata=None ):
"""
- If the combination of name, version and type of each element is defined in the <requirement> tag for at least one tool in the repository,
- then update the received metadata_dict with information from the parsed tool_dependencies_config.
+ If the combination of name, version and type of each element is defined in the <requirement> tag for
+ at least one tool in the repository, then update the received metadata_dict with information from the
+ parsed tool_dependencies_config.
"""
error_message = ''
if original_repository_metadata:
@@ -1171,7 +1181,7 @@
deleted_tool_dependency_names.append( original_dependency_val_dict[ 'name' ] )
return updated_tool_dependency_names, deleted_tool_dependency_names
-def handle_repository_elem( app, repository_elem, only_if_compiling_contained_td=False ):
+def handle_repository_elem( app, repository_elem, only_if_compiling_contained_td=False, updating_installed_repository=False ):
"""
Process the received repository_elem which is a <repository> tag either from a repository_dependencies.xml
file or a tool_dependencies.xml file. If the former, we're generating repository dependencies metadata for
@@ -1187,14 +1197,17 @@
changeset_revision = repository_elem.get( 'changeset_revision', None )
prior_installation_required = str( repository_elem.get( 'prior_installation_required', False ) )
if app.name == 'galaxy':
- # We're installing a repository into Galaxy, so make sure its contained repository dependency definition
- # is valid.
- if toolshed is None or name is None or owner is None or changeset_revision is None:
- # Raise an exception here instead of returning an error_message to keep the installation from
- # proceeding. Reaching here implies a bug in the Tool Shed framework.
- error_message = 'Installation halted because the following repository dependency definition is invalid:\n'
- error_message += xml_util.xml_to_string( repository_elem, use_indent=True )
- raise Exception( error_message )
+ if updating_installed_repository:
+ pass
+ else:
+ # We're installing a repository into Galaxy, so make sure its contained repository dependency definition
+ # is valid.
+ if toolshed is None or name is None or owner is None or changeset_revision is None:
+ # Raise an exception here instead of returning an error_message to keep the installation from
+ # proceeding. Reaching here implies a bug in the Tool Shed framework.
+ error_message = 'Installation halted because the following repository dependency definition is invalid:\n'
+ error_message += xml_util.xml_to_string( repository_elem, use_indent=True )
+ raise Exception( error_message )
if not toolshed:
# Default to the current tool shed.
toolshed = str( url_for( '/', qualified=True ) ).rstrip( '/' )
@@ -1230,6 +1243,14 @@
updated_changeset_revision )
if repository:
return repository_dependency_tup, is_valid, error_message
+ if updating_installed_repository:
+ # The repository dependency was included in an update to the installed repository, so it will
+ # not yet be installed. Return the tuple for later installation.
+ return repository_dependency_tup, is_valid, error_message
+ if updating_installed_repository:
+ # The repository dependency was included in an update to the installed repository, so it will not yet
+ # be installed. Return the tuple for later installation.
+ return repository_dependency_tup, is_valid, error_message
# Don't generate an error message for missing repository dependencies that are required only if compiling the
# dependent repository's tool dependency.
if not only_if_compiling_contained_td:
diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 lib/tool_shed/util/tool_dependency_util.py
--- a/lib/tool_shed/util/tool_dependency_util.py
+++ b/lib/tool_shed/util/tool_dependency_util.py
@@ -90,7 +90,6 @@
if tree is None:
return tool_dependency_objects
root = tree.getroot()
- fabric_version_checked = False
for elem in root:
tool_dependency_type = elem.tag
if tool_dependency_type == 'package':
@@ -574,8 +573,8 @@
sa_session.flush()
return tool_dependency
-def sync_database_with_file_system( app, tool_shed_repository, tool_dependency_name, tool_dependency_version, tool_dependency_install_dir,
- tool_dependency_type='package' ):
+def sync_database_with_file_system( app, tool_shed_repository, tool_dependency_name, tool_dependency_version,
+ tool_dependency_install_dir, tool_dependency_type='package' ):
"""
The installation directory defined by the received tool_dependency_install_dir exists, so check for the presence
of fabric_util.INSTALLATION_LOG. If the files exists, we'll assume the tool dependency is installed, but not
diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 templates/admin/tool_shed_repository/common.mako
--- a/templates/admin/tool_shed_repository/common.mako
+++ b/templates/admin/tool_shed_repository/common.mako
@@ -90,6 +90,7 @@
return str( self.count )
repository_dependencies_root_folder = containers_dict.get( 'repository_dependencies', None )
+ missing_repository_dependencies_root_folder = containers_dict.get( 'missing_repository_dependencies', None )
tool_dependencies_root_folder = containers_dict.get( 'tool_dependencies', None )
missing_tool_dependencies_root_folder = containers_dict.get( 'missing_tool_dependencies', None )
env_settings_heaader_row_displayed = False
@@ -112,7 +113,7 @@
</p></div></div>
- %if repository_dependencies_root_folder:
+ %if repository_dependencies_root_folder or missing_repository_dependencies_root_folder:
%if repository_dependencies_check_box is not None:
<div class="form-row">
%if export:
@@ -131,14 +132,26 @@
</div><div style="clear: both"></div>
%endif
- <div class="form-row">
- <p/>
- <% row_counter = RowCounter() %>
- <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table">
- ${render_folder( repository_dependencies_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
- </table>
- <div style="clear: both"></div>
- </div>
+ %if repository_dependencies_root_folder:
+ <div class="form-row">
+ <p/>
+ <% row_counter = RowCounter() %>
+ <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table">
+ ${render_folder( repository_dependencies_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
+ </table>
+ <div style="clear: both"></div>
+ </div>
+ %endif
+ %if missing_repository_dependencies_root_folder:
+ <div class="form-row">
+ <p/>
+ <% row_counter = RowCounter() %>
+ <table cellspacing="2" cellpadding="2" border="0" width="100%" class="tables container-table">
+ ${render_folder( missing_repository_dependencies_root_folder, 0, parent=None, row_counter=row_counter, is_root_folder=True )}
+ </table>
+ <div style="clear: both"></div>
+ </div>
+ %endif
%endif
%if tool_dependencies_root_folder or missing_tool_dependencies_root_folder:
%if install_tool_dependencies_check_box is not None:
diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 templates/admin/tool_shed_repository/install_tool_dependencies.mako
--- a/templates/admin/tool_shed_repository/install_tool_dependencies.mako
+++ /dev/null
@@ -1,81 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-<% import os %>
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-<div class="warningmessage">
- <p>
- The tool dependencies listed below can be automatically installed with the repository. Installing them provides significant
- benefits and Galaxy includes various features to manage them.
- </p>
- <p>
- Each of these dependencies may require their own build requirements (e.g., CMake, g++, etc). Galaxy will not attempt to install
- these build requirements, so if any are missing from your environment tool dependency installation may partially fail. The
- repository and all of it's contents will be installed in any case.
- </p>
- <p>
- If tool dependency installation fails in any way, you can install the missing build requirements and have Galaxy attempt to install
- the tool dependencies again using the <b>Install tool dependencies</b> pop-up menu option on the <b>Manage repository</b> page.
- </p>
-</div>
-
-<div class="toolForm">
- <div class="toolFormBody">
- <form name="install_tool_dependenceies" id="install_tool_dependenceies" action="${h.url_for( controller='admin_toolshed', action='install_tool_dependencies' )}" method="post" >
- <div class="form-row">
- <table class="grid">
- <tr><td colspan="4" bgcolor="#D8D8D8"><b>Tool dependencies</b></td></tr>
- <tr>
- <th>Name</th>
- <th>Version</th>
- <th>Type</th>
- <th>Install directory</th>
- </tr>
- <% tool_shed_repository = None %>
- %for tool_dependency in tool_dependencies:
- <input type="hidden" name="tool_dependency_ids" value="${trans.security.encode_id( tool_dependency.id )}"/>
- <%
- readme_text = None
- if tool_shed_repository is None:
- tool_shed_repository = tool_dependency.tool_shed_repository
- metadata = tool_shed_repository.metadata
- tool_dependencies_dict = metadata[ 'tool_dependencies' ]
- for key, requirements_dict in tool_dependencies_dict.items():
- key_items = key.split( '/' )
- key_name = key_items[ 0 ]
- key_version = key_items[ 1 ]
- if key_name == tool_dependency.name and key_version == tool_dependency.version:
- readme_text = requirements_dict.get( 'readme', None )
- install_dir = os.path.join( trans.app.config.tool_dependency_dir,
- tool_dependency.name,
- tool_dependency.version,
- tool_shed_repository.owner,
- tool_shed_repository.name,
- tool_shed_repository.installed_changeset_revision )
- %>
- %if not os.path.exists( install_dir ):
- <tr>
- <td>${tool_dependency.name}</td>
- <td>${tool_dependency.version}</td>
- <td>${tool_dependency.type}</td>
- <td>${install_dir}</td>
- </tr>
- %if readme_text:
- <tr><td colspan="4" bgcolor="#FFFFCC">${tool_dependency.name} ${tool_dependency.version} requirements and installation information</td></tr>
- <tr><td colspan="4"><pre>${readme_text}</pre></td></tr>
- %endif
- %endif
- %endfor
- </table>
- <div style="clear: both"></div>
- </div>
- <div class="form-row">
- <input type="submit" name="install_tool_dependencies_button" value="Install"/>
- </div>
- </form>
- </div>
-</div>
diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako
--- /dev/null
+++ b/templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako
@@ -0,0 +1,91 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" />
+<%namespace file="/message.mako" import="render_msg" />
+
+<%
+ import os
+ from tool_shed.util.common_util import parse_repository_dependency_tuple
+%>
+
+${render_galaxy_repository_actions( repository )}
+
+%if message:
+ ${render_msg( message, status )}
+%endif
+
+<div class="warningmessage">
+ <p>
+ The updates to the <b>${repository.name}</b> repository require the following packages. Click the <b>Install</b> button to install them.
+ Installing some packages may take a while, but you can continue to use Galaxy during installation.
+ </p>
+</div>
+
+<div class="toolForm">
+ <div class="toolFormBody">
+ <form name="install_tool_dependencies_with_update" id="install_tool_dependencies_with_update" action="${h.url_for( controller='admin_toolshed', action='install_tool_dependencies_with_update' )}" method="post" >
+ <input type="hidden" name="updating_repository_id" value="${updating_repository_id}"/>
+ <input type="hidden" name="updating_to_ctx_rev" value="${updating_to_ctx_rev}"/>
+ <input type="hidden" name="updating_to_changeset_revision" value="${updating_to_changeset_revision}"/>
+ <input type="hidden" name="encoded_updated_metadata" value="${encoded_updated_metadata}"/>
+ <input type="hidden" name="encoded_relative_install_dir" value="${encoded_relative_install_dir}"/>
+ <input type="hidden" name="encoded_tool_dependencies_dict" value="${encoded_tool_dependencies_dict}"/>
+ %if tool_dependencies_dict:
+ %if install_tool_dependencies_check_box is not None:
+ <div class="form-row">
+ <label>Handle tool dependencies?</label>
+ <% disabled = trans.app.config.tool_dependency_dir is None %>
+ ${install_tool_dependencies_check_box.get_html( disabled=disabled )}
+ <div class="toolParamHelp" style="clear: both;">
+ %if disabled:
+ Set the tool_dependency_dir configuration value in your Galaxy config to automatically handle tool dependencies.
+ %else:
+ Un-check to skip automatic handling of these tool dependencies.
+ %endif
+ </div>
+ </div>
+ <div style="clear: both"></div>
+ %endif
+ <div class="form-row">
+ <table class="grid">
+ <tr><td colspan="4" bgcolor="#D8D8D8"><b>New tool dependencies included in update</b></td></tr>
+ <tr>
+ <th>Name</th>
+ <th>Version</th>
+ <th>Install directory</th>
+ </tr>
+ %for key, requirements_dict in tool_dependencies_dict.items():
+ <%
+ readme_text = None
+ key_items = key.split( '/' )
+ key_name = key_items[ 0 ]
+ key_version = key_items[ 1 ]
+ readme_text = requirements_dict.get( 'readme', None )
+ install_dir = os.path.join( trans.app.config.tool_dependency_dir,
+ key_name,
+ key_version,
+ repository.owner,
+ repository.name,
+ repository.installed_changeset_revision )
+ %>
+ %if not os.path.exists( install_dir ):
+ <tr>
+ <td>${key_name}</td>
+ <td>${key_version}</td>
+ <td>${install_dir}</td>
+ </tr>
+ %if readme_text:
+ <tr><td colspan="4" bgcolor="#FFFFCC">${key_name} ${key_version} requirements and installation information</td></tr>
+ <tr><td colspan="4"><pre>${readme_text}</pre></td></tr>
+ %endif
+ %endif
+ %endfor
+ </table>
+ <div style="clear: both"></div>
+ </div>
+ %endif
+ <div class="form-row">
+ <input type="submit" name="install_tool_dependencies_with_update_button" value="Install"/>
+ </div>
+ </form>
+ </div>
+</div>
diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako
--- a/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako
+++ b/templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako
@@ -30,8 +30,6 @@
<tr><th bgcolor="#D8D8D8">Name</th><th bgcolor="#D8D8D8">Version</th><th bgcolor="#D8D8D8">Type</th><th bgcolor="#D8D8D8">Status</th><th bgcolor="#D8D8D8">Error</th></tr>
%for tool_dependency in repository.tool_dependencies:
<%
- # Tool dependencies cannot be uninstalled if they have a status of 'Installed'. Only the containing repository
- # can be uninstalled (only if it has no dependent repositories) if a tool dependency has been successfully installed.
if tool_dependency.error_message:
error_message = tool_dependency.error_message
else:
@@ -41,8 +39,7 @@
trans.install_model.ToolDependency.installation_status.UNINSTALLED ]:
can_install = True
if not can_uninstall:
- if tool_dependency.status not in [ trans.install_model.ToolDependency.installation_status.INSTALLED,
- trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
+ if tool_dependency.status not in [ trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
trans.install_model.ToolDependency.installation_status.UNINSTALLED ]:
can_uninstall = True
%>
diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
--- a/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
+++ b/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
@@ -46,8 +46,8 @@
<div class="warningmessage"><p>
- The core Galaxy development team does not maintain the contents of many Galaxy tool shed repositories. Some repository tools
- may include code that produces malicious behavior, so be aware of what you are installing.
+ The Galaxy development team does not maintain the contents of many Galaxy Tool Shed repositories. Some
+ repository tools may include code that produces malicious behavior, so be aware of what you are installing.
</p><p>
If you discover a repository that causes problems after installation, contact <a href="http://wiki.g2.bx.psu.edu/Support" target="_blank">Galaxy support</a>,
@@ -63,6 +63,11 @@
<form name="select_shed_tool_panel_config" id="select_shed_tool_panel_config" action="${h.url_for( controller='admin_toolshed', action='prepare_for_install' )}" method="post" ><div class="form-row"><input type="hidden" name="encoded_repo_info_dicts" value="${encoded_repo_info_dicts}" />
+ <input type="hidden" name="updating" value="${updating}" />
+ <input type="hidden" name="updating_repository_id" value="${updating_repository_id}" />
+ <input type="hidden" name="updating_to_ctx_rev" value="${updating_to_ctx_rev}" />
+ <input type="hidden" name="updating_to_changeset_revision" value="${updating_to_changeset_revision}" />
+ <input type="hidden" name="encoded_updated_metadata" value="${encoded_updated_metadata}" /><input type="hidden" name="includes_tools" value="${includes_tools}" /><input type="hidden" name="includes_tool_dependencies" value="${includes_tool_dependencies}" /><input type="hidden" name="includes_tools_for_display_in_tool_panel" value="${includes_tools_for_display_in_tool_panel}" />
diff -r 09985439d17f9bef026554938b05d0d6eedd06cb -r 90b4baa5c2b18d49bcea5a0807f0df8924abebb1 templates/admin/tool_shed_repository/select_tool_panel_section.mako
--- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako
+++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako
@@ -46,8 +46,8 @@
<div class="warningmessage"><p>
- The core Galaxy development team does not maintain the contents of many Galaxy tool shed repositories. Some repository tools
- may include code that produces malicious behavior, so be aware of what you are installing.
+ The Galaxy development team does not maintain the contents of many Galaxy Tool Shed repositories. Some
+ repository tools may include code that produces malicious behavior, so be aware of what you are installing.
</p><p>
If you discover a repository that causes problems after installation, contact <a href="http://wiki.g2.bx.psu.edu/Support" target="_blank">Galaxy support</a>,
@@ -67,6 +67,11 @@
<input type="hidden" name="includes_tools_for_display_in_tool_panel" value="${includes_tools_for_display_in_tool_panel}" /><input type="hidden" name="tool_shed_url" value="${tool_shed_url}" /><input type="hidden" name="encoded_repo_info_dicts" value="${encoded_repo_info_dicts}" />
+ <input type="hidden" name="updating" value="${updating}" />
+ <input type="hidden" name="updating_repository_id" value="${updating_repository_id}" />
+ <input type="hidden" name="updating_to_ctx_rev" value="${updating_to_ctx_rev}" />
+ <input type="hidden" name="updating_to_changeset_revision" value="${updating_to_changeset_revision}" />
+ <input type="hidden" name="encoded_updated_metadata" value="${encoded_updated_metadata}" /></div><div style="clear: both"></div><% readme_files_dict = containers_dict.get( 'readme_files', None ) %>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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