'+t.name+"
"}});return{View:a}}.apply(e,a),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var a,s;(function(n,l,o){a=[i(4),i(11)],s=function(t,e){var i=n.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new n.Model({visible:!0,data:[],id:t.uid(),error_text:"No options available.",wait_text:"Please wait...",multiple:!1,optional:!1,onchange:function(){}}).set(e),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:visible",this._changeVisible,this),this.on("change",function(){i.model.get("onchange")(i.value())}),this.render()},render:function(){var t=this;this.$el.empty().removeClass().addClass("ui-options").append(this.$message=l("")).append(this.$menu=l("").addClass("ui-options-menu")).append(this.$options=l(this._template())),this.all_button=null,this.model.get("multiple")&&(this.all_button=new e.ButtonCheck({onclick:function(){
-t.$("input").prop("checked",0!==t.all_button.value()),t.value(t._getValue()),t.trigger("change")}}),this.$menu.append(this.all_button.$el)),this._changeData(),this._changeWait(),this._changeVisible()},update:function(t){this.model.set("data",t)},_changeData:function(){var t=this;this.$options.empty(),this._templateOptions?this.$options.append(this._templateOptions(this.model.get("data"))):o.each(this.model.get("data"),function(e){t.$options.append(l(t._templateOption(e)).addClass("ui-option").tooltip({title:e.tooltip,placement:"bottom"}))});var t=this;this.$("input").on("change",function(){t.value(t._getValue()),t.trigger("change")}),this._changeValue(),this._changeWait()},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"]()},_changeWait:function(){this.model.get("wait")?0===this.length()&&(this._messageShow(this.model.get("wait_text"),"info"),this.$options.hide(),this.$menu.hide()):0===this.length()?(this._messageShow(this.model.get("error_text"),"danger"),this.$options.hide(),this.$menu.hide()):(this.$message.hide(),this.$options.css("display","inline-block"),this.$menu.show())},_changeValue:function(){this._setValue(this.model.get("value")),null!==this._getValue()||this.model.get("multiple")||this.model.get("optional")||this._setValue(this.first()),this.all_button&&this.all_button.value(l.isArray(this._getValue())?this._getValue().length:0,this.length())},value:function(t){return void 0!==t&&this.model.set("value",t),this._getValue()},first:function(){var t=this.$("input").first();return t.length>0?t.val():null},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},length:function(){return this.$(".ui-option").length},_setValue:function(t){var e=this;if(void 0!==t&&(this.$("input").prop("checked",!1),null!==t)){var i=l.isArray(t)?t:[t];o.each(i,function(t){e.$('input[value="'+t+'"]').first().prop("checked",!0)})}},_getValue:function(){var e=[];return this.$(":checked").each(function(){e.push(l(this).val())}),t.isEmpty(e)?null:this.model.get("multiple")?e:e[0]},_messageShow:function(t,e){this.$message.show().removeClass().addClass("ui-message alert alert-"+e).html(t)},_template:function(){return l("").addClass("ui-options-list")}}),a=i.extend({_templateOption:function(e){var i=t.uid();return l("").addClass("ui-option").append(l("").attr({id:i,type:this.model.get("type"),name:this.model.id,value:e.value})).append(l("").addClass("ui-options-label").attr("for",i).html(e.label))}}),s={};s.View=a.extend({initialize:function(t){t.type="radio",a.prototype.initialize.call(this,t)}});var r={};r.View=a.extend({initialize:function(t){t.type="checkbox",t.multiple=!0,a.prototype.initialize.call(this,t)}});var d={};return d.View=i.extend({initialize:function(t){i.prototype.initialize.call(this,t)},_setValue:function(t){void 0!==t&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+t+'"]').prop("checked",!0).closest("label").addClass("active"))},_templateOption:function(t){var e=l("").addClass("btn btn-default");return t.icon&&e.append(l("").addClass("fa").addClass(t.icon).addClass(!t.label&&"no-padding")),e.append(l("").attr({type:"radio",name:this.model.id,value:t.value})),t.label&&e.append(t.label),e},_template:function(){return l("").addClass("btn-group ui-radiobutton").attr("data-toggle","buttons")}}),{Base:i,BaseIcons:a,Radio:s,RadioButton:d,Checkbox:r}}.apply(e,a),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var a,s;(function(n,l,o){a=[i(4),i(11)],s=function(t,e){var i=n.View.extend({initialize:function(e){var i=this;this.data=[],this.data2=[],this.model=e&&e.model||new n.Model({id:t.uid(),cls:"ui-select",error_text:"No options available",empty_text:"Nothing selected",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1,disabled:!1,onchange:function(){},value:null,individual:!1,pagesize:20}).set(e),this.on("change",function(){i.model.get("onchange")&&i.model.get("onchange")(i.value())}),this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:disabled",this._changeDisabled,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:visible",this._changeVisible,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:multiple change:searchable change:cls change:id",this.render,this),this.render()},render:function(){var t=this;this.model.get("searchable")?this._renderSearchable():this._renderClassic(),this.$el.addClass(this.model.get("cls")).attr("id",this.model.get("id")),this.$select.empty().addClass("select").attr("id",this.model.get("id")+"_select").prop("multiple",this.model.get("multiple")).on("change",function(){t.value(t._getValue()),t.trigger("change")}),this._changeData(),this._changeWait(),this._changeVisible(),this._changeDisabled()},_renderClassic:function(){var t=this;this.$el.addClass(this.model.get("multiple")?"ui-select-multiple":"ui-select").append(this.$select=l("")).append(this.$dropdown=l("")).append(this.$resize=l("").append(this.$resize_icon=l(""))),this.model.get("multiple")?(this.$dropdown.hide(),this.$resize_icon.addClass("fa fa-angle-double-right fa-rotate-45").show(),this.$resize.removeClass().addClass("icon-resize").show().off("mousedown").on("mousedown",function(e){var i=e.pageY,a=t.$select.height();t.minHeight=t.minHeight||a,l("#dd-helper").show().on("mousemove",function(e){t.$select.height(Math.max(a+(e.pageY-i),t.minHeight))}).on("mouseup mouseleave",function(){l("#dd-helper").hide().off()})})):(this.$dropdown.show(),this.$resize.hide(),this.$resize_icon.hide())},_renderSearchable:function(){var t=this;this.$el.append(this.$select=l("")).append(this.$dropdown=l("")),this.$dropdown.hide(),this.model.get("multiple")||this.$dropdown.show().on("click",function(){t.$select.select2&&t.$select.select2("open")}),this.all_button=null,this.model.get("multiple")&&!this.model.get("individual")&&(this.all_button=new e.ButtonCheck({onclick:function(){var e=[];0!==t.all_button.value()&&o.each(t.model.get("data"),function(t){e.push(t.value)}),t.value(e),t.trigger("change")}}),this.$el.prepend(this.all_button.$el))},_match:function(t,e){return!t||""==t||String(e).toUpperCase().indexOf(t.toUpperCase())>=0},_changeData:function(){var t=this;this.data=[],!this.model.get("multiple")&&this.model.get("optional")&&this.data.push({value:"__null__",label:t.model.get("empty_text")}),o.each(this.model.get("data"),function(e){t.data.push(e)}),0==this.length()&&this.data.push({value:"__null__",label:this.model.get("error_text")}),this.model.get("searchable")?(this.data2=[],o.each(this.data,function(e,i){t.data2.push({order:i,id:e.value,text:e.label,tags:e.tags})}),this.$select.data("select2")&&this.$select.select2("destroy"),this.matched_tags={},this.$select.select2({data:t.data2,closeOnSelect:!this.model.get("multiple"),multiple:this.model.get("multiple"),query:function(e){t.matched_tags={};var i=t.model.get("pagesize"),a=o.filter(t.data2,function(i){var a=!1;return o.each(i.tags,function(i){t._match(e.term,i)&&(a=t.matched_tags[i]=!0)}),a||t._match(e.term,i.text)});e.callback({results:a.slice((e.page-1)*i,e.page*i),more:a.length>=e.page*i})},formatResult:function(e){return o.escape(e.text)+'"}}),this.$(".select2-container .select2-search input").off("blur")):(this.$select.find("option").remove(),o.each(this.data,function(e){t.$select.append(l("").attr("value",e.value).html(o.escape(e.label)))})),this.model.set("disabled",0==this.length()),this._changeValue()},_changeDisabled:function(){this.model.get("searchable")?this.$select.select2(this.model.get("disabled")?"disable":"enable"):this.$select.prop("disabled",this.model.get("disabled"))},_changeWait:function(){this.$dropdown.removeClass().addClass("icon-dropdown fa").addClass(this.model.get("wait")?"fa-spinner fa-spin":"fa-caret-down")},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"](),this.$select[this.model.get("visible")?"show":"hide"]()},_changeValue:function(){if(this._setValue(this.model.get("value")),this.model.get("multiple")){if(this.all_button){var t=this._getValue();this.all_button.value(l.isArray(t)?t.length:0,this.length())}}else null!==this._getValue()||this.model.get("optional")||this._setValue(this.first())},value:function(t){return void 0!==t&&this.model.set("value",t),this._getValue()},first:function(){return this.data.length>0?this.data[0].value:null},exists:function(t){return o.findWhere(this.data,{value:t})},text:function(){var t=this._getValue(),e=this.exists(l.isArray(t)?t[0]:t);return e?e.label:""},show:function(){this.model.set("visible",!0)},hide:function(){this.model.set("visible",!1)},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},disabled:function(){return this.model.get("disabled")},enable:function(){this.model.set("disabled",!1)},disable:function(){this.model.set("disabled",!0)},add:function(t,e){o.each(this.model.get("data"),function(e){e.keep&&!o.findWhere(t,{value:e.value})&&t.push(e)}),e&&t&&t.sort(e),this.model.set("data",t)},update:function(t){this.model.set("data",t)},setOnChange:function(t){this.model.set("onchange",t)},length:function(){return l.isArray(this.model.get("data"))?this.model.get("data").length:0},_setValue:function(t){var e=this;if(null!==t&&void 0!==t||(t="__null__"),this.model.get("multiple")?t=l.isArray(t)?t:[t]:l.isArray(t)&&(t=t.length>0?t[0]:"__null__"),this.model.get("searchable")){if(l.isArray(t)){var i=[];o.each(t,function(t){var a=o.findWhere(e.data2,{id:t});a&&i.push(a)}),t=i}else{var a=o.findWhere(this.data2,{id:t});t=a}this.$select.select2("data",t)}else this.$select.val(t)},_getValue:function(){var e=null;if(this.model.get("searchable")){var i=this.$select.select2("data");i&&(l.isArray(i)?(e=[],i.sort(function(t,e){return t.order-e.order}),o.each(i,function(t){e.push(t.id)})):e=i.id)}else e=this.$select.val();return t.isEmpty(e)?null:e}});return{View:i}}.apply(e,a),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},,,function(t,e,i){var a,s;(function(i,n,l,o){a=[],s=function(){var t=i.View.extend({initialize:function(t,e){this.$button=t,this.$button.length||(this.$button=n("")),this.options=e||[],this.$button.data("popupmenu",this);var i=this;this.$button.click(function(t){return n(".popmenu-wrapper").remove(),i._renderAndShow(t),!1})},_renderAndShow:function(t){this.render(),this.$el.appendTo("body").css(this._getShownPosition(t)).show(),this._setUpCloseBehavior()},render:function(){if(this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options)),this.options.length){var t=this;this.$el.find("li").each(function(e,i){var a=t.options[e];a.func&&n(this).children("a.popupmenu-option").click(function(e){a.func.call(t,e,a),e.preventDefault()})})}return this},template:function(t,e){return['"].join("")},_templateOptions:function(t){return t.length?l.map(t,function(t){if(t.divider)return'';if(t.header)return['"}});return{View:e}}.apply(e,a),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},,,,,,function(t,e,i){var a,s;(function(i,n,l){a=[],s=function(){return i.View.extend({initialize:function(t,e){this.app=t,this.app_options=t.model?t.model.attributes:{},this.field=e&&e.field||new i.View,this.model=e&&e.model||new i.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(e),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var a=this.model.get("collapsible_value");this.field.collapsed=void 0!==a&&JSON.stringify(this.model.get("value"))==JSON.stringify(a),this.listenTo(this.model,"change",this.render,this),this.render();var s=this;this.$collapsible.on("click",function(){s.field.collapsed=!s.field.collapsed,t.trigger&&t.trigger("change"),s.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){s.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(t){this.model.set("error_text",t)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){n(".tooltip").hide();var t=this.model.get("help",""),e=this.model.get("argument");e&&t.indexOf("("+e+")")==-1&&(t+=" ("+e+")"),this.$info.html(t),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(l.escape(this.model.get("text_value")));var i=this.model.get("error_text");if(this.$error[i?"show":"hide"](),this.$el[i?"addClass":"removeClass"]("ui-error"),this.$error_text.html(i),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var a=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+a)).attr("data-original-title",this.model.get("text_"+a)).tooltip({placement:"bottom"})}},_template:function(){return n("").addClass("ui-form-element").append(n("").addClass("ui-form-error ui-error").append(n("").addClass("fa fa-arrow-down")).append(n("").addClass("ui-form-error-text"))).append(n("").addClass("ui-form-title").append(n("").addClass("ui-form-collapsible").append(n("").addClass("ui-form-collapsible-icon")).append(n("").addClass("ui-form-collapsible-text"))).append(n("").addClass("ui-form-title-text"))).append(n("").addClass("ui-form-field").append(n("").addClass("ui-form-info")).append(n("").addClass("ui-form-backdrop"))).append(n("").addClass("ui-form-preview"))}})}.apply(e,a),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var a,s;(function(n,l,o){a=[i(4),i(5),i(38),i(41),i(39),i(40),i(36)],s=function(t,e,i,a,s,r,d){return n.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider",float:"_fieldSlider",boolean:"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(t){var e=this.types[t.type],i="function"==typeof this[e]?this[e].call(this,t):null;return i||(i=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0===t.value&&(t.value=null),i.value(t.value),i},_fieldData:function(t){return new i.View({id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,flavor:t.flavor,data:t.options,onchange:t.onchange})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var i=t.data;i||(i=[],l.each(t.options,function(t){i.push({label:t[0],value:t[1]})}));var a=e.Select;switch(t.display){case"checkboxes":a=e.Checkbox;break;case"radio":a=e.Radio;break;case"radiobutton":a=e.RadioButton}return new a.View({id:"field-"+t.id,data:i,error_text:t.error_text||"No options available",multiple:t.multiple,optional:t.optional,onchange:t.onchange,individual:t.individual,searchable:"workflow"!==t.flavor})},_fieldDrilldown:function(t){return t.is_workflow?this._fieldText(t):new e.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,optional:t.optional,onchange:t.onchange})},_fieldText:function(i){if(i.options&&i.data)if(i.area=i.multiple,t.isEmpty(i.value))i.value=null;else if(o.isArray(i.value)){var a="";for(var s in i.value){if(a+=String(i.value[s]),!i.multiple)break;a+="\n"}i.value=a}return new e.Input({id:"field-"+i.id,type:i.type,area:i.area,readonly:i.readonly,placeholder:i.placeholder,datalist:i.datalist,onchange:i.onchange})},_fieldSlider:function(t){return new e.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,min:t.min,max:t.max,onchange:t.onchange})},_fieldHidden:function(t){return new e.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){return new e.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:t.onchange})},_fieldColor:function(t){return new d({id:"field-"+t.id,onchange:t.onchange})},_fieldLibrary:function(t){return new a.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldFtp:function(t){return new s.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldGenomeSpace:function(t){var e=this;return new r.View({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldUpload:function(t){return new e.Upload({id:"field-"+t.id,onchange:t.onchange})}})}.apply(e,a),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var a,s;(function(n,l,o){a=[i(4),i(9),i(5)],s=function(t,e,i){var a=n.View.extend({initialize:function(e){this.list={},this.options=t.merge(e,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new i.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float form-repeat-add",onclick:function(){e.onnew&&e.onnew()}}),this.setElement(l("").append(this.$list=l("")).append(l("").append(this.button_new.$el)))},size:function(){return o.size(this.list)},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var a=new i.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){t.ondel&&t.ondel()}}),s=new e.View({id:t.id,title:"placeholder",cls:t.cls||"ui-portlet-repeat",operations:{button_delete:a}});s.append(t.$el),s.$el.addClass("section-row").hide(),this.list[t.id]=s,this.$list.append(s.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){return this.list[t]?(this.$list.find("#"+t).remove(),delete this.list[t],this.button_new.enable(),void this._refresh()):void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.")},delAll:function(){for(var t in this.list)this.del(t)},hideOptions:function(){this.button_new.$el.hide(),o.each(this.list,function(t){t.hideOperation("button_delete")}),o.isEmpty(this.list)&&this.$el.append(l("").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var i=this.list[e];i.title(++t+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});return{View:a}}.apply(e,a),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var a,s;(function(n,l,o,r){a=[i(4),i(5),i(9),i(31),i(29),i(30)],s=function(t,e,i,a,s,d){var c=n.View.extend({initialize:function(t,e){this.app=t,this.inputs=e.inputs,this.parameters=new d,this.setElement(l("")),this.render()},render:function(){var t=this;this.$el.empty(),o.each(this.inputs,function(e){t.add(e)})},add:function(e){var i=r.extend(!0,{},e);switch(i.id=e.id=t.uid(),this.app.input_list[i.id]=i,i.type){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(t){var e=this;t.test_param.id=t.id,this.app.model.get("sustain_conditionals")&&(t.test_param.disabled=!0);var i=this._addRow(t.test_param);i.model&&i.model.set("onchange",function(i){var a=e.app.data.matchCase(t,i);for(var s in t.cases){var n=t.cases[s],l=e.$("#"+t.id+"-section-"+s),o=!1;for(var r in n.inputs)if(!n.inputs[r].hidden){o=!0;break}s==a&&o?l.fadeIn("fast"):l.hide()}e.app.trigger("change")});for(var a in t.cases){var s=new c(this.app,{inputs:t.cases[a].inputs});this._append(s.$el.addClass("ui-form-section"),t.id+"-section-"+a)}i.trigger("change")},_addRepeat:function(t){function e(e){var a=t.id+"-section-"+n++,s=new c(i.app,{inputs:e});l.add({id:a,$el:s.$el,ondel:function(){l.del(a),i.app.trigger("change")}})}for(var 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",h+='
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'},_templateBox:function(t){return''},_template:function(){return'
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Token
Select Library
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t=this;this.$("input").on("change",function(){t.value(t._getValue()),t.trigger("change")}),this._changeValue(),this._changeWait()},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"]()},_changeWait:function(){this.model.get("wait")?0===this.length()&&(this._messageShow(this.model.get("wait_text"),"info"),this.$options.hide(),this.$menu.hide()):0===this.length()?(this._messageShow(this.model.get("error_text"),"danger"),this.$options.hide(),this.$menu.hide()):(this.$message.hide(),this.$options.css("display","inline-block"),this.$menu.show())},_changeValue:function(){this._setValue(this.model.get("value")),null!==this._getValue()||this.model.get("multiple")||this.model.get("optional")||this._setValue(this.first()),this.all_button&&this.all_button.value(l.isArray(this._getValue())?this._getValue().length:0,this.length())},value:function(t){return void 0!==t&&this.model.set("value",t),this._getValue()},first:function(){var t=this.$("input").first();return t.length>0?t.val():null},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},length:function(){return this.$(".ui-option").length},_setValue:function(t){var e=this;if(void 0!==t&&(this.$("input").prop("checked",!1),null!==t)){var i=l.isArray(t)?t:[t];o.each(i,function(t){e.$('input[value="'+t+'"]').first().prop("checked",!0)})}},_getValue:function(){var e=[];return this.$(":checked").each(function(){e.push(l(this).val())}),t.isEmpty(e)?null:this.model.get("multiple")?e:e[0]},_messageShow:function(t,e){this.$message.show().removeClass().addClass("ui-message alert alert-"+e).html(t)},_template:function(){return l("").addClass("ui-options-list")}}),a=i.extend({_templateOption:function(e){var i=t.uid();return l("").addClass("ui-option").append(l("").attr({id:i,type:this.model.get("type"),name:this.model.id,value:e.value})).append(l("").addClass("ui-options-label").attr("for",i).html(e.label))}}),s={};s.View=a.extend({initialize:function(t){t.type="radio",a.prototype.initialize.call(this,t)}});var r={};r.View=a.extend({initialize:function(t){t.type="checkbox",t.multiple=!0,a.prototype.initialize.call(this,t)}});var d={};return d.View=i.extend({initialize:function(t){i.prototype.initialize.call(this,t)},_setValue:function(t){void 0!==t&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+t+'"]').prop("checked",!0).closest("label").addClass("active"))},_templateOption:function(t){var e=l("").addClass("btn btn-default");return t.icon&&e.append(l("").addClass("fa").addClass(t.icon).addClass(!t.label&&"no-padding")),e.append(l("").attr({type:"radio",name:this.model.id,value:t.value})),t.label&&e.append(t.label),e},_template:function(){return l("").addClass("btn-group ui-radiobutton").attr("data-toggle","buttons")}}),{Base:i,BaseIcons:a,Radio:s,RadioButton:d,Checkbox:r}}.apply(e,a),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var a,s;(function(n,l,o){a=[i(4),i(11)],s=function(t,e){var i=n.View.extend({initialize:function(e){var i=this;this.data=[],this.data2=[],this.model=e&&e.model||new n.Model({id:t.uid(),cls:"ui-select",error_text:"No options available",empty_text:"Nothing selected",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1,disabled:!1,onchange:function(){},value:null,individual:!1,pagesize:20}).set(e),this.on("change",function(){i.model.get("onchange")&&i.model.get("onchange")(i.value())}),this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:disabled",this._changeDisabled,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:visible",this._changeVisible,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:multiple change:searchable change:cls change:id",this.render,this),this.render()},render:function(){var t=this;this.model.get("searchable")?this._renderSearchable():this._renderClassic(),this.$el.addClass(this.model.get("cls")).attr("id",this.model.get("id")),this.$select.empty().addClass("select").attr("id",this.model.get("id")+"_select").prop("multiple",this.model.get("multiple")).on("change",function(){t.value(t._getValue()),t.trigger("change")}),this._changeData(),this._changeWait(),this._changeVisible(),this._changeDisabled()},_renderClassic:function(){var t=this;this.$el.addClass(this.model.get("multiple")?"ui-select-multiple":"ui-select").append(this.$select=l("")).append(this.$dropdown=l("")).append(this.$resize=l("").append(this.$resize_icon=l(""))),this.model.get("multiple")?(this.$dropdown.hide(),this.$resize_icon.addClass("fa fa-angle-double-right fa-rotate-45").show(),this.$resize.removeClass().addClass("icon-resize").show().off("mousedown").on("mousedown",function(e){var i=e.pageY,a=t.$select.height();t.minHeight=t.minHeight||a,l("#dd-helper").show().on("mousemove",function(e){t.$select.height(Math.max(a+(e.pageY-i),t.minHeight))}).on("mouseup mouseleave",function(){l("#dd-helper").hide().off()})})):(this.$dropdown.show(),this.$resize.hide(),this.$resize_icon.hide())},_renderSearchable:function(){var t=this;this.$el.append(this.$select=l("")).append(this.$dropdown=l("")),this.$dropdown.hide(),this.model.get("multiple")||this.$dropdown.show().on("click",function(){t.$select.select2&&t.$select.select2("open")}),this.all_button=null,this.model.get("multiple")&&!this.model.get("individual")&&(this.all_button=new e.ButtonCheck({onclick:function(){var e=[];0!==t.all_button.value()&&o.each(t.model.get("data"),function(t){e.push(t.value)}),t.value(e),t.trigger("change")}}),this.$el.prepend(this.all_button.$el))},_match:function(t,e){return!t||""==t||String(e).toUpperCase().indexOf(t.toUpperCase())>=0},_changeData:function(){var t=this;this.data=[],!this.model.get("multiple")&&this.model.get("optional")&&this.data.push({value:"__null__",label:t.model.get("empty_text")}),o.each(this.model.get("data"),function(e){t.data.push(e)}),0==this.length()&&this.data.push({value:"__null__",label:this.model.get("error_text")}),this.model.get("searchable")?(this.data2=[],o.each(this.data,function(e,i){t.data2.push({order:i,id:e.value,text:e.label,tags:e.tags})}),this.$select.data("select2")&&this.$select.select2("destroy"),this.matched_tags={},this.$select.select2({data:t.data2,closeOnSelect:!this.model.get("multiple"),multiple:this.model.get("multiple"),query:function(e){t.matched_tags={};var i=t.model.get("pagesize"),a=o.filter(t.data2,function(i){var a=!1;return o.each(i.tags,function(i){t._match(e.term,i)&&(a=t.matched_tags[i]=!0)}),a||t._match(e.term,i.text)});e.callback({results:a.slice((e.page-1)*i,e.page*i),more:a.length>=e.page*i})},formatResult:function(e){return o.escape(e.text)+'"}}),this.$(".select2-container .select2-search input").off("blur")):(this.$select.find("option").remove(),o.each(this.data,function(e){t.$select.append(l("").attr("value",e.value).html(o.escape(e.label)))})),this.model.set("disabled",0==this.length()),this._changeValue()},_changeDisabled:function(){this.model.get("searchable")?this.$select.select2(this.model.get("disabled")?"disable":"enable"):this.$select.prop("disabled",this.model.get("disabled"))},_changeWait:function(){this.$dropdown.removeClass().addClass("icon-dropdown fa").addClass(this.model.get("wait")?"fa-spinner fa-spin":"fa-caret-down")},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"](),this.$select[this.model.get("visible")?"show":"hide"]()},_changeValue:function(){if(this._setValue(this.model.get("value")),this.model.get("multiple")){if(this.all_button){var t=this._getValue();this.all_button.value(l.isArray(t)?t.length:0,this.length())}}else null!==this._getValue()||this.model.get("optional")||this._setValue(this.first())},value:function(t){return void 0!==t&&this.model.set("value",t),this._getValue()},first:function(){return this.data.length>0?this.data[0].value:null},exists:function(t){return o.findWhere(this.data,{value:t})},text:function(){var t=this._getValue(),e=this.exists(l.isArray(t)?t[0]:t);return e?e.label:""},show:function(){this.model.set("visible",!0)},hide:function(){this.model.set("visible",!1)},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},disabled:function(){return this.model.get("disabled")},enable:function(){this.model.set("disabled",!1)},disable:function(){this.model.set("disabled",!0)},add:function(t,e){o.each(this.model.get("data"),function(e){e.keep&&!o.findWhere(t,{value:e.value})&&t.push(e)}),e&&t&&t.sort(e),this.model.set("data",t)},update:function(t){this.model.set("data",t)},setOnChange:function(t){this.model.set("onchange",t)},length:function(){return l.isArray(this.model.get("data"))?this.model.get("data").length:0},_setValue:function(t){var e=this;if(null!==t&&void 0!==t||(t="__null__"),this.model.get("multiple")?t=l.isArray(t)?t:[t]:l.isArray(t)&&(t=t.length>0?t[0]:"__null__"),this.model.get("searchable")){if(l.isArray(t)){var i=[];o.each(t,function(t){var a=o.findWhere(e.data2,{id:t});a&&i.push(a)}),t=i}else{var a=o.findWhere(this.data2,{id:t});t=a}this.$select.select2("data",t)}else this.$select.val(t)},_getValue:function(){var e=null;if(this.model.get("searchable")){var i=this.$select.select2("data");i&&(l.isArray(i)?(e=[],i.sort(function(t,e){return t.order-e.order}),o.each(i,function(t){e.push(t.id)})):e=i.id)}else e=this.$select.val();return t.isEmpty(e)?null:e}});return{View:i}}.apply(e,a),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},,,function(t,e,i){var a,s;(function(i,n,l,o){a=[],s=function(){var t=i.View.extend({initialize:function(t,e){this.$button=t,this.$button.length||(this.$button=n("")),this.options=e||[],this.$button.data("popupmenu",this);var i=this;this.$button.click(function(t){return n(".popmenu-wrapper").remove(),i._renderAndShow(t),!1})},_renderAndShow:function(t){this.render(),this.$el.appendTo("body").css(this._getShownPosition(t)).show(),this._setUpCloseBehavior()},render:function(){if(this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options)),this.options.length){var t=this;this.$el.find("li").each(function(e,i){var a=t.options[e];a.func&&n(this).children("a.popupmenu-option").click(function(e){a.func.call(t,e,a),e.preventDefault()})})}return this},template:function(t,e){return['"].join("")},_templateOptions:function(t){return t.length?l.map(t,function(t){if(t.divider)return'';if(t.header)return[''+n(t.title)+"
",'',""}});return{View:e}}.apply(e,a),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},,,,,,function(t,e,i){var a,s;(function(i,n,l){a=[],s=function(){return i.View.extend({initialize:function(t,e){this.app=t,this.app_options=t.model?t.model.attributes:{},this.field=e&&e.field||new i.View,this.model=e&&e.model||new i.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(e),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var a=this.model.get("collapsible_value");this.field.collapsed=void 0!==a&&JSON.stringify(this.model.get("value"))==JSON.stringify(a),this.listenTo(this.model,"change",this.render,this),this.render();var s=this;this.$collapsible.on("click",function(){s.field.collapsed=!s.field.collapsed,t.trigger&&t.trigger("change"),s.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){s.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(t){this.model.set("error_text",t)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){n(".tooltip").hide();var t=this.model.get("help",""),e=this.model.get("argument");e&&t.indexOf("("+e+")")==-1&&(t+=" ("+e+")"),this.$info.html(t),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(l.escape(this.model.get("text_value")));var i=this.model.get("error_text");if(this.$error[i?"show":"hide"](),this.$el[i?"addClass":"removeClass"]("ui-error"),this.$error_text.html(i),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var a=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+a)).attr("data-original-title",this.model.get("text_"+a)).tooltip({placement:"bottom"})}},_template:function(){return n("").addClass("ui-form-element").append(n("").addClass("ui-form-error ui-error").append(n("").addClass("fa fa-arrow-down")).append(n("").addClass("ui-form-error-text"))).append(n("").addClass("ui-form-title").append(n("").addClass("ui-form-collapsible").append(n("").addClass("ui-form-collapsible-icon")).append(n("").addClass("ui-form-collapsible-text"))).append(n("").addClass("ui-form-title-text"))).append(n("").addClass("ui-form-field").append(n("").addClass("ui-form-info")).append(n("").addClass("ui-form-backdrop"))).append(n("").addClass("ui-form-preview"))}})}.apply(e,a),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var a,s;(function(n,l,o){a=[i(4),i(5),i(38),i(41),i(39),i(40),i(36)],s=function(t,e,i,a,s,r,d){return n.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(t){var e=this.types[t.type],i="function"==typeof this[e]?this[e].call(this,t):null;return i||(i=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0===t.value&&(t.value=null),i.value(t.value),i},_fieldData:function(t){return new i.View({id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,flavor:t.flavor,data:t.options,onchange:t.onchange})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var i=t.data;i||(i=[],l.each(t.options,function(t){i.push({label:t[0],value:t[1]})}));var a=e.Select;switch(t.display){case"checkboxes":a=e.Checkbox;break;case"radio":a=e.Radio;break;case"radiobutton":a=e.RadioButton}return new a.View({id:"field-"+t.id,data:i,error_text:t.error_text||"No options available",multiple:t.multiple,optional:t.optional,onchange:t.onchange,individual:t.individual,searchable:"workflow"!==t.flavor})},_fieldDrilldown:function(t){return t.is_workflow?this._fieldText(t):new e.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,optional:t.optional,onchange:t.onchange})},_fieldText:function(i){if(i.options&&i.data)if(i.area=i.multiple,t.isEmpty(i.value))i.value=null;else if(o.isArray(i.value)){var a="";for(var s in i.value){if(a+=String(i.value[s]),!i.multiple)break;a+="\n"}i.value=a}return new e.Input({id:"field-"+i.id,type:i.type,area:i.area,readonly:i.readonly,placeholder:i.placeholder,datalist:i.datalist,onchange:i.onchange})},_fieldSlider:function(t){return new e.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,min:t.min,max:t.max,onchange:t.onchange})},_fieldHidden:function(t){return new e.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){return new e.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:t.onchange})},_fieldColor:function(t){return new d({id:"field-"+t.id,onchange:t.onchange})},_fieldLibrary:function(t){return new a.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldFtp:function(t){return new s.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:t.onchange})},_fieldGenomeSpace:function(t){var e=this;return new r.View({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldUpload:function(t){return new e.Upload({id:"field-"+t.id,onchange:t.onchange})}})}.apply(e,a),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var a,s;(function(n,l,o){a=[i(4),i(9),i(5)],s=function(t,e,i){var a=n.View.extend({initialize:function(e){this.list={},this.options=t.merge(e,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new i.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float form-repeat-add",onclick:function(){e.onnew&&e.onnew()}}),this.setElement(l("").append(this.$list=l("")).append(l("").append(this.button_new.$el)))},size:function(){return o.size(this.list)},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var a=new i.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){t.ondel&&t.ondel()}}),s=new e.View({id:t.id,title:"placeholder",cls:t.cls||"ui-portlet-repeat",operations:{button_delete:a}});s.append(t.$el),s.$el.addClass("section-row").hide(),this.list[t.id]=s,this.$list.append(s.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){return this.list[t]?(this.$list.find("#"+t).remove(),delete this.list[t],this.button_new.enable(),void this._refresh()):void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.")},delAll:function(){for(var t in this.list)this.del(t)},hideOptions:function(){this.button_new.$el.hide(),o.each(this.list,function(t){t.hideOperation("button_delete")}),o.isEmpty(this.list)&&this.$el.append(l("").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var i=this.list[e];i.title(++t+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});return{View:a}}.apply(e,a),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var a,s;(function(n,l,o,r){a=[i(4),i(5),i(9),i(31),i(29),i(30)],s=function(t,e,i,a,s,d){var c=n.View.extend({initialize:function(t,e){this.app=t,this.inputs=e.inputs,this.parameters=new d,this.setElement(l("")),this.render()},render:function(){var t=this;this.$el.empty(),o.each(this.inputs,function(e){t.add(e)})},add:function(e){var i=r.extend(!0,{},e);switch(i.id=e.id=t.uid(),this.app.input_list[i.id]=i,i.type){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(t){var e=this;t.test_param.id=t.id,this.app.model.get("sustain_conditionals")&&(t.test_param.disabled=!0);var i=this._addRow(t.test_param);i.model&&i.model.set("onchange",function(i){var a=e.app.data.matchCase(t,i);for(var s in t.cases){var n=t.cases[s],l=e.$("#"+t.id+"-section-"+s),o=!1;for(var r in n.inputs)if(!n.inputs[r].hidden){o=!0;break}s==a&&o?l.fadeIn("fast"):l.hide()}e.app.trigger("change")});for(var a in t.cases){var s=new c(this.app,{inputs:t.cases[a].inputs});this._append(s.$el.addClass("ui-form-section"),t.id+"-section-"+a)}i.trigger("change")},_addRepeat:function(t){function e(e){var a=t.id+"-section-"+n++,s=new c(i.app,{inputs:e});l.add({id:a,$el:s.$el,ondel:function(){l.del(a),i.app.trigger("change")}})}for(var i=this,n=0,l=new a.View({title:t.title||"Repeat",min:t.min,max:t.max,onnew:function(){e(t.inputs),i.app.trigger("change")}}),r=o.size(t.cache),d=0;d
'+this.grid_table(t),t.info_text&&(e+='
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index a1364e5aea5e..0679939d4423 100644
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0 */\n/***/ function(module, exports, __webpack_require__) {\n\n\t/* WEBPACK VAR INJECTION */(function(_) {var jQuery = __webpack_require__(1),\n\t $ = jQuery,\n\t GalaxyApp = __webpack_require__(52).GalaxyApp,\n\t AdminPanel = __webpack_require__(102),\n\t FormWrapper = __webpack_require__(62),\n\t GridView = __webpack_require__(12),\n\t Ui = __webpack_require__(5),\n\t QueryStringParsing = __webpack_require__(26),\n\t Router = __webpack_require__(55),\n\t Utils = __webpack_require__(4),\n\t Page = __webpack_require__(53);\n\t\n\twindow.app = function app(options, bootstrapped) {\n\t window.Galaxy = new GalaxyApp(options, bootstrapped);\n\t Galaxy.debug('admin app');\n\t\n\t /** Routes */\n\t var AdminRouter = Router.extend({\n\t routes: {\n\t '(/)admin(/)users': 'show_users',\n\t '(/)admin(/)roles': 'show_roles',\n\t '(/)admin(/)groups': 'show_groups',\n\t '(/)admin(/)tool_versions': 'show_tool_versions',\n\t '(/)admin(/)quotas': 'show_quotas',\n\t '(/)admin(/)forms(/)(:form_id)': 'show_forms'\n\t },\n\t\n\t authenticate: function (args, name) {\n\t return Galaxy.user && Galaxy.user.id && Galaxy.user.get('is_admin');\n\t },\n\t\n\t show_users: function () {\n\t this.page.display(new GridView({ url_base: Galaxy.root + 'admin/users_list', url_data: Galaxy.params, dict_format: true }));\n\t },\n\t\n\t show_roles: function () {\n\t this.page.display(new GridView({ url_base: Galaxy.root + 'admin/roles_list', url_data: Galaxy.params, dict_format: true }));\n\t },\n\t\n\t show_groups: function () {\n\t this.page.display(new GridView({ url_base: Galaxy.root + 'admin/groups_list', url_data: Galaxy.params, dict_format: true }));\n\t },\n\t\n\t show_tool_versions: function () {\n\t this.page.display(new GridView({ url_base: Galaxy.root + 'admin/tool_versions_list', url_data: Galaxy.params, dict_format: true }));\n\t },\n\t\n\t show_quotas: function () {\n\t this.page.display(new GridView({ url_base: Galaxy.root + 'admin/quotas_list', url_data: Galaxy.params, dict_format: true }));\n\t },\n\t\n\t show_forms: function (form_id) {\n\t var id = '?id=' + QueryStringParsing.get('id');\n\t var form_defs = {\n\t reset_user_password: {\n\t title: 'Reset passwords',\n\t url: 'admin/reset_user_password' + id,\n\t icon: 'fa-user',\n\t submit_title: 'Save new password',\n\t redirect: 'admin/users'\n\t },\n\t manage_roles_and_groups_for_user: {\n\t url: 'admin/manage_roles_and_groups_for_user' + id,\n\t icon: 'fa-users',\n\t redirect: 'admin/users'\n\t },\n\t manage_users_and_groups_for_role: {\n\t url: 'admin/manage_users_and_groups_for_role' + id,\n\t redirect: 'admin/roles'\n\t },\n\t manage_users_and_roles_for_group: {\n\t url: 'admin/manage_users_and_roles_for_group' + id,\n\t redirect: 'admin/groups'\n\t },\n\t manage_users_and_groups_for_quota: {\n\t url: 'admin/manage_users_and_groups_for_quota' + id,\n\t redirect: 'admin/quotas'\n\t },\n\t create_role: {\n\t url: 'admin/create_role',\n\t redirect: 'admin/roles'\n\t },\n\t create_group: {\n\t url: 'admin/create_group',\n\t redirect: 'admin/groups'\n\t },\n\t create_quota: {\n\t url: 'admin/create_quota',\n\t redirect: 'admin/quotas'\n\t },\n\t rename_role: {\n\t url: 'admin/rename_role' + id,\n\t redirect: 'admin/roles'\n\t },\n\t rename_group: {\n\t url: 'admin/rename_group' + id,\n\t redirect: 'admin/groups'\n\t },\n\t rename_quota: {\n\t url: 'admin/rename_quota' + id,\n\t redirect: 'admin/quotas'\n\t },\n\t edit_quota: {\n\t url: 'admin/edit_quota' + id,\n\t redirect: 'admin/quotas'\n\t },\n\t set_quota_default: {\n\t url: 'admin/set_quota_default' + id,\n\t redirect: 'admin/quotas'\n\t }\n\t };\n\t this.page.display(new FormWrapper.View(form_defs[form_id]));\n\t }\n\t });\n\t\n\t $(function () {\n\t _.extend(options.config, { active_view: 'admin' });\n\t Utils.setWindowTitle(\"Administration\");\n\t Galaxy.page = new Page.View(_.extend(options, {\n\t Left: AdminPanel,\n\t Router: AdminRouter\n\t }));\n\t });\n\t};\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3)))\n\n/***/ },\n/* 1 */,\n/* 2 */,\n/* 3 */,\n/* 4 */,\n/* 5 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/**\n\t * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc.\n\t */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(15), __webpack_require__(42), __webpack_require__(14), __webpack_require__(37), __webpack_require__(11), __webpack_require__(8)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Select, Slider, Options, Drilldown, Buttons, Modal) {\n\t\n\t /** Label wrapper */\n\t var Label = Backbone.View.extend({\n\t tagName: 'label',\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model(options);\n\t this.tagName = options.tagName || this.tagName;\n\t this.setElement($('<' + this.tagName + '/>'));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t title: function (new_title) {\n\t this.model.set('title', new_title);\n\t },\n\t value: function () {\n\t return this.model.get('title');\n\t },\n\t render: function () {\n\t this.$el.removeClass().addClass('ui-label').addClass(this.model.get('cls')).html(this.model.get('title'));\n\t return this;\n\t }\n\t });\n\t\n\t /** Displays messages used e.g. in the tool form */\n\t var Message = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t message: null,\n\t status: 'info',\n\t cls: '',\n\t persistent: false,\n\t fade: true\n\t }).set(options);\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t update: function (options) {\n\t this.model.set(options);\n\t },\n\t render: function () {\n\t this.$el.removeClass().addClass('ui-message').addClass(this.model.get('cls'));\n\t var status = this.model.get('status');\n\t if (this.model.get('large')) {\n\t this.$el.addClass((status == 'success' && 'done' || status == 'danger' && 'error' || status) + 'messagelarge');\n\t } else {\n\t this.$el.addClass('alert').addClass('alert-' + status);\n\t }\n\t if (this.model.get('message')) {\n\t this.$el.html(this.messageForDisplay());\n\t this.$el[this.model.get('fade') ? 'fadeIn' : 'show']();\n\t this.timeout && window.clearTimeout(this.timeout);\n\t if (!this.model.get('persistent')) {\n\t var self = this;\n\t this.timeout = window.setTimeout(function () {\n\t self.model.set('message', '');\n\t }, 3000);\n\t }\n\t } else {\n\t this.$el.fadeOut();\n\t }\n\t return this;\n\t },\n\t messageForDisplay: function () {\n\t return _.escape(this.model.get('message'));\n\t }\n\t });\n\t\n\t var UnescapedMessage = Message.extend({\n\t messageForDisplay: function () {\n\t return this.model.get('message');\n\t }\n\t });\n\t\n\t /** Renders an input element used e.g. in the tool form */\n\t var Input = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t type: 'text',\n\t placeholder: '',\n\t disabled: false,\n\t readonly: false,\n\t visible: true,\n\t cls: '',\n\t area: false,\n\t color: null,\n\t style: null\n\t }).set(options);\n\t this.tagName = this.model.get('area') ? 'textarea' : 'input';\n\t this.setElement($('<' + this.tagName + '/>'));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t events: {\n\t 'input': '_onchange'\n\t },\n\t value: function (new_val) {\n\t new_val !== undefined && this.model.set('value', typeof new_val === 'string' ? new_val : '');\n\t return this.model.get('value');\n\t },\n\t render: function () {\n\t var self = this;\n\t this.$el.removeClass().addClass('ui-' + this.tagName).addClass(this.model.get('cls')).addClass(this.model.get('style')).attr('id', this.model.id).attr('type', this.model.get('type')).attr('placeholder', this.model.get('placeholder')).css('color', this.model.get('color') || '').css('border-color', this.model.get('color') || '');\n\t var datalist = this.model.get('datalist');\n\t if ($.isArray(datalist) && datalist.length > 0) {\n\t this.$el.autocomplete({ source: function (request, response) {\n\t response(self.model.get('datalist'));\n\t },\n\t change: function () {\n\t self._onchange();\n\t } });\n\t }\n\t if (this.model.get('value') !== this.$el.val()) {\n\t this.$el.val(this.model.get('value'));\n\t }\n\t _.each(['readonly', 'disabled'], function (attr_name) {\n\t self.model.get(attr_name) ? self.$el.attr(attr_name, true) : self.$el.removeAttr(attr_name);\n\t });\n\t this.$el[this.model.get('visible') ? 'show' : 'hide']();\n\t return this;\n\t },\n\t _onchange: function () {\n\t this.value(this.$el.val());\n\t this.model.get('onchange') && this.model.get('onchange')(this.model.get('value'));\n\t }\n\t });\n\t\n\t /** Creates a hidden element input field used e.g. in the tool form */\n\t var Hidden = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model(options);\n\t this.setElement($('').append(this.$info = $('')).append(this.$hidden = $('')));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t value: function (new_val) {\n\t new_val !== undefined && this.model.set('value', new_val);\n\t return this.model.get('value');\n\t },\n\t render: function () {\n\t this.$el.attr('id', this.model.id);\n\t this.$hidden.val(this.model.get('value'));\n\t this.model.get('info') ? this.$info.show().text(this.model.get('info')) : this.$info.hide();\n\t return this;\n\t }\n\t });\n\t\n\t /** Creates a upload element input field */\n\t var Upload = Backbone.View.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.model = options && options.model || new Backbone.Model(options);\n\t this.setElement($('').append(this.$info = $('')).append(this.$file = $('').attr('type', 'file').addClass('ui-margin-bottom')).append(this.$text = $('').addClass('ui-textarea').attr('disabled', true)).append(this.$wait = $('').addClass('fa fa-spinner fa-spin')));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.$file.on('change', function (e) {\n\t self._readFile(e);\n\t });\n\t this.render();\n\t },\n\t value: function (new_val) {\n\t new_val !== undefined && this.model.set('value', new_val);\n\t return this.model.get('value');\n\t },\n\t render: function () {\n\t this.$el.attr('id', this.model.id);\n\t this.model.get('info') ? this.$info.show().text(this.model.get('info')) : this.$info.hide();\n\t this.model.get('value') ? this.$text.text(this.model.get('value')).show() : this.$text.hide();\n\t this.model.get('wait') ? this.$wait.show() : this.$wait.hide();\n\t return this;\n\t },\n\t _readFile: function (e) {\n\t var self = this;\n\t var file = e.target.files && e.target.files[0];\n\t if (file) {\n\t var reader = new FileReader();\n\t reader.onload = function () {\n\t self.model.set({ wait: false, value: this.result });\n\t };\n\t this.model.set({ wait: true, value: null });\n\t reader.readAsText(file);\n\t }\n\t }\n\t });\n\t\n\t return {\n\t Button: Buttons.ButtonDefault,\n\t ButtonIcon: Buttons.ButtonIcon,\n\t ButtonCheck: Buttons.ButtonCheck,\n\t ButtonMenu: Buttons.ButtonMenu,\n\t ButtonLink: Buttons.ButtonLink,\n\t Input: Input,\n\t Label: Label,\n\t Message: Message,\n\t UnescapedMessage: UnescapedMessage,\n\t Upload: Upload,\n\t Modal: Modal,\n\t RadioButton: Options.RadioButton,\n\t Checkbox: Options.Checkbox,\n\t Radio: Options.Radio,\n\t Select: Select,\n\t Hidden: Hidden,\n\t Slider: Slider,\n\t Drilldown: Drilldown\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 6 */,\n/* 7 */,\n/* 8 */,\n/* 9 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui) {\n\t var View = Backbone.View.extend({\n\t visible: false,\n\t initialize: function (options) {\n\t var self = this;\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t cls: 'ui-portlet',\n\t title: '',\n\t icon: '',\n\t buttons: null,\n\t body: null,\n\t scrollable: true,\n\t nopadding: false,\n\t operations: null,\n\t collapsible: false,\n\t collapsible_button: false,\n\t collapsed: false,\n\t onchange_title: null\n\t }).set(options);\n\t this.setElement(this._template());\n\t\n\t // link all dom elements\n\t this.$body = this.$('.portlet-body');\n\t this.$title_text = this.$('.portlet-title-text');\n\t this.$title_icon = this.$('.portlet-title-icon');\n\t this.$header = this.$('.portlet-header');\n\t this.$content = this.$('.portlet-content');\n\t this.$backdrop = this.$('.portlet-backdrop');\n\t this.$buttons = this.$('.portlet-buttons');\n\t this.$operations = this.$('.portlet-operations');\n\t\n\t // add body to component list\n\t this.model.get('body') && this.append(this.model.get('body'));\n\t\n\t // add icon for collapsible option\n\t this.collapsible_button = new Ui.ButtonIcon({\n\t icon: 'fa-eye',\n\t tooltip: 'Collapse/Expand',\n\t cls: 'ui-button-icon-plain',\n\t onclick: function () {\n\t self[self.collapsed ? 'expand' : 'collapse']();\n\t }\n\t });\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t var options = this.model.attributes;\n\t this.$el.removeClass().addClass(options.cls).attr('id', options.id);\n\t this.$header[options.title ? 'show' : 'hide']();\n\t this.$title_text.html(options.title);\n\t _.each([this.$content, this.$body], function ($el) {\n\t $el[options.nopadding ? 'addClass' : 'removeClass']('no-padding');\n\t });\n\t\n\t // render title icon\n\t if (options.icon) {\n\t this.$title_icon.removeClass().addClass('portlet-title-icon fa').addClass(options.icon).show();\n\t } else {\n\t this.$title_icon.hide();\n\t }\n\t\n\t // make portlet collapsible\n\t this.$title_text[options.collapsible ? 'addClass' : 'removeClass']('no-highlight collapsible').off();\n\t if (options.collapsible) {\n\t this.$title_text.on('click', function () {\n\t self[self.collapsed ? 'expand' : 'collapse']();\n\t });\n\t options.collapsed ? this.collapse() : this.expand();\n\t }\n\t\n\t // allow title editing\n\t this.$title_text.prop('disabled', !options.onchange_title);\n\t options.onchange_title && this.$title_text.make_text_editable({\n\t on_finish: function (new_title) {\n\t options.onchange_title(new_title);\n\t }\n\t });\n\t\n\t // render buttons\n\t if (options.buttons) {\n\t this.$buttons.empty().show();\n\t $.each(this.model.get('buttons'), function (name, item) {\n\t item.$el.prop('id', name);\n\t self.$buttons.append(item.$el);\n\t });\n\t } else {\n\t this.$buttons.hide();\n\t }\n\t\n\t // render operations\n\t this.$operations.empty;\n\t if (options.collapsible_button) {\n\t this.$operations.append(this.collapsible_button.$el);\n\t }\n\t if (options.operations) {\n\t $.each(options.operations, function (name, item) {\n\t item.$el.prop('id', name);\n\t self.$operations.append(item.$el);\n\t });\n\t }\n\t return this;\n\t },\n\t\n\t /** Append new doms to body */\n\t append: function ($el) {\n\t this.$body.append($el);\n\t },\n\t\n\t /** Remove all content */\n\t empty: function () {\n\t this.$body.empty();\n\t },\n\t\n\t /** Return header element */\n\t header: function () {\n\t return this.$header;\n\t },\n\t\n\t /** Return body element */\n\t body: function () {\n\t return this.$body;\n\t },\n\t\n\t /** Show portlet */\n\t show: function () {\n\t this.visible = true;\n\t this.$el.fadeIn('fast');\n\t },\n\t\n\t /** Hide portlet */\n\t hide: function () {\n\t this.visible = false;\n\t this.$el.hide();\n\t },\n\t\n\t /** Enable a particular button */\n\t enableButton: function (id) {\n\t this.$buttons.find('#' + id).prop('disabled', false);\n\t },\n\t\n\t /** Disable a particular button */\n\t disableButton: function (id) {\n\t this.$buttons.find('#' + id).prop('disabled', true);\n\t },\n\t\n\t /** Hide a particular operation */\n\t hideOperation: function (id) {\n\t this.$operations.find('#' + id).hide();\n\t },\n\t\n\t /** Show a particular operation */\n\t showOperation: function (id) {\n\t this.$operations.find('#' + id).show();\n\t },\n\t\n\t /** Replaces the event callback of an existing operation */\n\t setOperation: function (id, callback) {\n\t this.$operations.find('#' + id).off('click').on('click', callback);\n\t },\n\t\n\t /** Change title */\n\t title: function (new_title) {\n\t new_title && this.$title_text.html(new_title);\n\t return this.$title_text.html();\n\t },\n\t\n\t /** Collapse portlet */\n\t collapse: function () {\n\t this.collapsed = true;\n\t this.$content.height('0%');\n\t this.$body.hide();\n\t this.collapsible_button.setIcon('fa-eye-slash');\n\t },\n\t\n\t /** Expand portlet */\n\t expand: function () {\n\t this.collapsed = false;\n\t this.$content.height('100%');\n\t this.$body.fadeIn('fast');\n\t this.collapsible_button.setIcon('fa-eye');\n\t },\n\t\n\t /** Disable content access */\n\t disable: function () {\n\t this.$backdrop.show();\n\t },\n\t\n\t /** Enable content access */\n\t enable: function () {\n\t this.$backdrop.hide();\n\t },\n\t\n\t _template: function () {\n\t return $('').append($('').addClass('portlet-header').append($('').addClass('portlet-operations')).append($('').addClass('portlet-title').append($('').addClass('portlet-title-icon')).append($('').addClass('portlet-title-text')))).append($('').addClass('portlet-content').append($('').addClass('portlet-body')).append($('').addClass('portlet-buttons'))).append($('').addClass('portlet-backdrop'));\n\t }\n\t });\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ },\n/* 10 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {/**\n\t This is the main class of the form plugin. It is referenced as 'app' in lower level modules.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(9), __webpack_require__(5), __webpack_require__(32), __webpack_require__(19)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Portlet, Ui, FormSection, FormData) {\n\t return Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = new Backbone.Model({\n\t initial_errors: false,\n\t cls: 'ui-portlet-limited',\n\t icon: null,\n\t always_refresh: true,\n\t status: 'warning',\n\t onchange: function () {}\n\t }).set(options);\n\t this.setElement('');\n\t this.render();\n\t },\n\t\n\t /** Update available options */\n\t update: function (new_model) {\n\t var self = this;\n\t this.data.matchModel(new_model, function (node, input_id) {\n\t var input = self.input_list[input_id];\n\t if (input && input.options) {\n\t if (!_.isEqual(input.options, node.options)) {\n\t input.options = node.options;\n\t var field = self.field_list[input_id];\n\t if (field.update) {\n\t var new_options = [];\n\t if (['data', 'data_collection', 'drill_down'].indexOf(input.type) != -1) {\n\t new_options = input.options;\n\t } else {\n\t for (var i in node.options) {\n\t var opt = node.options[i];\n\t if (opt.length > 2) {\n\t new_options.push({ label: opt[0], value: opt[1] });\n\t }\n\t }\n\t }\n\t field.update(new_options);\n\t field.trigger('change');\n\t Galaxy.emit.debug('form-view::update()', 'Updating options for ' + input_id);\n\t }\n\t }\n\t }\n\t });\n\t },\n\t\n\t /** Set form into wait mode */\n\t wait: function (active) {\n\t for (var i in this.input_list) {\n\t var field = this.field_list[i];\n\t var input = this.input_list[i];\n\t if (input.is_dynamic && field.wait && field.unwait) {\n\t field[active ? 'wait' : 'unwait']();\n\t }\n\t }\n\t },\n\t\n\t /** Highlight and scroll to input element (currently only used for error notifications) */\n\t highlight: function (input_id, message, silent) {\n\t var input_element = this.element_list[input_id];\n\t if (input_element) {\n\t input_element.error(message || 'Please verify this parameter.');\n\t this.portlet.expand();\n\t this.trigger('expand', input_id);\n\t if (!silent) {\n\t var $panel = this.$el.parents().filter(function () {\n\t return ['auto', 'scroll'].indexOf($(this).css('overflow')) != -1;\n\t }).first();\n\t $panel.animate({ scrollTop: $panel.scrollTop() + input_element.$el.offset().top - 120 }, 500);\n\t }\n\t }\n\t },\n\t\n\t /** Highlights errors */\n\t errors: function (options) {\n\t this.trigger('reset');\n\t if (options && options.errors) {\n\t var error_messages = this.data.matchResponse(options.errors);\n\t for (var input_id in this.element_list) {\n\t var input = this.element_list[input_id];\n\t if (error_messages[input_id]) {\n\t this.highlight(input_id, error_messages[input_id], true);\n\t }\n\t }\n\t }\n\t },\n\t\n\t /** Render tool form */\n\t render: function () {\n\t var self = this;\n\t this.off('change');\n\t this.off('reset');\n\t // contains the dom field elements as created by the parameter factory i.e. form-parameters\n\t this.field_list = {};\n\t // contains input definitions/dictionaries as provided by the parameters to_dict() function through the api\n\t this.input_list = {};\n\t // contains the dom elements of each input element i.e. form-input which wraps the actual input field\n\t this.element_list = {};\n\t // converts the form into a json data structure\n\t this.data = new FormData.Manager(this);\n\t this._renderForm();\n\t this.data.create();\n\t this.model.get('initial_errors') && this.errors(this.model.attributes);\n\t // add listener which triggers on checksum change, and reset the form input wrappers\n\t var current_check = this.data.checksum();\n\t this.on('change', function (input_id) {\n\t var input = self.input_list[input_id];\n\t if (!input || input.refresh_on_change || self.model.get('always_refresh')) {\n\t var new_check = self.data.checksum();\n\t if (new_check != current_check) {\n\t current_check = new_check;\n\t self.model.get('onchange')();\n\t }\n\t }\n\t });\n\t this.on('reset', function () {\n\t _.each(self.element_list, function (input_element) {\n\t input_element.reset();\n\t });\n\t });\n\t return this;\n\t },\n\t\n\t /** Renders/appends dom elements of the form */\n\t _renderForm: function () {\n\t $('.tooltip').remove();\n\t var options = this.model.attributes;\n\t this.message = new Ui.UnescapedMessage();\n\t this.section = new FormSection.View(this, { inputs: options.inputs });\n\t this.portlet = new Portlet.View({\n\t icon: options.icon,\n\t title: options.title,\n\t cls: options.cls,\n\t operations: options.operations,\n\t buttons: options.buttons,\n\t collapsible: options.collapsible,\n\t collapsed: options.collapsed,\n\t onchange_title: options.onchange_title\n\t });\n\t this.portlet.append(this.message.$el);\n\t this.portlet.append(this.section.$el);\n\t this.$el.empty();\n\t options.inputs && this.$el.append(this.portlet.$el);\n\t options.message && this.message.update({ persistent: true, status: options.status, message: options.message });\n\t Galaxy.emit.debug('form-view::initialize()', 'Completed');\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ },\n/* 11 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/** This module contains all button views. */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t /** This renders the default button which is used e.g. at the bottom of the upload modal. */\n\t var ButtonDefault = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t title: '',\n\t icon: '',\n\t cls: 'btn btn-default',\n\t wait: false,\n\t wait_text: 'Sending...',\n\t wait_cls: 'btn btn-info',\n\t disabled: false,\n\t percentage: -1\n\t }).set(options);\n\t this.setElement($('').attr('type', 'button').append(this.$icon = $('')).append(this.$title = $('')).append(this.$progress = $('').append(this.$progress_bar = $(''))));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t var options = this.model.attributes;\n\t this.$el.removeClass().addClass('ui-button-default').addClass(options.disabled && 'disabled').attr('id', options.id).attr('disabled', options.disabled).off('click').on('click', function () {\n\t $('.tooltip').hide();\n\t options.onclick && !self.disabled && options.onclick();\n\t }).tooltip({ title: options.tooltip, placement: 'bottom' });\n\t this.$progress.addClass('progress').css('display', options.percentage !== -1 ? 'block' : 'none');\n\t this.$progress_bar.addClass('progress-bar').css({ width: options.percentage + '%' });\n\t this.$icon.removeClass().addClass('icon fa');\n\t this.$title.removeClass().addClass('title');\n\t if (options.wait) {\n\t this.$el.addClass(options.wait_cls).prop('disabled', true);\n\t this.$icon.addClass('fa-spinner fa-spin ui-margin-right');\n\t this.$title.html(options.wait_text);\n\t } else {\n\t this.$el.addClass(options.cls);\n\t this.$icon.addClass(options.icon);\n\t this.$title.html(options.title);\n\t options.icon && options.title && this.$icon.addClass('ui-margin-right');\n\t }\n\t },\n\t\n\t /** Show button */\n\t show: function () {\n\t this.$el.show();\n\t },\n\t\n\t /** Hide button */\n\t hide: function () {\n\t this.$el.hide();\n\t },\n\t\n\t /** Disable button */\n\t disable: function () {\n\t this.model.set('disabled', true);\n\t },\n\t\n\t /** Enable button */\n\t enable: function () {\n\t this.model.set('disabled', false);\n\t },\n\t\n\t /** Show spinner to indicate that the button is not ready to be clicked */\n\t wait: function () {\n\t this.model.set('wait', true);\n\t },\n\t\n\t /** Hide spinner to indicate that the button is ready to be clicked */\n\t unwait: function () {\n\t this.model.set('wait', false);\n\t },\n\t\n\t /** Change icon */\n\t setIcon: function (icon) {\n\t this.model.set('icon', icon);\n\t }\n\t });\n\t\n\t /** This button allows the right-click/open-in-new-tab feature, its used e.g. for panel buttons. */\n\t var ButtonLink = ButtonDefault.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t title: '',\n\t icon: '',\n\t cls: ''\n\t }).set(options);\n\t this.setElement($('').append(this.$icon = $('')));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var options = this.model.attributes;\n\t this.$el.removeClass().addClass(options.cls).attr({ id: options.id,\n\t href: options.href || 'javascript:void(0)',\n\t title: options.title,\n\t target: options.target || '_top',\n\t disabled: options.disabled }).tooltip({ placement: 'bottom' }).off('click').on('click', function () {\n\t options.onclick && !options.disabled && options.onclick();\n\t });\n\t this.$icon.removeClass().addClass(options.icon);\n\t }\n\t });\n\t\n\t /** The check button is used in the tool form and allows to distinguish between multiple states e.g. all, partially and nothing selected. */\n\t var ButtonCheck = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t title: 'Select/Unselect all',\n\t icons: ['fa-square-o', 'fa-minus-square-o', 'fa-check-square-o'],\n\t value: 0,\n\t onchange: function () {}\n\t }).set(options);\n\t this.setElement($('').append(this.$icon = $('')).append(this.$title = $('')));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function (options) {\n\t var self = this;\n\t var options = this.model.attributes;\n\t this.$el.addClass('ui-button-check').off('click').on('click', function () {\n\t self.model.set('value', self.model.get('value') === 0 && 2 || 0);\n\t options.onclick && options.onclick();\n\t });\n\t this.$title.html(options.title);\n\t this.$icon.removeClass().addClass('icon fa ui-margin-right').addClass(options.icons[options.value]);\n\t },\n\t\n\t /* Sets a new value and/or returns the value.\n\t * @param{Integer} new_val - Set a new value 0=unchecked, 1=partial and 2=checked.\n\t * OR:\n\t * @param{Integer} new_val - Number of selected options.\n\t * @param{Integer} total - Total number of available options.\n\t */\n\t value: function (new_val, total) {\n\t if (new_val !== undefined) {\n\t if (total && new_val !== 0) {\n\t new_val = new_val !== total && 1 || 2;\n\t }\n\t this.model.set('value', new_val);\n\t this.model.get('onchange')(this.model.get('value'));\n\t }\n\t return this.model.get('value');\n\t }\n\t });\n\t\n\t /** This renders a differently styled, more compact button version. */\n\t var ButtonIcon = ButtonDefault.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t title: '',\n\t icon: '',\n\t cls: 'ui-button-icon',\n\t disabled: false\n\t }).set(options);\n\t this.setElement($('').append(this.$button = $('').append(this.$icon = $('')).append(this.$title = $(''))));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function (options) {\n\t var self = this;\n\t var options = this.model.attributes;\n\t this.$el.removeClass().addClass(options.cls).addClass(options.disabled && 'disabled').attr('disabled', options.disabled).attr('id', options.id).off('click').on('click', function () {\n\t $('.tooltip').hide();\n\t !options.disabled && options.onclick && options.onclick();\n\t });\n\t this.$button.addClass('button').tooltip({ title: options.tooltip, placement: 'bottom' });\n\t this.$icon.removeClass().addClass('icon fa').addClass(options.icon);\n\t this.$title.addClass('title').html(options.title);\n\t options.icon && options.title && this.$icon.addClass('ui-margin-right');\n\t }\n\t });\n\t\n\t /** This class creates a button with dropdown menu. */\n\t var ButtonMenu = ButtonDefault.extend({\n\t $menu: null,\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: '',\n\t title: '',\n\t pull: 'right',\n\t icon: null,\n\t onclick: null,\n\t cls: 'ui-button-icon ui-button-menu',\n\t tooltip: '',\n\t target: '',\n\t href: '',\n\t onunload: null,\n\t visible: true,\n\t tag: ''\n\t }).set(options);\n\t this.collection = new Backbone.Collection();\n\t this.setElement($('').append(this.$root = $('').append(this.$icon = $('')).append(this.$title = $(''))));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.listenTo(this.collection, 'change add remove reset', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t var options = this.model.attributes;\n\t this.$el.removeClass().addClass('dropdown').addClass(options.cls).attr('id', options.id).css({ display: options.visible && this.collection.where({ visible: true }).length > 0 ? 'block' : 'none' });\n\t this.$root.addClass('root button dropdown-toggle').attr('data-toggle', 'dropdown').tooltip({ title: options.tooltip, placement: 'bottom' }).off('click').on('click', function (e) {\n\t $('.tooltip').hide();\n\t e.preventDefault();\n\t options.onclick && options.onclick();\n\t });\n\t this.$icon.removeClass().addClass('icon fa').addClass(options.icon);\n\t this.$title.removeClass().addClass('title').html(options.title);\n\t options.icon && options.title && this.$icon.addClass('ui-margin-right');\n\t this.$menu && this.$menu.remove();\n\t if (this.collection.length > 0) {\n\t this.$menu = $(''+n(t.title)+"
",'',"' + '
' + '
' + '' + '(no options) ';\n\t }\n\t return _.map(options, function (option) {\n\t if (option.divider) {\n\t return '';\n\t } else if (option.header) {\n\t return ['', option.html, ' '].join('');\n\t }\n\t var href = option.href || 'javascript:void(0);',\n\t target = option.target ? ' target=\"' + option.target + '\"' : '',\n\t check = option.checked ? '' : '';\n\t return ['', check, option.html, ' '].join('');\n\t }).join('');\n\t },\n\t\n\t // get the absolute position/offset for the menu\n\t _getShownPosition: function (clickEvent) {\n\t\n\t // display menu horiz. centered on click...\n\t var menuWidth = this.$el.width();\n\t var x = clickEvent.pageX - menuWidth / 2;\n\t\n\t // adjust to handle horiz. scroll and window dimensions ( draw entirely on visible screen area )\n\t x = Math.min(x, $(document).scrollLeft() + $(window).width() - menuWidth - 5);\n\t x = Math.max(x, $(document).scrollLeft() + 5);\n\t return {\n\t top: clickEvent.pageY,\n\t left: x\n\t };\n\t },\n\t\n\t // bind an event handler to all available frames so that when anything is clicked\n\t // the menu is removed from the DOM and the event handler unbinds itself\n\t _setUpCloseBehavior: function () {\n\t var menu = this;\n\t //TODO: alternately: focus hack, blocking overlay, jquery.blockui\n\t\n\t // function to close popup and unbind itself\n\t function closePopup(event) {\n\t $(document).off('click.close_popup');\n\t if (window && window.parent !== window) {\n\t try {\n\t $(window.parent.document).off(\"click.close_popup\");\n\t } catch (err) {}\n\t } else {\n\t try {\n\t $('iframe#galaxy_main').contents().off(\"click.close_popup\");\n\t } catch (err) {}\n\t }\n\t menu.remove();\n\t }\n\t\n\t $('html').one(\"click.close_popup\", closePopup);\n\t if (window && window.parent !== window) {\n\t try {\n\t $(window.parent.document).find('html').one(\"click.close_popup\", closePopup);\n\t } catch (err) {}\n\t } else {\n\t try {\n\t $('iframe#galaxy_main').contents().one(\"click.close_popup\", closePopup);\n\t } catch (err) {}\n\t }\n\t },\n\t\n\t // add a menu option/item at the given index\n\t addItem: function (item, index) {\n\t // append to end if no index\n\t index = index >= 0 ? index : this.options.length;\n\t this.options.splice(index, 0, item);\n\t return this;\n\t },\n\t\n\t // remove a menu option/item at the given index\n\t removeItem: function (index) {\n\t if (index >= 0) {\n\t this.options.splice(index, 1);\n\t }\n\t return this;\n\t },\n\t\n\t // search for a menu option by its html\n\t findIndexByHtml: function (html) {\n\t for (var i = 0; i < this.options.length; i++) {\n\t if (_.has(this.options[i], 'html') && this.options[i].html === html) {\n\t return i;\n\t }\n\t }\n\t return null;\n\t },\n\t\n\t // search for a menu option by its html\n\t findItemByHtml: function (html) {\n\t return this.options[this.findIndexByHtml(html)];\n\t },\n\t\n\t // string representation\n\t toString: function () {\n\t return 'PopupMenu';\n\t }\n\t });\n\t /** shortcut to new for when you don't need to preserve the ref */\n\t PopupMenu.create = function _create($button, options) {\n\t return new PopupMenu($button, options);\n\t };\n\t\n\t // -----------------------------------------------------------------------------\n\t // the following class functions are bridges from the original make_popupmenu and make_popup_menus\n\t // to the newer backbone.js PopupMenu\n\t\n\t /** Create a PopupMenu from simple map initial_options activated by clicking button_element.\n\t * Converts initial_options to object array used by PopupMenu.\n\t * @param {jQuery|DOMElement} button_element element which, when clicked, activates menu\n\t * @param {Object} initial_options map of key -> values, where\n\t * key is option text, value is fn to call when option is clicked\n\t * @returns {PopupMenu} the PopupMenu created\n\t */\n\t PopupMenu.make_popupmenu = function (button_element, initial_options) {\n\t var convertedOptions = [];\n\t _.each(initial_options, function (optionVal, optionKey) {\n\t var newOption = { html: optionKey };\n\t\n\t // keys with null values indicate: header\n\t if (optionVal === null) {\n\t // !optionVal? (null only?)\n\t newOption.header = true;\n\t\n\t // keys with function values indicate: a menu option\n\t } else if (jQuery.type(optionVal) === 'function') {\n\t newOption.func = optionVal;\n\t }\n\t //TODO:?? any other special optionVals?\n\t // there was no divider option originally\n\t convertedOptions.push(newOption);\n\t });\n\t return new PopupMenu($(button_element), convertedOptions);\n\t };\n\t\n\t /** Find all anchors in $parent (using selector) and covert anchors into a PopupMenu options map.\n\t * @param {jQuery} $parent the element that contains the links to convert to options\n\t * @param {String} selector jq selector string to find links\n\t * @returns {Object[]} the options array to initialize a PopupMenu\n\t */\n\t //TODO: lose parent and selector, pass in array of links, use map to return options\n\t PopupMenu.convertLinksToOptions = function ($parent, selector) {\n\t $parent = $($parent);\n\t selector = selector || 'a';\n\t var options = [];\n\t $parent.find(selector).each(function (elem, i) {\n\t var option = {},\n\t $link = $(elem);\n\t\n\t // convert link text to the option text (html) and the href into the option func\n\t option.html = $link.text();\n\t if ($link.attr('href')) {\n\t var linkHref = $link.attr('href'),\n\t linkTarget = $link.attr('target'),\n\t confirmText = $link.attr('confirm');\n\t\n\t option.func = function () {\n\t // if there's a \"confirm\" attribute, throw up a confirmation dialog, and\n\t // if the user cancels - do nothing\n\t if (confirmText && !confirm(confirmText)) {\n\t return;\n\t }\n\t\n\t // if there's no confirm attribute, or the user accepted the confirm dialog:\n\t switch (linkTarget) {\n\t // relocate the center panel\n\t case '_parent':\n\t window.parent.location = linkHref;\n\t break;\n\t\n\t // relocate the entire window\n\t case '_top':\n\t window.top.location = linkHref;\n\t break;\n\t\n\t // relocate this panel\n\t default:\n\t window.location = linkHref;\n\t }\n\t };\n\t }\n\t options.push(option);\n\t });\n\t return options;\n\t };\n\t\n\t /** Create a single popupmenu from existing DOM button and anchor elements\n\t * @param {jQuery} $buttonElement the element that when clicked will open the menu\n\t * @param {jQuery} $menuElement the element that contains the anchors to convert into a menu\n\t * @param {String} menuElementLinkSelector jq selector string used to find anchors to be made into menu options\n\t * @returns {PopupMenu} the PopupMenu (Backbone View) that can render, control the menu\n\t */\n\t PopupMenu.fromExistingDom = function ($buttonElement, $menuElement, menuElementLinkSelector) {\n\t $buttonElement = $($buttonElement);\n\t $menuElement = $($menuElement);\n\t var options = PopupMenu.convertLinksToOptions($menuElement, menuElementLinkSelector);\n\t // we're done with the menu (having converted it to an options map)\n\t $menuElement.remove();\n\t return new PopupMenu($buttonElement, options);\n\t };\n\t\n\t /** Create all popupmenus within a document or a more specific element\n\t * @param {DOMElement} parent the DOM element in which to search for popupmenus to build (defaults to document)\n\t * @param {String} menuSelector jq selector string to find popupmenu menu elements (defaults to \"div[popupmenu]\")\n\t * @param {Function} buttonSelectorBuildFn the function to build the jq button selector.\n\t * Will be passed $menuElement, parent.\n\t * (Defaults to return '#' + $menuElement.attr( 'popupmenu' ); )\n\t * @returns {PopupMenu[]} array of popupmenus created\n\t */\n\t PopupMenu.make_popup_menus = function (parent, menuSelector, buttonSelectorBuildFn) {\n\t parent = parent || document;\n\t // orig. Glx popupmenu menus have a (non-std) attribute 'popupmenu'\n\t // which contains the id of the button that activates the menu\n\t menuSelector = menuSelector || 'div[popupmenu]';\n\t // default to (orig. Glx) matching button to menu by using the popupmenu attr of the menu as the id of the button\n\t buttonSelectorBuildFn = buttonSelectorBuildFn || function ($menuElement, parent) {\n\t return '#' + $menuElement.attr('popupmenu');\n\t };\n\t\n\t // aggregate and return all PopupMenus\n\t var popupMenusCreated = [];\n\t $(parent).find(menuSelector).each(function () {\n\t var $menuElement = $(this),\n\t $buttonElement = $(parent).find(buttonSelectorBuildFn($menuElement, parent));\n\t popupMenusCreated.push(PopupMenu.fromDom($buttonElement, $menuElement));\n\t $buttonElement.addClass('popup');\n\t });\n\t return popupMenusCreated;\n\t };\n\t\n\t // =============================================================================\n\t return PopupMenu;\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ },\n/* 19 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/* This class maps the form dom to an api compatible javascript dictionary. */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t var Manager = Backbone.Model.extend({\n\t initialize: function (app) {\n\t this.app = app;\n\t },\n\t\n\t /** Creates a checksum. */\n\t checksum: function () {\n\t var sum = '';\n\t var self = this;\n\t this.app.section.$el.find('.section-row').each(function () {\n\t var id = $(this).attr('id');\n\t var field = self.app.field_list[id];\n\t if (field) {\n\t sum += id + ':' + JSON.stringify(field.value && field.value()) + ':' + field.collapsed + ';';\n\t }\n\t });\n\t return sum;\n\t },\n\t\n\t /** Convert dom into a dictionary of flat id/value pairs used e.g. on job submission. */\n\t create: function () {\n\t var self = this;\n\t\n\t // get raw dictionary from dom\n\t var dict = {};\n\t this._iterate(this.app.section.$el, dict);\n\t\n\t // add to result dictionary, label elements\n\t var result_dict = {};\n\t this.flat_dict = {};\n\t function add(flat_id, input_id, input_value) {\n\t self.flat_dict[flat_id] = input_id;\n\t result_dict[flat_id] = input_value;\n\t self.app.element_list[input_id] && self.app.element_list[input_id].$el.attr('tour_id', flat_id);\n\t }\n\t // converter between raw dictionary and job dictionary\n\t function convert(identifier, head) {\n\t for (var index in head) {\n\t var node = head[index];\n\t if (node.input) {\n\t var input = node.input;\n\t var flat_id = identifier;\n\t if (identifier != '') {\n\t flat_id += '|';\n\t }\n\t flat_id += input.name;\n\t switch (input.type) {\n\t case 'repeat':\n\t var section_label = 'section-';\n\t var block_indices = [];\n\t var block_prefix = null;\n\t for (var block_label in node) {\n\t var pos = block_label.indexOf(section_label);\n\t if (pos != -1) {\n\t pos += section_label.length;\n\t block_indices.push(parseInt(block_label.substr(pos)));\n\t if (!block_prefix) {\n\t block_prefix = block_label.substr(0, pos);\n\t }\n\t }\n\t }\n\t block_indices.sort(function (a, b) {\n\t return a - b;\n\t });\n\t var index = 0;\n\t for (var i in block_indices) {\n\t convert(flat_id + '_' + index++, node[block_prefix + block_indices[i]]);\n\t }\n\t break;\n\t case 'conditional':\n\t var value = self.app.field_list[input.id].value();\n\t add(flat_id + '|' + input.test_param.name, input.id, value);\n\t var selectedCase = matchCase(input, value);\n\t if (selectedCase != -1) {\n\t convert(flat_id, head[input.id + '-section-' + selectedCase]);\n\t }\n\t break;\n\t case 'section':\n\t convert(!input.flat && flat_id || '', node);\n\t break;\n\t default:\n\t var field = self.app.field_list[input.id];\n\t if (field && field.value) {\n\t var value = field.value();\n\t if (input.ignore === undefined || input.ignore != value) {\n\t if (field.collapsed && input.collapsible_value) {\n\t value = input.collapsible_value;\n\t }\n\t add(flat_id, input.id, value);\n\t if (input.payload) {\n\t for (var p_id in input.payload) {\n\t add(p_id, input.id, input.payload[p_id]);\n\t }\n\t }\n\t }\n\t }\n\t }\n\t }\n\t }\n\t }\n\t convert('', dict);\n\t return result_dict;\n\t },\n\t\n\t /** Matches flat ids to corresponding input element\n\t * @param{string} flat_id - Flat input id to be looked up.\n\t */\n\t match: function (flat_id) {\n\t return this.flat_dict && this.flat_dict[flat_id];\n\t },\n\t\n\t /** Match conditional values to selected cases\n\t */\n\t matchCase: function (input, value) {\n\t return matchCase(input, value);\n\t },\n\t\n\t /** Matches a new tool model to the current input elements e.g. used to update dynamic options\n\t */\n\t matchModel: function (model, callback) {\n\t var self = this;\n\t visitInputs(model.inputs, function (input, name) {\n\t self.flat_dict[name] && callback(input, self.flat_dict[name]);\n\t });\n\t },\n\t\n\t /** Matches identifier from api response to input elements e.g. used to display validation errors\n\t */\n\t matchResponse: function (response) {\n\t var result = {};\n\t var self = this;\n\t function search(id, head) {\n\t if (typeof head === 'string') {\n\t var input_id = self.flat_dict[id];\n\t input_id && (result[input_id] = head);\n\t } else {\n\t for (var i in head) {\n\t var new_id = i;\n\t if (id !== '') {\n\t var separator = '|';\n\t if (head instanceof Array) {\n\t separator = '_';\n\t }\n\t new_id = id + separator + new_id;\n\t }\n\t search(new_id, head[i]);\n\t }\n\t }\n\t }\n\t search('', response);\n\t return result;\n\t },\n\t\n\t /** Map dom tree to dictionary tree with input elements.\n\t */\n\t _iterate: function (parent, dict) {\n\t var self = this;\n\t var children = $(parent).children();\n\t children.each(function () {\n\t var child = this;\n\t var id = $(child).attr('id');\n\t if ($(child).hasClass('section-row')) {\n\t var input = self.app.input_list[id];\n\t dict[id] = input && { input: input } || {};\n\t self._iterate(child, dict[id]);\n\t } else {\n\t self._iterate(child, dict);\n\t }\n\t });\n\t }\n\t });\n\t\n\t /** Match conditional values to selected cases\n\t * @param{dict} input - Definition of conditional input parameter\n\t * @param{dict} value - Current value\n\t */\n\t var matchCase = function (input, value) {\n\t if (input.test_param.type == 'boolean') {\n\t if (value == 'true') {\n\t value = input.test_param.truevalue || 'true';\n\t } else {\n\t value = input.test_param.falsevalue || 'false';\n\t }\n\t }\n\t for (var i in input.cases) {\n\t if (input.cases[i].value == value) {\n\t return i;\n\t }\n\t }\n\t return -1;\n\t };\n\t\n\t /** Visits tool inputs\n\t * @param{dict} inputs - Nested dictionary of input elements\n\t * @param{dict} callback - Called with the mapped dictionary object and corresponding model node\n\t */\n\t var visitInputs = function (inputs, callback, prefix, context) {\n\t context = $.extend(true, {}, context);\n\t _.each(inputs, function (input) {\n\t if (input && input.type && input.name) {\n\t context[input.name] = input;\n\t }\n\t });\n\t for (var key in inputs) {\n\t var node = inputs[key];\n\t node.name = node.name || key;\n\t var name = prefix ? prefix + '|' + node.name : node.name;\n\t switch (node.type) {\n\t case 'repeat':\n\t _.each(node.cache, function (cache, j) {\n\t visitInputs(cache, callback, name + '_' + j, context);\n\t });\n\t break;\n\t case 'conditional':\n\t if (node.test_param) {\n\t callback(node.test_param, name + '|' + node.test_param.name, context);\n\t var selectedCase = matchCase(node, node.test_param.value);\n\t if (selectedCase != -1) {\n\t visitInputs(node.cases[selectedCase].inputs, callback, name, context);\n\t } else {\n\t Galaxy.emit.debug('form-data::visitInputs() - Invalid case for ' + name + '.');\n\t }\n\t } else {\n\t Galaxy.emit.debug('form-data::visitInputs() - Conditional test parameter missing for ' + name + '.');\n\t }\n\t break;\n\t case 'section':\n\t visitInputs(node.inputs, callback, name, context);\n\t break;\n\t default:\n\t callback(node, name, context);\n\t }\n\t }\n\t };\n\t\n\t return {\n\t Manager: Manager,\n\t visitInputs: visitInputs\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 20 */,\n/* 21 */,\n/* 22 */,\n/* 23 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/** This class creates a ui table element. */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t var View = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.options = Utils.merge(options, {\n\t content: 'No content available.',\n\t onchange: null,\n\t ondblclick: null,\n\t onconfirm: null,\n\t cls: 'ui-table',\n\t selectable: true,\n\t cls_tr: ''\n\t });\n\t this.setElement(this._template());\n\t this.$thead = this.$('thead');\n\t this.$tbody = this.$('tbody');\n\t this.$tmessage = this.$('tmessage');\n\t this.row = this._row();\n\t this.row_count = 0;\n\t },\n\t\n\t events: {\n\t 'click': '_onclick',\n\t 'dblclick': '_ondblclick'\n\t },\n\t\n\t /** Add cell to header row */\n\t addHeader: function ($el) {\n\t this.row.append($('
' + '
';\n\t },\n\t\n\t /** Row Template */\n\t _templateRow: function (options) {\n\t return '' + '' + '' + options.name + '' + '
';\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 14 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/** Base class for options based ui elements **/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(11)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Buttons) {\n\t var Base = Backbone.View.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.model = options && options.model || new Backbone.Model({\n\t visible: true,\n\t data: [],\n\t id: Utils.uid(),\n\t error_text: 'No options available.',\n\t wait_text: 'Please wait...',\n\t multiple: false,\n\t optional: false,\n\t onchange: function () {}\n\t }).set(options);\n\t this.listenTo(this.model, 'change:value', this._changeValue, this);\n\t this.listenTo(this.model, 'change:wait', this._changeWait, this);\n\t this.listenTo(this.model, 'change:data', this._changeData, this);\n\t this.listenTo(this.model, 'change:visible', this._changeVisible, this);\n\t this.on('change', function () {\n\t self.model.get('onchange')(self.value());\n\t });\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t this.$el.empty().removeClass().addClass('ui-options').append(this.$message = $('')).append(this.$menu = $('').addClass('ui-options-menu')).append(this.$options = $(this._template()));\n\t\n\t // add select/unselect all button\n\t this.all_button = null;\n\t if (this.model.get('multiple')) {\n\t this.all_button = new Buttons.ButtonCheck({\n\t onclick: function () {\n\t self.$('input').prop('checked', self.all_button.value() !== 0);\n\t self.value(self._getValue());\n\t self.trigger('change');\n\t }\n\t });\n\t this.$menu.append(this.all_button.$el);\n\t }\n\t\n\t // finalize dom\n\t this._changeData();\n\t this._changeWait();\n\t this._changeVisible();\n\t },\n\t\n\t /** Update available options */\n\t update: function (options) {\n\t this.model.set('data', options);\n\t },\n\t\n\t _changeData: function () {\n\t var self = this;\n\t this.$options.empty();\n\t if (this._templateOptions) {\n\t this.$options.append(this._templateOptions(this.model.get('data')));\n\t } else {\n\t _.each(this.model.get('data'), function (option) {\n\t self.$options.append($(self._templateOption(option)).addClass('ui-option').tooltip({ title: option.tooltip, placement: 'bottom' }));\n\t });\n\t }\n\t var self = this;\n\t this.$('input').on('change', function () {\n\t self.value(self._getValue());\n\t self.trigger('change');\n\t });\n\t this._changeValue();\n\t this._changeWait();\n\t },\n\t\n\t _changeVisible: function () {\n\t this.$el[this.model.get('visible') ? 'show' : 'hide']();\n\t },\n\t\n\t _changeWait: function () {\n\t if (this.model.get('wait')) {\n\t if (this.length() === 0) {\n\t this._messageShow(this.model.get('wait_text'), 'info');\n\t this.$options.hide();\n\t this.$menu.hide();\n\t }\n\t } else {\n\t if (this.length() === 0) {\n\t this._messageShow(this.model.get('error_text'), 'danger');\n\t this.$options.hide();\n\t this.$menu.hide();\n\t } else {\n\t this.$message.hide();\n\t this.$options.css('display', 'inline-block');\n\t this.$menu.show();\n\t }\n\t }\n\t },\n\t\n\t _changeValue: function () {\n\t this._setValue(this.model.get('value'));\n\t if (this._getValue() === null && !this.model.get('multiple') && !this.model.get('optional')) {\n\t this._setValue(this.first());\n\t }\n\t this.all_button && this.all_button.value($.isArray(this._getValue()) ? this._getValue().length : 0, this.length());\n\t },\n\t\n\t /** Return/Set current selection */\n\t value: function (new_value) {\n\t new_value !== undefined && this.model.set('value', new_value);\n\t return this._getValue();\n\t },\n\t\n\t /** Return first available option */\n\t first: function () {\n\t var options = this.$('input').first();\n\t return options.length > 0 ? options.val() : null;\n\t },\n\t\n\t /** Show a spinner indicating that the select options are currently loaded */\n\t wait: function () {\n\t this.model.set('wait', true);\n\t },\n\t\n\t /** Hide spinner indicating that the request has been completed */\n\t unwait: function () {\n\t this.model.set('wait', false);\n\t },\n\t\n\t /** Returns the number of options */\n\t length: function () {\n\t return this.$('.ui-option').length;\n\t },\n\t\n\t /** Set value to dom */\n\t _setValue: function (new_value) {\n\t var self = this;\n\t if (new_value !== undefined) {\n\t this.$('input').prop('checked', false);\n\t if (new_value !== null) {\n\t var values = $.isArray(new_value) ? new_value : [new_value];\n\t _.each(values, function (v) {\n\t self.$('input[value=\"' + v + '\"]').first().prop('checked', true);\n\t });\n\t }\n\t }\n\t },\n\t\n\t /** Return current selection */\n\t _getValue: function () {\n\t var selected = [];\n\t this.$(':checked').each(function () {\n\t selected.push($(this).val());\n\t });\n\t if (Utils.isEmpty(selected)) {\n\t return null;\n\t }\n\t return this.model.get('multiple') ? selected : selected[0];\n\t },\n\t\n\t /** Show message instead if options */\n\t _messageShow: function (text, status) {\n\t this.$message.show().removeClass().addClass('ui-message alert alert-' + status).html(text);\n\t },\n\t\n\t /** Main template function */\n\t _template: function () {\n\t return $('').addClass('ui-options-list');\n\t }\n\t });\n\t\n\t /** Iconized **/\n\t var BaseIcons = Base.extend({\n\t _templateOption: function (pair) {\n\t var id = Utils.uid();\n\t return $('').addClass('ui-option').append($('').attr({\n\t id: id,\n\t type: this.model.get('type'),\n\t name: this.model.id,\n\t value: pair.value })).append($('').addClass('ui-options-label').attr('for', id).html(pair.label));\n\t }\n\t });\n\t\n\t /** Radio button field **/\n\t var Radio = {};\n\t Radio.View = BaseIcons.extend({\n\t initialize: function (options) {\n\t options.type = 'radio';\n\t BaseIcons.prototype.initialize.call(this, options);\n\t }\n\t });\n\t\n\t /** Checkbox options field **/\n\t var Checkbox = {};\n\t Checkbox.View = BaseIcons.extend({\n\t initialize: function (options) {\n\t options.type = 'checkbox';\n\t options.multiple = true;\n\t BaseIcons.prototype.initialize.call(this, options);\n\t }\n\t });\n\t\n\t /** Radio button options field styled as classic buttons **/\n\t var RadioButton = {};\n\t RadioButton.View = Base.extend({\n\t initialize: function (options) {\n\t Base.prototype.initialize.call(this, options);\n\t },\n\t\n\t /** Set current value */\n\t _setValue: function (new_value) {\n\t if (new_value !== undefined) {\n\t this.$('input').prop('checked', false);\n\t this.$('label').removeClass('active');\n\t this.$('[value=\"' + new_value + '\"]').prop('checked', true).closest('label').addClass('active');\n\t }\n\t },\n\t\n\t /** Template for a single option */\n\t _templateOption: function (pair) {\n\t var $el = $('').addClass('btn btn-default');\n\t pair.icon && $el.append($('').addClass('fa').addClass(pair.icon).addClass(!pair.label && 'no-padding'));\n\t $el.append($('').attr({ type: 'radio', name: this.model.id, value: pair.value }));\n\t pair.label && $el.append(pair.label);\n\t return $el;\n\t },\n\t\n\t /** Main template function */\n\t _template: function () {\n\t return $('').addClass('btn-group ui-radiobutton').attr('data-toggle', 'buttons');\n\t }\n\t });\n\t\n\t return {\n\t Base: Base,\n\t BaseIcons: BaseIcons,\n\t Radio: Radio,\n\t RadioButton: RadioButton,\n\t Checkbox: Checkbox\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 15 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/**\n\t * This class creates/wraps a default html select field as backbone class.\n\t */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(11)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Buttons) {\n\t var View = Backbone.View.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.data = [];\n\t this.data2 = [];\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t cls: 'ui-select',\n\t error_text: 'No options available',\n\t empty_text: 'Nothing selected',\n\t visible: true,\n\t wait: false,\n\t multiple: false,\n\t searchable: true,\n\t optional: false,\n\t disabled: false,\n\t onchange: function () {},\n\t value: null,\n\t individual: false,\n\t pagesize: 20\n\t }).set(options);\n\t this.on('change', function () {\n\t self.model.get('onchange') && self.model.get('onchange')(self.value());\n\t });\n\t this.listenTo(this.model, 'change:data', this._changeData, this);\n\t this.listenTo(this.model, 'change:disabled', this._changeDisabled, this);\n\t this.listenTo(this.model, 'change:wait', this._changeWait, this);\n\t this.listenTo(this.model, 'change:visible', this._changeVisible, this);\n\t this.listenTo(this.model, 'change:value', this._changeValue, this);\n\t this.listenTo(this.model, 'change:multiple change:searchable change:cls change:id', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t this.model.get('searchable') ? this._renderSearchable() : this._renderClassic();\n\t this.$el.addClass(this.model.get('cls')).attr('id', this.model.get('id'));\n\t this.$select.empty().addClass('select').attr('id', this.model.get('id') + '_select').prop('multiple', this.model.get('multiple')).on('change', function () {\n\t self.value(self._getValue());\n\t self.trigger('change');\n\t });\n\t this._changeData();\n\t this._changeWait();\n\t this._changeVisible();\n\t this._changeDisabled();\n\t },\n\t\n\t /** Renders the classic selection field */\n\t _renderClassic: function () {\n\t var self = this;\n\t this.$el.addClass(this.model.get('multiple') ? 'ui-select-multiple' : 'ui-select').append(this.$select = $('')).append(this.$dropdown = $('')).append(this.$resize = $('').append(this.$resize_icon = $('')));\n\t if (this.model.get('multiple')) {\n\t this.$dropdown.hide();\n\t this.$resize_icon.addClass('fa fa-angle-double-right fa-rotate-45').show();\n\t this.$resize.removeClass().addClass('icon-resize').show().off('mousedown').on('mousedown', function (event) {\n\t var currentY = event.pageY;\n\t var currentHeight = self.$select.height();\n\t self.minHeight = self.minHeight || currentHeight;\n\t $('#dd-helper').show().on('mousemove', function (event) {\n\t self.$select.height(Math.max(currentHeight + (event.pageY - currentY), self.minHeight));\n\t }).on('mouseup mouseleave', function () {\n\t $('#dd-helper').hide().off();\n\t });\n\t });\n\t } else {\n\t this.$dropdown.show();\n\t this.$resize.hide();\n\t this.$resize_icon.hide();\n\t }\n\t },\n\t\n\t /** Renders the default select2 field */\n\t _renderSearchable: function () {\n\t var self = this;\n\t this.$el.append(this.$select = $('')).append(this.$dropdown = $(''));\n\t this.$dropdown.hide();\n\t if (!this.model.get('multiple')) {\n\t this.$dropdown.show().on('click', function () {\n\t self.$select.select2 && self.$select.select2('open');\n\t });\n\t }\n\t this.all_button = null;\n\t if (this.model.get('multiple') && !this.model.get('individual')) {\n\t this.all_button = new Buttons.ButtonCheck({\n\t onclick: function () {\n\t var new_value = [];\n\t self.all_button.value() !== 0 && _.each(self.model.get('data'), function (option) {\n\t new_value.push(option.value);\n\t });\n\t self.value(new_value);\n\t self.trigger('change');\n\t }\n\t });\n\t this.$el.prepend(this.all_button.$el);\n\t }\n\t },\n\t\n\t /** Matches a search term with a given text */\n\t _match: function (term, text) {\n\t return !term || term == '' || String(text).toUpperCase().indexOf(term.toUpperCase()) >= 0;\n\t },\n\t\n\t /** Updates the selection options */\n\t _changeData: function () {\n\t var self = this;\n\t this.data = [];\n\t if (!this.model.get('multiple') && this.model.get('optional')) {\n\t this.data.push({ value: '__null__', label: self.model.get('empty_text') });\n\t }\n\t _.each(this.model.get('data'), function (option) {\n\t self.data.push(option);\n\t });\n\t if (this.length() == 0) {\n\t this.data.push({ value: '__null__', label: this.model.get('error_text') });\n\t }\n\t if (this.model.get('searchable')) {\n\t this.data2 = [];\n\t _.each(this.data, function (option, index) {\n\t self.data2.push({ order: index, id: option.value, text: option.label, tags: option.tags });\n\t });\n\t this.$select.data('select2') && this.$select.select2('destroy');\n\t this.matched_tags = {};\n\t this.$select.select2({\n\t data: self.data2,\n\t closeOnSelect: !this.model.get('multiple'),\n\t multiple: this.model.get('multiple'),\n\t query: function (q) {\n\t self.matched_tags = {};\n\t var pagesize = self.model.get('pagesize');\n\t var results = _.filter(self.data2, function (e) {\n\t var found = false;\n\t _.each(e.tags, function (tag) {\n\t if (self._match(q.term, tag)) {\n\t found = self.matched_tags[tag] = true;\n\t }\n\t });\n\t return found || self._match(q.term, e.text);\n\t });\n\t q.callback({\n\t results: results.slice((q.page - 1) * pagesize, q.page * pagesize),\n\t more: results.length >= q.page * pagesize\n\t });\n\t },\n\t formatResult: function (result) {\n\t return _.escape(result.text) + '';\n\t }\n\t });\n\t this.$('.select2-container .select2-search input').off('blur');\n\t } else {\n\t this.$select.find('option').remove();\n\t _.each(this.data, function (option) {\n\t self.$select.append($('').attr('value', option.value).html(_.escape(option.label)));\n\t });\n\t }\n\t this.model.set('disabled', this.length() == 0);\n\t this._changeValue();\n\t },\n\t\n\t /** Handles field enabling/disabling, usually used when no options are available */\n\t _changeDisabled: function () {\n\t if (this.model.get('searchable')) {\n\t this.$select.select2(this.model.get('disabled') ? 'disable' : 'enable');\n\t } else {\n\t this.$select.prop('disabled', this.model.get('disabled'));\n\t }\n\t },\n\t\n\t /** Searchable fields may display a spinner e.g. while waiting for a server response */\n\t _changeWait: function () {\n\t this.$dropdown.removeClass().addClass('icon-dropdown fa').addClass(this.model.get('wait') ? 'fa-spinner fa-spin' : 'fa-caret-down');\n\t },\n\t\n\t /** Handles field visibility */\n\t _changeVisible: function () {\n\t this.$el[this.model.get('visible') ? 'show' : 'hide']();\n\t this.$select[this.model.get('visible') ? 'show' : 'hide']();\n\t },\n\t\n\t /** Synchronizes the model value with the actually selected field value */\n\t _changeValue: function () {\n\t this._setValue(this.model.get('value'));\n\t if (this.model.get('multiple')) {\n\t if (this.all_button) {\n\t var value = this._getValue();\n\t this.all_button.value($.isArray(value) ? value.length : 0, this.length());\n\t }\n\t } else if (this._getValue() === null && !this.model.get('optional')) {\n\t this._setValue(this.first());\n\t }\n\t },\n\t\n\t /** Return/Set current selection */\n\t value: function (new_value) {\n\t new_value !== undefined && this.model.set('value', new_value);\n\t return this._getValue();\n\t },\n\t\n\t /** Return the first select option */\n\t first: function () {\n\t return this.data.length > 0 ? this.data[0].value : null;\n\t },\n\t\n\t /** Check if a value is an existing option */\n\t exists: function (value) {\n\t return _.findWhere(this.data, { value: value });\n\t },\n\t\n\t /** Return the label/text of the current selection */\n\t text: function () {\n\t var v = this._getValue();\n\t var d = this.exists($.isArray(v) ? v[0] : v);\n\t return d ? d.label : '';\n\t },\n\t\n\t /** Show the select field */\n\t show: function () {\n\t this.model.set('visible', true);\n\t },\n\t\n\t /** Hide the select field */\n\t hide: function () {\n\t this.model.set('visible', false);\n\t },\n\t\n\t /** Show a spinner indicating that the select options are currently loaded */\n\t wait: function () {\n\t this.model.set('wait', true);\n\t },\n\t\n\t /** Hide spinner indicating that the request has been completed */\n\t unwait: function () {\n\t this.model.set('wait', false);\n\t },\n\t\n\t /** Returns true if the field is disabled */\n\t disabled: function () {\n\t return this.model.get('disabled');\n\t },\n\t\n\t /** Enable the select field */\n\t enable: function () {\n\t this.model.set('disabled', false);\n\t },\n\t\n\t /** Disable the select field */\n\t disable: function () {\n\t this.model.set('disabled', true);\n\t },\n\t\n\t /** Update all available options at once */\n\t add: function (options, sorter) {\n\t _.each(this.model.get('data'), function (v) {\n\t v.keep && !_.findWhere(options, { value: v.value }) && options.push(v);\n\t });\n\t sorter && options && options.sort(sorter);\n\t this.model.set('data', options);\n\t },\n\t\n\t /** Update available options */\n\t update: function (options) {\n\t this.model.set('data', options);\n\t },\n\t\n\t /** Set the custom onchange callback function */\n\t setOnChange: function (callback) {\n\t this.model.set('onchange', callback);\n\t },\n\t\n\t /** Number of available options */\n\t length: function () {\n\t return $.isArray(this.model.get('data')) ? this.model.get('data').length : 0;\n\t },\n\t\n\t /** Set value to dom */\n\t _setValue: function (new_value) {\n\t var self = this;\n\t if (new_value === null || new_value === undefined) {\n\t new_value = '__null__';\n\t }\n\t if (this.model.get('multiple')) {\n\t new_value = $.isArray(new_value) ? new_value : [new_value];\n\t } else if ($.isArray(new_value)) {\n\t if (new_value.length > 0) {\n\t new_value = new_value[0];\n\t } else {\n\t new_value = '__null__';\n\t }\n\t }\n\t if (this.model.get('searchable')) {\n\t if ($.isArray(new_value)) {\n\t var val = [];\n\t _.each(new_value, function (v) {\n\t var d = _.findWhere(self.data2, { id: v });\n\t d && val.push(d);\n\t });\n\t new_value = val;\n\t } else {\n\t var d = _.findWhere(this.data2, { id: new_value });\n\t new_value = d;\n\t }\n\t this.$select.select2('data', new_value);\n\t } else {\n\t this.$select.val(new_value);\n\t }\n\t },\n\t\n\t /** Get value from dom */\n\t _getValue: function () {\n\t var val = null;\n\t if (this.model.get('searchable')) {\n\t var selected = this.$select.select2('data');\n\t if (selected) {\n\t if ($.isArray(selected)) {\n\t val = [];\n\t selected.sort(function (a, b) {\n\t return a.order - b.order;\n\t });\n\t _.each(selected, function (v) {\n\t val.push(v.id);\n\t });\n\t } else {\n\t val = selected.id;\n\t }\n\t }\n\t } else {\n\t val = this.$select.val();\n\t }\n\t return Utils.isEmpty(val) ? null : val;\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 16 */,\n/* 17 */,\n/* 18 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _, jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [\n\t //jquery\n\t //backbone\n\t], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t // =============================================================================\n\t /**\n\t * view for a popup menu\n\t */\n\t var PopupMenu = Backbone.View.extend({\n\t //TODO: maybe better as singleton off the Galaxy obj\n\t /** Cache the desired button element and options, set up the button click handler\n\t * NOTE: attaches this view as HTML/jQ data on the button for later use.\n\t */\n\t initialize: function ($button, options) {\n\t // default settings\n\t this.$button = $button;\n\t if (!this.$button.length) {\n\t this.$button = $('');\n\t }\n\t this.options = options || [];\n\t this.$button.data('popupmenu', this);\n\t\n\t // set up button click -> open menu behavior\n\t var menu = this;\n\t this.$button.click(function (event) {\n\t // if there's already a menu open, remove it\n\t $('.popmenu-wrapper').remove();\n\t menu._renderAndShow(event);\n\t return false;\n\t });\n\t },\n\t\n\t // render the menu, append to the page body at the click position, and set up the 'click-away' handlers, show\n\t _renderAndShow: function (clickEvent) {\n\t this.render();\n\t this.$el.appendTo('body').css(this._getShownPosition(clickEvent)).show();\n\t this._setUpCloseBehavior();\n\t },\n\t\n\t // render the menu\n\t // this menu doesn't attach itself to the DOM ( see _renderAndShow )\n\t render: function () {\n\t // render the menu body absolute and hidden, fill with template\n\t this.$el.addClass('popmenu-wrapper').hide().css({ position: 'absolute' }).html(this.template(this.$button.attr('id'), this.options));\n\t\n\t // set up behavior on each link/anchor elem\n\t if (this.options.length) {\n\t var menu = this;\n\t //precondition: there should be one option per li\n\t this.$el.find('li').each(function (i, li) {\n\t var option = menu.options[i];\n\t\n\t // if the option has 'func', call that function when the anchor is clicked\n\t if (option.func) {\n\t $(this).children('a.popupmenu-option').click(function (event) {\n\t option.func.call(menu, event, option);\n\t // We must preventDefault otherwise clicking \"cancel\"\n\t // on a purge or something still navigates and causes\n\t // the action.\n\t event.preventDefault();\n\t // bubble up so that an option click will call the close behavior\n\t });\n\t }\n\t });\n\t }\n\t return this;\n\t },\n\t\n\t template: function (id, options) {\n\t return [''].join('');\n\t },\n\t\n\t _templateOptions: function (options) {\n\t if (!options.length) {\n\t return '' + '' + '' + '' + '
' + '' + this.options.content + ' ' + '
';\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 24 */,\n/* 25 */,\n/* 26 */,\n/* 27 */,\n/* 28 */,\n/* 29 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/**\n\t This class creates a form input element wrapper\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t return Backbone.View.extend({\n\t initialize: function (app, options) {\n\t this.app = app;\n\t this.app_options = app.model ? app.model.attributes : {};\n\t this.field = options && options.field || new Backbone.View();\n\t this.model = options && options.model || new Backbone.Model({\n\t text_enable: this.app_options.text_enable || 'Enable',\n\t text_disable: this.app_options.text_disable || 'Disable',\n\t cls_enable: this.app_options.cls_enable || 'fa fa-caret-square-o-down',\n\t cls_disable: this.app_options.cls_disable || 'fa fa-caret-square-o-up',\n\t always_refresh: this.app_options.always_refresh\n\t }).set(options);\n\t\n\t // set element and link components\n\t this.setElement(this._template());\n\t this.$field = this.$('.ui-form-field');\n\t this.$info = this.$('.ui-form-info');\n\t this.$preview = this.$('.ui-form-preview');\n\t this.$collapsible = this.$('.ui-form-collapsible');\n\t this.$collapsible_text = this.$('.ui-form-collapsible-text');\n\t this.$collapsible_icon = this.$('.ui-form-collapsible-icon');\n\t this.$title = this.$('.ui-form-title');\n\t this.$title_text = this.$('.ui-form-title-text');\n\t this.$error_text = this.$('.ui-form-error-text');\n\t this.$error = this.$('.ui-form-error');\n\t this.$backdrop = this.$('.ui-form-backdrop');\n\t\n\t // add field element\n\t this.$field.prepend(this.field.$el);\n\t\n\t // decide wether to expand or collapse fields\n\t var collapsible_value = this.model.get('collapsible_value');\n\t this.field.collapsed = collapsible_value !== undefined && JSON.stringify(this.model.get('value')) == JSON.stringify(collapsible_value);\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t\n\t // add click handler\n\t var self = this;\n\t this.$collapsible.on('click', function () {\n\t self.field.collapsed = !self.field.collapsed;\n\t app.trigger && app.trigger('change');\n\t self.render();\n\t });\n\t\n\t // hide error on value change\n\t if (this.field.model && !this.model.get('always_refresh')) {\n\t this.listenTo(this.field.model, 'change:value', function () {\n\t self.reset();\n\t });\n\t }\n\t },\n\t\n\t /** Set backdrop for input element */\n\t backdrop: function () {\n\t this.model.set('backdrop', true);\n\t },\n\t\n\t /** Set error text */\n\t error: function (text) {\n\t this.model.set('error_text', text);\n\t },\n\t\n\t /** Reset this view */\n\t reset: function () {\n\t !this.model.get('fixed') && this.model.set('error_text', null);\n\t },\n\t\n\t render: function () {\n\t // render help\n\t $('.tooltip').hide();\n\t var help_text = this.model.get('help', '');\n\t var help_argument = this.model.get('argument');\n\t if (help_argument && help_text.indexOf('(' + help_argument + ')') == -1) {\n\t help_text += ' (' + help_argument + ')';\n\t }\n\t this.$info.html(help_text);\n\t // render visibility\n\t this.$el[this.model.get('hidden') ? 'hide' : 'show']();\n\t // render preview view for collapsed fields\n\t this.$preview[this.field.collapsed && this.model.get('collapsible_preview') || this.model.get('disabled') ? 'show' : 'hide']().html(_.escape(this.model.get('text_value')));\n\t // render error messages\n\t var error_text = this.model.get('error_text');\n\t this.$error[error_text ? 'show' : 'hide']();\n\t this.$el[error_text ? 'addClass' : 'removeClass']('ui-error');\n\t this.$error_text.html(error_text);\n\t // render backdrop\n\t this.$backdrop[this.model.get('backdrop') ? 'show' : 'hide']();\n\t // render input field\n\t this.field.collapsed || this.model.get('disabled') ? this.$field.hide() : this.$field.show();\n\t // render input field color and style\n\t this.field.model && this.field.model.set({ 'color': this.model.get('color'), 'style': this.model.get('style') });\n\t // render collapsible options\n\t if (!this.model.get('disabled') && this.model.get('collapsible_value') !== undefined) {\n\t var collapsible_state = this.field.collapsed ? 'enable' : 'disable';\n\t this.$title_text.hide();\n\t this.$collapsible.show();\n\t this.$collapsible_text.text(this.model.get('label'));\n\t this.$collapsible_icon.removeClass().addClass('icon').addClass(this.model.get('cls_' + collapsible_state)).attr('data-original-title', this.model.get('text_' + collapsible_state)).tooltip({ placement: 'bottom' });\n\t } else {\n\t this.$title_text.show().text(this.model.get('label'));\n\t this.$collapsible.hide();\n\t }\n\t },\n\t\n\t _template: function () {\n\t return $('').addClass('ui-form-element').append($('').addClass('ui-form-error ui-error').append($('').addClass('fa fa-arrow-down')).append($('').addClass('ui-form-error-text'))).append($('').addClass('ui-form-title').append($('').addClass('ui-form-collapsible').append($('').addClass('ui-form-collapsible-icon')).append($('').addClass('ui-form-collapsible-text'))).append($('').addClass('ui-form-title-text'))).append($('').addClass('ui-form-field').append($('').addClass('ui-form-info')).append($('').addClass('ui-form-backdrop'))).append($('').addClass('ui-form-preview'));\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 30 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {/**\n\t This class creates input elements. New input parameter types should be added to the types dictionary.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(5), __webpack_require__(38), __webpack_require__(41), __webpack_require__(39), __webpack_require__(40), __webpack_require__(36)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui, SelectContent, SelectLibrary, SelectFtp, SelectGenomeSpace, ColorPicker) {\n\t\n\t // create form view\n\t return Backbone.Model.extend({\n\t /** Available parameter types */\n\t types: {\n\t 'text': '_fieldText',\n\t 'password': '_fieldText',\n\t 'select': '_fieldSelect',\n\t 'data_column': '_fieldSelect',\n\t 'genomebuild': '_fieldSelect',\n\t 'data': '_fieldData',\n\t 'data_collection': '_fieldData',\n\t 'integer': '_fieldSlider',\n\t 'float': '_fieldSlider',\n\t 'boolean': '_fieldBoolean',\n\t 'drill_down': '_fieldDrilldown',\n\t 'color': '_fieldColor',\n\t 'hidden': '_fieldHidden',\n\t 'hidden_data': '_fieldHidden',\n\t 'baseurl': '_fieldHidden',\n\t 'library_data': '_fieldLibrary',\n\t 'ftpfile': '_fieldFtp',\n\t 'upload': '_fieldUpload',\n\t 'genomespacefile': '_fieldGenomeSpace'\n\t },\n\t\n\t /** Returns an input field for a given field type */\n\t create: function (input_def) {\n\t var fieldClass = this.types[input_def.type];\n\t var field = typeof this[fieldClass] === 'function' ? this[fieldClass].call(this, input_def) : null;\n\t if (!field) {\n\t field = input_def.options ? this._fieldSelect(input_def) : this._fieldText(input_def);\n\t Galaxy.emit.debug('form-parameters::_addRow()', 'Auto matched field type (' + input_def.type + ').');\n\t }\n\t input_def.value === undefined && (input_def.value = null);\n\t field.value(input_def.value);\n\t return field;\n\t },\n\t\n\t /** Data input field */\n\t _fieldData: function (input_def) {\n\t return new SelectContent.View({\n\t id: 'field-' + input_def.id,\n\t extensions: input_def.extensions,\n\t optional: input_def.optional,\n\t multiple: input_def.multiple,\n\t type: input_def.type,\n\t flavor: input_def.flavor,\n\t data: input_def.options,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Select/Checkbox/Radio options field */\n\t _fieldSelect: function (input_def) {\n\t // show text field e.g. in workflow editor\n\t if (input_def.is_workflow) {\n\t return this._fieldText(input_def);\n\t }\n\t\n\t // customize properties\n\t if (input_def.type == 'data_column') {\n\t input_def.error_text = 'Missing columns in referenced dataset.';\n\t }\n\t\n\t // identify available options\n\t var data = input_def.data;\n\t if (!data) {\n\t data = [];\n\t _.each(input_def.options, function (option) {\n\t data.push({ label: option[0], value: option[1] });\n\t });\n\t }\n\t\n\t // identify display type\n\t var SelectClass = Ui.Select;\n\t switch (input_def.display) {\n\t case 'checkboxes':\n\t SelectClass = Ui.Checkbox;\n\t break;\n\t case 'radio':\n\t SelectClass = Ui.Radio;\n\t break;\n\t case 'radiobutton':\n\t SelectClass = Ui.RadioButton;\n\t break;\n\t }\n\t\n\t // create select field\n\t return new SelectClass.View({\n\t id: 'field-' + input_def.id,\n\t data: data,\n\t error_text: input_def.error_text || 'No options available',\n\t multiple: input_def.multiple,\n\t optional: input_def.optional,\n\t onchange: input_def.onchange,\n\t individual: input_def.individual,\n\t searchable: input_def.flavor !== 'workflow'\n\t });\n\t },\n\t\n\t /** Drill down options field */\n\t _fieldDrilldown: function (input_def) {\n\t // show text field e.g. in workflow editor\n\t if (input_def.is_workflow) {\n\t return this._fieldText(input_def);\n\t }\n\t\n\t // create drill down field\n\t return new Ui.Drilldown.View({\n\t id: 'field-' + input_def.id,\n\t data: input_def.options,\n\t display: input_def.display,\n\t optional: input_def.optional,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Text input field */\n\t _fieldText: function (input_def) {\n\t // field replaces e.g. a select field\n\t if (input_def.options && input_def.data) {\n\t input_def.area = input_def.multiple;\n\t if (Utils.isEmpty(input_def.value)) {\n\t input_def.value = null;\n\t } else {\n\t if ($.isArray(input_def.value)) {\n\t var str_value = '';\n\t for (var i in input_def.value) {\n\t str_value += String(input_def.value[i]);\n\t if (!input_def.multiple) {\n\t break;\n\t }\n\t str_value += '\\n';\n\t }\n\t input_def.value = str_value;\n\t }\n\t }\n\t }\n\t // create input element\n\t return new Ui.Input({\n\t id: 'field-' + input_def.id,\n\t type: input_def.type,\n\t area: input_def.area,\n\t readonly: input_def.readonly,\n\t placeholder: input_def.placeholder,\n\t datalist: input_def.datalist,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Slider field */\n\t _fieldSlider: function (input_def) {\n\t return new Ui.Slider.View({\n\t id: 'field-' + input_def.id,\n\t precise: input_def.type == 'float',\n\t is_workflow: input_def.is_workflow,\n\t min: input_def.min,\n\t max: input_def.max,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Hidden field */\n\t _fieldHidden: function (input_def) {\n\t return new Ui.Hidden({\n\t id: 'field-' + input_def.id,\n\t info: input_def.info\n\t });\n\t },\n\t\n\t /** Boolean field */\n\t _fieldBoolean: function (input_def) {\n\t return new Ui.RadioButton.View({\n\t id: 'field-' + input_def.id,\n\t data: [{ label: 'Yes', value: 'true' }, { label: 'No', value: 'false' }],\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Color picker field */\n\t _fieldColor: function (input_def) {\n\t return new ColorPicker({\n\t id: 'field-' + input_def.id,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Library dataset field */\n\t _fieldLibrary: function (input_def) {\n\t return new SelectLibrary.View({\n\t id: 'field-' + input_def.id,\n\t optional: input_def.optional,\n\t multiple: input_def.multiple,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** FTP file field */\n\t _fieldFtp: function (input_def) {\n\t return new SelectFtp.View({\n\t id: 'field-' + input_def.id,\n\t optional: input_def.optional,\n\t multiple: input_def.multiple,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** GenomeSpace file select field\n\t */\n\t _fieldGenomeSpace: function (input_def) {\n\t var self = this;\n\t return new SelectGenomeSpace.View({\n\t id: 'field-' + input_def.id,\n\t onchange: function () {\n\t self.app.trigger('change');\n\t }\n\t });\n\t },\n\t\n\t /** Upload file field */\n\t _fieldUpload: function (input_def) {\n\t return new Ui.Upload({\n\t id: 'field-' + input_def.id,\n\t onchange: input_def.onchange\n\t });\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ },\n/* 31 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/** This class creates a ui component which enables the dynamic creation of portlets */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(9), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Portlet, Ui) {\n\t var View = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.list = {};\n\t this.options = Utils.merge(options, {\n\t title: 'Repeat',\n\t empty_text: 'Not available.',\n\t max: null,\n\t min: null\n\t });\n\t this.button_new = new Ui.ButtonIcon({\n\t icon: 'fa-plus',\n\t title: 'Insert ' + this.options.title,\n\t tooltip: 'Add new ' + this.options.title + ' block',\n\t cls: 'ui-button-icon ui-clear-float form-repeat-add',\n\t onclick: function () {\n\t options.onnew && options.onnew();\n\t }\n\t });\n\t this.setElement($('').append(this.$list = $('')).append($('').append(this.button_new.$el)));\n\t },\n\t\n\t /** Number of repeat blocks */\n\t size: function () {\n\t return _.size(this.list);\n\t },\n\t\n\t /** Add new repeat block */\n\t add: function (options) {\n\t if (!options.id || this.list[options.id]) {\n\t Galaxy.emit.debug('form-repeat::add()', 'Duplicate or invalid repeat block id.');\n\t return;\n\t }\n\t var button_delete = new Ui.ButtonIcon({\n\t icon: 'fa-trash-o',\n\t tooltip: 'Delete this repeat block',\n\t cls: 'ui-button-icon-plain form-repeat-delete',\n\t onclick: function () {\n\t options.ondel && options.ondel();\n\t }\n\t });\n\t var portlet = new Portlet.View({\n\t id: options.id,\n\t title: 'placeholder',\n\t cls: options.cls || 'ui-portlet-repeat',\n\t operations: { button_delete: button_delete }\n\t });\n\t portlet.append(options.$el);\n\t portlet.$el.addClass('section-row').hide();\n\t this.list[options.id] = portlet;\n\t this.$list.append(portlet.$el.fadeIn('fast'));\n\t this.options.max > 0 && this.size() >= this.options.max && this.button_new.disable();\n\t this._refresh();\n\t },\n\t\n\t /** Delete repeat block */\n\t del: function (id) {\n\t if (!this.list[id]) {\n\t Galaxy.emit.debug('form-repeat::del()', 'Invalid repeat block id.');\n\t return;\n\t }\n\t this.$list.find('#' + id).remove();\n\t delete this.list[id];\n\t this.button_new.enable();\n\t this._refresh();\n\t },\n\t\n\t /** Remove all */\n\t delAll: function () {\n\t for (var id in this.list) {\n\t this.del(id);\n\t }\n\t },\n\t\n\t /** Hides add/del options */\n\t hideOptions: function () {\n\t this.button_new.$el.hide();\n\t _.each(this.list, function (portlet) {\n\t portlet.hideOperation('button_delete');\n\t });\n\t _.isEmpty(this.list) && this.$el.append($('').addClass('ui-form-info').html(this.options.empty_text));\n\t },\n\t\n\t /** Refresh view */\n\t _refresh: function () {\n\t var index = 0;\n\t for (var id in this.list) {\n\t var portlet = this.list[id];\n\t portlet.title(++index + ': ' + this.options.title);\n\t portlet[this.size() > this.options.min ? 'showOperation' : 'hideOperation']('button_delete');\n\t }\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 32 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _, jQuery) {/**\n\t This class creates a form section and populates it with input elements. It also handles repeat blocks and conditionals by recursively creating new sub sections.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(5), __webpack_require__(9), __webpack_require__(31), __webpack_require__(29), __webpack_require__(30)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui, Portlet, Repeat, InputElement, Parameters) {\n\t var View = Backbone.View.extend({\n\t initialize: function (app, options) {\n\t this.app = app;\n\t this.inputs = options.inputs;\n\t this.parameters = new Parameters();\n\t this.setElement($(''));\n\t this.render();\n\t },\n\t\n\t /** Render section view */\n\t render: function () {\n\t var self = this;\n\t this.$el.empty();\n\t _.each(this.inputs, function (input) {\n\t self.add(input);\n\t });\n\t },\n\t\n\t /** Add a new input element */\n\t add: function (input) {\n\t var input_def = jQuery.extend(true, {}, input);\n\t input_def.id = input.id = Utils.uid();\n\t this.app.input_list[input_def.id] = input_def;\n\t switch (input_def.type) {\n\t case 'conditional':\n\t this._addConditional(input_def);\n\t break;\n\t case 'repeat':\n\t this._addRepeat(input_def);\n\t break;\n\t case 'section':\n\t this._addSection(input_def);\n\t break;\n\t default:\n\t this._addRow(input_def);\n\t }\n\t },\n\t\n\t /** Add a conditional block */\n\t _addConditional: function (input_def) {\n\t var self = this;\n\t input_def.test_param.id = input_def.id;\n\t this.app.model.get('sustain_conditionals') && (input_def.test_param.disabled = true);\n\t var field = this._addRow(input_def.test_param);\n\t\n\t // set onchange event for test parameter\n\t field.model && field.model.set('onchange', function (value) {\n\t var selectedCase = self.app.data.matchCase(input_def, value);\n\t for (var i in input_def.cases) {\n\t var case_def = input_def.cases[i];\n\t var section_row = self.$('#' + input_def.id + '-section-' + i);\n\t var nonhidden = false;\n\t for (var j in case_def.inputs) {\n\t if (!case_def.inputs[j].hidden) {\n\t nonhidden = true;\n\t break;\n\t }\n\t }\n\t if (i == selectedCase && nonhidden) {\n\t section_row.fadeIn('fast');\n\t } else {\n\t section_row.hide();\n\t }\n\t }\n\t self.app.trigger('change');\n\t });\n\t\n\t // add conditional sub sections\n\t for (var i in input_def.cases) {\n\t var sub_section = new View(this.app, { inputs: input_def.cases[i].inputs });\n\t this._append(sub_section.$el.addClass('ui-form-section'), input_def.id + '-section-' + i);\n\t }\n\t\n\t // trigger refresh on conditional input field after all input elements have been created\n\t field.trigger('change');\n\t },\n\t\n\t /** Add a repeat block */\n\t _addRepeat: function (input_def) {\n\t var self = this;\n\t var block_index = 0;\n\t\n\t // create repeat block element\n\t var repeat = new Repeat.View({\n\t title: input_def.title || 'Repeat',\n\t min: input_def.min,\n\t max: input_def.max,\n\t onnew: function () {\n\t create(input_def.inputs);self.app.trigger('change');\n\t }\n\t });\n\t\n\t // helper function to create new repeat blocks\n\t function create(inputs) {\n\t var sub_section_id = input_def.id + '-section-' + block_index++;\n\t var sub_section = new View(self.app, { inputs: inputs });\n\t repeat.add({ id: sub_section_id,\n\t $el: sub_section.$el,\n\t ondel: function () {\n\t repeat.del(sub_section_id);self.app.trigger('change');\n\t } });\n\t }\n\t\n\t //\n\t // add parsed/minimum number of repeat blocks\n\t //\n\t var n_cache = _.size(input_def.cache);\n\t for (var i = 0; i < Math.max(Math.max(n_cache, input_def.min || 0), input_def.default || 0); i++) {\n\t create(i < n_cache ? input_def.cache[i] : input_def.inputs);\n\t }\n\t\n\t // hide options\n\t this.app.model.get('sustain_repeats') && repeat.hideOptions();\n\t\n\t // create input field wrapper\n\t var input_element = new InputElement(this.app, {\n\t label: input_def.title || input_def.name,\n\t help: input_def.help,\n\t field: repeat\n\t });\n\t this._append(input_element.$el, input_def.id);\n\t },\n\t\n\t /** Add a customized section */\n\t _addSection: function (input_def) {\n\t var portlet = new Portlet.View({\n\t title: input_def.title || input_def.name,\n\t cls: 'ui-portlet-section',\n\t collapsible: true,\n\t collapsible_button: true,\n\t collapsed: !input_def.expanded\n\t });\n\t portlet.append(new View(this.app, { inputs: input_def.inputs }).$el);\n\t portlet.append($('').addClass('ui-form-info').html(input_def.help));\n\t this.app.on('expand', function (input_id) {\n\t portlet.$('#' + input_id).length > 0 && portlet.expand();\n\t });\n\t this._append(portlet.$el, input_def.id);\n\t },\n\t\n\t /** Add a single input field element */\n\t _addRow: function (input_def) {\n\t var self = this;\n\t var id = input_def.id;\n\t input_def.onchange = input_def.onchange || function () {\n\t self.app.trigger('change', id);\n\t };\n\t var field = this.parameters.create(input_def);\n\t this.app.field_list[id] = field;\n\t var input_element = new InputElement(this.app, {\n\t name: input_def.name,\n\t label: input_def.hide_label ? '' : input_def.label || input_def.name,\n\t value: input_def.value,\n\t text_value: input_def.text_value,\n\t collapsible_value: input_def.collapsible_value,\n\t collapsible_preview: input_def.collapsible_preview,\n\t help: input_def.help,\n\t argument: input_def.argument,\n\t disabled: input_def.disabled,\n\t color: input_def.color,\n\t style: input_def.style,\n\t backdrop: input_def.backdrop,\n\t hidden: input_def.hidden,\n\t fixed: input_def.fixed,\n\t field: field\n\t });\n\t this.app.element_list[id] = input_element;\n\t this._append(input_element.$el, input_def.id);\n\t return field;\n\t },\n\t\n\t /** Append a new element to the form i.e. input element, repeat block, conditionals etc. */\n\t _append: function ($el, id) {\n\t this.$el.append($el.addClass('section-row').attr('id', id));\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ },\n/* 33 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t\n\t // grid model\n\t return Backbone.Model.extend({\n\t defaults: {\n\t url_base: '',\n\t async: false,\n\t async_ops: [],\n\t categorical_filters: [],\n\t filters: {},\n\t sort_key: null,\n\t show_item_checkboxes: false,\n\t advanced_search: false,\n\t cur_page: 1,\n\t num_pages: 1,\n\t operation: undefined,\n\t item_ids: undefined\n\t },\n\t\n\t /**\n\t * Return true if operation can be done asynchronously.\n\t */\n\t can_async_op: function (op) {\n\t return _.indexOf(this.attributes.async_ops, op) !== -1;\n\t },\n\t\n\t /**\n\t * Add filtering criterion.\n\t */\n\t add_filter: function (key, value, append) {\n\t // Update URL arg with new condition. \n\t if (append) {\n\t // Update or append value.\n\t var cur_val = this.attributes.filters[key],\n\t new_val;\n\t if (cur_val === null || cur_val === undefined) {\n\t new_val = value;\n\t } else if (typeof cur_val == 'string') {\n\t if (cur_val == 'All' || cur_val == value) {\n\t new_val = value;\n\t } else {\n\t // Replace string with array.\n\t var values = [];\n\t values[0] = cur_val;\n\t values[1] = value;\n\t new_val = values;\n\t }\n\t } else {\n\t // Current value is an array.\n\t new_val = cur_val;\n\t if (new_val.indexOf(value) === -1) {\n\t new_val.push(value);\n\t }\n\t }\n\t this.attributes.filters[key] = new_val;\n\t } else {\n\t // Replace value.\n\t this.attributes.filters[key] = value;\n\t }\n\t },\n\t\n\t /**\n\t * Remove filtering criterion.\n\t */\n\t remove_filter: function (key, condition) {\n\t var cur_val = this.attributes.filters[key];\n\t if (cur_val === null || cur_val === undefined) {\n\t return false;\n\t }\n\t\n\t if (typeof cur_val === 'string') {\n\t // overwrite/remove condition.\n\t this.attributes.filters[key] = '';\n\t } else {\n\t // filter contains an array of conditions.\n\t var condition_index = _.indexOf(cur_val, condition);\n\t if (condition_index !== -1) {\n\t cur_val[condition_index] = '';\n\t }\n\t }\n\t },\n\t\n\t /**\n\t * Returns URL data for obtaining a new grid.\n\t */\n\t get_url_data: function () {\n\t var url_data = {\n\t async: this.attributes.async,\n\t sort: this.attributes.sort_key,\n\t page: this.attributes.cur_page,\n\t show_item_checkboxes: this.attributes.show_item_checkboxes,\n\t advanced_search: this.attributes.advanced_search\n\t };\n\t\n\t // Add operation, item_ids only if they have values.\n\t if (this.attributes.operation) {\n\t url_data.operation = this.attributes.operation;\n\t }\n\t if (this.attributes.item_ids) {\n\t url_data.id = this.attributes.item_ids;\n\t }\n\t\n\t // Add filter arguments to data, placing \"f-\" in front of all arguments.\n\t var self = this;\n\t _.each(_.pairs(self.attributes.filters), function (k) {\n\t url_data['f-' + k[0]] = k[1];\n\t });\n\t return url_data;\n\t },\n\t\n\t // Return URL for obtaining a new grid\n\t get_url: function (args) {\n\t return this.get('url_base') + '?' + $.param(this.get_url_data()) + '&' + $.param(args);\n\t }\n\t\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ },\n/* 34 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(jQuery, _) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t\n\t // grid view templates\n\t return {\n\t // template\n\t grid: function (options) {\n\t var tmpl = '';\n\t if (options.embedded) {\n\t tmpl = this.grid_header(options) + this.grid_table(options);\n\t } else {\n\t tmpl = '' + '' + '
' + this.grid_table(options);\n\t }\n\t\n\t // add info text\n\t if (options.info_text) {\n\t tmpl += '
';\n\t\n\t // add checkbox\n\t if (options.show_item_checkboxes) {\n\t tmpl += '';\n\t if (options.items.length > 0) {\n\t tmpl += '' + '';\n\t }\n\t tmpl += ' ';\n\t }\n\t\n\t // create header elements\n\t for (var i in options.columns) {\n\t var column = options.columns[i];\n\t if (column.visible) {\n\t tmpl += '';\n\t if (column.href) {\n\t tmpl += '' + column.label + '';\n\t } else {\n\t tmpl += column.label;\n\t }\n\t tmpl += '' + column.extra + '' + ' ';\n\t }\n\t }\n\t\n\t // finalize\n\t tmpl += ' ';\n\t\n\t // return template\n\t return tmpl;\n\t },\n\t\n\t // template\n\t body: function (options) {\n\t // initialize\n\t var tmpl = '';\n\t var num_rows_rendered = 0;\n\t var items_length = options.items.length;\n\t\n\t // empty grid?\n\t if (items_length == 0) {\n\t // No results.\n\t tmpl += 'No Items ';\n\t\n\t // Link\n\t if (link) {\n\t if (options.operations.length != 0) {\n\t tmpl += ' ';\n\t }\n\t }\n\t tmpl += '';\n\t num_rows_rendered++;\n\t }\n\t return tmpl;\n\t },\n\t\n\t // template\n\t footer: function (options) {\n\t\n\t // create template string\n\t var tmpl = '';\n\t\n\t // paging\n\t if (options.use_paging && options.num_pages > 1) {\n\t // get configuration\n\t var num_page_links = options.num_page_links;\n\t var cur_page_num = options.cur_page_num;\n\t var num_pages = options.num_pages;\n\t\n\t // First pass on min page.\n\t var page_link_range = num_page_links / 2;\n\t var min_page = cur_page_num - page_link_range;\n\t var min_offset = 0;\n\t if (min_page <= 0) {\n\t // Min page is too low.\n\t min_page = 1;\n\t min_offset = page_link_range - (cur_page_num - min_page);\n\t }\n\t\n\t // Set max page.\n\t var max_range = page_link_range + min_offset;\n\t var max_page = cur_page_num + max_range;\n\t var max_offset;\n\t if (max_page <= num_pages) {\n\t // Max page is fine.\n\t max_offset = 0;\n\t } else {\n\t // Max page is too high.\n\t max_page = num_pages;\n\t // +1 to account for the +1 in the loop below.\n\t max_offset = max_range - (max_page + 1 - cur_page_num);\n\t }\n\t\n\t // Second and final pass on min page to add any unused\n\t // offset from max to min.\n\t if (max_offset != 0) {\n\t min_page -= max_offset;\n\t if (min_page < 1) {\n\t min_page = 1;\n\t }\n\t }\n\t\n\t // template header\n\t tmpl += '';\n\t if (options.show_item_checkboxes) {\n\t tmpl += '' + '' + 'Page:';\n\t\n\t if (min_page > 1) {\n\t tmpl += '1 ...';\n\t }\n\t\n\t // create page urls\n\t for (var page_index = min_page; page_index < max_page + 1; page_index++) {\n\t\n\t if (page_index == options.cur_page_num) {\n\t tmpl += '' + page_index + '';\n\t } else {\n\t tmpl += '' + page_index + '';\n\t }\n\t }\n\t\n\t // show last page\n\t if (max_page < num_pages) {\n\t tmpl += '...' + '' + num_pages + '';\n\t }\n\t tmpl += '';\n\t\n\t // Show all link\n\t tmpl += ' | Show All' + ' ' + ' ';\n\t }\n\t\n\t // Grid operations for multiple items.\n\t if (options.show_item_checkboxes) {\n\t // start template\n\t tmpl += '' + '' + '' + 'For selected items: ';\n\t\n\t // configure buttons for operations\n\t for (var i in options.operations) {\n\t var operation = options.operations[i];\n\t if (operation.allow_multiple) {\n\t tmpl += ' ';\n\t }\n\t }\n\t\n\t // finalize template\n\t tmpl += ' ' + ' ';\n\t }\n\t\n\t // count global operations\n\t var found_global = false;\n\t for (i in options.operations) {\n\t if (options.operations[i].global_operation) {\n\t found_global = true;\n\t break;\n\t }\n\t }\n\t\n\t // add global operations\n\t if (found_global) {\n\t tmpl += '' + '';\n\t for (i in options.operations) {\n\t var operation = options.operations[i];\n\t if (operation.global_operation) {\n\t tmpl += '' + operation.label + '';\n\t }\n\t }\n\t tmpl += ' ' + ' ';\n\t }\n\t\n\t // add legend\n\t if (options.legend) {\n\t tmpl += '' + '' + options.legend + ' ' + ' ';\n\t }\n\t\n\t // return\n\t return tmpl;\n\t },\n\t\n\t // template\n\t message: function (options) {\n\t var status = options.status == 'success' ? 'done' : options.status;\n\t return '';\n\t\n\t if (column.filterable == 'advanced') {\n\t tmpl += '' + column_label + ': ';\n\t }\n\t tmpl += '';\n\t if (column.is_text) {\n\t tmpl += '';\n\t } else {\n\t // filter criteria\n\t tmpl += '';\n\t\n\t // add category filters\n\t var seperator = false;\n\t for (var cf_label in options.categorical_filters[column_key]) {\n\t // get category filter\n\t var cf = options.categorical_filters[column_key][cf_label];\n\t\n\t // each filter will have only a single argument, so get that single argument\n\t var cf_key = '';\n\t var cf_arg = '';\n\t for (var key in cf) {\n\t cf_key = key;\n\t cf_arg = cf[key];\n\t }\n\t\n\t // add seperator\n\t if (seperator) {\n\t tmpl += ' | ';\n\t }\n\t seperator = true;\n\t\n\t // add category\n\t var filter = filters[column_key];\n\t if (filter && cf[column_key] && filter == cf_arg) {\n\t tmpl += '' + cf_label + '';\n\t } else {\n\t tmpl += '' + '' + cf_label + '' + '';\n\t }\n\t }\n\t tmpl += '';\n\t }\n\t tmpl += ' ' + ' ';\n\t\n\t // return template\n\t return tmpl;\n\t },\n\t\n\t // template for filter items\n\t filter_element: function (filter_key, filter_value) {\n\t filter_value = Utils.sanitize(filter_value);\n\t return '' + filter_value + '' + '' + '' + '';\n\t }\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 35 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;// Provides support for interacting with the GenomeSpace File Browser popup dialogue\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t\n\t // tool form templates\n\t return {\n\t openFileBrowser: function (options) {\n\t var GS_UI_URL = window.Galaxy.config.genomespace_ui_url;\n\t var GS_UPLOAD_URL = GS_UI_URL + 'upload/loadUrlToGenomespace.html?getLocation=true';\n\t\n\t var newWin = window.open(GS_UPLOAD_URL, \"GenomeSpace File Browser\", \"height=360px,width=600px\");\n\t\n\t successCalBack = options['successCallback'];\n\t window.addEventListener(\"message\", function (e) {\n\t successCalBack(e.data);\n\t }, false);\n\t\n\t newWin.focus();\n\t\n\t if (options['errorCallback'] != null) newWin.setCallbackOnGSUploadError = config['errorCallback'];\n\t }\n\t\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\n/***/ },\n/* 36 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/** Renders the color picker used e.g. in the tool form **/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t return Backbone.View.extend({\n\t colors: {\n\t standard: ['c00000', 'ff0000', 'ffc000', 'ffff00', '92d050', '00b050', '00b0f0', '0070c0', '002060', '7030a0'],\n\t base: ['ffffff', '000000', 'eeece1', '1f497d', '4f81bd', 'c0504d', '9bbb59', '8064a2', '4bacc6', 'f79646'],\n\t theme: [['f2f2f2', '7f7f7f', 'ddd9c3', 'c6d9f0', 'dbe5f1', 'f2dcdb', 'ebf1dd', 'e5e0ec', 'dbeef3', 'fdeada'], ['d8d8d8', '595959', 'c4bd97', '8db3e2', 'b8cce4', 'e5b9b7', 'd7e3bc', 'ccc1d9', 'b7dde8', 'fbd5b5'], ['bfbfbf', '3f3f3f', '938953', '548dd4', '95b3d7', 'd99694', 'c3d69b', 'b2a2c7', '92cddc', 'fac08f'], ['a5a5a5', '262626', '494429', '17365d', '366092', '953734', '76923c', '5f497a', '31859b', 'e36c09'], ['7f7f7e', '0c0c0c', '1d1b10', '0f243e', '244061', '632423', '4f6128', '3f3151', '205867', '974806']]\n\t },\n\t\n\t initialize: function (options) {\n\t this.options = Utils.merge(options, {});\n\t this.setElement(this._template());\n\t this.$panel = this.$('.ui-color-picker-panel');\n\t this.$view = this.$('.ui-color-picker-view');\n\t this.$value = this.$('.ui-color-picker-value');\n\t this.$header = this.$('.ui-color-picker-header');\n\t this._build();\n\t this.visible = false;\n\t this.value(this.options.value);\n\t this.$boxes = this.$('.ui-color-picker-box');\n\t var self = this;\n\t this.$boxes.on('click', function () {\n\t self.value($(this).css('background-color'));\n\t self.$header.trigger('click');\n\t });\n\t this.$header.on('click', function () {\n\t self.visible = !self.visible;\n\t if (self.visible) {\n\t self.$view.fadeIn('fast');\n\t } else {\n\t self.$view.fadeOut('fast');\n\t }\n\t });\n\t },\n\t\n\t /** Get/set value */\n\t value: function (new_val) {\n\t if (new_val !== undefined && new_val !== null) {\n\t this.$value.css('background-color', new_val);\n\t this.$('.ui-color-picker-box').empty();\n\t this.$(this._getValue()).html(this._templateCheck());\n\t this.options.onchange && this.options.onchange(new_val);\n\t }\n\t return this._getValue();\n\t },\n\t\n\t /** Get value from dom */\n\t _getValue: function () {\n\t var rgb = this.$value.css('background-color');\n\t rgb = rgb.match(/^rgb\\((\\d+),\\s*(\\d+),\\s*(\\d+)\\)$/);\n\t if (rgb) {\n\t function hex(x) {\n\t return ('0' + parseInt(x).toString(16)).slice(-2);\n\t }\n\t return '#' + hex(rgb[1]) + hex(rgb[2]) + hex(rgb[3]);\n\t } else {\n\t return null;\n\t }\n\t },\n\t\n\t /** Build color panel */\n\t _build: function () {\n\t this._content({ colors: this.colors.base });\n\t for (var i in this.colors.theme) {\n\t var line_def = {};\n\t if (i == 0) {\n\t line_def['bottom'] = true;\n\t } else if (i != this.colors.theme.length - 1) {\n\t line_def['top'] = true;\n\t line_def['bottom'] = true;\n\t } else {\n\t line_def['top'] = true;\n\t }\n\t line_def['colors'] = this.colors.theme[i];\n\t this._content(line_def);\n\t }\n\t this._content({ colors: this.colors.standard });\n\t },\n\t\n\t /** Create content */\n\t _content: function (options) {\n\t var colors = options.colors;\n\t var $content = $(this._templateContent());\n\t var $line = $content.find('.line');\n\t this.$panel.append($content);\n\t for (var i in colors) {\n\t var $box = $(this._templateBox(colors[i]));\n\t if (options.top) {\n\t $box.css('border-top', 'none');\n\t $box.css('border-top-left-radius', '0px');\n\t $box.css('border-top-right-radius', '0px');\n\t }\n\t if (options.bottom) {\n\t $box.css('border-bottom', 'none');\n\t $box.css('border-bottom-left-radius', '0px');\n\t $box.css('border-bottom-right-radius', '0px');\n\t }\n\t $line.append($box);\n\t }\n\t return $content;\n\t },\n\t\n\t /** Check icon */\n\t _templateCheck: function () {\n\t return '';\n\t },\n\t\n\t /** Content template */\n\t _templateContent: function () {\n\t return '
| ' + this.grid_header(options) + ' | ' + '' + ' | ' + ' |
| ' + ' | ' + ' | ' + ' |
' + options.info_text + '
';\n\t }\n\t\n\t // return\n\t return tmpl;\n\t },\n\t\n\t // template\n\t grid_table: function (options) {\n\t return '';\n\t },\n\t\n\t // template\n\t grid_header: function (options) {\n\t var tmpl = '';\n\t if (!options.embedded) {\n\t tmpl += '
';\n\t\n\t // return template\n\t return tmpl;\n\t },\n\t\n\t // template\n\t header: function (options) {\n\t\n\t // start\n\t var tmpl = '' + options.title + '
';\n\t }\n\t if (options.global_actions) {\n\t tmpl += '- ';\n\t var show_popup = options.global_actions.length >= 3;\n\t if (show_popup) {\n\t tmpl += '
- Actions ' + '
- ' + '' + action.label + '' + ' ';\n\t }\n\t if (show_popup) {\n\t tmpl += '
';\n\t }\n\t for (var i in options.global_actions) {\n\t var action = options.global_actions[i];\n\t tmpl += '
';\n\t }\n\t tmpl += '';\n\t }\n\t tmpl += '' + value + '';\n\t if (options.operations.length != 0) {\n\t tmpl += '
';\n\t }\n\t } else {\n\t tmpl += '';\n\t }\n\t tmpl += '' + '
' + _.escape(options.message) + '
' + '' + '';\n\t },\n\t\n\t // template\n\t grid_filters: function (options) {\n\t\n\t // get filters\n\t var default_filter_dict = options.default_filter_dict;\n\t var filters = options.filters;\n\t\n\t // show advanced search if flag set or if there are filters for advanced search fields\n\t var advanced_search_display = 'none';\n\t if (options.advanced_search) {\n\t advanced_search_display = 'block';\n\t }\n\t\n\t // identify columns with advanced filtering\n\t var show_advanced_search_link = false;\n\t for (var i in options.columns) {\n\t var column = options.columns[i];\n\t if (column.filterable == 'advanced') {\n\t var column_key = column.key;\n\t var f_key = filters[column_key];\n\t var d_key = default_filter_dict[column_key];\n\t if (f_key && d_key && f_key != d_key) {\n\t advanced_search_display = 'block';\n\t }\n\t show_advanced_search_link = true;\n\t }\n\t }\n\t\n\t // hide standard search if advanced is shown\n\t var standard_search_display = 'block';\n\t if (advanced_search_display == 'block') {\n\t standard_search_display = 'none';\n\t }\n\t\n\t //\n\t // standard search\n\t //\n\t var tmpl = '' + '' + '
' + '
';\n\t\n\t //\n\t // advanced search\n\t //\n\t tmpl += '| ' + ' | ' + '
| ';\n\t\n\t // show advanced search link in standard display\n\t if (show_advanced_search_link) {\n\t tmpl += 'Advanced Search';\n\t }\n\t\n\t // finalize standard search display\n\t tmpl += ' | ' + '
' + '' + '
' + '
';\n\t\n\t // return template\n\t return tmpl;\n\t },\n\t\n\t // template\n\t grid_column_filter: function (options, column) {\n\t\n\t // collect parameters\n\t var default_filter_dict = options.default_filter_dict;\n\t var filters = options.filters;\n\t var column_label = column.label;\n\t var column_key = column.key;\n\t if (column.filterable == 'advanced') {\n\t column_label = column_label.toLowerCase();\n\t }\n\t\n\t // start\n\t var tmpl = '| ' + 'Close Advanced Search' + ' | ' + '
' + '
' + '
';\n\t },\n\t\n\t /** Box template */\n\t _templateBox: function (color) {\n\t return '';\n\t },\n\t\n\t /** Main template */\n\t _template: function () {\n\t return '' + '
' + '
' + '
' + 'Select a color
' + '' + '
';\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 37 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function($, _) {/** This class creates/wraps a drill down element. */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(14)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Options) {\n\t\n\t var View = Options.BaseIcons.extend({\n\t initialize: function (options) {\n\t options.type = options.display || 'checkbox';\n\t options.multiple = options.type == 'checkbox';\n\t Options.BaseIcons.prototype.initialize.call(this, options);\n\t },\n\t\n\t /** Set states for selected values */\n\t _setValue: function (new_value) {\n\t Options.BaseIcons.prototype._setValue.call(this, new_value);\n\t if (new_value !== undefined && new_value !== null && this.header_index) {\n\t var self = this;\n\t var values = $.isArray(new_value) ? new_value : [new_value];\n\t _.each(values, function (v) {\n\t var list = self.header_index[v];\n\t _.each(list, function (element) {\n\t self._setState(element, true);\n\t });\n\t });\n\t }\n\t },\n\t\n\t /** Expand/collapse a sub group */\n\t _setState: function (header_id, is_expanded) {\n\t var $button = this.$('.button-' + header_id);\n\t var $subgroup = this.$('.subgroup-' + header_id);\n\t $button.data('is_expanded', is_expanded);\n\t if (is_expanded) {\n\t $subgroup.show();\n\t $button.removeClass('fa-plus-square').addClass('fa-minus-square');\n\t } else {\n\t $subgroup.hide();\n\t $button.removeClass('fa-minus-square').addClass('fa-plus-square');\n\t }\n\t },\n\t\n\t /** Template to create options tree */\n\t _templateOptions: function () {\n\t var self = this;\n\t this.header_index = {};\n\t\n\t // attach event handler\n\t function attach($el, header_id) {\n\t var $button = $el.find('.button-' + header_id);\n\t $button.on('click', function () {\n\t self._setState(header_id, !$button.data('is_expanded'));\n\t });\n\t }\n\t\n\t // recursive function which iterates through options\n\t function iterate($tmpl, options, header) {\n\t header = header || [];\n\t for (var i in options) {\n\t var level = options[i];\n\t var has_options = level.options && level.options.length > 0;\n\t var new_header = header.slice(0);\n\t self.header_index[level.value] = new_header.slice(0);\n\t var $group = $('');\n\t if (has_options) {\n\t var header_id = Utils.uid();\n\t var $button = $('').addClass('button-' + header_id).addClass('ui-drilldown-button fa fa-plus-square');\n\t var $subgroup = $('').addClass('subgroup-' + header_id).addClass('ui-drilldown-subgroup');\n\t $group.append($('').append($button).append(self._templateOption({ label: level.name, value: level.value })));\n\t new_header.push(header_id);\n\t iterate($subgroup, level.options, new_header);\n\t $group.append($subgroup);\n\t attach($group, header_id);\n\t } else {\n\t $group.append(self._templateOption({ label: level.name, value: level.value }));\n\t }\n\t $tmpl.append($group);\n\t }\n\t }\n\t\n\t // iterate through options and create dom\n\t var $tmpl = $('');\n\t iterate($tmpl, this.model.get('data'));\n\t return $tmpl;\n\t },\n\t\n\t /** Template for drill down view */\n\t _template: function () {\n\t return $('').addClass('ui-options-list drilldown-container').attr('id', this.model.id);\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 38 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(5), __webpack_require__(15)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui, Select) {\n\t\n\t /** Batch mode variations */\n\t var Batch = { DISABLED: 'disabled', ENABLED: 'enabled', LINKED: 'linked' };\n\t\n\t /** List of available content selectors options */\n\t var Configurations = {\n\t data: [{ src: 'hda', icon: 'fa-file-o', tooltip: 'Single dataset', multiple: false, batch: Batch.DISABLED }, { src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.LINKED }, { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.LINKED }],\n\t data_multiple: [{ src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.DISABLED }, { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collections', multiple: true, batch: Batch.DISABLED }],\n\t data_collection: [{ src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.DISABLED }],\n\t workflow_data: [{ src: 'hda', icon: 'fa-file-o', tooltip: 'Single dataset', multiple: false, batch: Batch.DISABLED }],\n\t workflow_data_multiple: [{ src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.DISABLED }],\n\t workflow_data_collection: [{ src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.DISABLED }],\n\t module_data: [{ src: 'hda', icon: 'fa-file-o', tooltip: 'Single dataset', multiple: false, batch: Batch.DISABLED }, { src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.ENABLED }],\n\t module_data_collection: [{ src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.DISABLED }, { src: 'hdca', icon: 'fa-folder', tooltip: 'Multiple collections', multiple: true, batch: Batch.ENABLED }]\n\t };\n\t\n\t /** View for hda and hdca content selector ui elements */\n\t var View = Backbone.View.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.model = options && options.model || new Backbone.Model({\n\t src_labels: { 'hda': 'dataset', 'hdca': 'dataset collection' },\n\t pagelimit: 100,\n\t statustimer: 1000\n\t }).set(options);\n\t this.setElement($('').addClass('ui-select-content'));\n\t this.button_product = new Ui.RadioButton.View({\n\t value: 'false',\n\t data: [{ icon: 'fa fa-chain', value: 'false',\n\t tooltip: 'Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads.' }, { icon: 'fa fa-chain-broken', value: 'true',\n\t tooltip: 'Unlinked dataset inputs will be run against *all* other inputs.' }] });\n\t var $batch_div = $('').addClass('ui-form-info').append($('').addClass('fa fa-sitemap')).append($('').html('This is a batch mode input field. Separate jobs will be triggered for each dataset selection.'));\n\t this.$batch = {\n\t linked: $batch_div.clone(),\n\t enabled: $batch_div.clone().append($('').append($('').addClass('ui-form-title').html('Batch options:')).append(this.button_product.$el)).append($('').css('clear', 'both'))\n\t };\n\t\n\t // add drag-drop event handlers\n\t this.$el.on('dragenter', function (e) {\n\t this.lastenter = e.target;self.$el.addClass('ui-dragover');\n\t }).on('dragover', function (e) {\n\t e.preventDefault();\n\t }).on('dragleave', function (e) {\n\t this.lastenter === e.target && self.$el.removeClass('ui-dragover');\n\t }).on('drop', function (e) {\n\t self._handleDrop(e);\n\t });\n\t\n\t // track current history elements\n\t this.history = {};\n\t\n\t // add listeners\n\t this.listenTo(this.model, 'change:data', this._changeData, this);\n\t this.listenTo(this.model, 'change:wait', this._changeWait, this);\n\t this.listenTo(this.model, 'change:current', this._changeCurrent, this);\n\t this.listenTo(this.model, 'change:value', this._changeValue, this);\n\t this.listenTo(this.model, 'change:type change:optional change:multiple change:extensions', this._changeType, this);\n\t this.render();\n\t\n\t // add change event\n\t this.on('change', function () {\n\t options.onchange && options.onchange(self.value());\n\t });\n\t },\n\t\n\t render: function () {\n\t this._changeType();\n\t this._changeValue();\n\t this._changeWait();\n\t },\n\t\n\t /** Indicate that select fields are being updated */\n\t wait: function () {\n\t this.model.set('wait', true);\n\t },\n\t\n\t /** Indicate that the options update has been completed */\n\t unwait: function () {\n\t this.model.set('wait', false);\n\t },\n\t\n\t /** Update data representing selectable options */\n\t update: function (options) {\n\t this.model.set('data', options);\n\t },\n\t\n\t /** Return the currently selected dataset values */\n\t value: function (new_value) {\n\t new_value !== undefined && this.model.set('value', new_value);\n\t var current = this.model.get('current');\n\t if (this.config[current]) {\n\t var id_list = this.fields[current].value();\n\t if (id_list !== null) {\n\t id_list = $.isArray(id_list) ? id_list : [id_list];\n\t if (id_list.length > 0) {\n\t var result = this._batch({ values: [] });\n\t for (var i in id_list) {\n\t var details = this.history[id_list[i] + '_' + this.config[current].src];\n\t if (details) {\n\t result.values.push(details);\n\t } else {\n\t Galaxy.emit.debug('ui-select-content::value()', 'Requested details not found for \\'' + id_list[i] + '\\'.');\n\t return null;\n\t }\n\t }\n\t result.values.sort(function (a, b) {\n\t return a.hid - b.hid;\n\t });\n\t return result;\n\t }\n\t }\n\t } else {\n\t Galaxy.emit.debug('ui-select-content::value()', 'Invalid value/source \\'' + new_value + '\\'.');\n\t }\n\t return null;\n\t },\n\t\n\t /** Change of current select field */\n\t _changeCurrent: function () {\n\t var self = this;\n\t _.each(this.fields, function (field, i) {\n\t if (self.model.get('current') == i) {\n\t field.$el.show();\n\t _.each(self.$batch, function ($batchfield, batchmode) {\n\t $batchfield[self.config[i].batch == batchmode ? 'show' : 'hide']();\n\t });\n\t self.button_type.value(i);\n\t } else {\n\t field.$el.hide();\n\t }\n\t });\n\t },\n\t\n\t /** Change of type */\n\t _changeType: function () {\n\t var self = this;\n\t\n\t // identify selector type identifier i.e. [ flavor ]_[ type ]_[ multiple ]\n\t var config_id = (this.model.get('flavor') ? this.model.get('flavor') + '_' : '') + String(this.model.get('type')) + (this.model.get('multiple') ? '_multiple' : '');\n\t if (Configurations[config_id]) {\n\t this.config = Configurations[config_id];\n\t } else {\n\t this.config = Configurations['data'];\n\t Galaxy.emit.debug('ui-select-content::_changeType()', 'Invalid configuration/type id \\'' + config_id + '\\'.');\n\t }\n\t\n\t // prepare extension component of error message\n\t var data = self.model.get('data');\n\t var extensions = Utils.textify(this.model.get('extensions'));\n\t var src_labels = this.model.get('src_labels');\n\t\n\t // build views\n\t this.fields = [];\n\t this.button_data = [];\n\t _.each(this.config, function (c, i) {\n\t self.button_data.push({\n\t value: i,\n\t icon: c.icon,\n\t tooltip: c.tooltip\n\t });\n\t self.fields.push(new Select.View({\n\t optional: self.model.get('optional'),\n\t multiple: c.multiple,\n\t searchable: !c.multiple || data && data[c.src] && data[c.src].length > self.model.get('pagelimit'),\n\t individual: true,\n\t error_text: 'No ' + (extensions ? extensions + ' ' : '') + (src_labels[c.src] || 'content') + ' available.',\n\t onchange: function () {\n\t self.trigger('change');\n\t }\n\t }));\n\t });\n\t this.button_type = new Ui.RadioButton.View({\n\t value: this.model.get('current'),\n\t data: this.button_data,\n\t onchange: function (value) {\n\t self.model.set('current', value);\n\t self.trigger('change');\n\t }\n\t });\n\t\n\t // append views\n\t this.$el.empty();\n\t var button_width = 0;\n\t if (this.fields.length > 1) {\n\t this.$el.append(this.button_type.$el);\n\t button_width = Math.max(0, this.fields.length * 36) + 'px';\n\t }\n\t _.each(this.fields, function (field) {\n\t self.$el.append(field.$el.css({ 'margin-left': button_width }));\n\t });\n\t _.each(this.$batch, function ($batchfield, batchmode) {\n\t self.$el.append($batchfield.css({ 'margin-left': button_width }));\n\t });\n\t this.model.set('current', 0);\n\t this._changeCurrent();\n\t this._changeData();\n\t },\n\t\n\t /** Change of wait flag */\n\t _changeWait: function () {\n\t var self = this;\n\t _.each(this.fields, function (field) {\n\t field[self.model.get('wait') ? 'wait' : 'unwait']();\n\t });\n\t },\n\t\n\t /** Change of available options */\n\t _changeData: function () {\n\t var options = this.model.get('data');\n\t var self = this;\n\t var select_options = {};\n\t _.each(options, function (items, src) {\n\t select_options[src] = [];\n\t _.each(items, function (item) {\n\t select_options[src].push({\n\t hid: item.hid,\n\t keep: item.keep,\n\t label: item.hid + ': ' + item.name,\n\t value: item.id,\n\t tags: item.tags\n\t });\n\t self.history[item.id + '_' + src] = item;\n\t });\n\t });\n\t _.each(this.config, function (c, i) {\n\t select_options[c.src] && self.fields[i].add(select_options[c.src], function (a, b) {\n\t return b.hid - a.hid;\n\t });\n\t });\n\t },\n\t\n\t /** Change of incoming value */\n\t _changeValue: function () {\n\t var new_value = this.model.get('value');\n\t if (new_value && new_value.values && new_value.values.length > 0) {\n\t // create list with content ids\n\t var list = [];\n\t _.each(new_value.values, function (value) {\n\t list.push(value.id);\n\t });\n\t // sniff first suitable field type from config list\n\t var src = new_value.values[0].src;\n\t var multiple = new_value.values.length > 1;\n\t for (var i = 0; i < this.config.length; i++) {\n\t var field = this.fields[i];\n\t var c = this.config[i];\n\t if (c.src == src && [multiple, true].indexOf(c.multiple) !== -1) {\n\t this.model.set('current', i);\n\t field.value(list);\n\t break;\n\t }\n\t }\n\t } else {\n\t _.each(this.fields, function (field) {\n\t field.value(null);\n\t });\n\t }\n\t },\n\t\n\t /** Handles drop events e.g. from history panel */\n\t _handleDrop: function (ev) {\n\t try {\n\t var data = this.model.get('data');\n\t var current = this.model.get('current');\n\t var config = this.config[current];\n\t var field = this.fields[current];\n\t var drop_data = JSON.parse(ev.originalEvent.dataTransfer.getData('text'))[0];\n\t var new_id = drop_data.id;\n\t var new_src = drop_data.history_content_type == 'dataset' ? 'hda' : 'hdca';\n\t var new_value = { id: new_id, src: new_src };\n\t if (data && _.findWhere(data[new_src], new_value)) {\n\t if (config.src == new_src) {\n\t var current_value = field.value();\n\t if (current_value && config.multiple) {\n\t if (current_value.indexOf(new_id) == -1) {\n\t current_value.push(new_id);\n\t }\n\t } else {\n\t current_value = new_id;\n\t }\n\t field.value(current_value);\n\t } else {\n\t this.model.set('value', { values: [new_value] });\n\t this.model.trigger('change:value');\n\t }\n\t this.trigger('change');\n\t this._handleDropStatus('success');\n\t } else {\n\t this._handleDropStatus('danger');\n\t }\n\t } catch (e) {\n\t this._handleDropStatus('danger');\n\t }\n\t ev.preventDefault();\n\t },\n\t\n\t /** Highlight drag result */\n\t _handleDropStatus: function (status) {\n\t var self = this;\n\t this.$el.removeClass('ui-dragover').addClass('ui-dragover-' + status);\n\t setTimeout(function () {\n\t self.$el.removeClass('ui-dragover-' + status);\n\t }, this.model.get('statustimer'));\n\t },\n\t\n\t /** Assists in identifying the batch mode */\n\t _batch: function (result) {\n\t result['batch'] = false;\n\t var current = this.model.get('current');\n\t var config = this.config[current];\n\t if (config.src == 'hdca' && !config.multiple) {\n\t var hdca = this.history[this.fields[current].value() + '_hdca'];\n\t if (hdca && hdca.map_over_type) {\n\t result['batch'] = true;\n\t }\n\t }\n\t if (config.batch == Batch.LINKED || config.batch == Batch.ENABLED) {\n\t result['batch'] = true;\n\t if (config.batch == Batch.ENABLED && this.button_product.value() === 'true') {\n\t result['product'] = true;\n\t }\n\t }\n\t return result;\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 39 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(13)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, List) {\n\t\n\t /**\n\t * FTP file selector\n\t */\n\t var View = Backbone.View.extend({\n\t // initialize\n\t initialize: function (options) {\n\t // link this\n\t var self = this;\n\t\n\t // create ui-list view to keep track of selected ftp files\n\t this.ftpfile_list = new List.View({\n\t name: 'file',\n\t optional: options.optional,\n\t multiple: options.multiple,\n\t onchange: function () {\n\t options.onchange && options.onchange(self.value());\n\t }\n\t });\n\t\n\t // create elements\n\t this.setElement(this.ftpfile_list.$el);\n\t\n\t // initial fetch of ftps\n\t Utils.get({\n\t url: Galaxy.root + 'api/remote_files',\n\t success: function (response) {\n\t var data = [];\n\t for (var i in response) {\n\t data.push({\n\t value: response[i]['path'],\n\t label: response[i]['path']\n\t });\n\t }\n\t self.ftpfile_list.update(data);\n\t }\n\t });\n\t },\n\t\n\t /** Return/Set currently selected ftp datasets */\n\t value: function (val) {\n\t return this.ftpfile_list.value(val);\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ },\n/* 40 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(5), __webpack_require__(35)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui, GenomespaceBrowser) {\n\t\n\t /**\n\t * GenomeSpace file selector\n\t */\n\t var View = Backbone.View.extend({\n\t // initialize\n\t initialize: function (options) {\n\t\n\t // link this\n\t var self = this;\n\t\n\t // create insert new list element button\n\t this.browse_button = new Ui.ButtonIcon({\n\t title: 'Browse',\n\t icon: 'fa fa-sign-in',\n\t tooltip: 'Browse GenomeSpace',\n\t onclick: function () {\n\t self.browseGenomeSpace();\n\t }\n\t });\n\t\n\t // create genomespace filepath textbox\n\t this.filename_textbox = new Ui.Input();\n\t\n\t // create genomespace token textbox\n\t this.token_textbox = new Ui.Input({\n\t type: 'password'\n\t });\n\t\n\t // create elements\n\t this.setElement(this._template(options));\n\t this.$('.ui-gs-browse-button').append(this.browse_button.$el);\n\t this.$('.ui-gs-filename-textbox').append(this.filename_textbox.$el);\n\t this.$('.ui-gs-token-textbox').append(this.token_textbox.$el);\n\t },\n\t\n\t /** Browse GenomeSpace */\n\t browseGenomeSpace: function (options) {\n\t var self = this;\n\t GenomespaceBrowser.openFileBrowser({\n\t successCallback: function (data) {\n\t self.value(data.destination + \"^\" + data.token);\n\t }\n\t });\n\t },\n\t\n\t /** Main Template */\n\t _template: function (options) {\n\t return '' + '
';\n\t '' + '
';\n\t },\n\t\n\t /** Return/Set currently selected genomespace filename/token */\n\t value: function (new_value) {\n\t // check if new_value is defined\n\t if (new_value !== undefined) {\n\t this._setValue(new_value);\n\t } else {\n\t return this._getValue();\n\t }\n\t },\n\t\n\t // get value\n\t _getValue: function () {\n\t return this.filename_textbox.value() + \"^\" + this.token_textbox.value();\n\t },\n\t\n\t // set value\n\t _setValue: function (new_value) {\n\t if (new_value) {\n\t values = new_value.split(\"^\");\n\t this.filename_textbox.value(values[0]);\n\t this.token_textbox.value(values[1]);\n\t }\n\t }\n\t\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ },\n/* 41 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(5), __webpack_require__(23), __webpack_require__(13)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui, Table, List) {\n\t\n\t // collection of libraries\n\t var Libraries = Backbone.Collection.extend({\n\t url: Galaxy.root + 'api/libraries?deleted=false'\n\t });\n\t\n\t // collection of dataset\n\t var LibraryDatasets = Backbone.Collection.extend({\n\t initialize: function () {\n\t var self = this;\n\t this.config = new Backbone.Model({ library_id: null });\n\t this.config.on('change', function () {\n\t self.fetch({ reset: true });\n\t });\n\t },\n\t url: function () {\n\t return Galaxy.root + 'api/libraries/' + this.config.get('library_id') + '/contents';\n\t }\n\t });\n\t\n\t // hda/hdca content selector ui element\n\t var View = Backbone.View.extend({\n\t // initialize\n\t initialize: function (options) {\n\t // link this\n\t var self = this;\n\t\n\t // collections\n\t this.libraries = new Libraries();\n\t this.datasets = new LibraryDatasets();\n\t\n\t // link app and options\n\t this.options = options;\n\t\n\t // select field for the library\n\t // TODO: Remove this once the library API supports searching for library datasets\n\t this.library_select = new Ui.Select.View({\n\t onchange: function (value) {\n\t self.datasets.config.set('library_id', value);\n\t }\n\t });\n\t\n\t // create ui-list view to keep track of selected data libraries\n\t this.dataset_list = new List.View({\n\t name: 'dataset',\n\t optional: options.optional,\n\t multiple: options.multiple,\n\t onchange: function () {\n\t self.trigger('change');\n\t }\n\t });\n\t\n\t // add reset handler for fetched libraries\n\t this.libraries.on('reset', function () {\n\t var data = [];\n\t self.libraries.each(function (model) {\n\t data.push({\n\t value: model.id,\n\t label: model.get('name')\n\t });\n\t });\n\t self.library_select.update(data);\n\t });\n\t\n\t // add reset handler for fetched library datasets\n\t this.datasets.on('reset', function () {\n\t var data = [];\n\t var library_current = self.library_select.text();\n\t if (library_current !== null) {\n\t self.datasets.each(function (model) {\n\t if (model.get('type') === 'file') {\n\t data.push({\n\t value: model.id,\n\t label: model.get('name')\n\t });\n\t }\n\t });\n\t }\n\t self.dataset_list.update(data);\n\t });\n\t\n\t // add change event. fires on trigger\n\t this.on('change', function () {\n\t options.onchange && options.onchange(self.value());\n\t });\n\t\n\t // create elements\n\t this.setElement(this._template());\n\t this.$('.library-select').append(this.library_select.$el);\n\t this.$el.append(this.dataset_list.$el);\n\t\n\t // initial fetch of libraries\n\t this.libraries.fetch({\n\t reset: true,\n\t success: function () {\n\t self.library_select.trigger('change');\n\t if (self.options.value !== undefined) {\n\t self.value(self.options.value);\n\t }\n\t }\n\t });\n\t },\n\t\n\t /** Return/Set currently selected library datasets */\n\t value: function (val) {\n\t return this.dataset_list.value(val);\n\t },\n\t\n\t /** Template */\n\t _template: function () {\n\t return '' + '' + '' + '
' + '' + '
' + 'Token
' + '' + '' + '
';\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ },\n/* 42 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t var View = Backbone.View.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t min: null,\n\t max: null,\n\t step: null,\n\t precise: false,\n\t split: 10000,\n\t value: null,\n\t onchange: function () {}\n\t }).set(options);\n\t\n\t // create new element\n\t this.setElement(this._template());\n\t this.$el.attr('id', this.model.id);\n\t this.$text = this.$('.ui-form-slider-text');\n\t this.$slider = this.$('.ui-form-slider-element');\n\t\n\t // add text field event\n\t var pressed = [];\n\t this.$text.on('change', function () {\n\t self.value($(this).val());\n\t }).on('keyup', function (e) {\n\t pressed[e.which] = false;\n\t }).on('keydown', function (e) {\n\t var v = e.which;\n\t pressed[v] = true;\n\t if (self.model.get('is_workflow') && pressed[16] && v == 52) {\n\t self.value('$');\n\t event.preventDefault();\n\t } else if (!(v == 8 || v == 9 || v == 13 || v == 37 || v == 39 || v >= 48 && v <= 57 && !pressed[16] || v >= 96 && v <= 105 || (v == 190 || v == 110) && $(this).val().indexOf('.') == -1 && self.model.get('precise') || (v == 189 || v == 109) && $(this).val().indexOf('-') == -1 || self._isParameter($(this).val()) || pressed[91] || pressed[17])) {\n\t event.preventDefault();\n\t }\n\t });\n\t\n\t // build slider, cannot be rebuild in render\n\t var opts = this.model.attributes;\n\t this.has_slider = opts.max !== null && opts.min !== null && opts.max > opts.min;\n\t var step = opts.step;\n\t if (!step) {\n\t if (opts.precise && this.has_slider) {\n\t step = (opts.max - opts.min) / opts.split;\n\t } else {\n\t step = 1.0;\n\t }\n\t }\n\t if (this.has_slider) {\n\t this.$text.addClass('ui-form-slider-left');\n\t this.$slider.slider({ min: opts.min, max: opts.max, step: step }).on('slide', function (event, ui) {\n\t self.value(ui.value);\n\t });\n\t } else {\n\t this.$slider.hide();\n\t }\n\t\n\t // add listeners\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var value = this.model.get('value');\n\t this.has_slider && this.$slider.slider('value', value);\n\t value !== this.$text.val() && this.$text.val(value);\n\t },\n\t\n\t /** Set and return the current value */\n\t value: function (new_val) {\n\t var options = this.model.attributes;\n\t if (new_val !== undefined) {\n\t if (new_val !== null && new_val !== '' && !this._isParameter(new_val)) {\n\t isNaN(new_val) && (new_val = 0);\n\t !options.precise && (new_val = Math.round(new_val));\n\t options.max !== null && (new_val = Math.min(new_val, options.max));\n\t options.min !== null && (new_val = Math.max(new_val, options.min));\n\t }\n\t this.model.set('value', new_val);\n\t this.model.trigger('change');\n\t options.onchange(new_val);\n\t }\n\t return this.model.get('value');\n\t },\n\t\n\t /** Return true if the field contains a workflow parameter i.e. $('name') */\n\t _isParameter: function (value) {\n\t return this.model.get('is_workflow') && String(value).substring(0, 1) === '$';\n\t },\n\t\n\t /** Slider template */\n\t _template: function () {\n\t return '' + 'Select Library' + '' + '
' + '' + '' + '';\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 43 */,\n/* 44 */,\n/* 45 */,\n/* 46 */,\n/* 47 */,\n/* 48 */,\n/* 49 */,\n/* 50 */,\n/* 51 */,\n/* 52 */,\n/* 53 */,\n/* 54 */,\n/* 55 */\n/***/ function(module, exports, __webpack_require__) {\n\n\t/* WEBPACK VAR INJECTION */(function(Backbone) {var jQuery = __webpack_require__(1),\n\t $ = jQuery,\n\t QUERY_STRING = __webpack_require__(26),\n\t Ui = __webpack_require__(5);\n\t\n\tvar Router = Backbone.Router.extend({\n\t // TODO: not many client routes at this point - fill and remove from server.\n\t // since we're at root here, this may be the last to be routed entirely on the client.\n\t initialize: function (page, options) {\n\t this.page = page;\n\t this.options = options;\n\t },\n\t\n\t /** helper to push a new navigation state */\n\t push: function (url, data) {\n\t data = data || {};\n\t data.__identifer = Math.random().toString(36).substr(2);\n\t if (!$.isEmptyObject(data)) {\n\t url += url.indexOf('?') == -1 ? '?' : '&';\n\t url += $.param(data, true);\n\t }\n\t Galaxy.params = {};\n\t this.navigate(url, { 'trigger': true });\n\t },\n\t\n\t /** override to parse query string into obj and send to each route */\n\t execute: function (callback, args, name) {\n\t Galaxy.debug('router execute:', callback, args, name);\n\t var queryObj = QUERY_STRING.parse(args.pop());\n\t args.push(queryObj);\n\t if (callback) {\n\t if (this.authenticate(args, name)) {\n\t callback.apply(this, args);\n\t } else {\n\t this.access_denied();\n\t }\n\t }\n\t },\n\t\n\t authenticate: function (args, name) {\n\t return true;\n\t },\n\t\n\t access_denied: function () {\n\t this.page.display(new Ui.Message({ status: 'danger', message: 'You must be logged in with proper credentials to make this request.', persistent: true }));\n\t }\n\t});\n\t\n\tmodule.exports = Router;\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ },\n/* 56 */,\n/* 57 */,\n/* 58 */,\n/* 59 */,\n/* 60 */,\n/* 61 */,\n/* 62 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/** Generic form view */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(10), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Form, Ui) {\n\t\n\t var View = Backbone.View.extend({\n\t\n\t initialize: function (options) {\n\t this.model = new Backbone.Model(options);\n\t this.url = this.model.get('url');\n\t this.redirect = this.model.get('redirect');\n\t this.setElement('');\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t $.ajax({\n\t url: Galaxy.root + this.url,\n\t type: 'GET'\n\t }).done(function (response) {\n\t var options = $.extend({}, self.model.attributes, response);\n\t var form = new Form({\n\t title: options.title,\n\t message: options.message,\n\t status: options.status || 'warning',\n\t icon: options.icon,\n\t inputs: options.inputs,\n\t buttons: {\n\t 'submit': new Ui.Button({\n\t tooltip: options.submit_tooltip,\n\t title: options.submit_title || 'Save',\n\t icon: options.submit_icon || 'fa-save',\n\t cls: 'btn btn-primary ui-clear-float',\n\t onclick: function () {\n\t self._submit(form);\n\t }\n\t })\n\t }\n\t });\n\t self.$el.empty().append(form.$el);\n\t }).fail(function (response) {\n\t self.$el.empty().append(new Ui.Message({\n\t message: 'Failed to load resource ' + self.url + '.',\n\t status: 'danger',\n\t persistent: true\n\t }).$el);\n\t });\n\t },\n\t\n\t _submit: function (form) {\n\t var self = this;\n\t $.ajax({\n\t url: Galaxy.root + self.url,\n\t data: JSON.stringify(form.data.create()),\n\t type: 'PUT',\n\t contentType: 'application/json'\n\t }).done(function (response) {\n\t var success_message = { message: response.message, status: 'success', persistent: false };\n\t if (self.redirect) {\n\t window.location = Galaxy.root + self.redirect + '?' + $.param(success_message);\n\t } else {\n\t form.data.matchModel(response, function (input, input_id) {\n\t form.field_list[input_id].value(input.value);\n\t });\n\t self._showMessage(form, success_message);\n\t }\n\t }).fail(function (response) {\n\t self._showMessage(form, { message: response.responseJSON.err_msg, status: 'danger', persistent: false });\n\t });\n\t },\n\t\n\t _showMessage: function (form, options) {\n\t var $panel = form.$el.parents().filter(function () {\n\t return ['auto', 'scroll'].indexOf($(this).css('overflow')) != -1;\n\t }).first();\n\t $panel.animate({ scrollTop: 0 }, 500);\n\t form.message.update(options);\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 63 */,\n/* 64 */,\n/* 65 */,\n/* 66 */,\n/* 67 */,\n/* 68 */,\n/* 69 */,\n/* 70 */,\n/* 71 */,\n/* 72 */,\n/* 73 */,\n/* 74 */,\n/* 75 */,\n/* 76 */,\n/* 77 */,\n/* 78 */,\n/* 79 */,\n/* 80 */,\n/* 81 */,\n/* 82 */,\n/* 83 */,\n/* 84 */,\n/* 85 */,\n/* 86 */,\n/* 87 */,\n/* 88 */,\n/* 89 */,\n/* 90 */,\n/* 91 */,\n/* 92 */,\n/* 93 */,\n/* 94 */,\n/* 95 */,\n/* 96 */,\n/* 97 */,\n/* 98 */,\n/* 99 */,\n/* 100 */,\n/* 101 */,\n/* 102 */\n/***/ function(module, exports, __webpack_require__) {\n\n\t/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {var _l = __webpack_require__(6);\n\t\n\tvar AdminPanel = Backbone.View.extend({\n\t initialize: function (page, options) {\n\t var self = this;\n\t this.page = page;\n\t this.root = options.root;\n\t this.config = options.config;\n\t this.settings = options.settings;\n\t this.message = options.message;\n\t this.status = options.status;\n\t this.model = new Backbone.Model({\n\t title: _l('Administration')\n\t });\n\t this.categories = new Backbone.Collection([{\n\t title: 'Server',\n\t items: [{\n\t title: 'Data types registry',\n\t url: 'admin/view_datatypes_registry'\n\t }, {\n\t title: 'Data tables registry',\n\t url: 'admin/view_tool_data_tables'\n\t }, {\n\t title: 'Display applications',\n\t url: 'admin/display_applications'\n\t }, {\n\t title: 'Manage jobs',\n\t url: 'admin/jobs'\n\t }]\n\t }, {\n\t title: 'Tools and Tool Shed',\n\t items: [{\n\t title: 'Search Tool Shed',\n\t url: 'admin_toolshed/browse_tool_sheds',\n\t enabled: self.settings.is_tool_shed_installed\n\t }, {\n\t title: 'Search Tool Shed (Beta)',\n\t url: 'admin_toolshed/browse_toolsheds',\n\t enabled: self.settings.is_tool_shed_installed && self.config.enable_beta_ts_api_install\n\t }, {\n\t title: 'Monitor installing repositories',\n\t url: 'admin_toolshed/monitor_repository_installation?installing_repository_ids=' + self.settings.installing_repository_ids,\n\t enabled: self.settings.installing_repository_ids\n\t }, {\n\t title: 'Manage installed tools',\n\t url: 'admin_toolshed/browse_repositories',\n\t enabled: self.settings.is_repo_installed\n\t }, {\n\t title: 'Reset metadata',\n\t url: 'admin_toolshed/reset_metadata_on_selected_installed_repositories',\n\t enabled: self.settings.is_repo_installed\n\t }, {\n\t title: 'Download local tool',\n\t url: 'admin/package_tool'\n\t }, {\n\t title: 'Tool lineage',\n\t url: 'admin/tool_versions',\n\t target: '__use_router__'\n\t }, {\n\t title: 'Reload a tool\\'s configuration',\n\t url: 'admin/reload_tool'\n\t }, {\n\t title: 'Review tool migration stages',\n\t url: 'admin/review_tool_migration_stages'\n\t }, {\n\t title: 'View Tool Error Logs',\n\t url: 'admin/tool_errors'\n\t }, {\n\t title: 'Manage Display Whitelist',\n\t url: 'admin/sanitize_whitelist'\n\t }, {\n\t title: 'Manage Tool Dependencies',\n\t url: 'admin/manage_tool_dependencies'\n\t }]\n\t }, {\n\t title: 'User Management',\n\t items: [{\n\t title: 'Users',\n\t url: 'admin/users',\n\t target: '__use_router__'\n\t }, {\n\t title: 'Groups',\n\t url: 'admin/groups',\n\t target: '__use_router__'\n\t }, {\n\t title: 'Roles',\n\t url: 'admin/roles',\n\t target: '__use_router__'\n\t }, {\n\t title: 'API keys',\n\t url: 'userskeys/all_users'\n\t }, {\n\t title: 'Impersonate a user',\n\t url: 'admin/impersonate',\n\t enabled: self.config.allow_user_impersonation\n\t }]\n\t }, {\n\t title: 'Data',\n\t items: [{\n\t title: 'Quotas',\n\t url: 'admin/quotas',\n\t target: '__use_router__',\n\t enabled: self.config.enable_quotas\n\t }, {\n\t title: 'Data libraries',\n\t url: 'library_admin/browse_libraries'\n\t }, {\n\t title: 'Roles',\n\t url: 'admin/roles',\n\t target: '__use_router__'\n\t }, {\n\t title: 'Local data',\n\t url: 'data_manager'\n\t }]\n\t }, {\n\t title: 'Form Definitions',\n\t items: [{\n\t title: 'Form definitions',\n\t url: 'forms/browse_form_definitions'\n\t }]\n\t }, {\n\t title: 'Sample Tracking',\n\t items: [{\n\t title: 'Sequencers and external services',\n\t url: 'external_service/browse_external_services'\n\t }, {\n\t title: 'Request types',\n\t url: 'request_type/browse_request_types'\n\t }, {\n\t title: 'Sequencing requests',\n\t url: 'requests_admin/browse_requests'\n\t }, {\n\t title: 'Find samples',\n\t url: 'requests_common/find_samples?cntrller=requests_admin'\n\t }]\n\t }]);\n\t this.setElement(this._template());\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t this.$el.empty();\n\t this.categories.each(function (category) {\n\t var $section = $(self._templateSection(category.attributes));\n\t var $entries = $section.find('.ui-side-section-body');\n\t _.each(category.get('items'), function (item) {\n\t if (item.enabled === undefined || item.enabled) {\n\t var $link = $('').attr({ href: self.root + item.url }).text(_l(item.title));\n\t if (item.target == '__use_router__') {\n\t $link.on('click', function (e) {\n\t e.preventDefault();self.page.router.push(item.url);\n\t });\n\t } else {\n\t $link.attr('target', 'galaxy_main');\n\t }\n\t $entries.append($('').addClass('ui-side-section-body-title').append($link));\n\t }\n\t });\n\t self.$el.append($section);\n\t });\n\t this.page.$('#galaxy_main').prop('src', this.root + 'admin/center?message=' + this.message + '&status=' + this.status);\n\t },\n\t\n\t _templateSection: function (options) {\n\t return ['
', '
' + _l(options.title) + '
', '', '
'].join('');\n\t },\n\t\n\t _template: function () {\n\t return '';\n\t },\n\t\n\t toString: function () {\n\t return 'adminPanel';\n\t }\n\t});\n\t\n\tmodule.exports = AdminPanel;\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ }\n]);\n\n\n// WEBPACK FOOTER //\n// admin.bundled.js","var jQuery = require( 'jquery' ),\n $ = jQuery,\n GalaxyApp = require( 'galaxy' ).GalaxyApp,\n AdminPanel = require( './panels/admin-panel' ),\n FormWrapper = require( 'mvc/form/form-wrapper' ),\n GridView = require( 'mvc/grid/grid-view' ),\n Ui = require( 'mvc/ui/ui-misc' ),\n QueryStringParsing = require( 'utils/query-string-parsing' ),\n Router = require( 'layout/router' ),\n Utils = require( 'utils/utils' ),\n Page = require( 'layout/page' );\n\nwindow.app = function app( options, bootstrapped ){\n window.Galaxy = new GalaxyApp( options, bootstrapped );\n Galaxy.debug( 'admin app' );\n\n /** Routes */\n var AdminRouter = Router.extend({\n routes: {\n '(/)admin(/)users' : 'show_users',\n '(/)admin(/)roles' : 'show_roles',\n '(/)admin(/)groups' : 'show_groups',\n '(/)admin(/)tool_versions' : 'show_tool_versions',\n '(/)admin(/)quotas' : 'show_quotas',\n '(/)admin(/)forms(/)(:form_id)' : 'show_forms'\n },\n\n authenticate: function( args, name ) {\n return Galaxy.user && Galaxy.user.id && Galaxy.user.get( 'is_admin' );\n },\n\n show_users: function() {\n this.page.display( new GridView( { url_base: Galaxy.root + 'admin/users_list', url_data: Galaxy.params, dict_format: true } ) );\n },\n\n show_roles: function() {\n this.page.display( new GridView( { url_base: Galaxy.root + 'admin/roles_list', url_data: Galaxy.params, dict_format: true } ) );\n },\n\n show_groups: function() {\n this.page.display( new GridView( { url_base: Galaxy.root + 'admin/groups_list', url_data: Galaxy.params, dict_format: true } ) );\n },\n\n show_tool_versions: function() {\n this.page.display( new GridView( { url_base: Galaxy.root + 'admin/tool_versions_list', url_data: Galaxy.params, dict_format: true } ) );\n },\n\n show_quotas: function() {\n this.page.display( new GridView( { url_base: Galaxy.root + 'admin/quotas_list', url_data: Galaxy.params, dict_format: true } ) );\n },\n\n show_forms : function( form_id ) {\n var id = '?id=' + QueryStringParsing.get( 'id' );\n var form_defs = {\n reset_user_password: {\n title : 'Reset passwords',\n url : 'admin/reset_user_password' + id,\n icon : 'fa-user',\n submit_title : 'Save new password',\n redirect : 'admin/users'\n },\n manage_roles_and_groups_for_user: {\n url : 'admin/manage_roles_and_groups_for_user' + id,\n icon : 'fa-users',\n redirect : 'admin/users'\n },\n manage_users_and_groups_for_role: {\n url : 'admin/manage_users_and_groups_for_role' + id,\n redirect : 'admin/roles'\n },\n manage_users_and_roles_for_group: {\n url : 'admin/manage_users_and_roles_for_group' + id,\n redirect : 'admin/groups'\n },\n manage_users_and_groups_for_quota: {\n url : 'admin/manage_users_and_groups_for_quota' + id,\n redirect : 'admin/quotas'\n },\n create_role: {\n url : 'admin/create_role',\n redirect : 'admin/roles'\n },\n create_group: {\n url : 'admin/create_group',\n redirect : 'admin/groups'\n },\n create_quota: {\n url : 'admin/create_quota',\n redirect : 'admin/quotas'\n },\n rename_role: {\n url : 'admin/rename_role' + id,\n redirect : 'admin/roles'\n },\n rename_group: {\n url : 'admin/rename_group' + id,\n redirect : 'admin/groups'\n },\n rename_quota: {\n url : 'admin/rename_quota' + id,\n redirect : 'admin/quotas'\n },\n edit_quota: {\n url : 'admin/edit_quota' + id,\n redirect : 'admin/quotas'\n },\n set_quota_default: {\n url : 'admin/set_quota_default' + id,\n redirect : 'admin/quotas'\n },\n };\n this.page.display( new FormWrapper.View ( form_defs[ form_id ] ) );\n }\n });\n\n $(function() {\n _.extend( options.config, { active_view : 'admin' } );\n Utils.setWindowTitle(\"Administration\");\n Galaxy.page = new Page.View( _.extend( options, {\n Left : AdminPanel,\n Router : AdminRouter\n } ) );\n });\n};\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/apps/admin.js","/**\n * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc.\n */\ndefine(['utils/utils',\n 'mvc/ui/ui-select-default',\n 'mvc/ui/ui-slider',\n 'mvc/ui/ui-options',\n 'mvc/ui/ui-drilldown',\n 'mvc/ui/ui-buttons',\n 'mvc/ui/ui-modal'],\n function( Utils, Select, Slider, Options, Drilldown, Buttons, Modal ) {\n\n /** Label wrapper */\n var Label = Backbone.View.extend({\n tagName: 'label',\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model( options );\n this.tagName = options.tagName || this.tagName;\n this.setElement( $( '<' + this.tagName + '/>' ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n title: function( new_title ) {\n this.model.set( 'title', new_title );\n },\n value: function() {\n return this.model.get( 'title' );\n },\n render: function() {\n this.$el.removeClass()\n .addClass( 'ui-label' )\n .addClass( this.model.get( 'cls' ) )\n .html( this.model.get( 'title' ) );\n return this;\n }\n });\n\n /** Displays messages used e.g. in the tool form */\n var Message = Backbone.View.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n message : null,\n status : 'info',\n cls : '',\n persistent : false,\n fade : true\n }).set( options );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n update: function( options ) {\n this.model.set( options );\n },\n render: function() {\n this.$el.removeClass().addClass( 'ui-message' ).addClass( this.model.get( 'cls' ) );\n var status = this.model.get( 'status' );\n if ( this.model.get( 'large' ) ) {\n this.$el.addClass((( status == 'success' && 'done' ) ||\n ( status == 'danger' && 'error' ) ||\n status ) + 'messagelarge' );\n } else {\n this.$el.addClass( 'alert' ).addClass( 'alert-' + status );\n }\n if ( this.model.get( 'message' ) ) {\n this.$el.html( this.messageForDisplay() );\n this.$el[ this.model.get( 'fade' ) ? 'fadeIn' : 'show' ]();\n this.timeout && window.clearTimeout( this.timeout );\n if ( !this.model.get( 'persistent' ) ) {\n var self = this;\n this.timeout = window.setTimeout( function() {\n self.model.set( 'message', '' );\n }, 3000 );\n }\n } else {\n this.$el.fadeOut();\n }\n return this;\n },\n messageForDisplay: function() {\n return _.escape( this.model.get( 'message' ) );\n }\n });\n\n var UnescapedMessage = Message.extend({\n messageForDisplay: function() {\n return this.model.get( 'message' );\n }\n });\n\n /** Renders an input element used e.g. in the tool form */\n var Input = Backbone.View.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n type : 'text',\n placeholder : '',\n disabled : false,\n readonly : false,\n visible : true,\n cls : '',\n area : false,\n color : null,\n style : null\n }).set( options );\n this.tagName = this.model.get( 'area' ) ? 'textarea' : 'input';\n this.setElement( $( '<' + this.tagName + '/>' ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n events: {\n 'input': '_onchange'\n },\n value: function( new_val ) {\n new_val !== undefined && this.model.set( 'value', typeof new_val === 'string' ? new_val : '' );\n return this.model.get( 'value' );\n },\n render: function() {\n var self = this;\n this.$el.removeClass()\n .addClass( 'ui-' + this.tagName )\n .addClass( this.model.get( 'cls' ) )\n .addClass( this.model.get( 'style' ) )\n .attr( 'id', this.model.id )\n .attr( 'type', this.model.get( 'type' ) )\n .attr( 'placeholder', this.model.get( 'placeholder' ) )\n .css( 'color', this.model.get( 'color' ) || '' )\n .css( 'border-color', this.model.get( 'color' ) || '' );\n var datalist = this.model.get( 'datalist' );\n if ( $.isArray( datalist ) && datalist.length > 0 ) {\n this.$el.autocomplete( { source : function( request, response ) { response( self.model.get( 'datalist' ) ) },\n change : function() { self._onchange() } } );\n }\n if ( this.model.get( 'value' ) !== this.$el.val() ) {\n this.$el.val( this.model.get( 'value' ) );\n }\n _.each( [ 'readonly', 'disabled' ], function( attr_name ) {\n self.model.get( attr_name ) ? self.$el.attr( attr_name, true ) : self.$el.removeAttr( attr_name );\n });\n this.$el[ this.model.get( 'visible' ) ? 'show' : 'hide' ]();\n return this;\n },\n _onchange: function() {\n this.value( this.$el.val() );\n this.model.get( 'onchange' ) && this.model.get( 'onchange' )( this.model.get( 'value' ) );\n }\n });\n\n /** Creates a hidden element input field used e.g. in the tool form */\n var Hidden = Backbone.View.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model( options );\n this.setElement( $ ( '' ).append( this.$info = $( '' ) )\n .append( this.$hidden = $( '' ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n value: function( new_val ) {\n new_val !== undefined && this.model.set( 'value', new_val );\n return this.model.get( 'value' );\n },\n render: function() {\n this.$el.attr( 'id', this.model.id );\n this.$hidden.val( this.model.get( 'value' ) );\n this.model.get( 'info' ) ? this.$info.show().text( this.model.get( 'info' ) ) : this.$info.hide();\n return this;\n }\n });\n\n /** Creates a upload element input field */\n var Upload = Backbone.View.extend({\n initialize: function( options ) {\n var self = this;\n this.model = options && options.model || new Backbone.Model( options );\n this.setElement( $ ( '' ).append( this.$info = $( '' ) )\n .append( this.$file = $( '' ).attr( 'type', 'file' ).addClass( 'ui-margin-bottom' ) )\n .append( this.$text = $( '' ).addClass( 'ui-textarea' ).attr( 'disabled', true ) )\n .append( this.$wait = $( '' ).addClass( 'fa fa-spinner fa-spin' ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.$file.on( 'change', function( e ) { self._readFile( e ) } );\n this.render();\n },\n value: function( new_val ) {\n new_val !== undefined && this.model.set( 'value', new_val );\n return this.model.get( 'value' );\n },\n render: function() {\n this.$el.attr( 'id', this.model.id );\n this.model.get( 'info' ) ? this.$info.show().text( this.model.get( 'info' ) ) : this.$info.hide();\n this.model.get( 'value' ) ? this.$text.text( this.model.get( 'value' ) ).show() : this.$text.hide();\n this.model.get( 'wait' ) ? this.$wait.show() : this.$wait.hide();\n return this;\n },\n _readFile: function( e ) {\n var self = this;\n var file = e.target.files && e.target.files[ 0 ];\n if ( file ) {\n var reader = new FileReader();\n reader.onload = function() {\n self.model.set( { wait: false, value: this.result } );\n }\n this.model.set( { wait: true, value: null } );\n reader.readAsText( file );\n }\n }\n });\n\n return {\n Button : Buttons.ButtonDefault,\n ButtonIcon : Buttons.ButtonIcon,\n ButtonCheck : Buttons.ButtonCheck,\n ButtonMenu : Buttons.ButtonMenu,\n ButtonLink : Buttons.ButtonLink,\n Input : Input,\n Label : Label,\n Message : Message,\n UnescapedMessage : UnescapedMessage,\n Upload : Upload,\n Modal : Modal,\n RadioButton : Options.RadioButton,\n Checkbox : Options.Checkbox,\n Radio : Options.Radio,\n Select : Select,\n Hidden : Hidden,\n Slider : Slider,\n Drilldown : Drilldown\n }\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/ui-misc.js","define([ 'utils/utils', 'mvc/ui/ui-misc' ], function( Utils, Ui ) {\nvar View = Backbone.View.extend({\n visible : false,\n initialize : function( options ) {\n var self = this;\n this.model = options && options.model || new Backbone.Model( {\n id : Utils.uid(),\n cls : 'ui-portlet',\n title : '',\n icon : '',\n buttons : null,\n body : null,\n scrollable : true,\n nopadding : false,\n operations : null,\n collapsible : false,\n collapsible_button : false,\n collapsed : false,\n onchange_title : null\n } ).set( options );\n this.setElement( this._template() );\n\n // link all dom elements\n this.$body = this.$( '.portlet-body' );\n this.$title_text = this.$( '.portlet-title-text' );\n this.$title_icon = this.$( '.portlet-title-icon' );\n this.$header = this.$( '.portlet-header' );\n this.$content = this.$( '.portlet-content' );\n this.$backdrop = this.$( '.portlet-backdrop' );\n this.$buttons = this.$( '.portlet-buttons' );\n this.$operations = this.$( '.portlet-operations' );\n\n // add body to component list\n this.model.get( 'body' ) && this.append( this.model.get( 'body' ) );\n\n // add icon for collapsible option\n this.collapsible_button = new Ui.ButtonIcon({\n icon : 'fa-eye',\n tooltip : 'Collapse/Expand',\n cls : 'ui-button-icon-plain',\n onclick : function() { self[ self.collapsed ? 'expand' : 'collapse' ]() }\n });\n this.render();\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n this.$el.removeClass().addClass( options.cls ).attr( 'id', options.id );\n this.$header[ options.title ? 'show' : 'hide' ]();\n this.$title_text.html( options.title );\n _.each( [ this.$content, this.$body ], function( $el ) {\n $el[ options.nopadding ? 'addClass' : 'removeClass' ]( 'no-padding' );\n });\n\n // render title icon\n if ( options.icon ) {\n this.$title_icon.removeClass().addClass( 'portlet-title-icon fa' ).addClass( options.icon ).show();\n } else {\n this.$title_icon.hide();\n }\n\n // make portlet collapsible\n this.$title_text[ options.collapsible ? 'addClass' : 'removeClass' ]( 'no-highlight collapsible' ).off();\n if ( options.collapsible ) {\n this.$title_text.on( 'click', function() { self[ self.collapsed ? 'expand' : 'collapse' ]() } );\n options.collapsed ? this.collapse() : this.expand();\n }\n\n // allow title editing\n this.$title_text.prop( 'disabled', !options.onchange_title );\n options.onchange_title && this.$title_text.make_text_editable({\n on_finish: function( new_title ) {\n options.onchange_title( new_title );\n }\n });\n\n // render buttons\n if ( options.buttons ) {\n this.$buttons.empty().show();\n $.each( this.model.get( 'buttons' ), function( name, item ) {\n item.$el.prop( 'id', name );\n self.$buttons.append( item.$el );\n });\n } else {\n this.$buttons.hide();\n }\n\n // render operations\n this.$operations.empty;\n if ( options.collapsible_button ) {\n this.$operations.append( this.collapsible_button.$el );\n }\n if ( options.operations ) {\n $.each( options.operations, function( name, item ) {\n item.$el.prop( 'id', name );\n self.$operations.append( item.$el );\n });\n }\n return this;\n },\n\n /** Append new doms to body */\n append: function( $el ) {\n this.$body.append( $el );\n },\n\n /** Remove all content */\n empty: function() {\n this.$body.empty();\n },\n\n /** Return header element */\n header: function() {\n return this.$header;\n },\n\n /** Return body element */\n body: function() {\n return this.$body;\n },\n\n /** Show portlet */\n show: function(){\n this.visible = true;\n this.$el.fadeIn( 'fast' );\n },\n\n /** Hide portlet */\n hide: function(){\n this.visible = false;\n this.$el.hide();\n },\n\n /** Enable a particular button */\n enableButton: function( id ) {\n this.$buttons.find( '#' + id ).prop( 'disabled', false );\n },\n\n /** Disable a particular button */\n disableButton: function( id ) {\n this.$buttons.find( '#' + id ).prop( 'disabled', true );\n },\n\n /** Hide a particular operation */\n hideOperation: function( id ) {\n this.$operations.find( '#' + id ).hide();\n },\n\n /** Show a particular operation */\n showOperation: function( id ) {\n this.$operations.find( '#' + id ).show();\n },\n\n /** Replaces the event callback of an existing operation */\n setOperation: function( id, callback ) {\n this.$operations.find( '#' + id ).off( 'click' ).on( 'click', callback );\n },\n\n /** Change title */\n title: function( new_title ) {\n new_title && this.$title_text.html( new_title );\n return this.$title_text.html();\n },\n\n /** Collapse portlet */\n collapse: function() {\n this.collapsed = true;\n this.$content.height( '0%' );\n this.$body.hide();\n this.collapsible_button.setIcon( 'fa-eye-slash' );\n },\n\n /** Expand portlet */\n expand: function() {\n this.collapsed = false;\n this.$content.height( '100%' );\n this.$body.fadeIn( 'fast' );\n this.collapsible_button.setIcon( 'fa-eye' );\n },\n\n /** Disable content access */\n disable: function() {\n this.$backdrop.show();\n },\n\n /** Enable content access */\n enable: function() {\n this.$backdrop.hide();\n },\n\n _template: function() {\n return $( '' ).append( $( '' ).addClass( 'portlet-header' )\n .append( $( '' ).addClass( 'portlet-operations' ) )\n .append( $( '' ).addClass( 'portlet-title' )\n .append( $( '' ).addClass( 'portlet-title-icon' ) )\n .append( $( '' ).addClass( 'portlet-title-text' ) ) ) )\n .append( $( '' ).addClass( 'portlet-content' )\n .append( $( '' ).addClass( 'portlet-body' ) )\n .append( $( '' ).addClass( 'portlet-buttons' ) ) )\n .append( $( '' ).addClass( 'portlet-backdrop' ) );\n }\n});\nreturn {\n View : View\n}\n});\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/ui-portlet.js","/**\n This is the main class of the form plugin. It is referenced as 'app' in lower level modules.\n*/\ndefine( [ 'utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'mvc/form/form-section', 'mvc/form/form-data' ],\nfunction( Utils, Portlet, Ui, FormSection, FormData ) {\n return Backbone.View.extend({\n initialize: function( options ) {\n this.model = new Backbone.Model({\n initial_errors : false,\n cls : 'ui-portlet-limited',\n icon : null,\n always_refresh : true,\n status : 'warning',\n onchange : function(){}\n }).set( options );\n this.setElement( '' );\n this.render();\n },\n\n /** Update available options */\n update: function( new_model ){\n var self = this;\n this.data.matchModel( new_model, function( node, input_id ) {\n var input = self.input_list[ input_id ];\n if ( input && input.options ) {\n if ( !_.isEqual( input.options, node.options ) ) {\n input.options = node.options;\n var field = self.field_list[ input_id ];\n if ( field.update ) {\n var new_options = [];\n if ( ( [ 'data', 'data_collection', 'drill_down' ] ).indexOf( input.type ) != -1 ) {\n new_options = input.options;\n } else {\n for ( var i in node.options ) {\n var opt = node.options[ i ];\n if ( opt.length > 2 ) {\n new_options.push( { label: opt[ 0 ], value: opt[ 1 ] } );\n }\n }\n }\n field.update( new_options );\n field.trigger( 'change' );\n Galaxy.emit.debug( 'form-view::update()', 'Updating options for ' + input_id );\n }\n }\n }\n });\n },\n\n /** Set form into wait mode */\n wait: function( active ) {\n for ( var i in this.input_list ) {\n var field = this.field_list[ i ];\n var input = this.input_list[ i ];\n if ( input.is_dynamic && field.wait && field.unwait ) {\n field[ active ? 'wait' : 'unwait' ]();\n }\n }\n },\n\n /** Highlight and scroll to input element (currently only used for error notifications) */\n highlight: function ( input_id, message, silent ) {\n var input_element = this.element_list[ input_id ];\n if ( input_element ) {\n input_element.error( message || 'Please verify this parameter.' );\n this.portlet.expand();\n this.trigger( 'expand', input_id );\n if ( !silent ) {\n var $panel = this.$el.parents().filter(function() {\n return [ 'auto', 'scroll' ].indexOf( $( this ).css( 'overflow' ) ) != -1;\n }).first();\n $panel.animate( { scrollTop : $panel.scrollTop() + input_element.$el.offset().top - 120 }, 500 );\n }\n }\n },\n\n /** Highlights errors */\n errors: function( options ) {\n this.trigger( 'reset' );\n if ( options && options.errors ) {\n var error_messages = this.data.matchResponse( options.errors );\n for ( var input_id in this.element_list ) {\n var input = this.element_list[ input_id ];\n if ( error_messages[ input_id ] ) {\n this.highlight( input_id, error_messages[ input_id ], true );\n }\n }\n }\n },\n\n /** Render tool form */\n render: function() {\n var self = this;\n this.off('change');\n this.off('reset');\n // contains the dom field elements as created by the parameter factory i.e. form-parameters\n this.field_list = {};\n // contains input definitions/dictionaries as provided by the parameters to_dict() function through the api\n this.input_list = {};\n // contains the dom elements of each input element i.e. form-input which wraps the actual input field\n this.element_list = {};\n // converts the form into a json data structure\n this.data = new FormData.Manager( this );\n this._renderForm();\n this.data.create();\n this.model.get( 'initial_errors' ) && this.errors( this.model.attributes );\n // add listener which triggers on checksum change, and reset the form input wrappers\n var current_check = this.data.checksum();\n this.on( 'change', function( input_id ) {\n var input = self.input_list[ input_id ];\n if ( !input || input.refresh_on_change || self.model.get( 'always_refresh' ) ) {\n var new_check = self.data.checksum();\n if ( new_check != current_check ) {\n current_check = new_check;\n self.model.get( 'onchange' )();\n }\n }\n });\n this.on('reset', function() {\n _.each( self.element_list, function( input_element ) { input_element.reset() } );\n });\n return this;\n },\n\n /** Renders/appends dom elements of the form */\n _renderForm: function() {\n $( '.tooltip' ).remove();\n var options = this.model.attributes;\n this.message = new Ui.UnescapedMessage();\n this.section = new FormSection.View( this, { inputs: options.inputs } );\n this.portlet = new Portlet.View({\n icon : options.icon,\n title : options.title,\n cls : options.cls,\n operations : options.operations,\n buttons : options.buttons,\n collapsible : options.collapsible,\n collapsed : options.collapsed,\n onchange_title : options.onchange_title\n });\n this.portlet.append( this.message.$el );\n this.portlet.append( this.section.$el );\n this.$el.empty();\n options.inputs && this.$el.append( this.portlet.$el );\n options.message && this.message.update( { persistent: true, status: options.status, message: options.message } );\n Galaxy.emit.debug( 'form-view::initialize()', 'Completed' );\n }\n });\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/form/form-view.js","/** This module contains all button views. */\ndefine( [ 'utils/utils' ], function( Utils ) {\n /** This renders the default button which is used e.g. at the bottom of the upload modal. */\n var ButtonDefault = Backbone.View.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : '',\n icon : '',\n cls : 'btn btn-default',\n wait : false,\n wait_text : 'Sending...',\n wait_cls : 'btn btn-info',\n disabled : false,\n percentage : -1\n }).set( options );\n this.setElement( $( '' ).attr( 'type', 'button' )\n .append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) )\n .append( this.$progress = $( '' ).append( this.$progress_bar = $( '' ) ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( 'ui-button-default' )\n .addClass( options.disabled && 'disabled' )\n .attr( 'id', options.id )\n .attr( 'disabled', options.disabled )\n .off( 'click' ).on( 'click' , function() {\n $( '.tooltip' ).hide();\n options.onclick && !self.disabled && options.onclick();\n })\n .tooltip( { title: options.tooltip, placement: 'bottom' } );\n this.$progress.addClass( 'progress' ).css( 'display', options.percentage !== -1 ? 'block' : 'none' );\n this.$progress_bar.addClass( 'progress-bar' ).css( { width : options.percentage + '%' } );\n this.$icon.removeClass().addClass( 'icon fa' );\n this.$title.removeClass().addClass( 'title' );\n if ( options.wait ) {\n this.$el.addClass( options.wait_cls ).prop( 'disabled', true );\n this.$icon.addClass( 'fa-spinner fa-spin ui-margin-right' );\n this.$title.html( options.wait_text );\n } else {\n this.$el.addClass( options.cls );\n this.$icon.addClass( options.icon );\n this.$title.html( options.title );\n options.icon && options.title && this.$icon.addClass( 'ui-margin-right' );\n }\n },\n\n /** Show button */\n show: function() {\n this.$el.show();\n },\n\n /** Hide button */\n hide: function() {\n this.$el.hide();\n },\n\n /** Disable button */\n disable: function() {\n this.model.set( 'disabled', true );\n },\n\n /** Enable button */\n enable: function() {\n this.model.set( 'disabled', false );\n },\n\n /** Show spinner to indicate that the button is not ready to be clicked */\n wait: function() {\n this.model.set( 'wait', true );\n },\n\n /** Hide spinner to indicate that the button is ready to be clicked */\n unwait: function() {\n this.model.set( 'wait', false );\n },\n\n /** Change icon */\n setIcon: function( icon ) {\n this.model.set( 'icon', icon );\n }\n });\n\n /** This button allows the right-click/open-in-new-tab feature, its used e.g. for panel buttons. */\n var ButtonLink = ButtonDefault.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : '',\n icon : '',\n cls : ''\n }).set( options );\n this.setElement( $( '' ).append( this.$icon = $( '' ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render: function() {\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( options.cls )\n .attr( { id : options.id,\n href : options.href || 'javascript:void(0)',\n title : options.title,\n target : options.target || '_top',\n disabled : options.disabled } )\n .tooltip( { placement: 'bottom' } )\n .off( 'click' ).on( 'click' , function() {\n options.onclick && !options.disabled && options.onclick();\n });\n this.$icon.removeClass().addClass( options.icon );\n }\n });\n\n /** The check button is used in the tool form and allows to distinguish between multiple states e.g. all, partially and nothing selected. */\n var ButtonCheck = Backbone.View.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : 'Select/Unselect all',\n icons : [ 'fa-square-o', 'fa-minus-square-o', 'fa-check-square-o' ],\n value : 0,\n onchange : function(){}\n }).set( options );\n this.setElement( $( '' ).append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render: function( options ) {\n var self = this;\n var options = this.model.attributes;\n this.$el.addClass( 'ui-button-check' )\n .off( 'click' ).on('click', function() {\n self.model.set( 'value', ( self.model.get( 'value' ) === 0 && 2 ) || 0 );\n options.onclick && options.onclick();\n });\n this.$title.html( options.title );\n this.$icon.removeClass()\n .addClass( 'icon fa ui-margin-right' )\n .addClass( options.icons[ options.value ] );\n },\n\n /* Sets a new value and/or returns the value.\n * @param{Integer} new_val - Set a new value 0=unchecked, 1=partial and 2=checked.\n * OR:\n * @param{Integer} new_val - Number of selected options.\n * @param{Integer} total - Total number of available options.\n */\n value: function ( new_val, total ) {\n if ( new_val !== undefined ) {\n if ( total && new_val !== 0 ) {\n new_val = ( new_val !== total ) && 1 || 2;\n }\n this.model.set( 'value', new_val );\n this.model.get( 'onchange' )( this.model.get( 'value' ) );\n }\n return this.model.get( 'value' );\n }\n });\n\n /** This renders a differently styled, more compact button version. */\n var ButtonIcon = ButtonDefault.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : '',\n icon : '',\n cls : 'ui-button-icon',\n disabled : false\n }).set( options );\n this.setElement( $( '' ).append( this.$button = $( '' ).append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render : function( options ) {\n var self = this;\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( options.cls )\n .addClass( options.disabled && 'disabled' )\n .attr( 'disabled', options.disabled )\n .attr( 'id', options.id )\n .off( 'click' ).on( 'click', function() {\n $( '.tooltip' ).hide();\n !options.disabled && options.onclick && options.onclick();\n });\n this.$button.addClass( 'button' ).tooltip( { title: options.tooltip, placement: 'bottom' } );\n this.$icon.removeClass().addClass( 'icon fa' ).addClass( options.icon );\n this.$title.addClass( 'title' ).html( options.title );\n options.icon && options.title && this.$icon.addClass( 'ui-margin-right' );\n }\n });\n\n /** This class creates a button with dropdown menu. */\n var ButtonMenu = ButtonDefault.extend({\n $menu: null,\n initialize: function ( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : '',\n title : '',\n pull : 'right',\n icon : null,\n onclick : null,\n cls : 'ui-button-icon ui-button-menu',\n tooltip : '',\n target : '',\n href : '',\n onunload : null,\n visible : true,\n tag : ''\n }).set( options );\n this.collection = new Backbone.Collection();\n this.setElement( $( '' ).append( this.$root = $( '' ).append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.listenTo( this.collection, 'change add remove reset', this.render, this );\n this.render();\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( 'dropdown' )\n .addClass( options.cls )\n .attr( 'id', options.id )\n .css( { display : options.visible && this.collection.where( { visible: true } ).length > 0 ? 'block' : 'none' } );\n this.$root.addClass( 'root button dropdown-toggle' )\n .attr( 'data-toggle', 'dropdown' )\n .tooltip( { title: options.tooltip, placement: 'bottom' } )\n .off( 'click' ).on( 'click', function( e ) {\n $( '.tooltip' ).hide();\n e.preventDefault();\n options.onclick && options.onclick();\n } );\n this.$icon.removeClass().addClass( 'icon fa' ).addClass( options.icon );\n this.$title.removeClass().addClass( 'title' ).html( options.title );\n options.icon && options.title && this.$icon.addClass( 'ui-margin-right' );\n this.$menu && this.$menu.remove();\n if ( this.collection.length > 0 ) {\n this.$menu = $( '\n cur_page = self.grid.get('cur_page'),\n text;\n if (page_num === new_page) {\n // Remove link to page since grid will be on this page. It is assumed that\n // this element has a single child, a hyperlink/anchor with text.\n text = $(this).children().text();\n $(this).empty();\n $(this).addClass('inactive-link');\n $(this).text(text);\n }\n else if (page_num === cur_page) {\n // Add hyperlink to this page since grid will no longer be on this page. It is assumed that\n // this element has a single child, a hyperlink/anchor.\n text = $(this).text();\n $(this).empty();\n $(this).removeClass('inactive-link');\n var t = $('' + text + '');\n t.click(function() {\n self.set_page(page_num);\n });\n $(this).append(t);\n }\n });\n\n if (new_page === 'all') {\n this.grid.set('cur_page', new_page);\n } else {\n this.grid.set('cur_page', parseInt(new_page, 10));\n }\n this.execute();\n },\n\n // confirmation/submission of operation request\n submit_operation: function (operation_button, confirmation_text) {\n // identify operation\n var operation_name = $(operation_button).val();\n\n // verify in any item is selected\n var number_of_checked_ids = this.$el.find('input[name=\"id\"]:checked').length;\n if (!number_of_checked_ids > 0) {\n return false;\n }\n\n // Check to see if there's grid confirmation text for this operation\n var operation = _.findWhere(this.grid.attributes.operations, {label: operation_name});\n if (operation && !confirmation_text){\n confirmation_text = operation.confirm || '';\n }\n\n // collect ids\n var item_ids = [];\n this.$el.find('input[name=id]:checked').each(function() {\n item_ids.push( $(this).val() );\n });\n\n // execute operation\n var options = {\n operation : operation_name,\n id : item_ids,\n confirmation_text : confirmation_text\n };\n if ( operation.target == 'top' ) {\n options = _.extend( options, {\n href : operation.href,\n target : operation.target\n });\n }\n this.execute( options );\n return true;\n },\n\n check_all_items: function () {\n var check = this.$('.grid-row-select-checkbox');\n var state = this.$( '#check_all' ).prop( 'checked' );\n _.each( check, function( c ) {\n $( c ).prop( 'checked', state );\n });\n this.init_grid_elements();\n },\n\n // Go back to page one; this is useful when a filter is applied.\n go_page_one: function () {\n // Need to go back to page 1 if not showing all.\n var cur_page = this.grid.get('cur_page');\n if (cur_page !== null && cur_page !== undefined && cur_page !== 'all') {\n this.grid.set('cur_page', 1);\n }\n },\n\n //\n // execute operations and hyperlink requests\n //\n execute: function (options) {\n // get url\n var id = null;\n var href = null;\n var operation = null;\n var confirmation_text = null;\n var target = null;\n\n // check for options\n if (options) {\n // get options\n href = options.href;\n operation = options.operation;\n id = options.id;\n confirmation_text = options.confirmation_text;\n target = options.target;\n\n // check if input contains the operation tag\n if (href !== undefined && href.indexOf('operation=') != -1) {\n // Get operation, id in hyperlink's href.\n var href_parts = href.split(\"?\");\n if (href_parts.length > 1) {\n var href_parms_str = href_parts[1];\n var href_parms = href_parms_str.split(\"&\");\n for (var index = 0; index < href_parms.length; index++) {\n if (href_parms[index].indexOf('operation') != -1) {\n // Found operation parm; get operation value.\n operation = href_parms[index].split('=')[1];\n operation = operation.replace (/\\+/g, ' ');\n } else if (href_parms[index].indexOf('id') != -1) {\n // Found id parm; get id value.\n id = href_parms[index].split('=')[1];\n }\n }\n }\n }\n }\n\n // check for operation details\n if (operation && id) {\n // show confirmation box\n if (confirmation_text && confirmation_text != '' && confirmation_text != 'None' && confirmation_text != 'null')\n if(!confirm(confirmation_text))\n return false;\n\n // use small characters for operation?!\n operation = operation.toLowerCase();\n\n // Update grid.\n this.grid.set({\n operation: operation,\n item_ids: id\n });\n\n // Do operation. If operation cannot be performed asynchronously, redirect to location.\n if ( target == 'top' ) {\n window.top.location = href + '?' + $.param( this.grid.get_url_data() );\n } else if ( this.grid.can_async_op(operation) || this.dict_format ) {\n this.update_grid();\n } else {\n this.go_to(target, href);\n }\n\n // done\n return false;\n }\n\n // refresh grid\n if (href) {\n this.go_to(target, href);\n return false;\n }\n\n // refresh grid\n if (this.grid.get('async') || this.dict_format) {\n this.update_grid();\n } else {\n this.go_to(target, href);\n }\n\n // done\n return false;\n },\n\n // go to url\n go_to: function (target, href) {\n // get aysnc status\n var async = this.grid.get('async');\n this.grid.set('async', false);\n\n // get slide status\n var advanced_search = this.$el.find('#advanced-search').is(':visible');\n this.grid.set('advanced_search', advanced_search);\n\n // get default url\n if(!href) {\n href = this.grid.get('url_base') + '?' + $.param(this.grid.get_url_data());\n }\n\n // clear grid of transient request attributes.\n this.grid.set({\n operation: undefined,\n item_ids: undefined,\n async: async\n });\n switch (target) {\n case 'inbound':\n // this currently assumes that there is only a single grid shown at a time\n var $div = $('.grid-header').closest('.inbound');\n if ($div.length !== 0) {\n $div.load(href);\n return;\n }\n break;\n case 'top':\n window.top.location = href;\n break;\n default:\n window.location = href;\n }\n },\n\n // Update grid.\n update_grid: function () {\n // If there's an operation, do POST; otherwise, do GET.\n var method = (this.grid.get('operation') ? 'POST' : 'GET' );\n\n // Show overlay to indicate loading and prevent user actions.\n this.$el.find('.loading-elt-overlay').show();\n var self = this;\n $.ajax({\n type: method,\n url: self.grid.get('url_base'),\n data: self.grid.get_url_data(),\n error: function(response) { alert( 'Grid refresh failed' );},\n success: function(response_text) {\n\n // backup\n var embedded = self.grid.get('embedded');\n var insert = self.grid.get('insert');\n var advanced_search = self.$el.find('#advanced-search').is(':visible');\n\n // request new configuration\n var json = self.dict_format ? response_text : $.parseJSON(response_text);\n\n // update\n json.embedded = embedded;\n json.insert = insert;\n json.advanced_search = advanced_search;\n\n // Initialize new grid config\n self.init_grid(json);\n\n // Hide loading overlay.\n self.$el.find('.loading-elt-overlay').hide();\n },\n complete: function() {\n // Clear grid of transient request attributes.\n self.grid.set({\n operation: undefined,\n item_ids: undefined\n });\n }\n });\n }\n});\n\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/grid/grid-view.js","// dependencies\ndefine(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc'], function(Utils, Portlet, Ui) {\n\n// ui list element\nvar View = Backbone.View.extend({\n // create portlet to keep track of selected list elements\n initialize : function(options) {\n // link this\n var self = this;\n\n // initialize options\n this.options = options;\n this.name = options.name || 'element';\n this.multiple = options.multiple || false;\n\n // create message handler\n this.message = new Ui.Message();\n\n // create portlet\n this.portlet = new Portlet.View({ cls: 'ui-portlet-section' });\n\n // create select field containing the options which can be inserted into the list\n this.select = new Ui.Select.View({ optional : options.optional });\n\n // create insert new list element button\n this.button = new Ui.ButtonIcon({\n icon : 'fa fa-sign-in',\n tooltip : 'Insert new ' + this.name,\n onclick : function() {\n self.add({\n id : self.select.value(),\n name : self.select.text()\n });\n }\n });\n\n // build main element\n this.setElement(this._template(options));\n this.$('.ui-list-message').append(this.message.$el);\n this.$('.ui-list-portlet').append(this.portlet.$el);\n this.$('.ui-list-button').append(this.button.$el);\n this.$('.ui-list-select').append(this.select.$el);\n },\n\n /** Return/Set currently selected list elements */\n value: function(val) {\n // set new value\n if (val !== undefined) {\n this.portlet.empty();\n if ($.isArray(val)) {\n for (var i in val) {\n var v = val[i];\n var v_id = null;\n var v_name = null;\n if ($.type(v) != 'string') {\n v_id = v.id;\n v_name = v.name;\n } else {\n v_id = v_name = v;\n }\n if (v_id != null) {\n this.add({\n id : v_id,\n name : v_name\n });\n }\n }\n }\n this._refresh();\n }\n // get current value\n var lst = [];\n this.$('.ui-list-id').each(function() {\n lst.push({\n id : $(this).prop('id'),\n name : $(this).find('.ui-list-name').html()\n });\n });\n if (lst.length == 0) {\n return null;\n }\n return lst;\n },\n\n /** Add row */\n add: function(options) {\n var self = this;\n if (this.$('[id=\"' + options.id + '\"]').length === 0) {\n if (!Utils.isEmpty(options.id)) {\n var $el = $(this._templateRow({\n id : options.id,\n name : options.name\n }));\n $el.on('click', function() {\n $el.remove();\n self._refresh();\n });\n $el.on('mouseover', function() {\n $el.addClass('portlet-highlight');\n });\n $el.on('mouseout', function() {\n $el.removeClass('portlet-highlight');\n });\n this.portlet.append($el);\n this._refresh();\n } else {\n this.message.update({ message: 'Please select a valid ' + this.name + '.', status: 'danger' });\n }\n } else {\n this.message.update({ message: 'This ' + this.name + ' is already in the list.' });\n }\n },\n\n /** Update available options */\n update: function(options) {\n this.select.update(options);\n },\n\n /** Refresh view */\n _refresh: function() {\n if (this.$('.ui-list-id').length > 0) {\n !this.multiple && this.button.disable();\n this.$('.ui-list-portlet').show();\n } else {\n this.button.enable();\n this.$('.ui-list-portlet').hide();\n }\n this.options.onchange && this.options.onchange();\n },\n\n /** Main Template */\n _template: function(options) {\n return '
' +\n '
' +\n '
' +\n '' +\n '(no options) ';\n }\n return _.map( options, function( option ){\n if( option.divider ){\n return '';\n } else if( option.header ){\n return [ '', option.html, ' ' ].join( '' );\n }\n var href = option.href || 'javascript:void(0);',\n target = ( option.target )?( ' target=\"' + option.target + '\"' ):( '' ),\n check = ( option.checked )?( '' ):( '' );\n return [\n '',\n check, option.html,\n ' '\n ].join( '' );\n }).join( '' );\n },\n\n // get the absolute position/offset for the menu\n _getShownPosition : function( clickEvent ){\n\n // display menu horiz. centered on click...\n var menuWidth = this.$el.width();\n var x = clickEvent.pageX - menuWidth / 2 ;\n\n // adjust to handle horiz. scroll and window dimensions ( draw entirely on visible screen area )\n x = Math.min( x, $( document ).scrollLeft() + $( window ).width() - menuWidth - 5 );\n x = Math.max( x, $( document ).scrollLeft() + 5 );\n return {\n top: clickEvent.pageY,\n left: x\n };\n },\n\n // bind an event handler to all available frames so that when anything is clicked\n // the menu is removed from the DOM and the event handler unbinds itself\n _setUpCloseBehavior: function(){\n var menu = this;\n//TODO: alternately: focus hack, blocking overlay, jquery.blockui\n\n // function to close popup and unbind itself\n function closePopup( event ){\n $( document ).off( 'click.close_popup' );\n if( window && window.parent !== window ){\n try {\n $( window.parent.document ).off( \"click.close_popup\" );\n } catch( err ){}\n } else {\n try {\n $( 'iframe#galaxy_main' ).contents().off( \"click.close_popup\" );\n } catch( err ){}\n }\n menu.remove();\n }\n\n $( 'html' ).one( \"click.close_popup\", closePopup );\n if( window && window.parent !== window ){\n try {\n $( window.parent.document ).find( 'html' ).one( \"click.close_popup\", closePopup );\n } catch( err ){}\n } else {\n try {\n $( 'iframe#galaxy_main' ).contents().one( \"click.close_popup\", closePopup );\n } catch( err ){}\n }\n },\n\n // add a menu option/item at the given index\n addItem: function( item, index ){\n // append to end if no index\n index = ( index >= 0 ) ? index : this.options.length;\n this.options.splice( index, 0, item );\n return this;\n },\n\n // remove a menu option/item at the given index\n removeItem: function( index ){\n if( index >=0 ){\n this.options.splice( index, 1 );\n }\n return this;\n },\n\n // search for a menu option by its html\n findIndexByHtml: function( html ){\n for( var i = 0; i < this.options.length; i++ ){\n if( _.has( this.options[i], 'html' ) && ( this.options[i].html === html )){\n return i;\n }\n }\n return null;\n },\n\n // search for a menu option by its html\n findItemByHtml: function( html ){\n return this.options[( this.findIndexByHtml( html ))];\n },\n\n // string representation\n toString: function(){\n return 'PopupMenu';\n }\n});\n/** shortcut to new for when you don't need to preserve the ref */\nPopupMenu.create = function _create( $button, options ){\n return new PopupMenu( $button, options );\n};\n\n// -----------------------------------------------------------------------------\n// the following class functions are bridges from the original make_popupmenu and make_popup_menus\n// to the newer backbone.js PopupMenu\n\n/** Create a PopupMenu from simple map initial_options activated by clicking button_element.\n * Converts initial_options to object array used by PopupMenu.\n * @param {jQuery|DOMElement} button_element element which, when clicked, activates menu\n * @param {Object} initial_options map of key -> values, where\n * key is option text, value is fn to call when option is clicked\n * @returns {PopupMenu} the PopupMenu created\n */\nPopupMenu.make_popupmenu = function( button_element, initial_options ){\n var convertedOptions = [];\n _.each( initial_options, function( optionVal, optionKey ){\n var newOption = { html: optionKey };\n\n // keys with null values indicate: header\n if( optionVal === null ){ // !optionVal? (null only?)\n newOption.header = true;\n\n // keys with function values indicate: a menu option\n } else if( jQuery.type( optionVal ) === 'function' ){\n newOption.func = optionVal;\n }\n //TODO:?? any other special optionVals?\n // there was no divider option originally\n convertedOptions.push( newOption );\n });\n return new PopupMenu( $( button_element ), convertedOptions );\n};\n\n/** Find all anchors in $parent (using selector) and covert anchors into a PopupMenu options map.\n * @param {jQuery} $parent the element that contains the links to convert to options\n * @param {String} selector jq selector string to find links\n * @returns {Object[]} the options array to initialize a PopupMenu\n */\n//TODO: lose parent and selector, pass in array of links, use map to return options\nPopupMenu.convertLinksToOptions = function( $parent, selector ){\n $parent = $( $parent );\n selector = selector || 'a';\n var options = [];\n $parent.find( selector ).each( function( elem, i ){\n var option = {}, $link = $( elem );\n\n // convert link text to the option text (html) and the href into the option func\n option.html = $link.text();\n if( $link.attr( 'href' ) ){\n var linkHref = $link.attr( 'href' ),\n linkTarget = $link.attr( 'target' ),\n confirmText = $link.attr( 'confirm' );\n\n option.func = function(){\n // if there's a \"confirm\" attribute, throw up a confirmation dialog, and\n // if the user cancels - do nothing\n if( ( confirmText ) && ( !confirm( confirmText ) ) ){ return; }\n\n // if there's no confirm attribute, or the user accepted the confirm dialog:\n switch( linkTarget ){\n // relocate the center panel\n case '_parent':\n window.parent.location = linkHref;\n break;\n\n // relocate the entire window\n case '_top':\n window.top.location = linkHref;\n break;\n\n // relocate this panel\n default:\n window.location = linkHref;\n }\n };\n }\n options.push( option );\n });\n return options;\n};\n\n/** Create a single popupmenu from existing DOM button and anchor elements\n * @param {jQuery} $buttonElement the element that when clicked will open the menu\n * @param {jQuery} $menuElement the element that contains the anchors to convert into a menu\n * @param {String} menuElementLinkSelector jq selector string used to find anchors to be made into menu options\n * @returns {PopupMenu} the PopupMenu (Backbone View) that can render, control the menu\n */\nPopupMenu.fromExistingDom = function( $buttonElement, $menuElement, menuElementLinkSelector ){\n $buttonElement = $( $buttonElement );\n $menuElement = $( $menuElement );\n var options = PopupMenu.convertLinksToOptions( $menuElement, menuElementLinkSelector );\n // we're done with the menu (having converted it to an options map)\n $menuElement.remove();\n return new PopupMenu( $buttonElement, options );\n};\n\n/** Create all popupmenus within a document or a more specific element\n * @param {DOMElement} parent the DOM element in which to search for popupmenus to build (defaults to document)\n * @param {String} menuSelector jq selector string to find popupmenu menu elements (defaults to \"div[popupmenu]\")\n * @param {Function} buttonSelectorBuildFn the function to build the jq button selector.\n * Will be passed $menuElement, parent.\n * (Defaults to return '#' + $menuElement.attr( 'popupmenu' ); )\n * @returns {PopupMenu[]} array of popupmenus created\n */\nPopupMenu.make_popup_menus = function( parent, menuSelector, buttonSelectorBuildFn ){\n parent = parent || document;\n // orig. Glx popupmenu menus have a (non-std) attribute 'popupmenu'\n // which contains the id of the button that activates the menu\n menuSelector = menuSelector || 'div[popupmenu]';\n // default to (orig. Glx) matching button to menu by using the popupmenu attr of the menu as the id of the button\n buttonSelectorBuildFn = buttonSelectorBuildFn || function( $menuElement, parent ){\n return '#' + $menuElement.attr( 'popupmenu' );\n };\n\n // aggregate and return all PopupMenus\n var popupMenusCreated = [];\n $( parent ).find( menuSelector ).each( function(){\n var $menuElement = $( this ),\n $buttonElement = $( parent ).find( buttonSelectorBuildFn( $menuElement, parent ) );\n popupMenusCreated.push( PopupMenu.fromDom( $buttonElement, $menuElement ) );\n $buttonElement.addClass( 'popup' );\n });\n return popupMenusCreated;\n};\n\n\n// =============================================================================\n return PopupMenu;\n});\n\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/popup-menu.js","/* This class maps the form dom to an api compatible javascript dictionary. */\ndefine([ 'utils/utils' ], function( Utils ) {\n var Manager = Backbone.Model.extend({\n initialize: function( app ) {\n this.app = app;\n },\n\n /** Creates a checksum. */\n checksum: function() {\n var sum = '';\n var self = this;\n this.app.section.$el.find( '.section-row' ).each( function() {\n var id = $(this).attr( 'id' );\n var field = self.app.field_list[ id ];\n if ( field ) {\n sum += id + ':' + JSON.stringify( field.value && field.value() ) + ':' + field.collapsed + ';';\n }\n });\n return sum;\n },\n\n /** Convert dom into a dictionary of flat id/value pairs used e.g. on job submission. */\n create: function() {\n var self = this;\n\n // get raw dictionary from dom\n var dict = {};\n this._iterate( this.app.section.$el, dict );\n\n // add to result dictionary, label elements\n var result_dict = {};\n this.flat_dict = {};\n function add( flat_id, input_id, input_value ) {\n self.flat_dict[ flat_id ] = input_id;\n result_dict[ flat_id ] = input_value;\n self.app.element_list[ input_id ] && self.app.element_list[ input_id ].$el.attr( 'tour_id', flat_id );\n }\n // converter between raw dictionary and job dictionary\n function convert( identifier, head ) {\n for ( var index in head ) {\n var node = head[ index ];\n if ( node.input ) {\n var input = node.input;\n var flat_id = identifier;\n if ( identifier != '' ) {\n flat_id += '|';\n }\n flat_id += input.name;\n switch ( input.type ) {\n case 'repeat':\n var section_label = 'section-';\n var block_indices = [];\n var block_prefix = null;\n for ( var block_label in node ) {\n var pos = block_label.indexOf( section_label );\n if ( pos != -1 ) {\n pos += section_label.length;\n block_indices.push( parseInt( block_label.substr( pos ) ));\n if ( !block_prefix ) {\n block_prefix = block_label.substr( 0, pos );\n }\n }\n }\n block_indices.sort( function( a, b ) { return a - b; });\n var index = 0;\n for ( var i in block_indices ) {\n convert( flat_id + '_' + index++, node[ block_prefix + block_indices[ i ] ]);\n }\n break;\n case 'conditional':\n var value = self.app.field_list[ input.id ].value();\n add( flat_id + '|' + input.test_param.name, input.id, value );\n var selectedCase = matchCase( input, value );\n if ( selectedCase != -1 ) {\n convert( flat_id, head[ input.id + '-section-' + selectedCase ] );\n }\n break;\n case 'section':\n convert( !input.flat && flat_id || '', node );\n break;\n default:\n var field = self.app.field_list[ input.id ];\n if ( field && field.value ) {\n var value = field.value();\n if ( input.ignore === undefined || input.ignore != value ) {\n if ( field.collapsed && input.collapsible_value ) {\n value = input.collapsible_value;\n }\n add( flat_id, input.id, value );\n if ( input.payload ) {\n for ( var p_id in input.payload ) {\n add( p_id, input.id, input.payload[ p_id ] );\n }\n }\n }\n }\n }\n }\n }\n }\n convert( '', dict );\n return result_dict;\n },\n\n /** Matches flat ids to corresponding input element\n * @param{string} flat_id - Flat input id to be looked up.\n */\n match: function ( flat_id ) {\n return this.flat_dict && this.flat_dict[ flat_id ];\n },\n\n /** Match conditional values to selected cases\n */\n matchCase: function( input, value ) {\n return matchCase( input, value );\n },\n\n /** Matches a new tool model to the current input elements e.g. used to update dynamic options\n */\n matchModel: function( model, callback ) {\n var self = this;\n visitInputs( model.inputs, function( input, name ) {\n self.flat_dict[ name ] && callback ( input, self.flat_dict[ name ] );\n });\n },\n\n /** Matches identifier from api response to input elements e.g. used to display validation errors\n */\n matchResponse: function( response ) {\n var result = {};\n var self = this;\n function search ( id, head ) {\n if ( typeof head === 'string' ) {\n var input_id = self.flat_dict[ id ];\n input_id && ( result[ input_id ] = head );\n } else {\n for ( var i in head ) {\n var new_id = i;\n if ( id !== '' ) {\n var separator = '|';\n if ( head instanceof Array ) {\n separator = '_';\n }\n new_id = id + separator + new_id;\n }\n search ( new_id, head[ i ] );\n }\n }\n }\n search( '', response );\n return result;\n },\n\n /** Map dom tree to dictionary tree with input elements.\n */\n _iterate: function( parent, dict ) {\n var self = this;\n var children = $( parent ).children();\n children.each( function() {\n var child = this;\n var id = $( child ).attr( 'id' );\n if ( $( child ).hasClass( 'section-row' ) ) {\n var input = self.app.input_list[ id ];\n dict[ id ] = ( input && { input : input } ) || {};\n self._iterate( child, dict[ id ] );\n } else {\n self._iterate( child, dict );\n }\n });\n }\n });\n\n /** Match conditional values to selected cases\n * @param{dict} input - Definition of conditional input parameter\n * @param{dict} value - Current value\n */\n var matchCase = function( input, value ) {\n if ( input.test_param.type == 'boolean' ) {\n if ( value == 'true' ) {\n value = input.test_param.truevalue || 'true';\n } else {\n value = input.test_param.falsevalue || 'false';\n }\n }\n for ( var i in input.cases ) {\n if ( input.cases[ i ].value == value ) {\n return i;\n }\n }\n return -1;\n };\n\n /** Visits tool inputs\n * @param{dict} inputs - Nested dictionary of input elements\n * @param{dict} callback - Called with the mapped dictionary object and corresponding model node\n */\n var visitInputs = function( inputs, callback, prefix, context ) {\n context = $.extend( true, {}, context );\n _.each( inputs, function ( input ) {\n if ( input && input.type && input.name ) {\n context[ input.name ] = input;\n }\n });\n for ( var key in inputs ) {\n var node = inputs[ key ];\n node.name = node.name || key;\n var name = prefix ? prefix + '|' + node.name : node.name;\n switch ( node.type ) {\n case 'repeat':\n _.each( node.cache, function( cache, j ) {\n visitInputs( cache, callback, name + '_' + j, context );\n });\n break;\n case 'conditional':\n if ( node.test_param ) {\n callback( node.test_param, name + '|' + node.test_param.name, context );\n var selectedCase = matchCase( node, node.test_param.value );\n if ( selectedCase != -1 ) {\n visitInputs( node.cases[ selectedCase ].inputs, callback, name, context );\n } else {\n Galaxy.emit.debug( 'form-data::visitInputs() - Invalid case for ' + name + '.' );\n }\n } else {\n Galaxy.emit.debug( 'form-data::visitInputs() - Conditional test parameter missing for ' + name + '.' );\n }\n break;\n case 'section':\n visitInputs( node.inputs, callback, name, context )\n break;\n default:\n callback( node, name, context );\n }\n }\n };\n\n return {\n Manager : Manager,\n visitInputs : visitInputs\n }\n});\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/form/form-data.js","/** This class creates a ui table element. */\ndefine( [ 'utils/utils' ], function( Utils ) {\n var View = Backbone.View.extend({\n initialize : function(options) {\n this.options = Utils.merge(options, {\n content : 'No content available.',\n onchange : null,\n ondblclick : null,\n onconfirm : null,\n cls : 'ui-table',\n selectable : true,\n cls_tr : ''\n });\n this.setElement( this._template() );\n this.$thead = this.$('thead');\n this.$tbody = this.$('tbody');\n this.$tmessage = this.$('tmessage');\n this.row = this._row();\n this.row_count = 0;\n },\n\n events : {\n 'click' : '_onclick',\n 'dblclick' : '_ondblclick'\n },\n\n /** Add cell to header row */\n addHeader: function( $el ) {\n this.row.append( $( '
' +\n '
';\n },\n\n /** Row Template */\n _templateRow: function(options) {\n return '' +\n '' +\n '' + options.name + '' +\n '
';\n }\n});\n\nreturn {\n View: View\n}\n\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/ui-list.js","/** Base class for options based ui elements **/\ndefine([ 'utils/utils', 'mvc/ui/ui-buttons' ], function( Utils, Buttons ) {\nvar Base = Backbone.View.extend({\n initialize: function( options ) {\n var self = this;\n this.model = options && options.model || new Backbone.Model({\n visible : true,\n data : [],\n id : Utils.uid(),\n error_text : 'No options available.',\n wait_text : 'Please wait...',\n multiple : false,\n optional : false,\n onchange : function(){}\n }).set( options );\n this.listenTo( this.model, 'change:value', this._changeValue, this );\n this.listenTo( this.model, 'change:wait', this._changeWait, this );\n this.listenTo( this.model, 'change:data', this._changeData, this );\n this.listenTo( this.model, 'change:visible', this._changeVisible, this );\n this.on( 'change', function() { self.model.get( 'onchange' )( self.value() ) } );\n this.render();\n },\n\n render: function() {\n var self = this;\n this.$el.empty()\n .removeClass()\n .addClass( 'ui-options' )\n .append( this.$message = $( '' ) )\n .append( this.$menu = $( '' ).addClass( 'ui-options-menu' ) )\n .append( this.$options = $( this._template() ) );\n\n // add select/unselect all button\n this.all_button = null;\n if ( this.model.get( 'multiple' ) ) {\n this.all_button = new Buttons.ButtonCheck({\n onclick: function() {\n self.$( 'input' ).prop( 'checked', self.all_button.value() !== 0 );\n self.value( self._getValue() );\n self.trigger( 'change' );\n }\n });\n this.$menu.append( this.all_button.$el );\n }\n\n // finalize dom\n this._changeData();\n this._changeWait();\n this._changeVisible();\n },\n\n /** Update available options */\n update: function( options ) {\n this.model.set( 'data', options );\n },\n\n _changeData: function() {\n var self = this;\n this.$options.empty();\n if ( this._templateOptions ) {\n this.$options.append( this._templateOptions( this.model.get( 'data' ) ) );\n } else {\n _.each( this.model.get( 'data' ), function( option ) {\n self.$options.append( $( self._templateOption( option ) )\n .addClass( 'ui-option' )\n .tooltip( { title: option.tooltip, placement: 'bottom' } ) );\n });\n }\n var self = this;\n this.$( 'input' ).on( 'change', function() {\n self.value( self._getValue() );\n self.trigger( 'change' );\n });\n this._changeValue();\n this._changeWait();\n },\n\n _changeVisible: function() {\n this.$el[ this.model.get( 'visible' ) ? 'show' : 'hide' ]();\n },\n\n _changeWait: function() {\n if ( this.model.get( 'wait' ) ) {\n if ( this.length() === 0 ) {\n this._messageShow( this.model.get( 'wait_text' ), 'info' );\n this.$options.hide();\n this.$menu.hide();\n }\n } else {\n if ( this.length() === 0 ) {\n this._messageShow( this.model.get( 'error_text' ), 'danger' );\n this.$options.hide();\n this.$menu.hide();\n } else {\n this.$message.hide();\n this.$options.css( 'display', 'inline-block' );\n this.$menu.show();\n }\n }\n },\n\n _changeValue: function() {\n this._setValue( this.model.get( 'value' ) );\n if ( this._getValue() === null && !this.model.get( 'multiple' ) && !this.model.get( 'optional' ) ) {\n this._setValue( this.first() );\n }\n this.all_button && this.all_button.value( $.isArray( this._getValue() ) ? this._getValue().length : 0, this.length() );\n },\n\n /** Return/Set current selection */\n value: function ( new_value ) {\n new_value !== undefined && this.model.set( 'value', new_value );\n return this._getValue();\n },\n\n /** Return first available option */\n first: function() {\n var options = this.$( 'input' ).first();\n return options.length > 0 ? options.val() : null;\n },\n\n /** Show a spinner indicating that the select options are currently loaded */\n wait: function() {\n this.model.set( 'wait', true );\n },\n\n /** Hide spinner indicating that the request has been completed */\n unwait: function() {\n this.model.set( 'wait', false );\n },\n\n /** Returns the number of options */\n length: function() {\n return this.$( '.ui-option' ).length;\n },\n\n /** Set value to dom */\n _setValue: function( new_value ) {\n var self = this;\n if ( new_value !== undefined ) {\n this.$( 'input' ).prop( 'checked', false );\n if ( new_value !== null ) {\n var values = $.isArray( new_value ) ? new_value : [ new_value ];\n _.each( values, function( v ) {\n self.$( 'input[value=\"' + v + '\"]' ).first().prop( 'checked', true );\n });\n }\n }\n },\n\n /** Return current selection */\n _getValue: function() {\n var selected = [];\n this.$( ':checked' ).each( function() {\n selected.push( $( this ).val() );\n });\n if ( Utils.isEmpty( selected ) ) {\n return null;\n }\n return this.model.get( 'multiple' ) ? selected : selected[ 0 ];\n },\n\n /** Show message instead if options */\n _messageShow: function( text, status ) {\n this.$message.show()\n .removeClass()\n .addClass( 'ui-message alert alert-' + status )\n .html( text );\n },\n\n /** Main template function */\n _template: function() {\n return $( '' ).addClass( 'ui-options-list' );\n }\n});\n\n/** Iconized **/\nvar BaseIcons = Base.extend({\n _templateOption: function( pair ) {\n var id = Utils.uid();\n return $( '' ).addClass( 'ui-option' )\n .append( $( '' ).attr( {\n id : id,\n type : this.model.get( 'type' ),\n name : this.model.id,\n value : pair.value } ) )\n .append( $( '' ).addClass( 'ui-options-label' )\n .attr( 'for', id )\n .html( pair.label ) );\n }\n});\n\n/** Radio button field **/\nvar Radio = {};\nRadio.View = BaseIcons.extend({\n initialize: function( options ) {\n options.type = 'radio';\n BaseIcons.prototype.initialize.call( this, options );\n }\n});\n\n/** Checkbox options field **/\nvar Checkbox = {};\nCheckbox.View = BaseIcons.extend({\n initialize: function( options ) {\n options.type = 'checkbox';\n options.multiple = true;\n BaseIcons.prototype.initialize.call( this, options );\n }\n});\n\n/** Radio button options field styled as classic buttons **/\nvar RadioButton = {};\nRadioButton.View = Base.extend({\n initialize: function( options ) {\n Base.prototype.initialize.call( this, options );\n },\n\n /** Set current value */\n _setValue: function ( new_value ) {\n if ( new_value !== undefined ) {\n this.$( 'input' ).prop( 'checked', false );\n this.$( 'label' ).removeClass( 'active' );\n this.$( '[value=\"' + new_value + '\"]' ).prop( 'checked', true ).closest( 'label' ).addClass( 'active' );\n }\n },\n\n /** Template for a single option */\n _templateOption: function( pair ) {\n var $el = $( '' ).addClass( 'btn btn-default' );\n pair.icon && $el.append( $( '' ).addClass( 'fa' ).addClass( pair.icon ).addClass( !pair.label && 'no-padding' ) );\n $el.append( $( '' ).attr( { type: 'radio', name: this.model.id, value: pair.value } ) );\n pair.label && $el.append( pair.label );\n return $el;\n },\n\n /** Main template function */\n _template: function() {\n return $( '' ).addClass( 'btn-group ui-radiobutton' ).attr( 'data-toggle', 'buttons' );\n }\n});\n\nreturn {\n Base : Base,\n BaseIcons : BaseIcons,\n Radio : Radio,\n RadioButton : RadioButton,\n Checkbox : Checkbox\n};\n\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/ui-options.js","/**\n * This class creates/wraps a default html select field as backbone class.\n */\ndefine([ 'utils/utils', 'mvc/ui/ui-buttons' ], function( Utils, Buttons ) {\nvar View = Backbone.View.extend({\n initialize: function( options ) {\n var self = this;\n this.data = [];\n this.data2 = [];\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n cls : 'ui-select',\n error_text : 'No options available',\n empty_text : 'Nothing selected',\n visible : true,\n wait : false,\n multiple : false,\n searchable : true,\n optional : false,\n disabled : false,\n onchange : function(){},\n value : null,\n individual : false,\n pagesize : 20\n }).set( options );\n this.on( 'change', function() { self.model.get( 'onchange' ) && self.model.get( 'onchange' )( self.value() ) } );\n this.listenTo( this.model, 'change:data', this._changeData, this );\n this.listenTo( this.model, 'change:disabled', this._changeDisabled, this );\n this.listenTo( this.model, 'change:wait', this._changeWait, this );\n this.listenTo( this.model, 'change:visible', this._changeVisible, this );\n this.listenTo( this.model, 'change:value', this._changeValue, this );\n this.listenTo( this.model, 'change:multiple change:searchable change:cls change:id', this.render, this );\n this.render();\n },\n\n render: function() {\n var self = this;\n this.model.get( 'searchable' ) ? this._renderSearchable() : this._renderClassic();\n this.$el.addClass( this.model.get( 'cls' ) )\n .attr( 'id', this.model.get( 'id' ) );\n this.$select.empty().addClass( 'select' )\n .attr( 'id', this.model.get( 'id' ) + '_select' )\n .prop( 'multiple', this.model.get( 'multiple' ) )\n .on( 'change', function() {\n self.value( self._getValue() );\n self.trigger( 'change' );\n });\n this._changeData();\n this._changeWait();\n this._changeVisible();\n this._changeDisabled();\n },\n\n /** Renders the classic selection field */\n _renderClassic: function() {\n var self = this;\n this.$el.addClass( this.model.get( 'multiple' ) ? 'ui-select-multiple' : 'ui-select' )\n .append( this.$select = $( '' ) )\n .append( this.$dropdown = $( '' ) )\n .append( this.$resize = $( '' )\n .append( this.$resize_icon = $( '' ) ) );\n if ( this.model.get( 'multiple' ) ) {\n this.$dropdown.hide();\n this.$resize_icon.addClass( 'fa fa-angle-double-right fa-rotate-45' ).show();\n this.$resize.removeClass()\n .addClass( 'icon-resize' )\n .show()\n .off( 'mousedown' ).on( 'mousedown', function( event ) {\n var currentY = event.pageY;\n var currentHeight = self.$select.height();\n self.minHeight = self.minHeight || currentHeight;\n $( '#dd-helper' ).show().on( 'mousemove', function( event ) {\n self.$select.height( Math.max( currentHeight + ( event.pageY - currentY ), self.minHeight ) );\n }).on( 'mouseup mouseleave', function() {\n $( '#dd-helper' ).hide().off();\n });\n });\n } else {\n this.$dropdown.show();\n this.$resize.hide();\n this.$resize_icon.hide();\n }\n },\n\n /** Renders the default select2 field */\n _renderSearchable: function() {\n var self = this;\n this.$el.append( this.$select = $( '' ) )\n .append( this.$dropdown = $( '' ) );\n this.$dropdown.hide();\n if ( !this.model.get( 'multiple' ) ) {\n this.$dropdown.show().on( 'click', function() {\n self.$select.select2 && self.$select.select2( 'open' );\n });\n }\n this.all_button = null;\n if ( this.model.get( 'multiple' ) && !this.model.get( 'individual' ) ) {\n this.all_button = new Buttons.ButtonCheck({\n onclick: function() {\n var new_value = [];\n self.all_button.value() !== 0 && _.each( self.model.get( 'data' ), function( option ) {\n new_value.push( option.value );\n });\n self.value( new_value );\n self.trigger( 'change' );\n }\n });\n this.$el.prepend( this.all_button.$el );\n }\n },\n\n /** Matches a search term with a given text */\n _match: function( term, text ) {\n return !term || term == '' || String( text ).toUpperCase().indexOf( term.toUpperCase() ) >= 0\n },\n\n /** Updates the selection options */\n _changeData: function() {\n var self = this;\n this.data = [];\n if ( !this.model.get( 'multiple' ) && this.model.get( 'optional' ) ) {\n this.data.push( { value: '__null__', label: self.model.get( 'empty_text' ) } );\n }\n _.each( this.model.get( 'data' ), function( option ) {\n self.data.push( option );\n });\n if ( this.length() == 0 ) {\n this.data.push( { value: '__null__', label: this.model.get( 'error_text' ) } );\n }\n if ( this.model.get( 'searchable' ) ) {\n this.data2 = [];\n _.each( this.data, function( option, index ) {\n self.data2.push( { order: index, id: option.value, text: option.label, tags: option.tags } );\n });\n this.$select.data( 'select2' ) && this.$select.select2( 'destroy' );\n this.matched_tags = {};\n this.$select.select2({\n data : self.data2,\n closeOnSelect : !this.model.get( 'multiple' ),\n multiple : this.model.get( 'multiple' ),\n query : function( q ) {\n self.matched_tags = {};\n var pagesize = self.model.get( 'pagesize' );\n var results = _.filter( self.data2, function ( e ) {\n var found = false;\n _.each( e.tags, function( tag ) {\n if ( self._match( q.term, tag ) ) {\n found = self.matched_tags[ tag ] = true;\n }\n });\n return found || self._match( q.term, e.text );\n });\n q.callback({\n results: results.slice( ( q.page - 1 ) * pagesize, q.page * pagesize ),\n more : results.length >= q.page * pagesize\n });\n },\n formatResult : function( result ) {\n return _.escape( result.text ) +\n '';\n }\n });\n this.$( '.select2-container .select2-search input' ).off( 'blur' );\n } else {\n this.$select.find( 'option' ).remove();\n _.each( this.data, function( option ) {\n self.$select.append( $( '' ).attr( 'value', option.value ).html( _.escape( option.label ) ) );\n });\n }\n this.model.set( 'disabled', this.length() == 0 );\n this._changeValue();\n },\n\n /** Handles field enabling/disabling, usually used when no options are available */\n _changeDisabled: function() {\n if ( this.model.get( 'searchable' ) ) {\n this.$select.select2( this.model.get( 'disabled' ) ? 'disable' : 'enable' );\n } else {\n this.$select.prop( 'disabled', this.model.get( 'disabled' ) );\n }\n },\n\n /** Searchable fields may display a spinner e.g. while waiting for a server response */\n _changeWait: function() {\n this.$dropdown.removeClass()\n .addClass( 'icon-dropdown fa' )\n .addClass( this.model.get( 'wait' ) ? 'fa-spinner fa-spin' : 'fa-caret-down' );\n },\n\n /** Handles field visibility */\n _changeVisible: function() {\n this.$el[ this.model.get( 'visible' ) ? 'show' : 'hide' ]();\n this.$select[ this.model.get( 'visible' ) ? 'show' : 'hide' ]();\n },\n\n /** Synchronizes the model value with the actually selected field value */\n _changeValue: function() {\n this._setValue( this.model.get( 'value' ) );\n if ( this.model.get( 'multiple' ) ) {\n if ( this.all_button ) {\n var value = this._getValue();\n this.all_button.value( $.isArray( value ) ? value.length : 0, this.length() );\n }\n } else if ( this._getValue() === null && !this.model.get( 'optional' ) ) {\n this._setValue( this.first() );\n }\n },\n\n /** Return/Set current selection */\n value: function ( new_value ) {\n new_value !== undefined && this.model.set( 'value', new_value );\n return this._getValue();\n },\n\n /** Return the first select option */\n first: function() {\n return this.data.length > 0 ? this.data[ 0 ].value : null;\n },\n\n /** Check if a value is an existing option */\n exists: function( value ) {\n return _.findWhere( this.data, { value: value } );\n },\n\n /** Return the label/text of the current selection */\n text: function () {\n var v = this._getValue();\n var d = this.exists( $.isArray( v ) ? v[ 0 ] : v );\n return d ? d.label : '';\n },\n\n /** Show the select field */\n show: function() {\n this.model.set( 'visible', true );\n },\n\n /** Hide the select field */\n hide: function() {\n this.model.set( 'visible', false );\n },\n\n /** Show a spinner indicating that the select options are currently loaded */\n wait: function() {\n this.model.set( 'wait', true );\n },\n\n /** Hide spinner indicating that the request has been completed */\n unwait: function() {\n this.model.set( 'wait', false );\n },\n\n /** Returns true if the field is disabled */\n disabled: function() {\n return this.model.get( 'disabled' );\n },\n\n /** Enable the select field */\n enable: function() {\n this.model.set( 'disabled', false );\n },\n\n /** Disable the select field */\n disable: function() {\n this.model.set( 'disabled', true );\n },\n\n /** Update all available options at once */\n add: function( options, sorter ) {\n _.each( this.model.get( 'data' ), function( v ) {\n v.keep && !_.findWhere( options, { value: v.value } ) && options.push( v );\n });\n sorter && options && options.sort( sorter );\n this.model.set( 'data', options );\n },\n\n /** Update available options */\n update: function( options ) {\n this.model.set( 'data', options );\n },\n\n /** Set the custom onchange callback function */\n setOnChange: function( callback ) {\n this.model.set( 'onchange', callback );\n },\n\n /** Number of available options */\n length: function() {\n return $.isArray( this.model.get( 'data' ) ) ? this.model.get( 'data' ).length : 0;\n },\n\n /** Set value to dom */\n _setValue: function( new_value ) {\n var self = this;\n if( new_value === null || new_value === undefined ) {\n new_value = '__null__';\n }\n if ( this.model.get( 'multiple' ) ) {\n new_value = $.isArray( new_value ) ? new_value : [ new_value ];\n } else if ( $.isArray( new_value ) ) {\n if ( new_value.length > 0 ) {\n new_value = new_value[ 0 ];\n } else {\n new_value = '__null__';\n }\n }\n if ( this.model.get( 'searchable' ) ) {\n if ( $.isArray( new_value ) ) {\n var val = [];\n _.each( new_value, function( v ) {\n var d = _.findWhere( self.data2, { id: v } );\n d && val.push( d );\n });\n new_value = val;\n } else {\n var d = _.findWhere( this.data2, { id: new_value } );\n new_value = d;\n }\n this.$select.select2( 'data', new_value );\n } else {\n this.$select.val( new_value );\n }\n },\n\n /** Get value from dom */\n _getValue: function() {\n var val = null;\n if ( this.model.get( 'searchable' ) ) {\n var selected = this.$select.select2( 'data' );\n if ( selected ) {\n if ( $.isArray( selected ) ) {\n val = [];\n selected.sort( function( a, b ) { return a.order - b.order } );\n _.each( selected, function( v ) { val.push( v.id ) } );\n } else {\n val = selected.id;\n }\n }\n } else {\n val = this.$select.val();\n }\n return Utils.isEmpty( val ) ? null : val;\n }\n});\n\nreturn {\n View: View\n}\n\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/ui-select-default.js","define([\n //jquery\n //backbone\n], function(){\n// =============================================================================\n/**\n * view for a popup menu\n */\nvar PopupMenu = Backbone.View.extend({\n//TODO: maybe better as singleton off the Galaxy obj\n /** Cache the desired button element and options, set up the button click handler\n * NOTE: attaches this view as HTML/jQ data on the button for later use.\n */\n initialize: function( $button, options ){\n // default settings\n this.$button = $button;\n if( !this.$button.length ){\n this.$button = $( '' );\n }\n this.options = options || [];\n this.$button.data( 'popupmenu', this );\n\n // set up button click -> open menu behavior\n var menu = this;\n this.$button.click( function( event ){\n // if there's already a menu open, remove it\n $( '.popmenu-wrapper' ).remove();\n menu._renderAndShow( event );\n return false;\n });\n },\n\n // render the menu, append to the page body at the click position, and set up the 'click-away' handlers, show\n _renderAndShow: function( clickEvent ){\n this.render();\n this.$el.appendTo( 'body' ).css( this._getShownPosition( clickEvent )).show();\n this._setUpCloseBehavior();\n },\n\n // render the menu\n // this menu doesn't attach itself to the DOM ( see _renderAndShow )\n render: function(){\n // render the menu body absolute and hidden, fill with template\n this.$el.addClass( 'popmenu-wrapper' ).hide()\n .css({ position : 'absolute' })\n .html( this.template( this.$button.attr( 'id' ), this.options ));\n\n // set up behavior on each link/anchor elem\n if( this.options.length ){\n var menu = this;\n //precondition: there should be one option per li\n this.$el.find( 'li' ).each( function( i, li ){\n var option = menu.options[i];\n\n // if the option has 'func', call that function when the anchor is clicked\n if( option.func ){\n $( this ).children( 'a.popupmenu-option' ).click( function( event ){\n option.func.call( menu, event, option );\n // We must preventDefault otherwise clicking \"cancel\"\n // on a purge or something still navigates and causes\n // the action.\n event.preventDefault();\n // bubble up so that an option click will call the close behavior\n });\n }\n });\n }\n return this;\n },\n\n template : function( id, options ){\n return [\n ''\n ].join( '' );\n },\n\n _templateOptions : function( options ){\n if( !options.length ){\n return '' +\n '' +\n '' +\n '' +\n '
' +\n '' + this.options.content + ' ' +\n '
';\n }\n });\n\n return {\n View: View\n }\n});\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/ui-table.js","/**\n This class creates a form input element wrapper\n*/\ndefine([], function() {\n return Backbone.View.extend({\n initialize: function( app, options ) {\n this.app = app;\n this.app_options = app.model ? app.model.attributes : {};\n this.field = options && options.field || new Backbone.View();\n this.model = options && options.model || new Backbone.Model({\n text_enable : this.app_options.text_enable || 'Enable',\n text_disable : this.app_options.text_disable || 'Disable',\n cls_enable : this.app_options.cls_enable || 'fa fa-caret-square-o-down',\n cls_disable : this.app_options.cls_disable || 'fa fa-caret-square-o-up',\n always_refresh : this.app_options.always_refresh\n }).set( options );\n\n // set element and link components\n this.setElement( this._template() );\n this.$field = this.$( '.ui-form-field' );\n this.$info = this.$( '.ui-form-info' );\n this.$preview = this.$( '.ui-form-preview' );\n this.$collapsible = this.$( '.ui-form-collapsible' );\n this.$collapsible_text = this.$( '.ui-form-collapsible-text' );\n this.$collapsible_icon = this.$( '.ui-form-collapsible-icon' );\n this.$title = this.$( '.ui-form-title' );\n this.$title_text = this.$( '.ui-form-title-text' );\n this.$error_text = this.$( '.ui-form-error-text' );\n this.$error = this.$( '.ui-form-error' );\n this.$backdrop = this.$( '.ui-form-backdrop' );\n\n // add field element\n this.$field.prepend( this.field.$el );\n\n // decide wether to expand or collapse fields\n var collapsible_value = this.model.get( 'collapsible_value' );\n this.field.collapsed = collapsible_value !== undefined && JSON.stringify( this.model.get( 'value' ) ) == JSON.stringify( collapsible_value );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n\n // add click handler\n var self = this;\n this.$collapsible.on( 'click', function() {\n self.field.collapsed = !self.field.collapsed;\n app.trigger && app.trigger( 'change' );\n self.render();\n });\n\n // hide error on value change\n if ( this.field.model && !this.model.get( 'always_refresh' ) ) {\n this.listenTo( this.field.model, 'change:value', function() { self.reset() } );\n }\n },\n\n /** Set backdrop for input element */\n backdrop: function() {\n this.model.set( 'backdrop', true );\n },\n\n /** Set error text */\n error: function( text ) {\n this.model.set( 'error_text', text );\n },\n\n /** Reset this view */\n reset: function() {\n !this.model.get( 'fixed' ) && this.model.set( 'error_text', null );\n },\n\n render: function() {\n // render help\n $( '.tooltip' ).hide();\n var help_text = this.model.get( 'help', '' );\n var help_argument = this.model.get( 'argument' );\n if ( help_argument && help_text.indexOf( '(' + help_argument + ')' ) == -1 ) {\n help_text += ' (' + help_argument + ')';\n }\n this.$info.html( help_text );\n // render visibility\n this.$el[ this.model.get( 'hidden' ) ? 'hide' : 'show' ]();\n // render preview view for collapsed fields\n this.$preview[ ( this.field.collapsed && this.model.get( 'collapsible_preview' ) || this.model.get( 'disabled' ) ) ? 'show' : 'hide' ]()\n .html( _.escape( this.model.get( 'text_value' ) ) );\n // render error messages\n var error_text = this.model.get( 'error_text' );\n this.$error[ error_text ? 'show' : 'hide' ]();\n this.$el[ error_text ? 'addClass' : 'removeClass' ]( 'ui-error' );\n this.$error_text.html( error_text );\n // render backdrop\n this.$backdrop[ this.model.get( 'backdrop' ) ? 'show' : 'hide' ]();\n // render input field\n this.field.collapsed || this.model.get( 'disabled' ) ? this.$field.hide() : this.$field.show();\n // render input field color and style\n this.field.model && this.field.model.set( { 'color': this.model.get( 'color' ), 'style': this.model.get( 'style' ) } );\n // render collapsible options\n if ( !this.model.get( 'disabled' ) && this.model.get( 'collapsible_value' ) !== undefined ) {\n var collapsible_state = this.field.collapsed ? 'enable' : 'disable';\n this.$title_text.hide();\n this.$collapsible.show();\n this.$collapsible_text.text( this.model.get( 'label' ) );\n this.$collapsible_icon.removeClass().addClass( 'icon' )\n .addClass( this.model.get( 'cls_' + collapsible_state ) )\n .attr( 'data-original-title', this.model.get( 'text_' + collapsible_state ) )\n .tooltip( { placement: 'bottom' } );\n } else {\n this.$title_text.show().text( this.model.get( 'label' ) );\n this.$collapsible.hide();\n }\n },\n\n _template: function() {\n return $( '' ).addClass( 'ui-form-element' )\n .append( $( '' ).addClass( 'ui-form-error ui-error' )\n .append( $( '' ).addClass( 'fa fa-arrow-down' ) )\n .append( $( '' ).addClass( 'ui-form-error-text' ) )\n )\n .append( $( '' ).addClass( 'ui-form-title' )\n .append( $( '' ).addClass( 'ui-form-collapsible' )\n .append( $( '' ).addClass( 'ui-form-collapsible-icon' ) )\n .append( $( '' ).addClass( 'ui-form-collapsible-text' ) )\n )\n .append( $( '' ).addClass( 'ui-form-title-text' ) )\n )\n .append( $( '' ).addClass( 'ui-form-field' )\n .append( $( '' ).addClass( 'ui-form-info' ) )\n .append( $( '' ).addClass( 'ui-form-backdrop' ) )\n )\n .append( $( '' ).addClass( 'ui-form-preview' ) );\n }\n });\n});\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/form/form-input.js","/**\n This class creates input elements. New input parameter types should be added to the types dictionary.\n*/\ndefine(['utils/utils',\n 'mvc/ui/ui-misc',\n 'mvc/ui/ui-select-content',\n 'mvc/ui/ui-select-library',\n 'mvc/ui/ui-select-ftp',\n 'mvc/ui/ui-select-genomespace',\n 'mvc/ui/ui-color-picker'],\n function( Utils, Ui, SelectContent, SelectLibrary, SelectFtp, SelectGenomeSpace, ColorPicker ) {\n\n // create form view\n return Backbone.Model.extend({\n /** Available parameter types */\n types: {\n 'text' : '_fieldText',\n 'password' : '_fieldText',\n 'select' : '_fieldSelect',\n 'data_column' : '_fieldSelect',\n 'genomebuild' : '_fieldSelect',\n 'data' : '_fieldData',\n 'data_collection' : '_fieldData',\n 'integer' : '_fieldSlider',\n 'float' : '_fieldSlider',\n 'boolean' : '_fieldBoolean',\n 'drill_down' : '_fieldDrilldown',\n 'color' : '_fieldColor',\n 'hidden' : '_fieldHidden',\n 'hidden_data' : '_fieldHidden',\n 'baseurl' : '_fieldHidden',\n 'library_data' : '_fieldLibrary',\n 'ftpfile' : '_fieldFtp',\n 'upload' : '_fieldUpload',\n 'genomespacefile' : '_fieldGenomeSpace'\n },\n\n /** Returns an input field for a given field type */\n create: function( input_def ) {\n var fieldClass = this.types[ input_def.type ];\n var field = typeof( this[ fieldClass ] ) === 'function' ? this[ fieldClass ].call( this, input_def ) : null;\n if ( !field ) {\n field = input_def.options ? this._fieldSelect( input_def ) : this._fieldText( input_def );\n Galaxy.emit.debug('form-parameters::_addRow()', 'Auto matched field type (' + input_def.type + ').');\n }\n input_def.value === undefined && ( input_def.value = null );\n field.value( input_def.value );\n return field;\n },\n\n /** Data input field */\n _fieldData: function( input_def ) {\n return new SelectContent.View({\n id : 'field-' + input_def.id,\n extensions : input_def.extensions,\n optional : input_def.optional,\n multiple : input_def.multiple,\n type : input_def.type,\n flavor : input_def.flavor,\n data : input_def.options,\n onchange : input_def.onchange\n });\n },\n\n /** Select/Checkbox/Radio options field */\n _fieldSelect: function ( input_def ) {\n // show text field e.g. in workflow editor\n if( input_def.is_workflow ) {\n return this._fieldText( input_def );\n }\n\n // customize properties\n if ( input_def.type == 'data_column' ) {\n input_def.error_text = 'Missing columns in referenced dataset.'\n }\n\n // identify available options\n var data = input_def.data;\n if( !data ) {\n data = [];\n _.each( input_def.options, function( option ) {\n data.push( { label: option[ 0 ], value: option[ 1 ] } );\n });\n }\n\n // identify display type\n var SelectClass = Ui.Select;\n switch ( input_def.display ) {\n case 'checkboxes':\n SelectClass = Ui.Checkbox;\n break;\n case 'radio':\n SelectClass = Ui.Radio;\n break;\n case 'radiobutton':\n SelectClass = Ui.RadioButton;\n break;\n }\n\n // create select field\n return new SelectClass.View({\n id : 'field-' + input_def.id,\n data : data,\n error_text : input_def.error_text || 'No options available',\n multiple : input_def.multiple,\n optional : input_def.optional,\n onchange : input_def.onchange,\n individual : input_def.individual,\n searchable : input_def.flavor !== 'workflow'\n });\n },\n\n /** Drill down options field */\n _fieldDrilldown: function ( input_def ) {\n // show text field e.g. in workflow editor\n if( input_def.is_workflow ) {\n return this._fieldText( input_def );\n }\n\n // create drill down field\n return new Ui.Drilldown.View({\n id : 'field-' + input_def.id,\n data : input_def.options,\n display : input_def.display,\n optional : input_def.optional,\n onchange : input_def.onchange\n });\n },\n\n /** Text input field */\n _fieldText: function( input_def ) {\n // field replaces e.g. a select field\n if ( input_def.options && input_def.data ) {\n input_def.area = input_def.multiple;\n if ( Utils.isEmpty( input_def.value ) ) {\n input_def.value = null;\n } else {\n if ( $.isArray( input_def.value ) ) {\n var str_value = '';\n for ( var i in input_def.value ) {\n str_value += String( input_def.value[ i ] );\n if ( !input_def.multiple ) {\n break;\n }\n str_value += '\\n';\n }\n input_def.value = str_value;\n }\n }\n }\n // create input element\n return new Ui.Input({\n id : 'field-' + input_def.id,\n type : input_def.type,\n area : input_def.area,\n readonly : input_def.readonly,\n placeholder : input_def.placeholder,\n datalist : input_def.datalist,\n onchange : input_def.onchange\n });\n },\n\n /** Slider field */\n _fieldSlider: function( input_def ) {\n return new Ui.Slider.View({\n id : 'field-' + input_def.id,\n precise : input_def.type == 'float',\n is_workflow : input_def.is_workflow,\n min : input_def.min,\n max : input_def.max,\n onchange : input_def.onchange\n });\n },\n\n /** Hidden field */\n _fieldHidden: function( input_def ) {\n return new Ui.Hidden({\n id : 'field-' + input_def.id,\n info : input_def.info\n });\n },\n\n /** Boolean field */\n _fieldBoolean: function( input_def ) {\n return new Ui.RadioButton.View({\n id : 'field-' + input_def.id,\n data : [ { label : 'Yes', value : 'true' },\n { label : 'No', value : 'false' }],\n onchange : input_def.onchange\n });\n },\n\n /** Color picker field */\n _fieldColor: function( input_def ) {\n return new ColorPicker({\n id : 'field-' + input_def.id,\n onchange : input_def.onchange\n });\n },\n\n /** Library dataset field */\n _fieldLibrary: function( input_def ) {\n return new SelectLibrary.View({\n id : 'field-' + input_def.id,\n optional : input_def.optional,\n multiple : input_def.multiple,\n onchange : input_def.onchange\n });\n },\n\n /** FTP file field */\n _fieldFtp: function( input_def ) {\n return new SelectFtp.View({\n id : 'field-' + input_def.id,\n optional : input_def.optional,\n multiple : input_def.multiple,\n onchange : input_def.onchange\n });\n },\n\n /** GenomeSpace file select field\n */\n _fieldGenomeSpace: function( input_def ) {\n var self = this;\n return new SelectGenomeSpace.View({\n id : 'field-' + input_def.id,\n onchange : function() {\n self.app.trigger( 'change' );\n }\n });\n },\n\n /** Upload file field */\n _fieldUpload: function( input_def ) {\n return new Ui.Upload({\n id : 'field-' + input_def.id,\n onchange : input_def.onchange\n });\n }\n });\n\n return {\n View: View\n };\n});\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/form/form-parameters.js","/** This class creates a ui component which enables the dynamic creation of portlets */\ndefine( [ 'utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc' ],\nfunction( Utils, Portlet, Ui ) {\n var View = Backbone.View.extend({\n initialize: function( options ) {\n this.list = {};\n this.options = Utils.merge( options, {\n title : 'Repeat',\n empty_text : 'Not available.',\n max : null,\n min : null\n });\n this.button_new = new Ui.ButtonIcon({\n icon : 'fa-plus',\n title : 'Insert ' + this.options.title,\n tooltip : 'Add new ' + this.options.title + ' block',\n cls : 'ui-button-icon ui-clear-float form-repeat-add',\n onclick : function() { options.onnew && options.onnew() }\n });\n this.setElement( $( '' ).append( this.$list = $( '' ) )\n .append( $( '' ).append( this.button_new.$el ) ) );\n },\n\n /** Number of repeat blocks */\n size: function() {\n return _.size( this.list );\n },\n\n /** Add new repeat block */\n add: function( options ) {\n if ( !options.id || this.list[ options.id ] ) {\n Galaxy.emit.debug( 'form-repeat::add()', 'Duplicate or invalid repeat block id.' );\n return;\n }\n var button_delete = new Ui.ButtonIcon({\n icon : 'fa-trash-o',\n tooltip : 'Delete this repeat block',\n cls : 'ui-button-icon-plain form-repeat-delete',\n onclick : function() { options.ondel && options.ondel() }\n });\n var portlet = new Portlet.View({\n id : options.id,\n title : 'placeholder',\n cls : options.cls || 'ui-portlet-repeat',\n operations : { button_delete: button_delete }\n });\n portlet.append( options.$el );\n portlet.$el.addClass( 'section-row' ).hide();\n this.list[ options.id ] = portlet;\n this.$list.append( portlet.$el.fadeIn( 'fast' ) );\n this.options.max > 0 && this.size() >= this.options.max && this.button_new.disable();\n this._refresh();\n },\n\n /** Delete repeat block */\n del: function( id ) {\n if ( !this.list[ id ] ) {\n Galaxy.emit.debug( 'form-repeat::del()', 'Invalid repeat block id.' );\n return;\n }\n this.$list.find( '#' + id ).remove();\n delete this.list[ id ];\n this.button_new.enable();\n this._refresh();\n },\n\n /** Remove all */\n delAll: function() {\n for( var id in this.list ) {\n this.del( id );\n }\n },\n\n /** Hides add/del options */\n hideOptions: function() {\n this.button_new.$el.hide();\n _.each( this.list, function( portlet ) { portlet.hideOperation( 'button_delete' ) } );\n _.isEmpty( this.list ) && this.$el.append( $( '' ).addClass( 'ui-form-info' ).html( this.options.empty_text ) );\n },\n\n /** Refresh view */\n _refresh: function() {\n var index = 0;\n for ( var id in this.list ) {\n var portlet = this.list[ id ];\n portlet.title( ++index + ': ' + this.options.title );\n portlet[ this.size() > this.options.min ? 'showOperation' : 'hideOperation' ]( 'button_delete' );\n }\n }\n });\n\n return {\n View : View\n }\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/form/form-repeat.js","/**\n This class creates a form section and populates it with input elements. It also handles repeat blocks and conditionals by recursively creating new sub sections.\n*/\ndefine([ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-portlet', 'mvc/form/form-repeat', 'mvc/form/form-input', 'mvc/form/form-parameters' ],\nfunction( Utils, Ui, Portlet, Repeat, InputElement, Parameters ) {\n var View = Backbone.View.extend({\n initialize: function( app, options ) {\n this.app = app;\n this.inputs = options.inputs;\n this.parameters = new Parameters();\n this.setElement( $( '' ) );\n this.render();\n },\n\n /** Render section view */\n render: function() {\n var self = this;\n this.$el.empty();\n _.each( this.inputs, function( input ) { self.add( input ) } );\n },\n\n /** Add a new input element */\n add: function( input ) {\n var input_def = jQuery.extend( true, {}, input );\n input_def.id = input.id = Utils.uid();\n this.app.input_list[ input_def.id ] = input_def;\n switch( input_def.type ) {\n case 'conditional':\n this._addConditional( input_def );\n break;\n case 'repeat':\n this._addRepeat( input_def );\n break;\n case 'section':\n this._addSection( input_def );\n break;\n default:\n this._addRow( input_def );\n }\n },\n\n /** Add a conditional block */\n _addConditional: function( input_def ) {\n var self = this;\n input_def.test_param.id = input_def.id;\n this.app.model.get( 'sustain_conditionals' ) && ( input_def.test_param.disabled = true );\n var field = this._addRow( input_def.test_param );\n\n // set onchange event for test parameter\n field.model && field.model.set( 'onchange', function( value ) {\n var selectedCase = self.app.data.matchCase( input_def, value );\n for ( var i in input_def.cases ) {\n var case_def = input_def.cases[ i ];\n var section_row = self.$( '#' + input_def.id + '-section-' + i );\n var nonhidden = false;\n for ( var j in case_def.inputs ) {\n if ( !case_def.inputs[ j ].hidden ) {\n nonhidden = true;\n break;\n }\n }\n if ( i == selectedCase && nonhidden ) {\n section_row.fadeIn( 'fast' );\n } else {\n section_row.hide();\n }\n }\n self.app.trigger( 'change' );\n });\n\n // add conditional sub sections\n for ( var i in input_def.cases ) {\n var sub_section = new View( this.app, { inputs: input_def.cases[ i ].inputs } );\n this._append( sub_section.$el.addClass( 'ui-form-section' ), input_def.id + '-section-' + i );\n }\n\n // trigger refresh on conditional input field after all input elements have been created\n field.trigger( 'change' );\n },\n\n /** Add a repeat block */\n _addRepeat: function( input_def ) {\n var self = this;\n var block_index = 0;\n\n // create repeat block element\n var repeat = new Repeat.View({\n title : input_def.title || 'Repeat',\n min : input_def.min,\n max : input_def.max,\n onnew : function() { create( input_def.inputs ); self.app.trigger( 'change' ); }\n });\n\n // helper function to create new repeat blocks\n function create ( inputs ) {\n var sub_section_id = input_def.id + '-section-' + ( block_index++ );\n var sub_section = new View( self.app, { inputs: inputs } );\n repeat.add( { id : sub_section_id,\n $el : sub_section.$el,\n ondel : function() { repeat.del( sub_section_id ); self.app.trigger( 'change' ); } } );\n }\n\n //\n // add parsed/minimum number of repeat blocks\n //\n var n_cache = _.size( input_def.cache );\n for ( var i = 0; i < Math.max( Math.max( n_cache, input_def.min || 0 ), input_def.default || 0 ); i++ ) {\n create( i < n_cache ? input_def.cache[ i ] : input_def.inputs );\n }\n\n // hide options\n this.app.model.get( 'sustain_repeats' ) && repeat.hideOptions();\n\n // create input field wrapper\n var input_element = new InputElement( this.app, {\n label : input_def.title || input_def.name,\n help : input_def.help,\n field : repeat\n });\n this._append( input_element.$el, input_def.id );\n },\n\n /** Add a customized section */\n _addSection: function( input_def ) {\n var portlet = new Portlet.View({\n title : input_def.title || input_def.name,\n cls : 'ui-portlet-section',\n collapsible : true,\n collapsible_button : true,\n collapsed : !input_def.expanded\n });\n portlet.append( new View( this.app, { inputs: input_def.inputs } ).$el );\n portlet.append( $( '' ).addClass( 'ui-form-info' ).html( input_def.help ) );\n this.app.on( 'expand', function( input_id ) { ( portlet.$( '#' + input_id ).length > 0 ) && portlet.expand(); } );\n this._append( portlet.$el, input_def.id );\n },\n\n /** Add a single input field element */\n _addRow: function( input_def ) {\n var self = this;\n var id = input_def.id;\n input_def.onchange = input_def.onchange || function() { self.app.trigger( 'change', id ) };\n var field = this.parameters.create( input_def );\n this.app.field_list[ id ] = field;\n var input_element = new InputElement( this.app, {\n name : input_def.name,\n label : input_def.hide_label ? '' : input_def.label || input_def.name,\n value : input_def.value,\n text_value : input_def.text_value,\n collapsible_value : input_def.collapsible_value,\n collapsible_preview : input_def.collapsible_preview,\n help : input_def.help,\n argument : input_def.argument,\n disabled : input_def.disabled,\n color : input_def.color,\n style : input_def.style,\n backdrop : input_def.backdrop,\n hidden : input_def.hidden,\n fixed : input_def.fixed,\n field : field\n });\n this.app.element_list[ id ] = input_element;\n this._append( input_element.$el, input_def.id );\n return field;\n },\n\n /** Append a new element to the form i.e. input element, repeat block, conditionals etc. */\n _append: function( $el, id ) {\n this.$el.append( $el.addClass( 'section-row' ).attr( 'id', id ) );\n }\n });\n\n return {\n View: View\n };\n});\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/form/form-section.js","// dependencies\ndefine([], function() {\n\n// grid model\nreturn Backbone.Model.extend({\n defaults: {\n url_base: '',\n async: false,\n async_ops: [],\n categorical_filters: [],\n filters: {},\n sort_key: null,\n show_item_checkboxes: false,\n advanced_search: false,\n cur_page: 1,\n num_pages: 1,\n operation: undefined,\n item_ids: undefined\n },\n\n /**\n * Return true if operation can be done asynchronously.\n */\n can_async_op: function(op) {\n return _.indexOf(this.attributes.async_ops, op) !== -1;\n },\n\n /**\n * Add filtering criterion.\n */\n add_filter: function(key, value, append) {\n // Update URL arg with new condition. \n if (append) {\n // Update or append value.\n var cur_val = this.attributes.filters[key],\n new_val;\n if (cur_val === null || cur_val === undefined) {\n new_val = value;\n } else if (typeof(cur_val) == 'string') {\n if (cur_val == 'All' || cur_val == value) {\n new_val = value;\n } else {\n // Replace string with array.\n var values = [];\n values[0] = cur_val;\n values[1] = value;\n new_val = values;\n }\n } else {\n // Current value is an array.\n new_val = cur_val;\n if ( new_val.indexOf( value ) === -1 ) {\n new_val.push(value);\n }\n }\n this.attributes.filters[key] = new_val;\n } \n else {\n // Replace value.\n this.attributes.filters[key] = value;\n }\n },\n\n /**\n * Remove filtering criterion.\n */\n remove_filter: function(key, condition) {\n var cur_val = this.attributes.filters[key];\n if (cur_val === null || cur_val === undefined) {\n return false; \n }\n\n if (typeof(cur_val) === 'string') {\n // overwrite/remove condition.\n this.attributes.filters[key] = '';\n } else {\n // filter contains an array of conditions.\n var condition_index = _.indexOf(cur_val, condition);\n if (condition_index !== -1) {\n cur_val[condition_index] = '';\n }\n }\n },\n\n /**\n * Returns URL data for obtaining a new grid.\n */\n get_url_data: function() {\n var url_data = {\n async: this.attributes.async,\n sort: this.attributes.sort_key,\n page: this.attributes.cur_page,\n show_item_checkboxes: this.attributes.show_item_checkboxes,\n advanced_search: this.attributes.advanced_search\n };\n\n // Add operation, item_ids only if they have values.\n if (this.attributes.operation) {\n url_data.operation = this.attributes.operation;\n }\n if (this.attributes.item_ids) {\n url_data.id = this.attributes.item_ids;\n }\n\n // Add filter arguments to data, placing \"f-\" in front of all arguments.\n var self = this;\n _.each(_.pairs(self.attributes.filters), function(k) {\n url_data['f-' + k[0]] = k[1];\n });\n return url_data;\n },\n \n // Return URL for obtaining a new grid\n get_url: function (args) {\n return this.get('url_base') + '?' + $.param(this.get_url_data()) + '&' + $.param(args);\n }\n \n});\n\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/grid/grid-model.js","// dependencies\ndefine(['utils/utils'], function(Utils) {\n\n// grid view templates\nreturn {\n // template\n grid: function(options) {\n var tmpl = '';\n if (options.embedded) {\n tmpl = this.grid_header(options) + this.grid_table(options);\n } else {\n tmpl = '' +\n '' +\n '
' +\n this.grid_table(options);\n }\n \n // add info text\n if (options.info_text) {\n tmpl += '
';\n \n // add checkbox\n if (options.show_item_checkboxes) {\n tmpl += '';\n if (options.items.length > 0) {\n tmpl += '' +\n '';\n }\n tmpl += ' ';\n }\n \n // create header elements\n for (var i in options.columns) {\n var column = options.columns[i];\n if (column.visible) {\n tmpl += '';\n if (column.href) {\n tmpl += '' + column.label + '';\n } else {\n tmpl += column.label;\n }\n tmpl += '' + column.extra + '' +\n ' ';\n }\n }\n \n // finalize\n tmpl += ' ';\n \n // return template\n return tmpl;\n },\n \n // template\n body: function(options) {\n // initialize\n var tmpl = '';\n var num_rows_rendered = 0;\n var items_length = options.items.length;\n \n // empty grid?\n if (items_length == 0) {\n // No results.\n tmpl += 'No Items ';\n \n // Link\n if (link) {\n if (options.operations.length != 0) {\n tmpl += ' ';\n }\n }\n tmpl += '';\n num_rows_rendered++;\n }\n return tmpl;\n },\n\n // template\n footer: function(options) {\n \n // create template string\n var tmpl = '';\n \n // paging\n if (options.use_paging && options.num_pages > 1) {\n // get configuration\n var num_page_links = options.num_page_links;\n var cur_page_num = options.cur_page_num;\n var num_pages = options.num_pages;\n \n // First pass on min page.\n var page_link_range = num_page_links / 2;\n var min_page = cur_page_num - page_link_range\n var min_offset = 0;\n if (min_page <= 0) {\n // Min page is too low.\n min_page = 1;\n min_offset = page_link_range - ( cur_page_num - min_page );\n }\n \n // Set max page.\n var max_range = page_link_range + min_offset;\n var max_page = cur_page_num + max_range;\n var max_offset;\n if (max_page <= num_pages) {\n // Max page is fine.\n max_offset = 0;\n } else {\n // Max page is too high.\n max_page = num_pages;\n // +1 to account for the +1 in the loop below.\n max_offset = max_range - ( max_page + 1 - cur_page_num );\n }\n \n // Second and final pass on min page to add any unused\n // offset from max to min.\n if (max_offset != 0) {\n min_page -= max_offset\n if (min_page < 1) {\n min_page = 1\n }\n }\n \n // template header\n tmpl += '';\n if (options.show_item_checkboxes) {\n tmpl += '' +\n '' +\n 'Page:';\n \n if (min_page > 1) {\n tmpl += '1 ...';\n }\n \n // create page urls\n for (var page_index = min_page; page_index < max_page + 1; page_index++) {\n \n if (page_index == options.cur_page_num) {\n tmpl += '' + page_index + '';\n } else {\n tmpl += '' + page_index + '';\n }\n }\n \n // show last page\n if (max_page < num_pages) {\n tmpl += '...' +\n '' + num_pages + '';\n }\n tmpl += '';\n \n // Show all link\n tmpl += ' | Show All' +\n ' ' +\n ' ';\n }\n \n // Grid operations for multiple items.\n if (options.show_item_checkboxes) {\n // start template\n tmpl += '' +\n '' +\n '' +\n 'For selected items: ';\n \n // configure buttons for operations\n for (var i in options.operations) {\n var operation = options.operations[i];\n if (operation.allow_multiple) {\n tmpl += ' ';\n }\n }\n \n // finalize template\n tmpl += ' ' +\n ' ';\n }\n \n // count global operations\n var found_global = false;\n for (i in options.operations) {\n if (options.operations[i].global_operation) {\n found_global = true;\n break;\n }\n }\n \n // add global operations\n if (found_global) {\n tmpl += '' +\n '';\n for (i in options.operations) {\n var operation = options.operations[i];\n if (operation.global_operation) {\n tmpl += '' + operation.label + '';\n }\n }\n tmpl += ' ' +\n ' ';\n }\n \n // add legend\n if (options.legend) {\n tmpl += '' +\n '' + options.legend + ' ' +\n ' ';\n }\n \n // return\n return tmpl;\n },\n \n // template\n message: function(options) {\n var status = options.status == 'success' ? 'done' : options.status;\n return '';\n \n if (column.filterable == 'advanced') {\n tmpl += '' + column_label + ': ';\n }\n tmpl += '';\n if (column.is_text) {\n tmpl += '';\n } else {\n // filter criteria\n tmpl += '';\n \n // add category filters\n var seperator = false;\n for (var cf_label in options.categorical_filters[column_key]) {\n // get category filter\n var cf = options.categorical_filters[column_key][cf_label];\n \n // each filter will have only a single argument, so get that single argument\n var cf_key = '';\n var cf_arg = '';\n for (var key in cf) {\n cf_key = key;\n cf_arg = cf[key];\n }\n \n // add seperator\n if (seperator) {\n tmpl += ' | ';\n }\n seperator = true;\n \n // add category\n var filter = filters[column_key];\n if (filter && cf[column_key] && filter == cf_arg) {\n tmpl += '' + cf_label + '';\n } else {\n tmpl += '' +\n '' + cf_label + '' +\n '';\n }\n }\n tmpl += '';\n }\n tmpl += ' ' +\n ' ';\n \n // return template\n return tmpl;\n },\n \n // template for filter items\n filter_element: function(filter_key, filter_value) {\n filter_value = Utils.sanitize(filter_value);\n return '' + filter_value +\n '' +\n '' +\n '' +\n '';\n\n }\n};\n\n});\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/grid/grid-template.js","// Provides support for interacting with the GenomeSpace File Browser popup dialogue\ndefine([], function() {\n\n// tool form templates\nreturn {\n openFileBrowser: function( options ) {\n var GS_UI_URL = window.Galaxy.config.genomespace_ui_url;\n var GS_UPLOAD_URL = GS_UI_URL + 'upload/loadUrlToGenomespace.html?getLocation=true'\n\n var newWin = window.open(GS_UPLOAD_URL, \"GenomeSpace File Browser\", \"height=360px,width=600px\");\n \n successCalBack = options['successCallback'];\n window.addEventListener( \"message\", function (e) {\n successCalBack(e.data); \n }, false);\n \n newWin.focus();\n \n if (options['errorCallback'] != null) newWin.setCallbackOnGSUploadError = config['errorCallback']; \n }\n\n};\n\n});\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/tool/tool-genomespace.js","/** Renders the color picker used e.g. in the tool form **/\ndefine(['utils/utils'], function( Utils ) {\n return Backbone.View.extend({\n colors: {\n standard: ['c00000','ff0000','ffc000','ffff00','92d050','00b050','00b0f0','0070c0','002060','7030a0'],\n base : ['ffffff','000000','eeece1','1f497d','4f81bd','c0504d','9bbb59','8064a2','4bacc6','f79646'],\n theme :[['f2f2f2','7f7f7f','ddd9c3','c6d9f0','dbe5f1','f2dcdb','ebf1dd','e5e0ec','dbeef3','fdeada'],\n ['d8d8d8','595959','c4bd97','8db3e2','b8cce4','e5b9b7','d7e3bc','ccc1d9','b7dde8','fbd5b5'],\n ['bfbfbf','3f3f3f','938953','548dd4','95b3d7','d99694','c3d69b','b2a2c7','92cddc','fac08f'],\n ['a5a5a5','262626','494429','17365d','366092','953734','76923c','5f497a','31859b','e36c09'],\n ['7f7f7e','0c0c0c','1d1b10','0f243e','244061','632423','4f6128','3f3151','205867','974806']]\n },\n\n initialize : function( options ) {\n this.options = Utils.merge( options, {} );\n this.setElement( this._template() );\n this.$panel = this.$( '.ui-color-picker-panel' );\n this.$view = this.$( '.ui-color-picker-view' );\n this.$value = this.$( '.ui-color-picker-value' );\n this.$header = this.$( '.ui-color-picker-header' );\n this._build();\n this.visible = false;\n this.value( this.options.value );\n this.$boxes = this.$( '.ui-color-picker-box' );\n var self = this;\n this.$boxes.on( 'click', function() {\n self.value( $( this ).css( 'background-color' ) );\n self.$header.trigger( 'click' );\n } );\n this.$header.on( 'click', function() {\n self.visible = !self.visible;\n if ( self.visible ) {\n self.$view.fadeIn( 'fast' );\n } else {\n self.$view.fadeOut( 'fast' );\n }\n } );\n },\n\n /** Get/set value */\n value : function ( new_val ) {\n if ( new_val !== undefined && new_val !== null ) {\n this.$value.css( 'background-color', new_val );\n this.$( '.ui-color-picker-box' ).empty();\n this.$( this._getValue() ).html( this._templateCheck() );\n this.options.onchange && this.options.onchange( new_val );\n }\n return this._getValue();\n },\n\n /** Get value from dom */\n _getValue: function() {\n var rgb = this.$value.css( 'background-color' );\n rgb = rgb.match(/^rgb\\((\\d+),\\s*(\\d+),\\s*(\\d+)\\)$/);\n if ( rgb ) {\n function hex( x ) {\n return ( '0' + parseInt( x ).toString( 16 ) ).slice( -2 );\n }\n return '#' + hex( rgb[ 1] ) + hex( rgb[ 2 ] ) + hex( rgb[ 3 ] );\n } else {\n return null;\n }\n },\n\n /** Build color panel */\n _build: function() {\n this._content( { colors : this.colors.base } );\n for ( var i in this.colors.theme ) {\n var line_def = {};\n if ( i == 0 ) {\n line_def[ 'bottom' ] = true;\n } else if ( i != this.colors.theme.length - 1 ) {\n line_def[ 'top' ] = true;\n line_def[ 'bottom' ] = true;\n } else {\n line_def[ 'top' ] = true;\n }\n line_def[ 'colors' ] = this.colors.theme[ i ];\n this._content( line_def );\n }\n this._content( { colors : this.colors.standard } );\n },\n\n /** Create content */\n _content: function( options ) {\n var colors = options.colors;\n var $content = $( this._templateContent() );\n var $line = $content.find( '.line' );\n this.$panel.append( $content );\n for ( var i in colors ) {\n var $box = $( this._templateBox( colors[ i ] ) );\n if ( options.top ) {\n $box.css( 'border-top', 'none' );\n $box.css( 'border-top-left-radius', '0px' );\n $box.css( 'border-top-right-radius', '0px' );\n }\n if ( options.bottom ) {\n $box.css( 'border-bottom', 'none' );\n $box.css( 'border-bottom-left-radius', '0px' );\n $box.css( 'border-bottom-right-radius', '0px' );\n }\n $line.append( $box );\n }\n return $content;\n },\n\n /** Check icon */\n _templateCheck: function() {\n return '';\n },\n\n /** Content template */\n _templateContent: function() {\n return '
| ' +\n this.grid_header(options) +\n ' | ' +\n '' +\n ' | ' +\n ' |
| ' +\n ' | ' +\n ' | ' +\n ' |
' + options.info_text + '
';\n }\n \n // return\n return tmpl;\n },\n \n // template\n grid_table: function(options) {\n return '';\n },\n \n // template\n grid_header: function(options) {\n var tmpl = '';\n if (!options.embedded) {\n tmpl += '
'\n \n // return template\n return tmpl;\n },\n\n // template\n header: function(options) {\n \n // start\n var tmpl = '' + options.title + '
';\n }\n if (options.global_actions) {\n tmpl += '- ';\n var show_popup = (options.global_actions.length >= 3);\n if (show_popup) {\n tmpl += '
- Actions ' +\n '
- ' +\n '' + action.label + '' +\n ' ';\n }\n if (show_popup) {\n tmpl += '
';\n }\n for (var i in options.global_actions) {\n var action = options.global_actions[i];\n tmpl += '
';\n }\n tmpl += '';\n }\n tmpl += '' + value + '';\n if (options.operations.length != 0) {\n tmpl += '
';\n }\n } else {\n tmpl += '';\n }\n tmpl += '' +\n '
' + _.escape( options.message ) + '
' +\n '' +\n '';\n },\n \n // template\n grid_filters: function (options) {\n \n // get filters\n var default_filter_dict = options.default_filter_dict;\n var filters = options.filters;\n\n // show advanced search if flag set or if there are filters for advanced search fields\n var advanced_search_display = 'none';\n if (options.advanced_search) {\n advanced_search_display = 'block';\n }\n \n // identify columns with advanced filtering\n var show_advanced_search_link = false;\n for (var i in options.columns) {\n var column = options.columns[i];\n if (column.filterable == 'advanced') {\n var column_key = column.key;\n var f_key = filters[column_key];\n var d_key = default_filter_dict[column_key];\n if (f_key && d_key && f_key != d_key) {\n advanced_search_display = 'block';\n }\n show_advanced_search_link = true;\n }\n }\n \n // hide standard search if advanced is shown\n var standard_search_display = 'block';\n if (advanced_search_display == 'block') {\n standard_search_display = 'none';\n }\n\n //\n // standard search\n //\n var tmpl = '' +\n '' +\n '
' +\n '
';\n \n //\n // advanced search\n //\n tmpl += '| ' +\n ' | ' +\n '
| ';\n \n // show advanced search link in standard display\n if (show_advanced_search_link) {\n tmpl += 'Advanced Search';\n }\n \n // finalize standard search display\n tmpl += ' | ' +\n '
' +\n '' +\n '
' +\n '
';\n\n // return template\n return tmpl;\n },\n \n // template\n grid_column_filter: function(options, column) {\n \n // collect parameters\n var default_filter_dict = options.default_filter_dict;\n var filters = options.filters;\n var column_label = column.label;\n var column_key = column.key;\n if (column.filterable == 'advanced') {\n column_label = column_label.toLowerCase();\n }\n \n // start\n var tmpl = '| ' +\n 'Close Advanced Search' +\n ' | ' +\n '
' +\n '
' +\n '
';\n },\n\n /** Box template */\n _templateBox: function( color ) {\n return '';\n },\n\n /** Main template */\n _template: function() {\n return '' +\n '
' +\n '
' +\n '
' +\n 'Select a color
' +\n '' +\n '
';\n }\n });\n});\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/ui-color-picker.js","/** This class creates/wraps a drill down element. */\ndefine([ 'utils/utils', 'mvc/ui/ui-options' ], function( Utils, Options ) {\n\nvar View = Options.BaseIcons.extend({\n initialize: function( options ) {\n options.type = options.display || 'checkbox';\n options.multiple = ( options.type == 'checkbox' );\n Options.BaseIcons.prototype.initialize.call( this, options );\n },\n\n /** Set states for selected values */\n _setValue: function ( new_value ) {\n Options.BaseIcons.prototype._setValue.call( this, new_value );\n if ( new_value !== undefined && new_value !== null && this.header_index ) {\n var self = this;\n var values = $.isArray( new_value ) ? new_value : [ new_value ];\n _.each( values, function( v ) {\n var list = self.header_index[ v ];\n _.each( list, function( element ) {\n self._setState( element, true );\n });\n });\n }\n },\n\n /** Expand/collapse a sub group */\n _setState: function ( header_id, is_expanded ) {\n var $button = this.$( '.button-' + header_id );\n var $subgroup = this.$( '.subgroup-' + header_id );\n $button.data( 'is_expanded', is_expanded );\n if ( is_expanded ) {\n $subgroup.show();\n $button.removeClass( 'fa-plus-square' ).addClass( 'fa-minus-square' );\n } else {\n $subgroup.hide();\n $button.removeClass( 'fa-minus-square' ).addClass( 'fa-plus-square' );\n }\n },\n\n /** Template to create options tree */\n _templateOptions: function() {\n var self = this;\n this.header_index = {};\n\n // attach event handler\n function attach( $el, header_id ) {\n var $button = $el.find( '.button-' + header_id );\n $button.on( 'click', function() {\n self._setState( header_id, !$button.data( 'is_expanded' ) );\n });\n }\n\n // recursive function which iterates through options\n function iterate ( $tmpl, options, header ) {\n header = header || [];\n for (var i in options ) {\n var level = options[ i ];\n var has_options = level.options && level.options.length > 0;\n var new_header = header.slice( 0 );\n self.header_index[ level.value ] = new_header.slice( 0 );\n var $group = $( '' );\n if ( has_options ) {\n var header_id = Utils.uid();\n var $button = $( '' ).addClass( 'button-' + header_id ).addClass( 'ui-drilldown-button fa fa-plus-square' );\n var $subgroup = $( '' ).addClass( 'subgroup-' + header_id ).addClass( 'ui-drilldown-subgroup' );\n $group.append( $( '' )\n .append( $button )\n .append( self._templateOption( { label: level.name, value: level.value } ) ) );\n new_header.push( header_id );\n iterate ( $subgroup, level.options, new_header );\n $group.append( $subgroup );\n attach( $group, header_id );\n } else {\n $group.append( self._templateOption( { label: level.name, value: level.value } ) );\n }\n $tmpl.append( $group );\n }\n }\n\n // iterate through options and create dom\n var $tmpl = $( '' );\n iterate( $tmpl, this.model.get( 'data' ) );\n return $tmpl;\n },\n\n /** Template for drill down view */\n _template: function() {\n return $( '' ).addClass( 'ui-options-list drilldown-container' ).attr( 'id', this.model.id );\n }\n});\n\nreturn {\n View: View\n}\n\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/ui-drilldown.js","define([ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-select-default' ], function( Utils, Ui, Select ) {\n\n/** Batch mode variations */\nvar Batch = { DISABLED: 'disabled', ENABLED: 'enabled', LINKED: 'linked' };\n\n/** List of available content selectors options */\nvar Configurations = {\n data: [\n { src: 'hda', icon: 'fa-file-o', tooltip: 'Single dataset', multiple: false, batch: Batch.DISABLED },\n { src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.LINKED },\n { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.LINKED } ],\n data_multiple: [\n { src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.DISABLED },\n { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collections', multiple: true, batch: Batch.DISABLED } ],\n data_collection: [\n { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.DISABLED } ],\n workflow_data: [\n { src: 'hda', icon: 'fa-file-o', tooltip: 'Single dataset', multiple: false, batch: Batch.DISABLED } ],\n workflow_data_multiple: [\n { src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.DISABLED } ],\n workflow_data_collection: [\n { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.DISABLED } ],\n module_data: [\n { src: 'hda', icon: 'fa-file-o', tooltip: 'Single dataset', multiple: false, batch: Batch.DISABLED },\n { src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.ENABLED } ],\n module_data_collection: [\n { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.DISABLED },\n { src: 'hdca', icon: 'fa-folder', tooltip: 'Multiple collections', multiple: true, batch: Batch.ENABLED } ]\n};\n\n/** View for hda and hdca content selector ui elements */\nvar View = Backbone.View.extend({\n initialize : function( options ) {\n var self = this;\n this.model = options && options.model || new Backbone.Model({\n src_labels : { 'hda' : 'dataset', 'hdca': 'dataset collection' },\n pagelimit : 100,\n statustimer : 1000\n }).set( options );\n this.setElement( $( '' ).addClass( 'ui-select-content' ) );\n this.button_product = new Ui.RadioButton.View( {\n value : 'false',\n data : [ { icon: 'fa fa-chain', value: 'false',\n tooltip: 'Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads.' },\n { icon: 'fa fa-chain-broken', value: 'true',\n tooltip: 'Unlinked dataset inputs will be run against *all* other inputs.' } ] } );\n var $batch_div = $( '' ).addClass( 'ui-form-info' )\n .append( $( '' ).addClass( 'fa fa-sitemap' ) )\n .append( $( '' ).html( 'This is a batch mode input field. Separate jobs will be triggered for each dataset selection.' ) );\n this.$batch = {\n linked : $batch_div.clone(),\n enabled : $batch_div.clone().append( $( '' )\n .append( $( '' ).addClass( 'ui-form-title' ).html( 'Batch options:' ) )\n .append( this.button_product.$el ) )\n .append( $( '' ).css( 'clear', 'both' ) )\n };\n\n // add drag-drop event handlers\n this.$el.on( 'dragenter', function( e ) { this.lastenter = e.target; self.$el.addClass( 'ui-dragover' ); } )\n .on( 'dragover', function( e ) { e.preventDefault(); } )\n .on( 'dragleave', function( e ) { this.lastenter === e.target && self.$el.removeClass( 'ui-dragover' ); } )\n .on( 'drop', function( e ) { self._handleDrop( e ); } );\n\n // track current history elements\n this.history = {};\n\n // add listeners\n this.listenTo( this.model, 'change:data', this._changeData, this );\n this.listenTo( this.model, 'change:wait', this._changeWait, this );\n this.listenTo( this.model, 'change:current', this._changeCurrent, this );\n this.listenTo( this.model, 'change:value', this._changeValue, this );\n this.listenTo( this.model, 'change:type change:optional change:multiple change:extensions', this._changeType, this );\n this.render();\n\n // add change event\n this.on( 'change', function() { options.onchange && options.onchange( self.value() ) } );\n },\n\n render: function() {\n this._changeType();\n this._changeValue();\n this._changeWait();\n },\n\n /** Indicate that select fields are being updated */\n wait: function() {\n this.model.set( 'wait', true );\n },\n\n /** Indicate that the options update has been completed */\n unwait: function() {\n this.model.set( 'wait', false );\n },\n\n /** Update data representing selectable options */\n update: function( options ) {\n this.model.set( 'data', options );\n },\n\n /** Return the currently selected dataset values */\n value: function ( new_value ) {\n new_value !== undefined && this.model.set( 'value', new_value );\n var current = this.model.get( 'current' );\n if ( this.config[ current ] ) {\n var id_list = this.fields[ current ].value();\n if (id_list !== null) {\n id_list = $.isArray( id_list ) ? id_list : [ id_list ];\n if ( id_list.length > 0 ) {\n var result = this._batch( { values: [] } );\n for ( var i in id_list ) {\n var details = this.history[ id_list[ i ] + '_' + this.config[ current ].src ];\n if ( details ) {\n result.values.push( details );\n } else {\n Galaxy.emit.debug( 'ui-select-content::value()', 'Requested details not found for \\'' + id_list[ i ] + '\\'.' );\n return null;\n }\n }\n result.values.sort( function( a, b ) { return a.hid - b.hid } );\n return result;\n }\n }\n } else {\n Galaxy.emit.debug( 'ui-select-content::value()', 'Invalid value/source \\'' + new_value + '\\'.' );\n }\n return null;\n },\n\n /** Change of current select field */\n _changeCurrent: function() {\n var self = this;\n _.each( this.fields, function( field, i ) {\n if ( self.model.get( 'current' ) == i ) {\n field.$el.show();\n _.each( self.$batch, function( $batchfield, batchmode ) {\n $batchfield[ self.config[ i ].batch == batchmode ? 'show' : 'hide' ]();\n });\n self.button_type.value( i );\n } else {\n field.$el.hide();\n }\n });\n },\n\n /** Change of type */\n _changeType: function() {\n var self = this;\n\n // identify selector type identifier i.e. [ flavor ]_[ type ]_[ multiple ]\n var config_id = ( this.model.get( 'flavor' ) ? this.model.get( 'flavor' ) + '_' : '' ) +\n String( this.model.get( 'type' ) ) + ( this.model.get( 'multiple' ) ? '_multiple' : '' );\n if ( Configurations[ config_id ] ) {\n this.config = Configurations[ config_id ];\n } else {\n this.config = Configurations[ 'data' ];\n Galaxy.emit.debug( 'ui-select-content::_changeType()', 'Invalid configuration/type id \\'' + config_id + '\\'.' );\n }\n\n // prepare extension component of error message\n var data = self.model.get( 'data' );\n var extensions = Utils.textify( this.model.get( 'extensions' ) );\n var src_labels = this.model.get( 'src_labels' );\n\n // build views\n this.fields = [];\n this.button_data = [];\n _.each( this.config, function( c, i ) {\n self.button_data.push({\n value : i,\n icon : c.icon,\n tooltip : c.tooltip\n });\n self.fields.push(\n new Select.View({\n optional : self.model.get( 'optional' ),\n multiple : c.multiple,\n searchable : !c.multiple || ( data && data[ c.src ] && data[ c.src ].length > self.model.get( 'pagelimit' ) ),\n individual : true,\n error_text : 'No ' + ( extensions ? extensions + ' ' : '' ) + ( src_labels[ c.src ] || 'content' ) + ' available.',\n onchange : function() {\n self.trigger( 'change' );\n }\n })\n );\n });\n this.button_type = new Ui.RadioButton.View({\n value : this.model.get( 'current' ),\n data : this.button_data,\n onchange: function( value ) {\n self.model.set( 'current', value );\n self.trigger( 'change' );\n }\n });\n\n // append views\n this.$el.empty();\n var button_width = 0;\n if ( this.fields.length > 1 ) {\n this.$el.append( this.button_type.$el );\n button_width = Math.max( 0, this.fields.length * 36 ) + 'px';\n }\n _.each( this.fields, function( field ) {\n self.$el.append( field.$el.css( { 'margin-left': button_width } ) );\n });\n _.each( this.$batch, function( $batchfield, batchmode ) {\n self.$el.append( $batchfield.css( { 'margin-left': button_width } ) );\n });\n this.model.set( 'current', 0 );\n this._changeCurrent();\n this._changeData();\n },\n\n /** Change of wait flag */\n _changeWait: function() {\n var self = this;\n _.each( this.fields, function( field ) { field[ self.model.get( 'wait' ) ? 'wait' : 'unwait' ]() } );\n },\n\n /** Change of available options */\n _changeData: function() {\n var options = this.model.get( 'data' );\n var self = this;\n var select_options = {};\n _.each( options, function( items, src ) {\n select_options[ src ] = [];\n _.each( items, function( item ) {\n select_options[ src ].push({\n hid : item.hid,\n keep : item.keep,\n label: item.hid + ': ' + item.name,\n value: item.id,\n tags : item.tags\n });\n self.history[ item.id + '_' + src ] = item;\n });\n });\n _.each( this.config, function( c, i ) {\n select_options[ c.src ] && self.fields[ i ].add( select_options[ c.src ], function( a, b ) { return b.hid - a.hid } );\n });\n },\n\n /** Change of incoming value */\n _changeValue: function () {\n var new_value = this.model.get( 'value' );\n if ( new_value && new_value.values && new_value.values.length > 0 ) {\n // create list with content ids\n var list = [];\n _.each( new_value.values, function( value ) {\n list.push( value.id );\n });\n // sniff first suitable field type from config list\n var src = new_value.values[ 0 ].src;\n var multiple = new_value.values.length > 1;\n for( var i = 0; i < this.config.length; i++ ) {\n var field = this.fields[ i ];\n var c = this.config[ i ];\n if ( c.src == src && [ multiple, true ].indexOf( c.multiple ) !== -1 ) {\n this.model.set( 'current', i );\n field.value( list );\n break;\n }\n }\n } else {\n _.each( this.fields, function( field ) {\n field.value( null );\n });\n }\n },\n\n /** Handles drop events e.g. from history panel */\n _handleDrop: function( ev ) {\n try {\n var data = this.model.get( 'data' );\n var current = this.model.get( 'current' );\n var config = this.config[ current ];\n var field = this.fields[ current ];\n var drop_data = JSON.parse( ev.originalEvent.dataTransfer.getData( 'text' ) )[ 0 ];\n var new_id = drop_data.id;\n var new_src = drop_data.history_content_type == 'dataset' ? 'hda' : 'hdca';\n var new_value = { id: new_id, src: new_src };\n if ( data && _.findWhere( data[ new_src ], new_value ) ) {\n if ( config.src == new_src ) {\n var current_value = field.value();\n if ( current_value && config.multiple ) {\n if ( current_value.indexOf( new_id ) == -1 ) {\n current_value.push( new_id );\n }\n } else {\n current_value = new_id;\n }\n field.value( current_value );\n } else {\n this.model.set( 'value', { values: [ new_value ] } );\n this.model.trigger( 'change:value' );\n }\n this.trigger( 'change' );\n this._handleDropStatus( 'success' );\n } else {\n this._handleDropStatus( 'danger' );\n }\n } catch( e ) {\n this._handleDropStatus( 'danger' );\n }\n ev.preventDefault();\n },\n\n /** Highlight drag result */\n _handleDropStatus: function( status ) {\n var self = this;\n this.$el.removeClass( 'ui-dragover' ).addClass( 'ui-dragover-' + status );\n setTimeout( function() { self.$el.removeClass( 'ui-dragover-' + status ) }, this.model.get( 'statustimer' ) );\n },\n\n /** Assists in identifying the batch mode */\n _batch: function( result ) {\n result[ 'batch' ] = false;\n var current = this.model.get( 'current' );\n var config = this.config[ current ];\n if ( config.src == 'hdca' && !config.multiple ) {\n var hdca = this.history[ this.fields[ current ].value() + '_hdca' ];\n if ( hdca && hdca.map_over_type ) {\n result[ 'batch' ] = true;\n }\n }\n if ( config.batch == Batch.LINKED || config.batch == Batch.ENABLED ) {\n result[ 'batch' ] = true;\n if ( config.batch == Batch.ENABLED && this.button_product.value() === 'true' ) {\n result[ 'product' ] = true;\n }\n }\n return result;\n }\n});\n\nreturn {\n View: View\n}\n\n});\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/ui-select-content.js","// dependencies\ndefine(['utils/utils', 'mvc/ui/ui-list'],\n function(Utils, List) {\n\n/**\n * FTP file selector\n */\nvar View = Backbone.View.extend({\n // initialize\n initialize : function(options) {\n // link this\n var self = this;\n\n // create ui-list view to keep track of selected ftp files\n this.ftpfile_list = new List.View({\n name : 'file',\n optional : options.optional,\n multiple : options.multiple,\n onchange : function() {\n options.onchange && options.onchange(self.value());\n }\n });\n\n // create elements\n this.setElement(this.ftpfile_list.$el);\n\n // initial fetch of ftps\n Utils.get({\n url : Galaxy.root + 'api/remote_files',\n success : function(response) {\n var data = [];\n for (var i in response) {\n data.push({\n value : response[i]['path'],\n label : response[i]['path']\n });\n }\n self.ftpfile_list.update(data);\n }\n });\n },\n\n /** Return/Set currently selected ftp datasets */\n value: function(val) {\n return this.ftpfile_list.value(val);\n }\n});\n\nreturn {\n View: View\n}\n\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/ui-select-ftp.js","// dependencies\ndefine(['utils/utils', 'mvc/ui/ui-misc', 'mvc/tool/tool-genomespace'],\n function(Utils, Ui, GenomespaceBrowser) {\n\n/**\n * GenomeSpace file selector\n */\nvar View = Backbone.View.extend({\n // initialize\n initialize : function(options) {\n\n // link this\n var self = this;\n\n // create insert new list element button\n this.browse_button = new Ui.ButtonIcon({\n title : 'Browse',\n icon : 'fa fa-sign-in',\n tooltip : 'Browse GenomeSpace',\n onclick : function() {\n self.browseGenomeSpace();\n }\n });\n\n // create genomespace filepath textbox\n this.filename_textbox = new Ui.Input();\n\n // create genomespace token textbox\n this.token_textbox = new Ui.Input({\n type : 'password' \n });\n\n // create elements\n this.setElement(this._template(options));\n this.$('.ui-gs-browse-button').append(this.browse_button.$el);\n this.$('.ui-gs-filename-textbox').append(this.filename_textbox.$el);\n this.$('.ui-gs-token-textbox').append(this.token_textbox.$el);\n },\n\n /** Browse GenomeSpace */\n browseGenomeSpace: function(options) {\n var self = this;\n GenomespaceBrowser.openFileBrowser({\n successCallback: function(data) {\n self.value(data.destination + \"^\" + data.token);\n }\n });\n },\n \n /** Main Template */\n _template: function(options) {\n return '' +\n '
'\n '' +\n '
';\n },\n \n /** Return/Set currently selected genomespace filename/token */\n value : function (new_value) {\n // check if new_value is defined\n if (new_value !== undefined) {\n this._setValue(new_value);\n }\n else {\n return this._getValue();\n }\n },\n \n // get value\n _getValue: function() {\n return this.filename_textbox.value() +\n \"^\" + this.token_textbox.value();\n },\n \n // set value\n _setValue: function(new_value) {\n if (new_value) {\n values = new_value.split(\"^\");\n this.filename_textbox.value(values[0]);\n this.token_textbox.value(values[1]);\n }\n },\n \n});\n\nreturn {\n View: View\n}\n\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/ui-select-genomespace.js","// dependencies\ndefine(['utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-table', 'mvc/ui/ui-list'],\n function(Utils, Ui, Table, List) {\n\n// collection of libraries\nvar Libraries = Backbone.Collection.extend({\n url: Galaxy.root + 'api/libraries?deleted=false'\n});\n\n// collection of dataset\nvar LibraryDatasets = Backbone.Collection.extend({\n initialize: function() {\n var self = this;\n this.config = new Backbone.Model({ library_id: null });\n this.config.on('change', function() {\n self.fetch({ reset: true });\n });\n },\n url: function() {\n return Galaxy.root + 'api/libraries/' + this.config.get('library_id') + '/contents';\n }\n});\n\n// hda/hdca content selector ui element\nvar View = Backbone.View.extend({\n // initialize\n initialize : function(options) {\n // link this\n var self = this;\n\n // collections\n this.libraries = new Libraries();\n this.datasets = new LibraryDatasets();\n\n // link app and options\n this.options = options;\n\n // select field for the library\n // TODO: Remove this once the library API supports searching for library datasets\n this.library_select = new Ui.Select.View({\n onchange : function(value) {\n self.datasets.config.set('library_id', value);\n }\n });\n\n // create ui-list view to keep track of selected data libraries\n this.dataset_list = new List.View({\n name : 'dataset',\n optional : options.optional,\n multiple : options.multiple,\n onchange : function() {\n self.trigger('change');\n }\n });\n\n // add reset handler for fetched libraries\n this.libraries.on('reset', function() {\n var data = [];\n self.libraries.each(function(model) {\n data.push({\n value : model.id,\n label : model.get('name')\n });\n });\n self.library_select.update(data);\n });\n\n // add reset handler for fetched library datasets\n this.datasets.on('reset', function() {\n var data = [];\n var library_current = self.library_select.text();\n if (library_current !== null) {\n self.datasets.each(function(model) {\n if (model.get('type') === 'file') {\n data.push({\n value : model.id,\n label : model.get('name')\n });\n }\n });\n }\n self.dataset_list.update(data);\n });\n\n // add change event. fires on trigger\n this.on('change', function() {\n options.onchange && options.onchange(self.value());\n });\n\n // create elements\n this.setElement(this._template());\n this.$('.library-select').append(this.library_select.$el);\n this.$el.append(this.dataset_list.$el);\n\n // initial fetch of libraries\n this.libraries.fetch({\n reset: true,\n success: function() {\n self.library_select.trigger('change');\n if (self.options.value !== undefined) {\n self.value(self.options.value);\n }\n }\n });\n },\n\n /** Return/Set currently selected library datasets */\n value: function(val) {\n return this.dataset_list.value(val);\n },\n\n /** Template */\n _template: function() {\n return '' +\n '' +\n '' +\n '
' +\n '' +\n '
' +\n 'Token
' +\n '' +\n '' +\n '
';\n }\n});\n\nreturn {\n View: View\n}\n\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/ui-select-library.js","define([ 'utils/utils' ], function( Utils ) {\n var View = Backbone.View.extend({\n initialize : function( options ) {\n var self = this;\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n min : null,\n max : null,\n step : null,\n precise : false,\n split : 10000,\n value : null,\n onchange : function(){}\n }).set( options );\n\n // create new element\n this.setElement( this._template() );\n this.$el.attr( 'id', this.model.id );\n this.$text = this.$( '.ui-form-slider-text' );\n this.$slider = this.$( '.ui-form-slider-element' );\n\n // add text field event\n var pressed = [];\n this.$text.on( 'change', function () {\n self.value( $( this ).val() );\n }).on( 'keyup', function( e ) {\n pressed[e.which] = false;\n }).on( 'keydown', function ( e ) {\n var v = e.which;\n pressed[ v ] = true;\n if ( self.model.get( 'is_workflow' ) && pressed[ 16 ] && v == 52 ) {\n self.value( '$' );\n event.preventDefault();\n } else if (!( v == 8 || v == 9 || v == 13 || v == 37 || v == 39 || ( v >= 48 && v <= 57 && !pressed[ 16 ] ) || ( v >= 96 && v <= 105 )\n || ( ( v == 190 || v == 110 ) && $( this ).val().indexOf( '.' ) == -1 && self.model.get( 'precise' ) )\n || ( ( v == 189 || v == 109 ) && $( this ).val().indexOf( '-' ) == -1 )\n || self._isParameter( $( this ).val() )\n || pressed[ 91 ] || pressed[ 17 ] ) ) {\n event.preventDefault();\n }\n });\n\n // build slider, cannot be rebuild in render\n var opts = this.model.attributes;\n this.has_slider = opts.max !== null && opts.min !== null && opts.max > opts.min;\n var step = opts.step;\n if ( !step ) {\n if ( opts.precise && this.has_slider ) {\n step = ( opts.max - opts.min ) / opts.split;\n } else {\n step = 1.0;\n }\n }\n if ( this.has_slider ) {\n this.$text.addClass( 'ui-form-slider-left' );\n this.$slider.slider( { min: opts.min, max: opts.max, step: step } )\n .on( 'slide', function ( event, ui ) { self.value( ui.value ) } );\n } else {\n this.$slider.hide();\n }\n\n // add listeners\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render: function() {\n var value = this.model.get( 'value' );\n this.has_slider && this.$slider.slider( 'value', value );\n value !== this.$text.val() && this.$text.val( value );\n },\n\n /** Set and return the current value */\n value : function ( new_val ) {\n var options = this.model.attributes;\n if ( new_val !== undefined ) {\n if ( new_val !== null && new_val !== '' && !this._isParameter( new_val ) ) {\n isNaN( new_val ) && ( new_val = 0 );\n !options.precise && ( new_val = Math.round( new_val ) );\n options.max !== null && ( new_val = Math.min( new_val, options.max ) );\n options.min !== null && ( new_val = Math.max( new_val, options.min ) );\n }\n this.model.set( 'value', new_val );\n this.model.trigger( 'change' );\n options.onchange( new_val );\n }\n return this.model.get( 'value' );\n },\n\n /** Return true if the field contains a workflow parameter i.e. $('name') */\n _isParameter: function( value ) {\n return this.model.get( 'is_workflow' ) && String( value ).substring( 0, 1 ) === '$';\n },\n\n /** Slider template */\n _template: function() {\n return '' +\n 'Select Library' +\n '' +\n '
' +\n '' +\n '' +\n '';\n }\n });\n\n return {\n View : View\n };\n});\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/ui/ui-slider.js","var jQuery = require( 'jquery' ),\n $ = jQuery,\n QUERY_STRING = require( 'utils/query-string-parsing' ),\n Ui = require( 'mvc/ui/ui-misc' );\n\nvar Router = Backbone.Router.extend({\n // TODO: not many client routes at this point - fill and remove from server.\n // since we're at root here, this may be the last to be routed entirely on the client.\n initialize : function( page, options ){\n this.page = page;\n this.options = options;\n },\n\n /** helper to push a new navigation state */\n push: function( url, data ) {\n data = data || {};\n data.__identifer = Math.random().toString( 36 ).substr( 2 );\n if ( !$.isEmptyObject( data ) ) {\n url += url.indexOf( '?' ) == -1 ? '?' : '&';\n url += $.param( data , true );\n }\n Galaxy.params = {};\n this.navigate( url, { 'trigger': true } );\n },\n\n /** override to parse query string into obj and send to each route */\n execute: function( callback, args, name ){\n Galaxy.debug( 'router execute:', callback, args, name );\n var queryObj = QUERY_STRING.parse( args.pop() );\n args.push( queryObj );\n if( callback ){\n if ( this.authenticate( args, name ) ) {\n callback.apply( this, args );\n } else {\n this.access_denied();\n }\n }\n },\n\n authenticate: function( args, name ) {\n return true;\n },\n\n access_denied: function() {\n this.page.display( new Ui.Message( { status: 'danger', message: 'You must be logged in with proper credentials to make this request.', persistent: true } ) );\n }\n});\n\nmodule.exports = Router\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/layout/router.js","/** Generic form view */\ndefine( [ 'mvc/form/form-view', 'mvc/ui/ui-misc' ], function( Form, Ui ) {\n\n var View = Backbone.View.extend({\n\n initialize: function( options ) {\n this.model = new Backbone.Model( options );\n this.url = this.model.get( 'url' );\n this.redirect = this.model.get( 'redirect' );\n this.setElement( '' );\n this.render();\n },\n\n render: function() {\n var self = this;\n $.ajax({\n url : Galaxy.root + this.url,\n type : 'GET'\n }).done( function( response ) {\n var options = $.extend( {}, self.model.attributes, response );\n var form = new Form({\n title : options.title,\n message: options.message,\n status : options.status || 'warning',\n icon : options.icon,\n inputs : options.inputs,\n buttons: {\n 'submit': new Ui.Button({\n tooltip : options.submit_tooltip,\n title : options.submit_title || 'Save',\n icon : options.submit_icon || 'fa-save',\n cls : 'btn btn-primary ui-clear-float',\n onclick : function() { self._submit( form ) }\n })\n }\n });\n self.$el.empty().append( form.$el );\n }).fail( function( response ) {\n self.$el.empty().append( new Ui.Message({\n message : 'Failed to load resource ' + self.url + '.',\n status : 'danger',\n persistent : true\n }).$el );\n });\n },\n\n _submit: function( form ) {\n var self = this;\n $.ajax( {\n url : Galaxy.root + self.url,\n data : JSON.stringify( form.data.create() ),\n type : 'PUT',\n contentType : 'application/json'\n }).done( function( response ) {\n var success_message = { message: response.message, status: 'success', persistent: false };\n if ( self.redirect ) {\n window.location = Galaxy.root + self.redirect + '?' + $.param( success_message );\n } else {\n form.data.matchModel( response, function ( input, input_id ) {\n form.field_list[ input_id ].value( input.value );\n });\n self._showMessage( form, success_message );\n }\n }).fail( function( response ) {\n self._showMessage( form, { message: response.responseJSON.err_msg, status: 'danger', persistent: false } );\n });\n },\n\n _showMessage: function( form, options ) {\n var $panel = form.$el.parents().filter(function() {\n return [ 'auto', 'scroll' ].indexOf( $( this ).css( 'overflow' ) ) != -1;\n }).first();\n $panel.animate( { scrollTop : 0 }, 500 );\n form.message.update( options );\n }\n });\n\n return {\n View : View\n };\n});\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/mvc/form/form-wrapper.js","var _l = require( 'utils/localization' );\n\nvar AdminPanel = Backbone.View.extend({\n initialize: function( page, options ) {\n var self = this;\n this.page = page;\n this.root = options.root;\n this.config = options.config;\n this.settings = options.settings;\n this.message = options.message;\n this.status = options.status;\n this.model = new Backbone.Model({\n title : _l( 'Administration' )\n });\n this.categories = new Backbone.Collection([{\n title : 'Server',\n items : [ {\n title : 'Data types registry',\n url : 'admin/view_datatypes_registry'\n },{\n title : 'Data tables registry',\n url : 'admin/view_tool_data_tables'\n },{\n title : 'Display applications',\n url : 'admin/display_applications'\n },{\n title : 'Manage jobs',\n url : 'admin/jobs'\n } ]\n },{\n title : 'Tools and Tool Shed',\n items : [ {\n title : 'Search Tool Shed',\n url : 'admin_toolshed/browse_tool_sheds',\n enabled : self.settings.is_tool_shed_installed\n },{\n title : 'Search Tool Shed (Beta)',\n url : 'admin_toolshed/browse_toolsheds',\n enabled : self.settings.is_tool_shed_installed && self.config.enable_beta_ts_api_install\n },{\n title : 'Monitor installing repositories',\n url : 'admin_toolshed/monitor_repository_installation?installing_repository_ids=' + self.settings.installing_repository_ids,\n enabled : self.settings.installing_repository_ids\n },{\n title : 'Manage installed tools',\n url : 'admin_toolshed/browse_repositories',\n enabled : self.settings.is_repo_installed\n },{\n title : 'Reset metadata',\n url : 'admin_toolshed/reset_metadata_on_selected_installed_repositories',\n enabled : self.settings.is_repo_installed\n },{\n title : 'Download local tool',\n url : 'admin/package_tool'\n },{\n title : 'Tool lineage',\n url : 'admin/tool_versions',\n target : '__use_router__'\n },{\n title : 'Reload a tool\\'s configuration',\n url : 'admin/reload_tool'\n },{\n title : 'Review tool migration stages',\n url : 'admin/review_tool_migration_stages'\n },{\n title : 'View Tool Error Logs',\n url : 'admin/tool_errors'\n },{\n title : 'Manage Display Whitelist',\n url : 'admin/sanitize_whitelist'\n },{\n title : 'Manage Tool Dependencies',\n url : 'admin/manage_tool_dependencies'\n } ]\n },{\n title : 'User Management',\n items : [ {\n title : 'Users',\n url : 'admin/users',\n target : '__use_router__'\n },{\n title : 'Groups',\n url : 'admin/groups',\n target : '__use_router__'\n },{\n title : 'Roles',\n url : 'admin/roles',\n target : '__use_router__'\n },{\n title : 'API keys',\n url : 'userskeys/all_users'\n },{\n title : 'Impersonate a user',\n url : 'admin/impersonate',\n enabled : self.config.allow_user_impersonation\n } ]\n },{\n title : 'Data',\n items : [ {\n title : 'Quotas',\n url : 'admin/quotas',\n target : '__use_router__',\n enabled : self.config.enable_quotas\n },{\n title : 'Data libraries',\n url : 'library_admin/browse_libraries'\n },{\n title : 'Roles',\n url : 'admin/roles',\n target : '__use_router__'\n },{\n title : 'Local data',\n url : 'data_manager'\n } ]\n },{\n title : 'Form Definitions',\n items : [ {\n title : 'Form definitions',\n url : 'forms/browse_form_definitions'\n } ]\n },{\n title : 'Sample Tracking',\n items : [ {\n title : 'Sequencers and external services',\n url : 'external_service/browse_external_services'\n },{\n title : 'Request types',\n url : 'request_type/browse_request_types'\n },{\n title : 'Sequencing requests',\n url : 'requests_admin/browse_requests'\n },{\n title : 'Find samples',\n url : 'requests_common/find_samples?cntrller=requests_admin'\n } ]\n }]);\n this.setElement( this._template() );\n },\n\n render : function() {\n var self = this;\n this.$el.empty();\n this.categories.each( function( category ) {\n var $section = $( self._templateSection( category.attributes ) );\n var $entries = $section.find( '.ui-side-section-body' );\n _.each( category.get( 'items' ), function( item ) {\n if ( item.enabled === undefined || item.enabled ) {\n var $link = $( '' ).attr( { href : self.root + item.url } ).text( _l( item.title ) );\n if ( item.target == '__use_router__' ) {\n $link.on( 'click', function( e ) { e.preventDefault(); self.page.router.push( item.url ); } );\n } else {\n $link.attr( 'target', 'galaxy_main' );\n }\n $entries.append( $( '' ).addClass( 'ui-side-section-body-title' ).append( $link ) );\n }\n });\n self.$el.append( $section );\n });\n this.page.$( '#galaxy_main' ).prop( 'src', this.root + 'admin/center?message=' + this.message + '&status=' + this.status );\n },\n\n _templateSection : function( options ) {\n return [\n '
',\n '
' + _l( options.title ) + '
',\n '',\n '
'\n ].join('');\n },\n\n _template : function() {\n return '';\n },\n\n toString : function() { return 'adminPanel' }\n});\n\nmodule.exports = AdminPanel;\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/apps/panels/admin-panel.js"],"sourceRoot":""}
\ No newline at end of file
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0 */\n/***/ function(module, exports, __webpack_require__) {\n\n\t/* WEBPACK VAR INJECTION */(function(_) {var jQuery = __webpack_require__(1),\n\t $ = jQuery,\n\t GalaxyApp = __webpack_require__(52).GalaxyApp,\n\t AdminPanel = __webpack_require__(102),\n\t FormWrapper = __webpack_require__(62),\n\t GridView = __webpack_require__(12),\n\t Ui = __webpack_require__(5),\n\t QueryStringParsing = __webpack_require__(26),\n\t Router = __webpack_require__(55),\n\t Utils = __webpack_require__(4),\n\t Page = __webpack_require__(53);\n\t\n\twindow.app = function app(options, bootstrapped) {\n\t window.Galaxy = new GalaxyApp(options, bootstrapped);\n\t Galaxy.debug('admin app');\n\t\n\t /** Routes */\n\t var AdminRouter = Router.extend({\n\t routes: {\n\t '(/)admin(/)users': 'show_users',\n\t '(/)admin(/)roles': 'show_roles',\n\t '(/)admin(/)groups': 'show_groups',\n\t '(/)admin(/)tool_versions': 'show_tool_versions',\n\t '(/)admin(/)quotas': 'show_quotas',\n\t '(/)admin(/)forms(/)(:form_id)': 'show_forms'\n\t },\n\t\n\t authenticate: function (args, name) {\n\t return Galaxy.user && Galaxy.user.id && Galaxy.user.get('is_admin');\n\t },\n\t\n\t show_users: function () {\n\t this.page.display(new GridView({ url_base: Galaxy.root + 'admin/users_list', url_data: Galaxy.params, dict_format: true }));\n\t },\n\t\n\t show_roles: function () {\n\t this.page.display(new GridView({ url_base: Galaxy.root + 'admin/roles_list', url_data: Galaxy.params, dict_format: true }));\n\t },\n\t\n\t show_groups: function () {\n\t this.page.display(new GridView({ url_base: Galaxy.root + 'admin/groups_list', url_data: Galaxy.params, dict_format: true }));\n\t },\n\t\n\t show_tool_versions: function () {\n\t this.page.display(new GridView({ url_base: Galaxy.root + 'admin/tool_versions_list', url_data: Galaxy.params, dict_format: true }));\n\t },\n\t\n\t show_quotas: function () {\n\t this.page.display(new GridView({ url_base: Galaxy.root + 'admin/quotas_list', url_data: Galaxy.params, dict_format: true }));\n\t },\n\t\n\t show_forms: function (form_id) {\n\t var id = '?id=' + QueryStringParsing.get('id');\n\t var form_defs = {\n\t reset_user_password: {\n\t title: 'Reset passwords',\n\t url: 'admin/reset_user_password' + id,\n\t icon: 'fa-user',\n\t submit_title: 'Save new password',\n\t redirect: 'admin/users'\n\t },\n\t manage_roles_and_groups_for_user: {\n\t url: 'admin/manage_roles_and_groups_for_user' + id,\n\t icon: 'fa-users',\n\t redirect: 'admin/users'\n\t },\n\t manage_users_and_groups_for_role: {\n\t url: 'admin/manage_users_and_groups_for_role' + id,\n\t redirect: 'admin/roles'\n\t },\n\t manage_users_and_roles_for_group: {\n\t url: 'admin/manage_users_and_roles_for_group' + id,\n\t redirect: 'admin/groups'\n\t },\n\t manage_users_and_groups_for_quota: {\n\t url: 'admin/manage_users_and_groups_for_quota' + id,\n\t redirect: 'admin/quotas'\n\t },\n\t create_role: {\n\t url: 'admin/create_role',\n\t redirect: 'admin/roles'\n\t },\n\t create_group: {\n\t url: 'admin/create_group',\n\t redirect: 'admin/groups'\n\t },\n\t create_quota: {\n\t url: 'admin/create_quota',\n\t redirect: 'admin/quotas'\n\t },\n\t rename_role: {\n\t url: 'admin/rename_role' + id,\n\t redirect: 'admin/roles'\n\t },\n\t rename_group: {\n\t url: 'admin/rename_group' + id,\n\t redirect: 'admin/groups'\n\t },\n\t rename_quota: {\n\t url: 'admin/rename_quota' + id,\n\t redirect: 'admin/quotas'\n\t },\n\t edit_quota: {\n\t url: 'admin/edit_quota' + id,\n\t redirect: 'admin/quotas'\n\t },\n\t set_quota_default: {\n\t url: 'admin/set_quota_default' + id,\n\t redirect: 'admin/quotas'\n\t }\n\t };\n\t this.page.display(new FormWrapper.View(form_defs[form_id]));\n\t }\n\t });\n\t\n\t $(function () {\n\t _.extend(options.config, { active_view: 'admin' });\n\t Utils.setWindowTitle(\"Administration\");\n\t Galaxy.page = new Page.View(_.extend(options, {\n\t Left: AdminPanel,\n\t Router: AdminRouter\n\t }));\n\t });\n\t};\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3)))\n\n/***/ },\n/* 1 */,\n/* 2 */,\n/* 3 */,\n/* 4 */,\n/* 5 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/**\n\t * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc.\n\t */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(15), __webpack_require__(42), __webpack_require__(14), __webpack_require__(37), __webpack_require__(11), __webpack_require__(8)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Select, Slider, Options, Drilldown, Buttons, Modal) {\n\t\n\t /** Label wrapper */\n\t var Label = Backbone.View.extend({\n\t tagName: 'label',\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model(options);\n\t this.tagName = options.tagName || this.tagName;\n\t this.setElement($('<' + this.tagName + '/>'));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t title: function (new_title) {\n\t this.model.set('title', new_title);\n\t },\n\t value: function () {\n\t return this.model.get('title');\n\t },\n\t render: function () {\n\t this.$el.removeClass().addClass('ui-label').addClass(this.model.get('cls')).html(this.model.get('title'));\n\t return this;\n\t }\n\t });\n\t\n\t /** Displays messages used e.g. in the tool form */\n\t var Message = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t message: null,\n\t status: 'info',\n\t cls: '',\n\t persistent: false,\n\t fade: true\n\t }).set(options);\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t update: function (options) {\n\t this.model.set(options);\n\t },\n\t render: function () {\n\t this.$el.removeClass().addClass('ui-message').addClass(this.model.get('cls'));\n\t var status = this.model.get('status');\n\t if (this.model.get('large')) {\n\t this.$el.addClass((status == 'success' && 'done' || status == 'danger' && 'error' || status) + 'messagelarge');\n\t } else {\n\t this.$el.addClass('alert').addClass('alert-' + status);\n\t }\n\t if (this.model.get('message')) {\n\t this.$el.html(this.messageForDisplay());\n\t this.$el[this.model.get('fade') ? 'fadeIn' : 'show']();\n\t this.timeout && window.clearTimeout(this.timeout);\n\t if (!this.model.get('persistent')) {\n\t var self = this;\n\t this.timeout = window.setTimeout(function () {\n\t self.model.set('message', '');\n\t }, 3000);\n\t }\n\t } else {\n\t this.$el.fadeOut();\n\t }\n\t return this;\n\t },\n\t messageForDisplay: function () {\n\t return _.escape(this.model.get('message'));\n\t }\n\t });\n\t\n\t var UnescapedMessage = Message.extend({\n\t messageForDisplay: function () {\n\t return this.model.get('message');\n\t }\n\t });\n\t\n\t /** Renders an input element used e.g. in the tool form */\n\t var Input = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t type: 'text',\n\t placeholder: '',\n\t disabled: false,\n\t readonly: false,\n\t visible: true,\n\t cls: '',\n\t area: false,\n\t color: null,\n\t style: null\n\t }).set(options);\n\t this.tagName = this.model.get('area') ? 'textarea' : 'input';\n\t this.setElement($('<' + this.tagName + '/>'));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t events: {\n\t 'input': '_onchange'\n\t },\n\t value: function (new_val) {\n\t new_val !== undefined && this.model.set('value', typeof new_val === 'string' ? new_val : '');\n\t return this.model.get('value');\n\t },\n\t render: function () {\n\t var self = this;\n\t this.$el.removeClass().addClass('ui-' + this.tagName).addClass(this.model.get('cls')).addClass(this.model.get('style')).attr('id', this.model.id).attr('type', this.model.get('type')).attr('placeholder', this.model.get('placeholder')).css('color', this.model.get('color') || '').css('border-color', this.model.get('color') || '');\n\t var datalist = this.model.get('datalist');\n\t if ($.isArray(datalist) && datalist.length > 0) {\n\t this.$el.autocomplete({ source: function (request, response) {\n\t response(self.model.get('datalist'));\n\t },\n\t change: function () {\n\t self._onchange();\n\t } });\n\t }\n\t if (this.model.get('value') !== this.$el.val()) {\n\t this.$el.val(this.model.get('value'));\n\t }\n\t _.each(['readonly', 'disabled'], function (attr_name) {\n\t self.model.get(attr_name) ? self.$el.attr(attr_name, true) : self.$el.removeAttr(attr_name);\n\t });\n\t this.$el[this.model.get('visible') ? 'show' : 'hide']();\n\t return this;\n\t },\n\t _onchange: function () {\n\t this.value(this.$el.val());\n\t this.model.get('onchange') && this.model.get('onchange')(this.model.get('value'));\n\t }\n\t });\n\t\n\t /** Creates a hidden element input field used e.g. in the tool form */\n\t var Hidden = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model(options);\n\t this.setElement($('').append(this.$info = $('')).append(this.$hidden = $('')));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t value: function (new_val) {\n\t new_val !== undefined && this.model.set('value', new_val);\n\t return this.model.get('value');\n\t },\n\t render: function () {\n\t this.$el.attr('id', this.model.id);\n\t this.$hidden.val(this.model.get('value'));\n\t this.model.get('info') ? this.$info.show().text(this.model.get('info')) : this.$info.hide();\n\t return this;\n\t }\n\t });\n\t\n\t /** Creates a upload element input field */\n\t var Upload = Backbone.View.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.model = options && options.model || new Backbone.Model(options);\n\t this.setElement($('').append(this.$info = $('')).append(this.$file = $('').attr('type', 'file').addClass('ui-margin-bottom')).append(this.$text = $('').addClass('ui-textarea').attr('disabled', true)).append(this.$wait = $('').addClass('fa fa-spinner fa-spin')));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.$file.on('change', function (e) {\n\t self._readFile(e);\n\t });\n\t this.render();\n\t },\n\t value: function (new_val) {\n\t new_val !== undefined && this.model.set('value', new_val);\n\t return this.model.get('value');\n\t },\n\t render: function () {\n\t this.$el.attr('id', this.model.id);\n\t this.model.get('info') ? this.$info.show().text(this.model.get('info')) : this.$info.hide();\n\t this.model.get('value') ? this.$text.text(this.model.get('value')).show() : this.$text.hide();\n\t this.model.get('wait') ? this.$wait.show() : this.$wait.hide();\n\t return this;\n\t },\n\t _readFile: function (e) {\n\t var self = this;\n\t var file = e.target.files && e.target.files[0];\n\t if (file) {\n\t var reader = new FileReader();\n\t reader.onload = function () {\n\t self.model.set({ wait: false, value: this.result });\n\t };\n\t this.model.set({ wait: true, value: null });\n\t reader.readAsText(file);\n\t }\n\t }\n\t });\n\t\n\t return {\n\t Button: Buttons.ButtonDefault,\n\t ButtonIcon: Buttons.ButtonIcon,\n\t ButtonCheck: Buttons.ButtonCheck,\n\t ButtonMenu: Buttons.ButtonMenu,\n\t ButtonLink: Buttons.ButtonLink,\n\t Input: Input,\n\t Label: Label,\n\t Message: Message,\n\t UnescapedMessage: UnescapedMessage,\n\t Upload: Upload,\n\t Modal: Modal,\n\t RadioButton: Options.RadioButton,\n\t Checkbox: Options.Checkbox,\n\t Radio: Options.Radio,\n\t Select: Select,\n\t Hidden: Hidden,\n\t Slider: Slider,\n\t Drilldown: Drilldown\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 6 */,\n/* 7 */,\n/* 8 */,\n/* 9 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui) {\n\t var View = Backbone.View.extend({\n\t visible: false,\n\t initialize: function (options) {\n\t var self = this;\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t cls: 'ui-portlet',\n\t title: '',\n\t icon: '',\n\t buttons: null,\n\t body: null,\n\t scrollable: true,\n\t nopadding: false,\n\t operations: null,\n\t collapsible: false,\n\t collapsible_button: false,\n\t collapsed: false,\n\t onchange_title: null\n\t }).set(options);\n\t this.setElement(this._template());\n\t\n\t // link all dom elements\n\t this.$body = this.$('.portlet-body');\n\t this.$title_text = this.$('.portlet-title-text');\n\t this.$title_icon = this.$('.portlet-title-icon');\n\t this.$header = this.$('.portlet-header');\n\t this.$content = this.$('.portlet-content');\n\t this.$backdrop = this.$('.portlet-backdrop');\n\t this.$buttons = this.$('.portlet-buttons');\n\t this.$operations = this.$('.portlet-operations');\n\t\n\t // add body to component list\n\t this.model.get('body') && this.append(this.model.get('body'));\n\t\n\t // add icon for collapsible option\n\t this.collapsible_button = new Ui.ButtonIcon({\n\t icon: 'fa-eye',\n\t tooltip: 'Collapse/Expand',\n\t cls: 'ui-button-icon-plain',\n\t onclick: function () {\n\t self[self.collapsed ? 'expand' : 'collapse']();\n\t }\n\t });\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t var options = this.model.attributes;\n\t this.$el.removeClass().addClass(options.cls).attr('id', options.id);\n\t this.$header[options.title ? 'show' : 'hide']();\n\t this.$title_text.html(options.title);\n\t _.each([this.$content, this.$body], function ($el) {\n\t $el[options.nopadding ? 'addClass' : 'removeClass']('no-padding');\n\t });\n\t\n\t // render title icon\n\t if (options.icon) {\n\t this.$title_icon.removeClass().addClass('portlet-title-icon fa').addClass(options.icon).show();\n\t } else {\n\t this.$title_icon.hide();\n\t }\n\t\n\t // make portlet collapsible\n\t this.$title_text[options.collapsible ? 'addClass' : 'removeClass']('no-highlight collapsible').off();\n\t if (options.collapsible) {\n\t this.$title_text.on('click', function () {\n\t self[self.collapsed ? 'expand' : 'collapse']();\n\t });\n\t options.collapsed ? this.collapse() : this.expand();\n\t }\n\t\n\t // allow title editing\n\t this.$title_text.prop('disabled', !options.onchange_title);\n\t options.onchange_title && this.$title_text.make_text_editable({\n\t on_finish: function (new_title) {\n\t options.onchange_title(new_title);\n\t }\n\t });\n\t\n\t // render buttons\n\t if (options.buttons) {\n\t this.$buttons.empty().show();\n\t $.each(this.model.get('buttons'), function (name, item) {\n\t item.$el.prop('id', name);\n\t self.$buttons.append(item.$el);\n\t });\n\t } else {\n\t this.$buttons.hide();\n\t }\n\t\n\t // render operations\n\t this.$operations.empty;\n\t if (options.collapsible_button) {\n\t this.$operations.append(this.collapsible_button.$el);\n\t }\n\t if (options.operations) {\n\t $.each(options.operations, function (name, item) {\n\t item.$el.prop('id', name);\n\t self.$operations.append(item.$el);\n\t });\n\t }\n\t return this;\n\t },\n\t\n\t /** Append new doms to body */\n\t append: function ($el) {\n\t this.$body.append($el);\n\t },\n\t\n\t /** Remove all content */\n\t empty: function () {\n\t this.$body.empty();\n\t },\n\t\n\t /** Return header element */\n\t header: function () {\n\t return this.$header;\n\t },\n\t\n\t /** Return body element */\n\t body: function () {\n\t return this.$body;\n\t },\n\t\n\t /** Show portlet */\n\t show: function () {\n\t this.visible = true;\n\t this.$el.fadeIn('fast');\n\t },\n\t\n\t /** Hide portlet */\n\t hide: function () {\n\t this.visible = false;\n\t this.$el.hide();\n\t },\n\t\n\t /** Enable a particular button */\n\t enableButton: function (id) {\n\t this.$buttons.find('#' + id).prop('disabled', false);\n\t },\n\t\n\t /** Disable a particular button */\n\t disableButton: function (id) {\n\t this.$buttons.find('#' + id).prop('disabled', true);\n\t },\n\t\n\t /** Hide a particular operation */\n\t hideOperation: function (id) {\n\t this.$operations.find('#' + id).hide();\n\t },\n\t\n\t /** Show a particular operation */\n\t showOperation: function (id) {\n\t this.$operations.find('#' + id).show();\n\t },\n\t\n\t /** Replaces the event callback of an existing operation */\n\t setOperation: function (id, callback) {\n\t this.$operations.find('#' + id).off('click').on('click', callback);\n\t },\n\t\n\t /** Change title */\n\t title: function (new_title) {\n\t new_title && this.$title_text.html(new_title);\n\t return this.$title_text.html();\n\t },\n\t\n\t /** Collapse portlet */\n\t collapse: function () {\n\t this.collapsed = true;\n\t this.$content.height('0%');\n\t this.$body.hide();\n\t this.collapsible_button.setIcon('fa-eye-slash');\n\t },\n\t\n\t /** Expand portlet */\n\t expand: function () {\n\t this.collapsed = false;\n\t this.$content.height('100%');\n\t this.$body.fadeIn('fast');\n\t this.collapsible_button.setIcon('fa-eye');\n\t },\n\t\n\t /** Disable content access */\n\t disable: function () {\n\t this.$backdrop.show();\n\t },\n\t\n\t /** Enable content access */\n\t enable: function () {\n\t this.$backdrop.hide();\n\t },\n\t\n\t _template: function () {\n\t return $('').append($('').addClass('portlet-header').append($('').addClass('portlet-operations')).append($('').addClass('portlet-title').append($('').addClass('portlet-title-icon')).append($('').addClass('portlet-title-text')))).append($('').addClass('portlet-content').append($('').addClass('portlet-body')).append($('').addClass('portlet-buttons'))).append($('').addClass('portlet-backdrop'));\n\t }\n\t });\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ },\n/* 10 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {/**\n\t This is the main class of the form plugin. It is referenced as 'app' in lower level modules.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(9), __webpack_require__(5), __webpack_require__(32), __webpack_require__(19)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Portlet, Ui, FormSection, FormData) {\n\t return Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = new Backbone.Model({\n\t initial_errors: false,\n\t cls: 'ui-portlet-limited',\n\t icon: null,\n\t always_refresh: true,\n\t status: 'warning',\n\t onchange: function () {}\n\t }).set(options);\n\t this.setElement('');\n\t this.render();\n\t },\n\t\n\t /** Update available options */\n\t update: function (new_model) {\n\t var self = this;\n\t this.data.matchModel(new_model, function (node, input_id) {\n\t var input = self.input_list[input_id];\n\t if (input && input.options) {\n\t if (!_.isEqual(input.options, node.options)) {\n\t input.options = node.options;\n\t var field = self.field_list[input_id];\n\t if (field.update) {\n\t var new_options = [];\n\t if (['data', 'data_collection', 'drill_down'].indexOf(input.type) != -1) {\n\t new_options = input.options;\n\t } else {\n\t for (var i in node.options) {\n\t var opt = node.options[i];\n\t if (opt.length > 2) {\n\t new_options.push({ label: opt[0], value: opt[1] });\n\t }\n\t }\n\t }\n\t field.update(new_options);\n\t field.trigger('change');\n\t Galaxy.emit.debug('form-view::update()', 'Updating options for ' + input_id);\n\t }\n\t }\n\t }\n\t });\n\t },\n\t\n\t /** Set form into wait mode */\n\t wait: function (active) {\n\t for (var i in this.input_list) {\n\t var field = this.field_list[i];\n\t var input = this.input_list[i];\n\t if (input.is_dynamic && field.wait && field.unwait) {\n\t field[active ? 'wait' : 'unwait']();\n\t }\n\t }\n\t },\n\t\n\t /** Highlight and scroll to input element (currently only used for error notifications) */\n\t highlight: function (input_id, message, silent) {\n\t var input_element = this.element_list[input_id];\n\t if (input_element) {\n\t input_element.error(message || 'Please verify this parameter.');\n\t this.portlet.expand();\n\t this.trigger('expand', input_id);\n\t if (!silent) {\n\t var $panel = this.$el.parents().filter(function () {\n\t return ['auto', 'scroll'].indexOf($(this).css('overflow')) != -1;\n\t }).first();\n\t $panel.animate({ scrollTop: $panel.scrollTop() + input_element.$el.offset().top - 120 }, 500);\n\t }\n\t }\n\t },\n\t\n\t /** Highlights errors */\n\t errors: function (options) {\n\t this.trigger('reset');\n\t if (options && options.errors) {\n\t var error_messages = this.data.matchResponse(options.errors);\n\t for (var input_id in this.element_list) {\n\t var input = this.element_list[input_id];\n\t if (error_messages[input_id]) {\n\t this.highlight(input_id, error_messages[input_id], true);\n\t }\n\t }\n\t }\n\t },\n\t\n\t /** Render tool form */\n\t render: function () {\n\t var self = this;\n\t this.off('change');\n\t this.off('reset');\n\t // contains the dom field elements as created by the parameter factory i.e. form-parameters\n\t this.field_list = {};\n\t // contains input definitions/dictionaries as provided by the parameters to_dict() function through the api\n\t this.input_list = {};\n\t // contains the dom elements of each input element i.e. form-input which wraps the actual input field\n\t this.element_list = {};\n\t // converts the form into a json data structure\n\t this.data = new FormData.Manager(this);\n\t this._renderForm();\n\t this.data.create();\n\t this.model.get('initial_errors') && this.errors(this.model.attributes);\n\t // add listener which triggers on checksum change, and reset the form input wrappers\n\t var current_check = this.data.checksum();\n\t this.on('change', function (input_id) {\n\t var input = self.input_list[input_id];\n\t if (!input || input.refresh_on_change || self.model.get('always_refresh')) {\n\t var new_check = self.data.checksum();\n\t if (new_check != current_check) {\n\t current_check = new_check;\n\t self.model.get('onchange')();\n\t }\n\t }\n\t });\n\t this.on('reset', function () {\n\t _.each(self.element_list, function (input_element) {\n\t input_element.reset();\n\t });\n\t });\n\t return this;\n\t },\n\t\n\t /** Renders/appends dom elements of the form */\n\t _renderForm: function () {\n\t $('.tooltip').remove();\n\t var options = this.model.attributes;\n\t this.message = new Ui.UnescapedMessage();\n\t this.section = new FormSection.View(this, { inputs: options.inputs });\n\t this.portlet = new Portlet.View({\n\t icon: options.icon,\n\t title: options.title,\n\t cls: options.cls,\n\t operations: options.operations,\n\t buttons: options.buttons,\n\t collapsible: options.collapsible,\n\t collapsed: options.collapsed,\n\t onchange_title: options.onchange_title\n\t });\n\t this.portlet.append(this.message.$el);\n\t this.portlet.append(this.section.$el);\n\t this.$el.empty();\n\t options.inputs && this.$el.append(this.portlet.$el);\n\t options.message && this.message.update({ persistent: true, status: options.status, message: options.message });\n\t Galaxy.emit.debug('form-view::initialize()', 'Completed');\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ },\n/* 11 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/** This module contains all button views. */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t /** This renders the default button which is used e.g. at the bottom of the upload modal. */\n\t var ButtonDefault = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t title: '',\n\t icon: '',\n\t cls: 'btn btn-default',\n\t wait: false,\n\t wait_text: 'Sending...',\n\t wait_cls: 'btn btn-info',\n\t disabled: false,\n\t percentage: -1\n\t }).set(options);\n\t this.setElement($('').attr('type', 'button').append(this.$icon = $('')).append(this.$title = $('')).append(this.$progress = $('').append(this.$progress_bar = $(''))));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t var options = this.model.attributes;\n\t this.$el.removeClass().addClass('ui-button-default').addClass(options.disabled && 'disabled').attr('id', options.id).attr('disabled', options.disabled).off('click').on('click', function () {\n\t $('.tooltip').hide();\n\t options.onclick && !self.disabled && options.onclick();\n\t }).tooltip({ title: options.tooltip, placement: 'bottom' });\n\t this.$progress.addClass('progress').css('display', options.percentage !== -1 ? 'block' : 'none');\n\t this.$progress_bar.addClass('progress-bar').css({ width: options.percentage + '%' });\n\t this.$icon.removeClass().addClass('icon fa');\n\t this.$title.removeClass().addClass('title');\n\t if (options.wait) {\n\t this.$el.addClass(options.wait_cls).prop('disabled', true);\n\t this.$icon.addClass('fa-spinner fa-spin ui-margin-right');\n\t this.$title.html(options.wait_text);\n\t } else {\n\t this.$el.addClass(options.cls);\n\t this.$icon.addClass(options.icon);\n\t this.$title.html(options.title);\n\t options.icon && options.title && this.$icon.addClass('ui-margin-right');\n\t }\n\t },\n\t\n\t /** Show button */\n\t show: function () {\n\t this.$el.show();\n\t },\n\t\n\t /** Hide button */\n\t hide: function () {\n\t this.$el.hide();\n\t },\n\t\n\t /** Disable button */\n\t disable: function () {\n\t this.model.set('disabled', true);\n\t },\n\t\n\t /** Enable button */\n\t enable: function () {\n\t this.model.set('disabled', false);\n\t },\n\t\n\t /** Show spinner to indicate that the button is not ready to be clicked */\n\t wait: function () {\n\t this.model.set('wait', true);\n\t },\n\t\n\t /** Hide spinner to indicate that the button is ready to be clicked */\n\t unwait: function () {\n\t this.model.set('wait', false);\n\t },\n\t\n\t /** Change icon */\n\t setIcon: function (icon) {\n\t this.model.set('icon', icon);\n\t }\n\t });\n\t\n\t /** This button allows the right-click/open-in-new-tab feature, its used e.g. for panel buttons. */\n\t var ButtonLink = ButtonDefault.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t title: '',\n\t icon: '',\n\t cls: ''\n\t }).set(options);\n\t this.setElement($('').append(this.$icon = $('')));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var options = this.model.attributes;\n\t this.$el.removeClass().addClass(options.cls).attr({ id: options.id,\n\t href: options.href || 'javascript:void(0)',\n\t title: options.title,\n\t target: options.target || '_top',\n\t disabled: options.disabled }).tooltip({ placement: 'bottom' }).off('click').on('click', function () {\n\t options.onclick && !options.disabled && options.onclick();\n\t });\n\t this.$icon.removeClass().addClass(options.icon);\n\t }\n\t });\n\t\n\t /** The check button is used in the tool form and allows to distinguish between multiple states e.g. all, partially and nothing selected. */\n\t var ButtonCheck = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t title: 'Select/Unselect all',\n\t icons: ['fa-square-o', 'fa-minus-square-o', 'fa-check-square-o'],\n\t value: 0,\n\t onchange: function () {}\n\t }).set(options);\n\t this.setElement($('').append(this.$icon = $('')).append(this.$title = $('')));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function (options) {\n\t var self = this;\n\t var options = this.model.attributes;\n\t this.$el.addClass('ui-button-check').off('click').on('click', function () {\n\t self.model.set('value', self.model.get('value') === 0 && 2 || 0);\n\t options.onclick && options.onclick();\n\t });\n\t this.$title.html(options.title);\n\t this.$icon.removeClass().addClass('icon fa ui-margin-right').addClass(options.icons[options.value]);\n\t },\n\t\n\t /* Sets a new value and/or returns the value.\n\t * @param{Integer} new_val - Set a new value 0=unchecked, 1=partial and 2=checked.\n\t * OR:\n\t * @param{Integer} new_val - Number of selected options.\n\t * @param{Integer} total - Total number of available options.\n\t */\n\t value: function (new_val, total) {\n\t if (new_val !== undefined) {\n\t if (total && new_val !== 0) {\n\t new_val = new_val !== total && 1 || 2;\n\t }\n\t this.model.set('value', new_val);\n\t this.model.get('onchange')(this.model.get('value'));\n\t }\n\t return this.model.get('value');\n\t }\n\t });\n\t\n\t /** This renders a differently styled, more compact button version. */\n\t var ButtonIcon = ButtonDefault.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t title: '',\n\t icon: '',\n\t cls: 'ui-button-icon',\n\t disabled: false\n\t }).set(options);\n\t this.setElement($('').append(this.$button = $('').append(this.$icon = $('')).append(this.$title = $(''))));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function (options) {\n\t var self = this;\n\t var options = this.model.attributes;\n\t this.$el.removeClass().addClass(options.cls).addClass(options.disabled && 'disabled').attr('disabled', options.disabled).attr('id', options.id).off('click').on('click', function () {\n\t $('.tooltip').hide();\n\t !options.disabled && options.onclick && options.onclick();\n\t });\n\t this.$button.addClass('button').tooltip({ title: options.tooltip, placement: 'bottom' });\n\t this.$icon.removeClass().addClass('icon fa').addClass(options.icon);\n\t this.$title.addClass('title').html(options.title);\n\t options.icon && options.title && this.$icon.addClass('ui-margin-right');\n\t }\n\t });\n\t\n\t /** This class creates a button with dropdown menu. */\n\t var ButtonMenu = ButtonDefault.extend({\n\t $menu: null,\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: '',\n\t title: '',\n\t pull: 'right',\n\t icon: null,\n\t onclick: null,\n\t cls: 'ui-button-icon ui-button-menu',\n\t tooltip: '',\n\t target: '',\n\t href: '',\n\t onunload: null,\n\t visible: true,\n\t tag: ''\n\t }).set(options);\n\t this.collection = new Backbone.Collection();\n\t this.setElement($('').append(this.$root = $('').append(this.$icon = $('')).append(this.$title = $(''))));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.listenTo(this.collection, 'change add remove reset', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t var options = this.model.attributes;\n\t this.$el.removeClass().addClass('dropdown').addClass(options.cls).attr('id', options.id).css({ display: options.visible && this.collection.where({ visible: true }).length > 0 ? 'block' : 'none' });\n\t this.$root.addClass('root button dropdown-toggle').attr('data-toggle', 'dropdown').tooltip({ title: options.tooltip, placement: 'bottom' }).off('click').on('click', function (e) {\n\t $('.tooltip').hide();\n\t e.preventDefault();\n\t options.onclick && options.onclick();\n\t });\n\t this.$icon.removeClass().addClass('icon fa').addClass(options.icon);\n\t this.$title.removeClass().addClass('title').html(options.title);\n\t options.icon && options.title && this.$icon.addClass('ui-margin-right');\n\t this.$menu && this.$menu.remove();\n\t if (this.collection.length > 0) {\n\t this.$menu = $('\n\t cur_page = self.grid.get('cur_page'),\n\t text;\n\t if (page_num === new_page) {\n\t // Remove link to page since grid will be on this page. It is assumed that\n\t // this element has a single child, a hyperlink/anchor with text.\n\t text = $(this).children().text();\n\t $(this).empty();\n\t $(this).addClass('inactive-link');\n\t $(this).text(text);\n\t } else if (page_num === cur_page) {\n\t // Add hyperlink to this page since grid will no longer be on this page. It is assumed that\n\t // this element has a single child, a hyperlink/anchor.\n\t text = $(this).text();\n\t $(this).empty();\n\t $(this).removeClass('inactive-link');\n\t var t = $('' + text + '');\n\t t.click(function () {\n\t self.set_page(page_num);\n\t });\n\t $(this).append(t);\n\t }\n\t });\n\t\n\t if (new_page === 'all') {\n\t this.grid.set('cur_page', new_page);\n\t } else {\n\t this.grid.set('cur_page', parseInt(new_page, 10));\n\t }\n\t this.execute();\n\t },\n\t\n\t // confirmation/submission of operation request\n\t submit_operation: function (operation_button, confirmation_text) {\n\t // identify operation\n\t var operation_name = $(operation_button).val();\n\t\n\t // verify in any item is selected\n\t var number_of_checked_ids = this.$el.find('input[name=\"id\"]:checked').length;\n\t if (!number_of_checked_ids > 0) {\n\t return false;\n\t }\n\t\n\t // Check to see if there's grid confirmation text for this operation\n\t var operation = _.findWhere(this.grid.attributes.operations, { label: operation_name });\n\t if (operation && !confirmation_text) {\n\t confirmation_text = operation.confirm || '';\n\t }\n\t\n\t // collect ids\n\t var item_ids = [];\n\t this.$el.find('input[name=id]:checked').each(function () {\n\t item_ids.push($(this).val());\n\t });\n\t\n\t // execute operation\n\t var options = {\n\t operation: operation_name,\n\t id: item_ids,\n\t confirmation_text: confirmation_text\n\t };\n\t if (operation.target == 'top') {\n\t options = _.extend(options, {\n\t href: operation.href,\n\t target: operation.target\n\t });\n\t }\n\t this.execute(options);\n\t return true;\n\t },\n\t\n\t check_all_items: function () {\n\t var check = this.$('.grid-row-select-checkbox');\n\t var state = this.$('#check_all').prop('checked');\n\t _.each(check, function (c) {\n\t $(c).prop('checked', state);\n\t });\n\t this.init_grid_elements();\n\t },\n\t\n\t // Go back to page one; this is useful when a filter is applied.\n\t go_page_one: function () {\n\t // Need to go back to page 1 if not showing all.\n\t var cur_page = this.grid.get('cur_page');\n\t if (cur_page !== null && cur_page !== undefined && cur_page !== 'all') {\n\t this.grid.set('cur_page', 1);\n\t }\n\t },\n\t\n\t //\n\t // execute operations and hyperlink requests\n\t //\n\t execute: function (options) {\n\t // get url\n\t var id = null;\n\t var href = null;\n\t var operation = null;\n\t var confirmation_text = null;\n\t var target = null;\n\t\n\t // check for options\n\t if (options) {\n\t // get options\n\t href = options.href;\n\t operation = options.operation;\n\t id = options.id;\n\t confirmation_text = options.confirmation_text;\n\t target = options.target;\n\t\n\t // check if input contains the operation tag\n\t if (href !== undefined && href.indexOf('operation=') != -1) {\n\t // Get operation, id in hyperlink's href.\n\t var href_parts = href.split(\"?\");\n\t if (href_parts.length > 1) {\n\t var href_parms_str = href_parts[1];\n\t var href_parms = href_parms_str.split(\"&\");\n\t for (var index = 0; index < href_parms.length; index++) {\n\t if (href_parms[index].indexOf('operation') != -1) {\n\t // Found operation parm; get operation value.\n\t operation = href_parms[index].split('=')[1];\n\t operation = operation.replace(/\\+/g, ' ');\n\t } else if (href_parms[index].indexOf('id') != -1) {\n\t // Found id parm; get id value.\n\t id = href_parms[index].split('=')[1];\n\t }\n\t }\n\t }\n\t }\n\t }\n\t\n\t // check for operation details\n\t if (operation && id) {\n\t // show confirmation box\n\t if (confirmation_text && confirmation_text != '' && confirmation_text != 'None' && confirmation_text != 'null') if (!confirm(confirmation_text)) return false;\n\t\n\t // use small characters for operation?!\n\t operation = operation.toLowerCase();\n\t\n\t // Update grid.\n\t this.grid.set({\n\t operation: operation,\n\t item_ids: id\n\t });\n\t\n\t // Do operation. If operation cannot be performed asynchronously, redirect to location.\n\t if (target == 'top') {\n\t window.top.location = href + '?' + $.param(this.grid.get_url_data());\n\t } else if (this.grid.can_async_op(operation) || this.dict_format) {\n\t this.update_grid();\n\t } else {\n\t this.go_to(target, href);\n\t }\n\t\n\t // done\n\t return false;\n\t }\n\t\n\t // refresh grid\n\t if (href) {\n\t this.go_to(target, href);\n\t return false;\n\t }\n\t\n\t // refresh grid\n\t if (this.grid.get('async') || this.dict_format) {\n\t this.update_grid();\n\t } else {\n\t this.go_to(target, href);\n\t }\n\t\n\t // done\n\t return false;\n\t },\n\t\n\t // go to url\n\t go_to: function (target, href) {\n\t // get aysnc status\n\t var async = this.grid.get('async');\n\t this.grid.set('async', false);\n\t\n\t // get slide status\n\t var advanced_search = this.$el.find('#advanced-search').is(':visible');\n\t this.grid.set('advanced_search', advanced_search);\n\t\n\t // get default url\n\t if (!href) {\n\t href = this.grid.get('url_base') + '?' + $.param(this.grid.get_url_data());\n\t }\n\t\n\t // clear grid of transient request attributes.\n\t this.grid.set({\n\t operation: undefined,\n\t item_ids: undefined,\n\t async: async\n\t });\n\t switch (target) {\n\t case 'inbound':\n\t // this currently assumes that there is only a single grid shown at a time\n\t var $div = $('.grid-header').closest('.inbound');\n\t if ($div.length !== 0) {\n\t $div.load(href);\n\t return;\n\t }\n\t break;\n\t case 'top':\n\t window.top.location = href;\n\t break;\n\t default:\n\t window.location = href;\n\t }\n\t },\n\t\n\t // Update grid.\n\t update_grid: function () {\n\t // If there's an operation, do POST; otherwise, do GET.\n\t var method = this.grid.get('operation') ? 'POST' : 'GET';\n\t\n\t // Show overlay to indicate loading and prevent user actions.\n\t this.$el.find('.loading-elt-overlay').show();\n\t var self = this;\n\t $.ajax({\n\t type: method,\n\t url: self.grid.get('url_base'),\n\t data: self.grid.get_url_data(),\n\t error: function (response) {\n\t alert('Grid refresh failed');\n\t },\n\t success: function (response_text) {\n\t\n\t // backup\n\t var embedded = self.grid.get('embedded');\n\t var insert = self.grid.get('insert');\n\t var advanced_search = self.$el.find('#advanced-search').is(':visible');\n\t\n\t // request new configuration\n\t var json = self.dict_format ? response_text : $.parseJSON(response_text);\n\t\n\t // update\n\t json.embedded = embedded;\n\t json.insert = insert;\n\t json.advanced_search = advanced_search;\n\t\n\t // Initialize new grid config\n\t self.init_grid(json);\n\t\n\t // Hide loading overlay.\n\t self.$el.find('.loading-elt-overlay').hide();\n\t },\n\t complete: function () {\n\t // Clear grid of transient request attributes.\n\t self.grid.set({\n\t operation: undefined,\n\t item_ids: undefined\n\t });\n\t }\n\t });\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 13 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(9), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Portlet, Ui) {\n\t\n\t // ui list element\n\t var View = Backbone.View.extend({\n\t // create portlet to keep track of selected list elements\n\t initialize: function (options) {\n\t // link this\n\t var self = this;\n\t\n\t // initialize options\n\t this.options = options;\n\t this.name = options.name || 'element';\n\t this.multiple = options.multiple || false;\n\t\n\t // create message handler\n\t this.message = new Ui.Message();\n\t\n\t // create portlet\n\t this.portlet = new Portlet.View({ cls: 'ui-portlet-section' });\n\t\n\t // create select field containing the options which can be inserted into the list\n\t this.select = new Ui.Select.View({ optional: options.optional });\n\t\n\t // create insert new list element button\n\t this.button = new Ui.ButtonIcon({\n\t icon: 'fa fa-sign-in',\n\t tooltip: 'Insert new ' + this.name,\n\t onclick: function () {\n\t self.add({\n\t id: self.select.value(),\n\t name: self.select.text()\n\t });\n\t }\n\t });\n\t\n\t // build main element\n\t this.setElement(this._template(options));\n\t this.$('.ui-list-message').append(this.message.$el);\n\t this.$('.ui-list-portlet').append(this.portlet.$el);\n\t this.$('.ui-list-button').append(this.button.$el);\n\t this.$('.ui-list-select').append(this.select.$el);\n\t },\n\t\n\t /** Return/Set currently selected list elements */\n\t value: function (val) {\n\t // set new value\n\t if (val !== undefined) {\n\t this.portlet.empty();\n\t if ($.isArray(val)) {\n\t for (var i in val) {\n\t var v = val[i];\n\t var v_id = null;\n\t var v_name = null;\n\t if ($.type(v) != 'string') {\n\t v_id = v.id;\n\t v_name = v.name;\n\t } else {\n\t v_id = v_name = v;\n\t }\n\t if (v_id != null) {\n\t this.add({\n\t id: v_id,\n\t name: v_name\n\t });\n\t }\n\t }\n\t }\n\t this._refresh();\n\t }\n\t // get current value\n\t var lst = [];\n\t this.$('.ui-list-id').each(function () {\n\t lst.push({\n\t id: $(this).prop('id'),\n\t name: $(this).find('.ui-list-name').html()\n\t });\n\t });\n\t if (lst.length == 0) {\n\t return null;\n\t }\n\t return lst;\n\t },\n\t\n\t /** Add row */\n\t add: function (options) {\n\t var self = this;\n\t if (this.$('[id=\"' + options.id + '\"]').length === 0) {\n\t if (!Utils.isEmpty(options.id)) {\n\t var $el = $(this._templateRow({\n\t id: options.id,\n\t name: options.name\n\t }));\n\t $el.on('click', function () {\n\t $el.remove();\n\t self._refresh();\n\t });\n\t $el.on('mouseover', function () {\n\t $el.addClass('portlet-highlight');\n\t });\n\t $el.on('mouseout', function () {\n\t $el.removeClass('portlet-highlight');\n\t });\n\t this.portlet.append($el);\n\t this._refresh();\n\t } else {\n\t this.message.update({ message: 'Please select a valid ' + this.name + '.', status: 'danger' });\n\t }\n\t } else {\n\t this.message.update({ message: 'This ' + this.name + ' is already in the list.' });\n\t }\n\t },\n\t\n\t /** Update available options */\n\t update: function (options) {\n\t this.select.update(options);\n\t },\n\t\n\t /** Refresh view */\n\t _refresh: function () {\n\t if (this.$('.ui-list-id').length > 0) {\n\t !this.multiple && this.button.disable();\n\t this.$('.ui-list-portlet').show();\n\t } else {\n\t this.button.enable();\n\t this.$('.ui-list-portlet').hide();\n\t }\n\t this.options.onchange && this.options.onchange();\n\t },\n\t\n\t /** Main Template */\n\t _template: function (options) {\n\t return '
' + '
' + '
' + '' + '(no options) ';\n\t }\n\t return _.map(options, function (option) {\n\t if (option.divider) {\n\t return '';\n\t } else if (option.header) {\n\t return ['', option.html, ' '].join('');\n\t }\n\t var href = option.href || 'javascript:void(0);',\n\t target = option.target ? ' target=\"' + option.target + '\"' : '',\n\t check = option.checked ? '' : '';\n\t return ['', check, option.html, ' '].join('');\n\t }).join('');\n\t },\n\t\n\t // get the absolute position/offset for the menu\n\t _getShownPosition: function (clickEvent) {\n\t\n\t // display menu horiz. centered on click...\n\t var menuWidth = this.$el.width();\n\t var x = clickEvent.pageX - menuWidth / 2;\n\t\n\t // adjust to handle horiz. scroll and window dimensions ( draw entirely on visible screen area )\n\t x = Math.min(x, $(document).scrollLeft() + $(window).width() - menuWidth - 5);\n\t x = Math.max(x, $(document).scrollLeft() + 5);\n\t return {\n\t top: clickEvent.pageY,\n\t left: x\n\t };\n\t },\n\t\n\t // bind an event handler to all available frames so that when anything is clicked\n\t // the menu is removed from the DOM and the event handler unbinds itself\n\t _setUpCloseBehavior: function () {\n\t var menu = this;\n\t //TODO: alternately: focus hack, blocking overlay, jquery.blockui\n\t\n\t // function to close popup and unbind itself\n\t function closePopup(event) {\n\t $(document).off('click.close_popup');\n\t if (window && window.parent !== window) {\n\t try {\n\t $(window.parent.document).off(\"click.close_popup\");\n\t } catch (err) {}\n\t } else {\n\t try {\n\t $('iframe#galaxy_main').contents().off(\"click.close_popup\");\n\t } catch (err) {}\n\t }\n\t menu.remove();\n\t }\n\t\n\t $('html').one(\"click.close_popup\", closePopup);\n\t if (window && window.parent !== window) {\n\t try {\n\t $(window.parent.document).find('html').one(\"click.close_popup\", closePopup);\n\t } catch (err) {}\n\t } else {\n\t try {\n\t $('iframe#galaxy_main').contents().one(\"click.close_popup\", closePopup);\n\t } catch (err) {}\n\t }\n\t },\n\t\n\t // add a menu option/item at the given index\n\t addItem: function (item, index) {\n\t // append to end if no index\n\t index = index >= 0 ? index : this.options.length;\n\t this.options.splice(index, 0, item);\n\t return this;\n\t },\n\t\n\t // remove a menu option/item at the given index\n\t removeItem: function (index) {\n\t if (index >= 0) {\n\t this.options.splice(index, 1);\n\t }\n\t return this;\n\t },\n\t\n\t // search for a menu option by its html\n\t findIndexByHtml: function (html) {\n\t for (var i = 0; i < this.options.length; i++) {\n\t if (_.has(this.options[i], 'html') && this.options[i].html === html) {\n\t return i;\n\t }\n\t }\n\t return null;\n\t },\n\t\n\t // search for a menu option by its html\n\t findItemByHtml: function (html) {\n\t return this.options[this.findIndexByHtml(html)];\n\t },\n\t\n\t // string representation\n\t toString: function () {\n\t return 'PopupMenu';\n\t }\n\t });\n\t /** shortcut to new for when you don't need to preserve the ref */\n\t PopupMenu.create = function _create($button, options) {\n\t return new PopupMenu($button, options);\n\t };\n\t\n\t // -----------------------------------------------------------------------------\n\t // the following class functions are bridges from the original make_popupmenu and make_popup_menus\n\t // to the newer backbone.js PopupMenu\n\t\n\t /** Create a PopupMenu from simple map initial_options activated by clicking button_element.\n\t * Converts initial_options to object array used by PopupMenu.\n\t * @param {jQuery|DOMElement} button_element element which, when clicked, activates menu\n\t * @param {Object} initial_options map of key -> values, where\n\t * key is option text, value is fn to call when option is clicked\n\t * @returns {PopupMenu} the PopupMenu created\n\t */\n\t PopupMenu.make_popupmenu = function (button_element, initial_options) {\n\t var convertedOptions = [];\n\t _.each(initial_options, function (optionVal, optionKey) {\n\t var newOption = { html: optionKey };\n\t\n\t // keys with null values indicate: header\n\t if (optionVal === null) {\n\t // !optionVal? (null only?)\n\t newOption.header = true;\n\t\n\t // keys with function values indicate: a menu option\n\t } else if (jQuery.type(optionVal) === 'function') {\n\t newOption.func = optionVal;\n\t }\n\t //TODO:?? any other special optionVals?\n\t // there was no divider option originally\n\t convertedOptions.push(newOption);\n\t });\n\t return new PopupMenu($(button_element), convertedOptions);\n\t };\n\t\n\t /** Find all anchors in $parent (using selector) and covert anchors into a PopupMenu options map.\n\t * @param {jQuery} $parent the element that contains the links to convert to options\n\t * @param {String} selector jq selector string to find links\n\t * @returns {Object[]} the options array to initialize a PopupMenu\n\t */\n\t //TODO: lose parent and selector, pass in array of links, use map to return options\n\t PopupMenu.convertLinksToOptions = function ($parent, selector) {\n\t $parent = $($parent);\n\t selector = selector || 'a';\n\t var options = [];\n\t $parent.find(selector).each(function (elem, i) {\n\t var option = {},\n\t $link = $(elem);\n\t\n\t // convert link text to the option text (html) and the href into the option func\n\t option.html = $link.text();\n\t if ($link.attr('href')) {\n\t var linkHref = $link.attr('href'),\n\t linkTarget = $link.attr('target'),\n\t confirmText = $link.attr('confirm');\n\t\n\t option.func = function () {\n\t // if there's a \"confirm\" attribute, throw up a confirmation dialog, and\n\t // if the user cancels - do nothing\n\t if (confirmText && !confirm(confirmText)) {\n\t return;\n\t }\n\t\n\t // if there's no confirm attribute, or the user accepted the confirm dialog:\n\t switch (linkTarget) {\n\t // relocate the center panel\n\t case '_parent':\n\t window.parent.location = linkHref;\n\t break;\n\t\n\t // relocate the entire window\n\t case '_top':\n\t window.top.location = linkHref;\n\t break;\n\t\n\t // relocate this panel\n\t default:\n\t window.location = linkHref;\n\t }\n\t };\n\t }\n\t options.push(option);\n\t });\n\t return options;\n\t };\n\t\n\t /** Create a single popupmenu from existing DOM button and anchor elements\n\t * @param {jQuery} $buttonElement the element that when clicked will open the menu\n\t * @param {jQuery} $menuElement the element that contains the anchors to convert into a menu\n\t * @param {String} menuElementLinkSelector jq selector string used to find anchors to be made into menu options\n\t * @returns {PopupMenu} the PopupMenu (Backbone View) that can render, control the menu\n\t */\n\t PopupMenu.fromExistingDom = function ($buttonElement, $menuElement, menuElementLinkSelector) {\n\t $buttonElement = $($buttonElement);\n\t $menuElement = $($menuElement);\n\t var options = PopupMenu.convertLinksToOptions($menuElement, menuElementLinkSelector);\n\t // we're done with the menu (having converted it to an options map)\n\t $menuElement.remove();\n\t return new PopupMenu($buttonElement, options);\n\t };\n\t\n\t /** Create all popupmenus within a document or a more specific element\n\t * @param {DOMElement} parent the DOM element in which to search for popupmenus to build (defaults to document)\n\t * @param {String} menuSelector jq selector string to find popupmenu menu elements (defaults to \"div[popupmenu]\")\n\t * @param {Function} buttonSelectorBuildFn the function to build the jq button selector.\n\t * Will be passed $menuElement, parent.\n\t * (Defaults to return '#' + $menuElement.attr( 'popupmenu' ); )\n\t * @returns {PopupMenu[]} array of popupmenus created\n\t */\n\t PopupMenu.make_popup_menus = function (parent, menuSelector, buttonSelectorBuildFn) {\n\t parent = parent || document;\n\t // orig. Glx popupmenu menus have a (non-std) attribute 'popupmenu'\n\t // which contains the id of the button that activates the menu\n\t menuSelector = menuSelector || 'div[popupmenu]';\n\t // default to (orig. Glx) matching button to menu by using the popupmenu attr of the menu as the id of the button\n\t buttonSelectorBuildFn = buttonSelectorBuildFn || function ($menuElement, parent) {\n\t return '#' + $menuElement.attr('popupmenu');\n\t };\n\t\n\t // aggregate and return all PopupMenus\n\t var popupMenusCreated = [];\n\t $(parent).find(menuSelector).each(function () {\n\t var $menuElement = $(this),\n\t $buttonElement = $(parent).find(buttonSelectorBuildFn($menuElement, parent));\n\t popupMenusCreated.push(PopupMenu.fromDom($buttonElement, $menuElement));\n\t $buttonElement.addClass('popup');\n\t });\n\t return popupMenusCreated;\n\t };\n\t\n\t // =============================================================================\n\t return PopupMenu;\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ },\n/* 19 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/* This class maps the form dom to an api compatible javascript dictionary. */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t var Manager = Backbone.Model.extend({\n\t initialize: function (app) {\n\t this.app = app;\n\t },\n\t\n\t /** Creates a checksum. */\n\t checksum: function () {\n\t var sum = '';\n\t var self = this;\n\t this.app.section.$el.find('.section-row').each(function () {\n\t var id = $(this).attr('id');\n\t var field = self.app.field_list[id];\n\t if (field) {\n\t sum += id + ':' + JSON.stringify(field.value && field.value()) + ':' + field.collapsed + ';';\n\t }\n\t });\n\t return sum;\n\t },\n\t\n\t /** Convert dom into a dictionary of flat id/value pairs used e.g. on job submission. */\n\t create: function () {\n\t var self = this;\n\t\n\t // get raw dictionary from dom\n\t var dict = {};\n\t this._iterate(this.app.section.$el, dict);\n\t\n\t // add to result dictionary, label elements\n\t var result_dict = {};\n\t this.flat_dict = {};\n\t function add(flat_id, input_id, input_value) {\n\t self.flat_dict[flat_id] = input_id;\n\t result_dict[flat_id] = input_value;\n\t self.app.element_list[input_id] && self.app.element_list[input_id].$el.attr('tour_id', flat_id);\n\t }\n\t // converter between raw dictionary and job dictionary\n\t function convert(identifier, head) {\n\t for (var index in head) {\n\t var node = head[index];\n\t if (node.input) {\n\t var input = node.input;\n\t var flat_id = identifier;\n\t if (identifier != '') {\n\t flat_id += '|';\n\t }\n\t flat_id += input.name;\n\t switch (input.type) {\n\t case 'repeat':\n\t var section_label = 'section-';\n\t var block_indices = [];\n\t var block_prefix = null;\n\t for (var block_label in node) {\n\t var pos = block_label.indexOf(section_label);\n\t if (pos != -1) {\n\t pos += section_label.length;\n\t block_indices.push(parseInt(block_label.substr(pos)));\n\t if (!block_prefix) {\n\t block_prefix = block_label.substr(0, pos);\n\t }\n\t }\n\t }\n\t block_indices.sort(function (a, b) {\n\t return a - b;\n\t });\n\t var index = 0;\n\t for (var i in block_indices) {\n\t convert(flat_id + '_' + index++, node[block_prefix + block_indices[i]]);\n\t }\n\t break;\n\t case 'conditional':\n\t var value = self.app.field_list[input.id].value();\n\t add(flat_id + '|' + input.test_param.name, input.id, value);\n\t var selectedCase = matchCase(input, value);\n\t if (selectedCase != -1) {\n\t convert(flat_id, head[input.id + '-section-' + selectedCase]);\n\t }\n\t break;\n\t case 'section':\n\t convert(!input.flat && flat_id || '', node);\n\t break;\n\t default:\n\t var field = self.app.field_list[input.id];\n\t if (field && field.value) {\n\t var value = field.value();\n\t if (input.ignore === undefined || input.ignore != value) {\n\t if (field.collapsed && input.collapsible_value) {\n\t value = input.collapsible_value;\n\t }\n\t add(flat_id, input.id, value);\n\t if (input.payload) {\n\t for (var p_id in input.payload) {\n\t add(p_id, input.id, input.payload[p_id]);\n\t }\n\t }\n\t }\n\t }\n\t }\n\t }\n\t }\n\t }\n\t convert('', dict);\n\t return result_dict;\n\t },\n\t\n\t /** Matches flat ids to corresponding input element\n\t * @param{string} flat_id - Flat input id to be looked up.\n\t */\n\t match: function (flat_id) {\n\t return this.flat_dict && this.flat_dict[flat_id];\n\t },\n\t\n\t /** Match conditional values to selected cases\n\t */\n\t matchCase: function (input, value) {\n\t return matchCase(input, value);\n\t },\n\t\n\t /** Matches a new tool model to the current input elements e.g. used to update dynamic options\n\t */\n\t matchModel: function (model, callback) {\n\t var self = this;\n\t visitInputs(model.inputs, function (input, name) {\n\t self.flat_dict[name] && callback(input, self.flat_dict[name]);\n\t });\n\t },\n\t\n\t /** Matches identifier from api response to input elements e.g. used to display validation errors\n\t */\n\t matchResponse: function (response) {\n\t var result = {};\n\t var self = this;\n\t function search(id, head) {\n\t if (typeof head === 'string') {\n\t var input_id = self.flat_dict[id];\n\t input_id && (result[input_id] = head);\n\t } else {\n\t for (var i in head) {\n\t var new_id = i;\n\t if (id !== '') {\n\t var separator = '|';\n\t if (head instanceof Array) {\n\t separator = '_';\n\t }\n\t new_id = id + separator + new_id;\n\t }\n\t search(new_id, head[i]);\n\t }\n\t }\n\t }\n\t search('', response);\n\t return result;\n\t },\n\t\n\t /** Map dom tree to dictionary tree with input elements.\n\t */\n\t _iterate: function (parent, dict) {\n\t var self = this;\n\t var children = $(parent).children();\n\t children.each(function () {\n\t var child = this;\n\t var id = $(child).attr('id');\n\t if ($(child).hasClass('section-row')) {\n\t var input = self.app.input_list[id];\n\t dict[id] = input && { input: input } || {};\n\t self._iterate(child, dict[id]);\n\t } else {\n\t self._iterate(child, dict);\n\t }\n\t });\n\t }\n\t });\n\t\n\t /** Match conditional values to selected cases\n\t * @param{dict} input - Definition of conditional input parameter\n\t * @param{dict} value - Current value\n\t */\n\t var matchCase = function (input, value) {\n\t if (input.test_param.type == 'boolean') {\n\t if (value == 'true') {\n\t value = input.test_param.truevalue || 'true';\n\t } else {\n\t value = input.test_param.falsevalue || 'false';\n\t }\n\t }\n\t for (var i in input.cases) {\n\t if (input.cases[i].value == value) {\n\t return i;\n\t }\n\t }\n\t return -1;\n\t };\n\t\n\t /** Visits tool inputs\n\t * @param{dict} inputs - Nested dictionary of input elements\n\t * @param{dict} callback - Called with the mapped dictionary object and corresponding model node\n\t */\n\t var visitInputs = function (inputs, callback, prefix, context) {\n\t context = $.extend(true, {}, context);\n\t _.each(inputs, function (input) {\n\t if (input && input.type && input.name) {\n\t context[input.name] = input;\n\t }\n\t });\n\t for (var key in inputs) {\n\t var node = inputs[key];\n\t node.name = node.name || key;\n\t var name = prefix ? prefix + '|' + node.name : node.name;\n\t switch (node.type) {\n\t case 'repeat':\n\t _.each(node.cache, function (cache, j) {\n\t visitInputs(cache, callback, name + '_' + j, context);\n\t });\n\t break;\n\t case 'conditional':\n\t if (node.test_param) {\n\t callback(node.test_param, name + '|' + node.test_param.name, context);\n\t var selectedCase = matchCase(node, node.test_param.value);\n\t if (selectedCase != -1) {\n\t visitInputs(node.cases[selectedCase].inputs, callback, name, context);\n\t } else {\n\t Galaxy.emit.debug('form-data::visitInputs() - Invalid case for ' + name + '.');\n\t }\n\t } else {\n\t Galaxy.emit.debug('form-data::visitInputs() - Conditional test parameter missing for ' + name + '.');\n\t }\n\t break;\n\t case 'section':\n\t visitInputs(node.inputs, callback, name, context);\n\t break;\n\t default:\n\t callback(node, name, context);\n\t }\n\t }\n\t };\n\t\n\t return {\n\t Manager: Manager,\n\t visitInputs: visitInputs\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 20 */,\n/* 21 */,\n/* 22 */,\n/* 23 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/** This class creates a ui table element. */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t var View = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.options = Utils.merge(options, {\n\t content: 'No content available.',\n\t onchange: null,\n\t ondblclick: null,\n\t onconfirm: null,\n\t cls: 'ui-table',\n\t selectable: true,\n\t cls_tr: ''\n\t });\n\t this.setElement(this._template());\n\t this.$thead = this.$('thead');\n\t this.$tbody = this.$('tbody');\n\t this.$tmessage = this.$('tmessage');\n\t this.row = this._row();\n\t this.row_count = 0;\n\t },\n\t\n\t events: {\n\t 'click': '_onclick',\n\t 'dblclick': '_ondblclick'\n\t },\n\t\n\t /** Add cell to header row */\n\t addHeader: function ($el) {\n\t this.row.append($('
' + '
';\n\t },\n\t\n\t /** Row Template */\n\t _templateRow: function (options) {\n\t return '' + '' + '' + options.name + '' + '
';\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 14 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/** Base class for options based ui elements **/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(11)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Buttons) {\n\t var Base = Backbone.View.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.model = options && options.model || new Backbone.Model({\n\t visible: true,\n\t data: [],\n\t id: Utils.uid(),\n\t error_text: 'No options available.',\n\t wait_text: 'Please wait...',\n\t multiple: false,\n\t optional: false,\n\t onchange: function () {}\n\t }).set(options);\n\t this.listenTo(this.model, 'change:value', this._changeValue, this);\n\t this.listenTo(this.model, 'change:wait', this._changeWait, this);\n\t this.listenTo(this.model, 'change:data', this._changeData, this);\n\t this.listenTo(this.model, 'change:visible', this._changeVisible, this);\n\t this.on('change', function () {\n\t self.model.get('onchange')(self.value());\n\t });\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t this.$el.empty().removeClass().addClass('ui-options').append(this.$message = $('')).append(this.$menu = $('').addClass('ui-options-menu')).append(this.$options = $(this._template()));\n\t\n\t // add select/unselect all button\n\t this.all_button = null;\n\t if (this.model.get('multiple')) {\n\t this.all_button = new Buttons.ButtonCheck({\n\t onclick: function () {\n\t self.$('input').prop('checked', self.all_button.value() !== 0);\n\t self.value(self._getValue());\n\t self.trigger('change');\n\t }\n\t });\n\t this.$menu.append(this.all_button.$el);\n\t }\n\t\n\t // finalize dom\n\t this._changeData();\n\t this._changeWait();\n\t this._changeVisible();\n\t },\n\t\n\t /** Update available options */\n\t update: function (options) {\n\t this.model.set('data', options);\n\t },\n\t\n\t _changeData: function () {\n\t var self = this;\n\t this.$options.empty();\n\t if (this._templateOptions) {\n\t this.$options.append(this._templateOptions(this.model.get('data')));\n\t } else {\n\t _.each(this.model.get('data'), function (option) {\n\t self.$options.append($(self._templateOption(option)).addClass('ui-option').tooltip({ title: option.tooltip, placement: 'bottom' }));\n\t });\n\t }\n\t var self = this;\n\t this.$('input').on('change', function () {\n\t self.value(self._getValue());\n\t self.trigger('change');\n\t });\n\t this._changeValue();\n\t this._changeWait();\n\t },\n\t\n\t _changeVisible: function () {\n\t this.$el[this.model.get('visible') ? 'show' : 'hide']();\n\t },\n\t\n\t _changeWait: function () {\n\t if (this.model.get('wait')) {\n\t if (this.length() === 0) {\n\t this._messageShow(this.model.get('wait_text'), 'info');\n\t this.$options.hide();\n\t this.$menu.hide();\n\t }\n\t } else {\n\t if (this.length() === 0) {\n\t this._messageShow(this.model.get('error_text'), 'danger');\n\t this.$options.hide();\n\t this.$menu.hide();\n\t } else {\n\t this.$message.hide();\n\t this.$options.css('display', 'inline-block');\n\t this.$menu.show();\n\t }\n\t }\n\t },\n\t\n\t _changeValue: function () {\n\t this._setValue(this.model.get('value'));\n\t if (this._getValue() === null && !this.model.get('multiple') && !this.model.get('optional')) {\n\t this._setValue(this.first());\n\t }\n\t this.all_button && this.all_button.value($.isArray(this._getValue()) ? this._getValue().length : 0, this.length());\n\t },\n\t\n\t /** Return/Set current selection */\n\t value: function (new_value) {\n\t new_value !== undefined && this.model.set('value', new_value);\n\t return this._getValue();\n\t },\n\t\n\t /** Return first available option */\n\t first: function () {\n\t var options = this.$('input').first();\n\t return options.length > 0 ? options.val() : null;\n\t },\n\t\n\t /** Show a spinner indicating that the select options are currently loaded */\n\t wait: function () {\n\t this.model.set('wait', true);\n\t },\n\t\n\t /** Hide spinner indicating that the request has been completed */\n\t unwait: function () {\n\t this.model.set('wait', false);\n\t },\n\t\n\t /** Returns the number of options */\n\t length: function () {\n\t return this.$('.ui-option').length;\n\t },\n\t\n\t /** Set value to dom */\n\t _setValue: function (new_value) {\n\t var self = this;\n\t if (new_value !== undefined) {\n\t this.$('input').prop('checked', false);\n\t if (new_value !== null) {\n\t var values = $.isArray(new_value) ? new_value : [new_value];\n\t _.each(values, function (v) {\n\t self.$('input[value=\"' + v + '\"]').first().prop('checked', true);\n\t });\n\t }\n\t }\n\t },\n\t\n\t /** Return current selection */\n\t _getValue: function () {\n\t var selected = [];\n\t this.$(':checked').each(function () {\n\t selected.push($(this).val());\n\t });\n\t if (Utils.isEmpty(selected)) {\n\t return null;\n\t }\n\t return this.model.get('multiple') ? selected : selected[0];\n\t },\n\t\n\t /** Show message instead if options */\n\t _messageShow: function (text, status) {\n\t this.$message.show().removeClass().addClass('ui-message alert alert-' + status).html(text);\n\t },\n\t\n\t /** Main template function */\n\t _template: function () {\n\t return $('').addClass('ui-options-list');\n\t }\n\t });\n\t\n\t /** Iconized **/\n\t var BaseIcons = Base.extend({\n\t _templateOption: function (pair) {\n\t var id = Utils.uid();\n\t return $('').addClass('ui-option').append($('').attr({\n\t id: id,\n\t type: this.model.get('type'),\n\t name: this.model.id,\n\t value: pair.value })).append($('').addClass('ui-options-label').attr('for', id).html(pair.label));\n\t }\n\t });\n\t\n\t /** Radio button field **/\n\t var Radio = {};\n\t Radio.View = BaseIcons.extend({\n\t initialize: function (options) {\n\t options.type = 'radio';\n\t BaseIcons.prototype.initialize.call(this, options);\n\t }\n\t });\n\t\n\t /** Checkbox options field **/\n\t var Checkbox = {};\n\t Checkbox.View = BaseIcons.extend({\n\t initialize: function (options) {\n\t options.type = 'checkbox';\n\t options.multiple = true;\n\t BaseIcons.prototype.initialize.call(this, options);\n\t }\n\t });\n\t\n\t /** Radio button options field styled as classic buttons **/\n\t var RadioButton = {};\n\t RadioButton.View = Base.extend({\n\t initialize: function (options) {\n\t Base.prototype.initialize.call(this, options);\n\t },\n\t\n\t /** Set current value */\n\t _setValue: function (new_value) {\n\t if (new_value !== undefined) {\n\t this.$('input').prop('checked', false);\n\t this.$('label').removeClass('active');\n\t this.$('[value=\"' + new_value + '\"]').prop('checked', true).closest('label').addClass('active');\n\t }\n\t },\n\t\n\t /** Template for a single option */\n\t _templateOption: function (pair) {\n\t var $el = $('').addClass('btn btn-default');\n\t pair.icon && $el.append($('').addClass('fa').addClass(pair.icon).addClass(!pair.label && 'no-padding'));\n\t $el.append($('').attr({ type: 'radio', name: this.model.id, value: pair.value }));\n\t pair.label && $el.append(pair.label);\n\t return $el;\n\t },\n\t\n\t /** Main template function */\n\t _template: function () {\n\t return $('').addClass('btn-group ui-radiobutton').attr('data-toggle', 'buttons');\n\t }\n\t });\n\t\n\t return {\n\t Base: Base,\n\t BaseIcons: BaseIcons,\n\t Radio: Radio,\n\t RadioButton: RadioButton,\n\t Checkbox: Checkbox\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 15 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/**\n\t * This class creates/wraps a default html select field as backbone class.\n\t */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(11)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Buttons) {\n\t var View = Backbone.View.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.data = [];\n\t this.data2 = [];\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t cls: 'ui-select',\n\t error_text: 'No options available',\n\t empty_text: 'Nothing selected',\n\t visible: true,\n\t wait: false,\n\t multiple: false,\n\t searchable: true,\n\t optional: false,\n\t disabled: false,\n\t onchange: function () {},\n\t value: null,\n\t individual: false,\n\t pagesize: 20\n\t }).set(options);\n\t this.on('change', function () {\n\t self.model.get('onchange') && self.model.get('onchange')(self.value());\n\t });\n\t this.listenTo(this.model, 'change:data', this._changeData, this);\n\t this.listenTo(this.model, 'change:disabled', this._changeDisabled, this);\n\t this.listenTo(this.model, 'change:wait', this._changeWait, this);\n\t this.listenTo(this.model, 'change:visible', this._changeVisible, this);\n\t this.listenTo(this.model, 'change:value', this._changeValue, this);\n\t this.listenTo(this.model, 'change:multiple change:searchable change:cls change:id', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t this.model.get('searchable') ? this._renderSearchable() : this._renderClassic();\n\t this.$el.addClass(this.model.get('cls')).attr('id', this.model.get('id'));\n\t this.$select.empty().addClass('select').attr('id', this.model.get('id') + '_select').prop('multiple', this.model.get('multiple')).on('change', function () {\n\t self.value(self._getValue());\n\t self.trigger('change');\n\t });\n\t this._changeData();\n\t this._changeWait();\n\t this._changeVisible();\n\t this._changeDisabled();\n\t },\n\t\n\t /** Renders the classic selection field */\n\t _renderClassic: function () {\n\t var self = this;\n\t this.$el.addClass(this.model.get('multiple') ? 'ui-select-multiple' : 'ui-select').append(this.$select = $('')).append(this.$dropdown = $('')).append(this.$resize = $('').append(this.$resize_icon = $('')));\n\t if (this.model.get('multiple')) {\n\t this.$dropdown.hide();\n\t this.$resize_icon.addClass('fa fa-angle-double-right fa-rotate-45').show();\n\t this.$resize.removeClass().addClass('icon-resize').show().off('mousedown').on('mousedown', function (event) {\n\t var currentY = event.pageY;\n\t var currentHeight = self.$select.height();\n\t self.minHeight = self.minHeight || currentHeight;\n\t $('#dd-helper').show().on('mousemove', function (event) {\n\t self.$select.height(Math.max(currentHeight + (event.pageY - currentY), self.minHeight));\n\t }).on('mouseup mouseleave', function () {\n\t $('#dd-helper').hide().off();\n\t });\n\t });\n\t } else {\n\t this.$dropdown.show();\n\t this.$resize.hide();\n\t this.$resize_icon.hide();\n\t }\n\t },\n\t\n\t /** Renders the default select2 field */\n\t _renderSearchable: function () {\n\t var self = this;\n\t this.$el.append(this.$select = $('')).append(this.$dropdown = $(''));\n\t this.$dropdown.hide();\n\t if (!this.model.get('multiple')) {\n\t this.$dropdown.show().on('click', function () {\n\t self.$select.select2 && self.$select.select2('open');\n\t });\n\t }\n\t this.all_button = null;\n\t if (this.model.get('multiple') && !this.model.get('individual')) {\n\t this.all_button = new Buttons.ButtonCheck({\n\t onclick: function () {\n\t var new_value = [];\n\t self.all_button.value() !== 0 && _.each(self.model.get('data'), function (option) {\n\t new_value.push(option.value);\n\t });\n\t self.value(new_value);\n\t self.trigger('change');\n\t }\n\t });\n\t this.$el.prepend(this.all_button.$el);\n\t }\n\t },\n\t\n\t /** Matches a search term with a given text */\n\t _match: function (term, text) {\n\t return !term || term == '' || String(text).toUpperCase().indexOf(term.toUpperCase()) >= 0;\n\t },\n\t\n\t /** Updates the selection options */\n\t _changeData: function () {\n\t var self = this;\n\t this.data = [];\n\t if (!this.model.get('multiple') && this.model.get('optional')) {\n\t this.data.push({ value: '__null__', label: self.model.get('empty_text') });\n\t }\n\t _.each(this.model.get('data'), function (option) {\n\t self.data.push(option);\n\t });\n\t if (this.length() == 0) {\n\t this.data.push({ value: '__null__', label: this.model.get('error_text') });\n\t }\n\t if (this.model.get('searchable')) {\n\t this.data2 = [];\n\t _.each(this.data, function (option, index) {\n\t self.data2.push({ order: index, id: option.value, text: option.label, tags: option.tags });\n\t });\n\t this.$select.data('select2') && this.$select.select2('destroy');\n\t this.matched_tags = {};\n\t this.$select.select2({\n\t data: self.data2,\n\t closeOnSelect: !this.model.get('multiple'),\n\t multiple: this.model.get('multiple'),\n\t query: function (q) {\n\t self.matched_tags = {};\n\t var pagesize = self.model.get('pagesize');\n\t var results = _.filter(self.data2, function (e) {\n\t var found = false;\n\t _.each(e.tags, function (tag) {\n\t if (self._match(q.term, tag)) {\n\t found = self.matched_tags[tag] = true;\n\t }\n\t });\n\t return found || self._match(q.term, e.text);\n\t });\n\t q.callback({\n\t results: results.slice((q.page - 1) * pagesize, q.page * pagesize),\n\t more: results.length >= q.page * pagesize\n\t });\n\t },\n\t formatResult: function (result) {\n\t return _.escape(result.text) + '';\n\t }\n\t });\n\t this.$('.select2-container .select2-search input').off('blur');\n\t } else {\n\t this.$select.find('option').remove();\n\t _.each(this.data, function (option) {\n\t self.$select.append($('').attr('value', option.value).html(_.escape(option.label)));\n\t });\n\t }\n\t this.model.set('disabled', this.length() == 0);\n\t this._changeValue();\n\t },\n\t\n\t /** Handles field enabling/disabling, usually used when no options are available */\n\t _changeDisabled: function () {\n\t if (this.model.get('searchable')) {\n\t this.$select.select2(this.model.get('disabled') ? 'disable' : 'enable');\n\t } else {\n\t this.$select.prop('disabled', this.model.get('disabled'));\n\t }\n\t },\n\t\n\t /** Searchable fields may display a spinner e.g. while waiting for a server response */\n\t _changeWait: function () {\n\t this.$dropdown.removeClass().addClass('icon-dropdown fa').addClass(this.model.get('wait') ? 'fa-spinner fa-spin' : 'fa-caret-down');\n\t },\n\t\n\t /** Handles field visibility */\n\t _changeVisible: function () {\n\t this.$el[this.model.get('visible') ? 'show' : 'hide']();\n\t this.$select[this.model.get('visible') ? 'show' : 'hide']();\n\t },\n\t\n\t /** Synchronizes the model value with the actually selected field value */\n\t _changeValue: function () {\n\t this._setValue(this.model.get('value'));\n\t if (this.model.get('multiple')) {\n\t if (this.all_button) {\n\t var value = this._getValue();\n\t this.all_button.value($.isArray(value) ? value.length : 0, this.length());\n\t }\n\t } else if (this._getValue() === null && !this.model.get('optional')) {\n\t this._setValue(this.first());\n\t }\n\t },\n\t\n\t /** Return/Set current selection */\n\t value: function (new_value) {\n\t new_value !== undefined && this.model.set('value', new_value);\n\t return this._getValue();\n\t },\n\t\n\t /** Return the first select option */\n\t first: function () {\n\t return this.data.length > 0 ? this.data[0].value : null;\n\t },\n\t\n\t /** Check if a value is an existing option */\n\t exists: function (value) {\n\t return _.findWhere(this.data, { value: value });\n\t },\n\t\n\t /** Return the label/text of the current selection */\n\t text: function () {\n\t var v = this._getValue();\n\t var d = this.exists($.isArray(v) ? v[0] : v);\n\t return d ? d.label : '';\n\t },\n\t\n\t /** Show the select field */\n\t show: function () {\n\t this.model.set('visible', true);\n\t },\n\t\n\t /** Hide the select field */\n\t hide: function () {\n\t this.model.set('visible', false);\n\t },\n\t\n\t /** Show a spinner indicating that the select options are currently loaded */\n\t wait: function () {\n\t this.model.set('wait', true);\n\t },\n\t\n\t /** Hide spinner indicating that the request has been completed */\n\t unwait: function () {\n\t this.model.set('wait', false);\n\t },\n\t\n\t /** Returns true if the field is disabled */\n\t disabled: function () {\n\t return this.model.get('disabled');\n\t },\n\t\n\t /** Enable the select field */\n\t enable: function () {\n\t this.model.set('disabled', false);\n\t },\n\t\n\t /** Disable the select field */\n\t disable: function () {\n\t this.model.set('disabled', true);\n\t },\n\t\n\t /** Update all available options at once */\n\t add: function (options, sorter) {\n\t _.each(this.model.get('data'), function (v) {\n\t v.keep && !_.findWhere(options, { value: v.value }) && options.push(v);\n\t });\n\t sorter && options && options.sort(sorter);\n\t this.model.set('data', options);\n\t },\n\t\n\t /** Update available options */\n\t update: function (options) {\n\t this.model.set('data', options);\n\t },\n\t\n\t /** Set the custom onchange callback function */\n\t setOnChange: function (callback) {\n\t this.model.set('onchange', callback);\n\t },\n\t\n\t /** Number of available options */\n\t length: function () {\n\t return $.isArray(this.model.get('data')) ? this.model.get('data').length : 0;\n\t },\n\t\n\t /** Set value to dom */\n\t _setValue: function (new_value) {\n\t var self = this;\n\t if (new_value === null || new_value === undefined) {\n\t new_value = '__null__';\n\t }\n\t if (this.model.get('multiple')) {\n\t new_value = $.isArray(new_value) ? new_value : [new_value];\n\t } else if ($.isArray(new_value)) {\n\t if (new_value.length > 0) {\n\t new_value = new_value[0];\n\t } else {\n\t new_value = '__null__';\n\t }\n\t }\n\t if (this.model.get('searchable')) {\n\t if ($.isArray(new_value)) {\n\t var val = [];\n\t _.each(new_value, function (v) {\n\t var d = _.findWhere(self.data2, { id: v });\n\t d && val.push(d);\n\t });\n\t new_value = val;\n\t } else {\n\t var d = _.findWhere(this.data2, { id: new_value });\n\t new_value = d;\n\t }\n\t this.$select.select2('data', new_value);\n\t } else {\n\t this.$select.val(new_value);\n\t }\n\t },\n\t\n\t /** Get value from dom */\n\t _getValue: function () {\n\t var val = null;\n\t if (this.model.get('searchable')) {\n\t var selected = this.$select.select2('data');\n\t if (selected) {\n\t if ($.isArray(selected)) {\n\t val = [];\n\t selected.sort(function (a, b) {\n\t return a.order - b.order;\n\t });\n\t _.each(selected, function (v) {\n\t val.push(v.id);\n\t });\n\t } else {\n\t val = selected.id;\n\t }\n\t }\n\t } else {\n\t val = this.$select.val();\n\t }\n\t return Utils.isEmpty(val) ? null : val;\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 16 */,\n/* 17 */,\n/* 18 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _, jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [\n\t //jquery\n\t //backbone\n\t], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t // =============================================================================\n\t /**\n\t * view for a popup menu\n\t */\n\t var PopupMenu = Backbone.View.extend({\n\t //TODO: maybe better as singleton off the Galaxy obj\n\t /** Cache the desired button element and options, set up the button click handler\n\t * NOTE: attaches this view as HTML/jQ data on the button for later use.\n\t */\n\t initialize: function ($button, options) {\n\t // default settings\n\t this.$button = $button;\n\t if (!this.$button.length) {\n\t this.$button = $('');\n\t }\n\t this.options = options || [];\n\t this.$button.data('popupmenu', this);\n\t\n\t // set up button click -> open menu behavior\n\t var menu = this;\n\t this.$button.click(function (event) {\n\t // if there's already a menu open, remove it\n\t $('.popmenu-wrapper').remove();\n\t menu._renderAndShow(event);\n\t return false;\n\t });\n\t },\n\t\n\t // render the menu, append to the page body at the click position, and set up the 'click-away' handlers, show\n\t _renderAndShow: function (clickEvent) {\n\t this.render();\n\t this.$el.appendTo('body').css(this._getShownPosition(clickEvent)).show();\n\t this._setUpCloseBehavior();\n\t },\n\t\n\t // render the menu\n\t // this menu doesn't attach itself to the DOM ( see _renderAndShow )\n\t render: function () {\n\t // render the menu body absolute and hidden, fill with template\n\t this.$el.addClass('popmenu-wrapper').hide().css({ position: 'absolute' }).html(this.template(this.$button.attr('id'), this.options));\n\t\n\t // set up behavior on each link/anchor elem\n\t if (this.options.length) {\n\t var menu = this;\n\t //precondition: there should be one option per li\n\t this.$el.find('li').each(function (i, li) {\n\t var option = menu.options[i];\n\t\n\t // if the option has 'func', call that function when the anchor is clicked\n\t if (option.func) {\n\t $(this).children('a.popupmenu-option').click(function (event) {\n\t option.func.call(menu, event, option);\n\t // We must preventDefault otherwise clicking \"cancel\"\n\t // on a purge or something still navigates and causes\n\t // the action.\n\t event.preventDefault();\n\t // bubble up so that an option click will call the close behavior\n\t });\n\t }\n\t });\n\t }\n\t return this;\n\t },\n\t\n\t template: function (id, options) {\n\t return [''].join('');\n\t },\n\t\n\t _templateOptions: function (options) {\n\t if (!options.length) {\n\t return '' + '' + '' + '' + '
' + '' + this.options.content + ' ' + '
';\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 24 */,\n/* 25 */,\n/* 26 */,\n/* 27 */,\n/* 28 */,\n/* 29 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/**\n\t This class creates a form input element wrapper\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t return Backbone.View.extend({\n\t initialize: function (app, options) {\n\t this.app = app;\n\t this.app_options = app.model ? app.model.attributes : {};\n\t this.field = options && options.field || new Backbone.View();\n\t this.model = options && options.model || new Backbone.Model({\n\t text_enable: this.app_options.text_enable || 'Enable',\n\t text_disable: this.app_options.text_disable || 'Disable',\n\t cls_enable: this.app_options.cls_enable || 'fa fa-caret-square-o-down',\n\t cls_disable: this.app_options.cls_disable || 'fa fa-caret-square-o-up',\n\t always_refresh: this.app_options.always_refresh\n\t }).set(options);\n\t\n\t // set element and link components\n\t this.setElement(this._template());\n\t this.$field = this.$('.ui-form-field');\n\t this.$info = this.$('.ui-form-info');\n\t this.$preview = this.$('.ui-form-preview');\n\t this.$collapsible = this.$('.ui-form-collapsible');\n\t this.$collapsible_text = this.$('.ui-form-collapsible-text');\n\t this.$collapsible_icon = this.$('.ui-form-collapsible-icon');\n\t this.$title = this.$('.ui-form-title');\n\t this.$title_text = this.$('.ui-form-title-text');\n\t this.$error_text = this.$('.ui-form-error-text');\n\t this.$error = this.$('.ui-form-error');\n\t this.$backdrop = this.$('.ui-form-backdrop');\n\t\n\t // add field element\n\t this.$field.prepend(this.field.$el);\n\t\n\t // decide wether to expand or collapse fields\n\t var collapsible_value = this.model.get('collapsible_value');\n\t this.field.collapsed = collapsible_value !== undefined && JSON.stringify(this.model.get('value')) == JSON.stringify(collapsible_value);\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t\n\t // add click handler\n\t var self = this;\n\t this.$collapsible.on('click', function () {\n\t self.field.collapsed = !self.field.collapsed;\n\t app.trigger && app.trigger('change');\n\t self.render();\n\t });\n\t\n\t // hide error on value change\n\t if (this.field.model && !this.model.get('always_refresh')) {\n\t this.listenTo(this.field.model, 'change:value', function () {\n\t self.reset();\n\t });\n\t }\n\t },\n\t\n\t /** Set backdrop for input element */\n\t backdrop: function () {\n\t this.model.set('backdrop', true);\n\t },\n\t\n\t /** Set error text */\n\t error: function (text) {\n\t this.model.set('error_text', text);\n\t },\n\t\n\t /** Reset this view */\n\t reset: function () {\n\t !this.model.get('fixed') && this.model.set('error_text', null);\n\t },\n\t\n\t render: function () {\n\t // render help\n\t $('.tooltip').hide();\n\t var help_text = this.model.get('help', '');\n\t var help_argument = this.model.get('argument');\n\t if (help_argument && help_text.indexOf('(' + help_argument + ')') == -1) {\n\t help_text += ' (' + help_argument + ')';\n\t }\n\t this.$info.html(help_text);\n\t // render visibility\n\t this.$el[this.model.get('hidden') ? 'hide' : 'show']();\n\t // render preview view for collapsed fields\n\t this.$preview[this.field.collapsed && this.model.get('collapsible_preview') || this.model.get('disabled') ? 'show' : 'hide']().html(_.escape(this.model.get('text_value')));\n\t // render error messages\n\t var error_text = this.model.get('error_text');\n\t this.$error[error_text ? 'show' : 'hide']();\n\t this.$el[error_text ? 'addClass' : 'removeClass']('ui-error');\n\t this.$error_text.html(error_text);\n\t // render backdrop\n\t this.$backdrop[this.model.get('backdrop') ? 'show' : 'hide']();\n\t // render input field\n\t this.field.collapsed || this.model.get('disabled') ? this.$field.hide() : this.$field.show();\n\t // render input field color and style\n\t this.field.model && this.field.model.set({ 'color': this.model.get('color'), 'style': this.model.get('style') });\n\t // render collapsible options\n\t if (!this.model.get('disabled') && this.model.get('collapsible_value') !== undefined) {\n\t var collapsible_state = this.field.collapsed ? 'enable' : 'disable';\n\t this.$title_text.hide();\n\t this.$collapsible.show();\n\t this.$collapsible_text.text(this.model.get('label'));\n\t this.$collapsible_icon.removeClass().addClass('icon').addClass(this.model.get('cls_' + collapsible_state)).attr('data-original-title', this.model.get('text_' + collapsible_state)).tooltip({ placement: 'bottom' });\n\t } else {\n\t this.$title_text.show().text(this.model.get('label'));\n\t this.$collapsible.hide();\n\t }\n\t },\n\t\n\t _template: function () {\n\t return $('').addClass('ui-form-element').append($('').addClass('ui-form-error ui-error').append($('').addClass('fa fa-arrow-down')).append($('').addClass('ui-form-error-text'))).append($('').addClass('ui-form-title').append($('').addClass('ui-form-collapsible').append($('').addClass('ui-form-collapsible-icon')).append($('').addClass('ui-form-collapsible-text'))).append($('').addClass('ui-form-title-text'))).append($('').addClass('ui-form-field').append($('').addClass('ui-form-info')).append($('').addClass('ui-form-backdrop'))).append($('').addClass('ui-form-preview'));\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 30 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {/**\n\t This class creates input elements. New input parameter types should be added to the types dictionary.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(5), __webpack_require__(38), __webpack_require__(41), __webpack_require__(39), __webpack_require__(40), __webpack_require__(36)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui, SelectContent, SelectLibrary, SelectFtp, SelectGenomeSpace, ColorPicker) {\n\t\n\t // create form view\n\t return Backbone.Model.extend({\n\t /** Available parameter types */\n\t types: {\n\t 'text': '_fieldText',\n\t 'password': '_fieldText',\n\t 'select': '_fieldSelect',\n\t 'data_column': '_fieldSelect',\n\t 'genomebuild': '_fieldSelect',\n\t 'data': '_fieldData',\n\t 'data_collection': '_fieldData',\n\t 'integer': '_fieldSlider',\n\t 'float': '_fieldSlider',\n\t 'boolean': '_fieldBoolean',\n\t 'drill_down': '_fieldDrilldown',\n\t 'color': '_fieldColor',\n\t 'hidden': '_fieldHidden',\n\t 'hidden_data': '_fieldHidden',\n\t 'baseurl': '_fieldHidden',\n\t 'library_data': '_fieldLibrary',\n\t 'ftpfile': '_fieldFtp',\n\t 'upload': '_fieldUpload',\n\t 'genomespacefile': '_fieldGenomeSpace'\n\t },\n\t\n\t /** Returns an input field for a given field type */\n\t create: function (input_def) {\n\t var fieldClass = this.types[input_def.type];\n\t var field = typeof this[fieldClass] === 'function' ? this[fieldClass].call(this, input_def) : null;\n\t if (!field) {\n\t field = input_def.options ? this._fieldSelect(input_def) : this._fieldText(input_def);\n\t Galaxy.emit.debug('form-parameters::_addRow()', 'Auto matched field type (' + input_def.type + ').');\n\t }\n\t input_def.value === undefined && (input_def.value = null);\n\t field.value(input_def.value);\n\t return field;\n\t },\n\t\n\t /** Data input field */\n\t _fieldData: function (input_def) {\n\t return new SelectContent.View({\n\t id: 'field-' + input_def.id,\n\t extensions: input_def.extensions,\n\t optional: input_def.optional,\n\t multiple: input_def.multiple,\n\t type: input_def.type,\n\t flavor: input_def.flavor,\n\t data: input_def.options,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Select/Checkbox/Radio options field */\n\t _fieldSelect: function (input_def) {\n\t // show text field e.g. in workflow editor\n\t if (input_def.is_workflow) {\n\t return this._fieldText(input_def);\n\t }\n\t\n\t // customize properties\n\t if (input_def.type == 'data_column') {\n\t input_def.error_text = 'Missing columns in referenced dataset.';\n\t }\n\t\n\t // identify available options\n\t var data = input_def.data;\n\t if (!data) {\n\t data = [];\n\t _.each(input_def.options, function (option) {\n\t data.push({ label: option[0], value: option[1] });\n\t });\n\t }\n\t\n\t // identify display type\n\t var SelectClass = Ui.Select;\n\t switch (input_def.display) {\n\t case 'checkboxes':\n\t SelectClass = Ui.Checkbox;\n\t break;\n\t case 'radio':\n\t SelectClass = Ui.Radio;\n\t break;\n\t case 'radiobutton':\n\t SelectClass = Ui.RadioButton;\n\t break;\n\t }\n\t\n\t // create select field\n\t return new SelectClass.View({\n\t id: 'field-' + input_def.id,\n\t data: data,\n\t error_text: input_def.error_text || 'No options available',\n\t multiple: input_def.multiple,\n\t optional: input_def.optional,\n\t onchange: input_def.onchange,\n\t individual: input_def.individual,\n\t searchable: input_def.flavor !== 'workflow'\n\t });\n\t },\n\t\n\t /** Drill down options field */\n\t _fieldDrilldown: function (input_def) {\n\t // show text field e.g. in workflow editor\n\t if (input_def.is_workflow) {\n\t return this._fieldText(input_def);\n\t }\n\t\n\t // create drill down field\n\t return new Ui.Drilldown.View({\n\t id: 'field-' + input_def.id,\n\t data: input_def.options,\n\t display: input_def.display,\n\t optional: input_def.optional,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Text input field */\n\t _fieldText: function (input_def) {\n\t // field replaces e.g. a select field\n\t if (input_def.options && input_def.data) {\n\t input_def.area = input_def.multiple;\n\t if (Utils.isEmpty(input_def.value)) {\n\t input_def.value = null;\n\t } else {\n\t if ($.isArray(input_def.value)) {\n\t var str_value = '';\n\t for (var i in input_def.value) {\n\t str_value += String(input_def.value[i]);\n\t if (!input_def.multiple) {\n\t break;\n\t }\n\t str_value += '\\n';\n\t }\n\t input_def.value = str_value;\n\t }\n\t }\n\t }\n\t // create input element\n\t return new Ui.Input({\n\t id: 'field-' + input_def.id,\n\t type: input_def.type,\n\t area: input_def.area,\n\t readonly: input_def.readonly,\n\t placeholder: input_def.placeholder,\n\t datalist: input_def.datalist,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Slider field */\n\t _fieldSlider: function (input_def) {\n\t return new Ui.Slider.View({\n\t id: 'field-' + input_def.id,\n\t precise: input_def.type == 'float',\n\t is_workflow: input_def.is_workflow,\n\t min: input_def.min,\n\t max: input_def.max,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Hidden field */\n\t _fieldHidden: function (input_def) {\n\t return new Ui.Hidden({\n\t id: 'field-' + input_def.id,\n\t info: input_def.info\n\t });\n\t },\n\t\n\t /** Boolean field */\n\t _fieldBoolean: function (input_def) {\n\t return new Ui.RadioButton.View({\n\t id: 'field-' + input_def.id,\n\t data: [{ label: 'Yes', value: 'true' }, { label: 'No', value: 'false' }],\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Color picker field */\n\t _fieldColor: function (input_def) {\n\t return new ColorPicker({\n\t id: 'field-' + input_def.id,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** Library dataset field */\n\t _fieldLibrary: function (input_def) {\n\t return new SelectLibrary.View({\n\t id: 'field-' + input_def.id,\n\t optional: input_def.optional,\n\t multiple: input_def.multiple,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** FTP file field */\n\t _fieldFtp: function (input_def) {\n\t return new SelectFtp.View({\n\t id: 'field-' + input_def.id,\n\t optional: input_def.optional,\n\t multiple: input_def.multiple,\n\t onchange: input_def.onchange\n\t });\n\t },\n\t\n\t /** GenomeSpace file select field\n\t */\n\t _fieldGenomeSpace: function (input_def) {\n\t var self = this;\n\t return new SelectGenomeSpace.View({\n\t id: 'field-' + input_def.id,\n\t onchange: function () {\n\t self.app.trigger('change');\n\t }\n\t });\n\t },\n\t\n\t /** Upload file field */\n\t _fieldUpload: function (input_def) {\n\t return new Ui.Upload({\n\t id: 'field-' + input_def.id,\n\t onchange: input_def.onchange\n\t });\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ },\n/* 31 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/** This class creates a ui component which enables the dynamic creation of portlets */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(9), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Portlet, Ui) {\n\t var View = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.list = {};\n\t this.options = Utils.merge(options, {\n\t title: 'Repeat',\n\t empty_text: 'Not available.',\n\t max: null,\n\t min: null\n\t });\n\t this.button_new = new Ui.ButtonIcon({\n\t icon: 'fa-plus',\n\t title: 'Insert ' + this.options.title,\n\t tooltip: 'Add new ' + this.options.title + ' block',\n\t cls: 'ui-button-icon ui-clear-float form-repeat-add',\n\t onclick: function () {\n\t options.onnew && options.onnew();\n\t }\n\t });\n\t this.setElement($('').append(this.$list = $('')).append($('').append(this.button_new.$el)));\n\t },\n\t\n\t /** Number of repeat blocks */\n\t size: function () {\n\t return _.size(this.list);\n\t },\n\t\n\t /** Add new repeat block */\n\t add: function (options) {\n\t if (!options.id || this.list[options.id]) {\n\t Galaxy.emit.debug('form-repeat::add()', 'Duplicate or invalid repeat block id.');\n\t return;\n\t }\n\t var button_delete = new Ui.ButtonIcon({\n\t icon: 'fa-trash-o',\n\t tooltip: 'Delete this repeat block',\n\t cls: 'ui-button-icon-plain form-repeat-delete',\n\t onclick: function () {\n\t options.ondel && options.ondel();\n\t }\n\t });\n\t var portlet = new Portlet.View({\n\t id: options.id,\n\t title: 'placeholder',\n\t cls: options.cls || 'ui-portlet-repeat',\n\t operations: { button_delete: button_delete }\n\t });\n\t portlet.append(options.$el);\n\t portlet.$el.addClass('section-row').hide();\n\t this.list[options.id] = portlet;\n\t this.$list.append(portlet.$el.fadeIn('fast'));\n\t this.options.max > 0 && this.size() >= this.options.max && this.button_new.disable();\n\t this._refresh();\n\t },\n\t\n\t /** Delete repeat block */\n\t del: function (id) {\n\t if (!this.list[id]) {\n\t Galaxy.emit.debug('form-repeat::del()', 'Invalid repeat block id.');\n\t return;\n\t }\n\t this.$list.find('#' + id).remove();\n\t delete this.list[id];\n\t this.button_new.enable();\n\t this._refresh();\n\t },\n\t\n\t /** Remove all */\n\t delAll: function () {\n\t for (var id in this.list) {\n\t this.del(id);\n\t }\n\t },\n\t\n\t /** Hides add/del options */\n\t hideOptions: function () {\n\t this.button_new.$el.hide();\n\t _.each(this.list, function (portlet) {\n\t portlet.hideOperation('button_delete');\n\t });\n\t _.isEmpty(this.list) && this.$el.append($('').addClass('ui-form-info').html(this.options.empty_text));\n\t },\n\t\n\t /** Refresh view */\n\t _refresh: function () {\n\t var index = 0;\n\t for (var id in this.list) {\n\t var portlet = this.list[id];\n\t portlet.title(++index + ': ' + this.options.title);\n\t portlet[this.size() > this.options.min ? 'showOperation' : 'hideOperation']('button_delete');\n\t }\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 32 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _, jQuery) {/**\n\t This class creates a form section and populates it with input elements. It also handles repeat blocks and conditionals by recursively creating new sub sections.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(5), __webpack_require__(9), __webpack_require__(31), __webpack_require__(29), __webpack_require__(30)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui, Portlet, Repeat, InputElement, Parameters) {\n\t var View = Backbone.View.extend({\n\t initialize: function (app, options) {\n\t this.app = app;\n\t this.inputs = options.inputs;\n\t this.parameters = new Parameters();\n\t this.setElement($(''));\n\t this.render();\n\t },\n\t\n\t /** Render section view */\n\t render: function () {\n\t var self = this;\n\t this.$el.empty();\n\t _.each(this.inputs, function (input) {\n\t self.add(input);\n\t });\n\t },\n\t\n\t /** Add a new input element */\n\t add: function (input) {\n\t var input_def = jQuery.extend(true, {}, input);\n\t input_def.id = input.id = Utils.uid();\n\t this.app.input_list[input_def.id] = input_def;\n\t switch (input_def.type) {\n\t case 'conditional':\n\t this._addConditional(input_def);\n\t break;\n\t case 'repeat':\n\t this._addRepeat(input_def);\n\t break;\n\t case 'section':\n\t this._addSection(input_def);\n\t break;\n\t default:\n\t this._addRow(input_def);\n\t }\n\t },\n\t\n\t /** Add a conditional block */\n\t _addConditional: function (input_def) {\n\t var self = this;\n\t input_def.test_param.id = input_def.id;\n\t this.app.model.get('sustain_conditionals') && (input_def.test_param.disabled = true);\n\t var field = this._addRow(input_def.test_param);\n\t\n\t // set onchange event for test parameter\n\t field.model && field.model.set('onchange', function (value) {\n\t var selectedCase = self.app.data.matchCase(input_def, value);\n\t for (var i in input_def.cases) {\n\t var case_def = input_def.cases[i];\n\t var section_row = self.$('#' + input_def.id + '-section-' + i);\n\t var nonhidden = false;\n\t for (var j in case_def.inputs) {\n\t if (!case_def.inputs[j].hidden) {\n\t nonhidden = true;\n\t break;\n\t }\n\t }\n\t if (i == selectedCase && nonhidden) {\n\t section_row.fadeIn('fast');\n\t } else {\n\t section_row.hide();\n\t }\n\t }\n\t self.app.trigger('change');\n\t });\n\t\n\t // add conditional sub sections\n\t for (var i in input_def.cases) {\n\t var sub_section = new View(this.app, { inputs: input_def.cases[i].inputs });\n\t this._append(sub_section.$el.addClass('ui-form-section'), input_def.id + '-section-' + i);\n\t }\n\t\n\t // trigger refresh on conditional input field after all input elements have been created\n\t field.trigger('change');\n\t },\n\t\n\t /** Add a repeat block */\n\t _addRepeat: function (input_def) {\n\t var self = this;\n\t var block_index = 0;\n\t\n\t // create repeat block element\n\t var repeat = new Repeat.View({\n\t title: input_def.title || 'Repeat',\n\t min: input_def.min,\n\t max: input_def.max,\n\t onnew: function () {\n\t create(input_def.inputs);self.app.trigger('change');\n\t }\n\t });\n\t\n\t // helper function to create new repeat blocks\n\t function create(inputs) {\n\t var sub_section_id = input_def.id + '-section-' + block_index++;\n\t var sub_section = new View(self.app, { inputs: inputs });\n\t repeat.add({ id: sub_section_id,\n\t $el: sub_section.$el,\n\t ondel: function () {\n\t repeat.del(sub_section_id);self.app.trigger('change');\n\t } });\n\t }\n\t\n\t //\n\t // add parsed/minimum number of repeat blocks\n\t //\n\t var n_cache = _.size(input_def.cache);\n\t for (var i = 0; i < Math.max(Math.max(n_cache, input_def.min || 0), input_def.default || 0); i++) {\n\t create(i < n_cache ? input_def.cache[i] : input_def.inputs);\n\t }\n\t\n\t // hide options\n\t this.app.model.get('sustain_repeats') && repeat.hideOptions();\n\t\n\t // create input field wrapper\n\t var input_element = new InputElement(this.app, {\n\t label: input_def.title || input_def.name,\n\t help: input_def.help,\n\t field: repeat\n\t });\n\t this._append(input_element.$el, input_def.id);\n\t },\n\t\n\t /** Add a customized section */\n\t _addSection: function (input_def) {\n\t var portlet = new Portlet.View({\n\t title: input_def.title || input_def.name,\n\t cls: 'ui-portlet-section',\n\t collapsible: true,\n\t collapsible_button: true,\n\t collapsed: !input_def.expanded\n\t });\n\t portlet.append(new View(this.app, { inputs: input_def.inputs }).$el);\n\t portlet.append($('').addClass('ui-form-info').html(input_def.help));\n\t this.app.on('expand', function (input_id) {\n\t portlet.$('#' + input_id).length > 0 && portlet.expand();\n\t });\n\t this._append(portlet.$el, input_def.id);\n\t },\n\t\n\t /** Add a single input field element */\n\t _addRow: function (input_def) {\n\t var self = this;\n\t var id = input_def.id;\n\t input_def.onchange = input_def.onchange || function () {\n\t self.app.trigger('change', id);\n\t };\n\t var field = this.parameters.create(input_def);\n\t this.app.field_list[id] = field;\n\t var input_element = new InputElement(this.app, {\n\t name: input_def.name,\n\t label: input_def.hide_label ? '' : input_def.label || input_def.name,\n\t value: input_def.value,\n\t text_value: input_def.text_value,\n\t collapsible_value: input_def.collapsible_value,\n\t collapsible_preview: input_def.collapsible_preview,\n\t help: input_def.help,\n\t argument: input_def.argument,\n\t disabled: input_def.disabled,\n\t color: input_def.color,\n\t style: input_def.style,\n\t backdrop: input_def.backdrop,\n\t hidden: input_def.hidden,\n\t fixed: input_def.fixed,\n\t field: field\n\t });\n\t this.app.element_list[id] = input_element;\n\t this._append(input_element.$el, input_def.id);\n\t return field;\n\t },\n\t\n\t /** Append a new element to the form i.e. input element, repeat block, conditionals etc. */\n\t _append: function ($el, id) {\n\t this.$el.append($el.addClass('section-row').attr('id', id));\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ },\n/* 33 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t\n\t // grid model\n\t return Backbone.Model.extend({\n\t defaults: {\n\t url_base: '',\n\t async: false,\n\t async_ops: [],\n\t categorical_filters: [],\n\t filters: {},\n\t sort_key: null,\n\t show_item_checkboxes: false,\n\t advanced_search: false,\n\t cur_page: 1,\n\t num_pages: 1,\n\t operation: undefined,\n\t item_ids: undefined\n\t },\n\t\n\t /**\n\t * Return true if operation can be done asynchronously.\n\t */\n\t can_async_op: function (op) {\n\t return _.indexOf(this.attributes.async_ops, op) !== -1;\n\t },\n\t\n\t /**\n\t * Add filtering criterion.\n\t */\n\t add_filter: function (key, value, append) {\n\t // Update URL arg with new condition. \n\t if (append) {\n\t // Update or append value.\n\t var cur_val = this.attributes.filters[key],\n\t new_val;\n\t if (cur_val === null || cur_val === undefined) {\n\t new_val = value;\n\t } else if (typeof cur_val == 'string') {\n\t if (cur_val == 'All' || cur_val == value) {\n\t new_val = value;\n\t } else {\n\t // Replace string with array.\n\t var values = [];\n\t values[0] = cur_val;\n\t values[1] = value;\n\t new_val = values;\n\t }\n\t } else {\n\t // Current value is an array.\n\t new_val = cur_val;\n\t if (new_val.indexOf(value) === -1) {\n\t new_val.push(value);\n\t }\n\t }\n\t this.attributes.filters[key] = new_val;\n\t } else {\n\t // Replace value.\n\t this.attributes.filters[key] = value;\n\t }\n\t },\n\t\n\t /**\n\t * Remove filtering criterion.\n\t */\n\t remove_filter: function (key, condition) {\n\t var cur_val = this.attributes.filters[key];\n\t if (cur_val === null || cur_val === undefined) {\n\t return false;\n\t }\n\t\n\t if (typeof cur_val === 'string') {\n\t // overwrite/remove condition.\n\t this.attributes.filters[key] = '';\n\t } else {\n\t // filter contains an array of conditions.\n\t var condition_index = _.indexOf(cur_val, condition);\n\t if (condition_index !== -1) {\n\t cur_val[condition_index] = '';\n\t }\n\t }\n\t },\n\t\n\t /**\n\t * Returns URL data for obtaining a new grid.\n\t */\n\t get_url_data: function () {\n\t var url_data = {\n\t async: this.attributes.async,\n\t sort: this.attributes.sort_key,\n\t page: this.attributes.cur_page,\n\t show_item_checkboxes: this.attributes.show_item_checkboxes,\n\t advanced_search: this.attributes.advanced_search\n\t };\n\t\n\t // Add operation, item_ids only if they have values.\n\t if (this.attributes.operation) {\n\t url_data.operation = this.attributes.operation;\n\t }\n\t if (this.attributes.item_ids) {\n\t url_data.id = this.attributes.item_ids;\n\t }\n\t\n\t // Add filter arguments to data, placing \"f-\" in front of all arguments.\n\t var self = this;\n\t _.each(_.pairs(self.attributes.filters), function (k) {\n\t url_data['f-' + k[0]] = k[1];\n\t });\n\t return url_data;\n\t },\n\t\n\t // Return URL for obtaining a new grid\n\t get_url: function (args) {\n\t return this.get('url_base') + '?' + $.param(this.get_url_data()) + '&' + $.param(args);\n\t }\n\t\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ },\n/* 34 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(jQuery, _) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t\n\t // grid view templates\n\t return {\n\t // template\n\t grid: function (options) {\n\t var tmpl = '';\n\t if (options.embedded) {\n\t tmpl = this.grid_header(options) + this.grid_table(options);\n\t } else {\n\t tmpl = '' + '' + '
' + this.grid_table(options);\n\t }\n\t\n\t // add info text\n\t if (options.info_text) {\n\t tmpl += '
';\n\t\n\t // add checkbox\n\t if (options.show_item_checkboxes) {\n\t tmpl += '';\n\t if (options.items.length > 0) {\n\t tmpl += '' + '';\n\t }\n\t tmpl += ' ';\n\t }\n\t\n\t // create header elements\n\t for (var i in options.columns) {\n\t var column = options.columns[i];\n\t if (column.visible) {\n\t tmpl += '';\n\t if (column.href) {\n\t tmpl += '' + column.label + '';\n\t } else {\n\t tmpl += column.label;\n\t }\n\t tmpl += '' + column.extra + '' + ' ';\n\t }\n\t }\n\t\n\t // finalize\n\t tmpl += ' ';\n\t\n\t // return template\n\t return tmpl;\n\t },\n\t\n\t // template\n\t body: function (options) {\n\t // initialize\n\t var tmpl = '';\n\t var num_rows_rendered = 0;\n\t var items_length = options.items.length;\n\t\n\t // empty grid?\n\t if (items_length == 0) {\n\t // No results.\n\t tmpl += 'No Items ';\n\t\n\t // Link\n\t if (link) {\n\t if (options.operations.length != 0) {\n\t tmpl += ' ';\n\t }\n\t }\n\t tmpl += '';\n\t num_rows_rendered++;\n\t }\n\t return tmpl;\n\t },\n\t\n\t // template\n\t footer: function (options) {\n\t\n\t // create template string\n\t var tmpl = '';\n\t\n\t // paging\n\t if (options.use_paging && options.num_pages > 1) {\n\t // get configuration\n\t var num_page_links = options.num_page_links;\n\t var cur_page_num = options.cur_page_num;\n\t var num_pages = options.num_pages;\n\t\n\t // First pass on min page.\n\t var page_link_range = num_page_links / 2;\n\t var min_page = cur_page_num - page_link_range;\n\t var min_offset = 0;\n\t if (min_page <= 0) {\n\t // Min page is too low.\n\t min_page = 1;\n\t min_offset = page_link_range - (cur_page_num - min_page);\n\t }\n\t\n\t // Set max page.\n\t var max_range = page_link_range + min_offset;\n\t var max_page = cur_page_num + max_range;\n\t var max_offset;\n\t if (max_page <= num_pages) {\n\t // Max page is fine.\n\t max_offset = 0;\n\t } else {\n\t // Max page is too high.\n\t max_page = num_pages;\n\t // +1 to account for the +1 in the loop below.\n\t max_offset = max_range - (max_page + 1 - cur_page_num);\n\t }\n\t\n\t // Second and final pass on min page to add any unused\n\t // offset from max to min.\n\t if (max_offset != 0) {\n\t min_page -= max_offset;\n\t if (min_page < 1) {\n\t min_page = 1;\n\t }\n\t }\n\t\n\t // template header\n\t tmpl += '';\n\t if (options.show_item_checkboxes) {\n\t tmpl += '' + '' + 'Page:';\n\t\n\t if (min_page > 1) {\n\t tmpl += '1 ...';\n\t }\n\t\n\t // create page urls\n\t for (var page_index = min_page; page_index < max_page + 1; page_index++) {\n\t\n\t if (page_index == options.cur_page_num) {\n\t tmpl += '' + page_index + '';\n\t } else {\n\t tmpl += '' + page_index + '';\n\t }\n\t }\n\t\n\t // show last page\n\t if (max_page < num_pages) {\n\t tmpl += '...' + '' + num_pages + '';\n\t }\n\t tmpl += '';\n\t\n\t // Show all link\n\t tmpl += ' | Show All' + ' ' + ' ';\n\t }\n\t\n\t // Grid operations for multiple items.\n\t if (options.show_item_checkboxes) {\n\t // start template\n\t tmpl += '' + '' + '' + 'For selected items: ';\n\t\n\t // configure buttons for operations\n\t for (var i in options.operations) {\n\t var operation = options.operations[i];\n\t if (operation.allow_multiple) {\n\t tmpl += ' ';\n\t }\n\t }\n\t\n\t // finalize template\n\t tmpl += ' ' + ' ';\n\t }\n\t\n\t // count global operations\n\t var found_global = false;\n\t for (i in options.operations) {\n\t if (options.operations[i].global_operation) {\n\t found_global = true;\n\t break;\n\t }\n\t }\n\t\n\t // add global operations\n\t if (found_global) {\n\t tmpl += '' + '';\n\t for (i in options.operations) {\n\t var operation = options.operations[i];\n\t if (operation.global_operation) {\n\t tmpl += '' + operation.label + '';\n\t }\n\t }\n\t tmpl += ' ' + ' ';\n\t }\n\t\n\t // add legend\n\t if (options.legend) {\n\t tmpl += '' + '' + options.legend + ' ' + ' ';\n\t }\n\t\n\t // return\n\t return tmpl;\n\t },\n\t\n\t // template\n\t message: function (options) {\n\t var status = options.status == 'success' ? 'done' : options.status;\n\t return '';\n\t\n\t if (column.filterable == 'advanced') {\n\t tmpl += '' + column_label + ': ';\n\t }\n\t tmpl += '';\n\t if (column.is_text) {\n\t tmpl += '';\n\t } else {\n\t // filter criteria\n\t tmpl += '';\n\t\n\t // add category filters\n\t var seperator = false;\n\t for (var cf_label in options.categorical_filters[column_key]) {\n\t // get category filter\n\t var cf = options.categorical_filters[column_key][cf_label];\n\t\n\t // each filter will have only a single argument, so get that single argument\n\t var cf_key = '';\n\t var cf_arg = '';\n\t for (var key in cf) {\n\t cf_key = key;\n\t cf_arg = cf[key];\n\t }\n\t\n\t // add seperator\n\t if (seperator) {\n\t tmpl += ' | ';\n\t }\n\t seperator = true;\n\t\n\t // add category\n\t var filter = filters[column_key];\n\t if (filter && cf[column_key] && filter == cf_arg) {\n\t tmpl += '' + cf_label + '';\n\t } else {\n\t tmpl += '' + '' + cf_label + '' + '';\n\t }\n\t }\n\t tmpl += '';\n\t }\n\t tmpl += ' ' + ' ';\n\t\n\t // return template\n\t return tmpl;\n\t },\n\t\n\t // template for filter items\n\t filter_element: function (filter_key, filter_value) {\n\t filter_value = Utils.sanitize(filter_value);\n\t return '' + filter_value + '' + '' + '' + '';\n\t }\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 35 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;// Provides support for interacting with the GenomeSpace File Browser popup dialogue\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t\n\t // tool form templates\n\t return {\n\t openFileBrowser: function (options) {\n\t var GS_UI_URL = window.Galaxy.config.genomespace_ui_url;\n\t var GS_UPLOAD_URL = GS_UI_URL + 'upload/loadUrlToGenomespace.html?getLocation=true';\n\t\n\t var newWin = window.open(GS_UPLOAD_URL, \"GenomeSpace File Browser\", \"height=360px,width=600px\");\n\t\n\t successCalBack = options['successCallback'];\n\t window.addEventListener(\"message\", function (e) {\n\t successCalBack(e.data);\n\t }, false);\n\t\n\t newWin.focus();\n\t\n\t if (options['errorCallback'] != null) newWin.setCallbackOnGSUploadError = config['errorCallback'];\n\t }\n\t\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\n/***/ },\n/* 36 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/** Renders the color picker used e.g. in the tool form **/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t return Backbone.View.extend({\n\t colors: {\n\t standard: ['c00000', 'ff0000', 'ffc000', 'ffff00', '92d050', '00b050', '00b0f0', '0070c0', '002060', '7030a0'],\n\t base: ['ffffff', '000000', 'eeece1', '1f497d', '4f81bd', 'c0504d', '9bbb59', '8064a2', '4bacc6', 'f79646'],\n\t theme: [['f2f2f2', '7f7f7f', 'ddd9c3', 'c6d9f0', 'dbe5f1', 'f2dcdb', 'ebf1dd', 'e5e0ec', 'dbeef3', 'fdeada'], ['d8d8d8', '595959', 'c4bd97', '8db3e2', 'b8cce4', 'e5b9b7', 'd7e3bc', 'ccc1d9', 'b7dde8', 'fbd5b5'], ['bfbfbf', '3f3f3f', '938953', '548dd4', '95b3d7', 'd99694', 'c3d69b', 'b2a2c7', '92cddc', 'fac08f'], ['a5a5a5', '262626', '494429', '17365d', '366092', '953734', '76923c', '5f497a', '31859b', 'e36c09'], ['7f7f7e', '0c0c0c', '1d1b10', '0f243e', '244061', '632423', '4f6128', '3f3151', '205867', '974806']]\n\t },\n\t\n\t initialize: function (options) {\n\t this.options = Utils.merge(options, {});\n\t this.setElement(this._template());\n\t this.$panel = this.$('.ui-color-picker-panel');\n\t this.$view = this.$('.ui-color-picker-view');\n\t this.$value = this.$('.ui-color-picker-value');\n\t this.$header = this.$('.ui-color-picker-header');\n\t this._build();\n\t this.visible = false;\n\t this.value(this.options.value);\n\t this.$boxes = this.$('.ui-color-picker-box');\n\t var self = this;\n\t this.$boxes.on('click', function () {\n\t self.value($(this).css('background-color'));\n\t self.$header.trigger('click');\n\t });\n\t this.$header.on('click', function () {\n\t self.visible = !self.visible;\n\t if (self.visible) {\n\t self.$view.fadeIn('fast');\n\t } else {\n\t self.$view.fadeOut('fast');\n\t }\n\t });\n\t },\n\t\n\t /** Get/set value */\n\t value: function (new_val) {\n\t if (new_val !== undefined && new_val !== null) {\n\t this.$value.css('background-color', new_val);\n\t this.$('.ui-color-picker-box').empty();\n\t this.$(this._getValue()).html(this._templateCheck());\n\t this.options.onchange && this.options.onchange(new_val);\n\t }\n\t return this._getValue();\n\t },\n\t\n\t /** Get value from dom */\n\t _getValue: function () {\n\t var rgb = this.$value.css('background-color');\n\t rgb = rgb.match(/^rgb\\((\\d+),\\s*(\\d+),\\s*(\\d+)\\)$/);\n\t if (rgb) {\n\t function hex(x) {\n\t return ('0' + parseInt(x).toString(16)).slice(-2);\n\t }\n\t return '#' + hex(rgb[1]) + hex(rgb[2]) + hex(rgb[3]);\n\t } else {\n\t return null;\n\t }\n\t },\n\t\n\t /** Build color panel */\n\t _build: function () {\n\t this._content({ colors: this.colors.base });\n\t for (var i in this.colors.theme) {\n\t var line_def = {};\n\t if (i == 0) {\n\t line_def['bottom'] = true;\n\t } else if (i != this.colors.theme.length - 1) {\n\t line_def['top'] = true;\n\t line_def['bottom'] = true;\n\t } else {\n\t line_def['top'] = true;\n\t }\n\t line_def['colors'] = this.colors.theme[i];\n\t this._content(line_def);\n\t }\n\t this._content({ colors: this.colors.standard });\n\t },\n\t\n\t /** Create content */\n\t _content: function (options) {\n\t var colors = options.colors;\n\t var $content = $(this._templateContent());\n\t var $line = $content.find('.line');\n\t this.$panel.append($content);\n\t for (var i in colors) {\n\t var $box = $(this._templateBox(colors[i]));\n\t if (options.top) {\n\t $box.css('border-top', 'none');\n\t $box.css('border-top-left-radius', '0px');\n\t $box.css('border-top-right-radius', '0px');\n\t }\n\t if (options.bottom) {\n\t $box.css('border-bottom', 'none');\n\t $box.css('border-bottom-left-radius', '0px');\n\t $box.css('border-bottom-right-radius', '0px');\n\t }\n\t $line.append($box);\n\t }\n\t return $content;\n\t },\n\t\n\t /** Check icon */\n\t _templateCheck: function () {\n\t return '';\n\t },\n\t\n\t /** Content template */\n\t _templateContent: function () {\n\t return '
| ' + this.grid_header(options) + ' | ' + '' + ' | ' + ' |
| ' + ' | ' + ' | ' + ' |
' + options.info_text + '
';\n\t }\n\t\n\t // return\n\t return tmpl;\n\t },\n\t\n\t // template\n\t grid_table: function (options) {\n\t return '';\n\t },\n\t\n\t // template\n\t grid_header: function (options) {\n\t var tmpl = '';\n\t if (!options.embedded) {\n\t tmpl += '
';\n\t\n\t // return template\n\t return tmpl;\n\t },\n\t\n\t // template\n\t header: function (options) {\n\t\n\t // start\n\t var tmpl = '' + options.title + '
';\n\t }\n\t if (options.global_actions) {\n\t tmpl += '- ';\n\t var show_popup = options.global_actions.length >= 3;\n\t if (show_popup) {\n\t tmpl += '
- Actions ' + '
- ' + '' + action.label + '' + ' ';\n\t }\n\t if (show_popup) {\n\t tmpl += '
';\n\t }\n\t for (var i in options.global_actions) {\n\t var action = options.global_actions[i];\n\t tmpl += '
';\n\t }\n\t tmpl += '';\n\t }\n\t tmpl += '' + value + '';\n\t if (options.operations.length != 0) {\n\t tmpl += '
';\n\t }\n\t } else {\n\t tmpl += '';\n\t }\n\t tmpl += '' + '
' + _.escape(options.message) + '
' + '' + '';\n\t },\n\t\n\t // template\n\t grid_filters: function (options) {\n\t\n\t // get filters\n\t var default_filter_dict = options.default_filter_dict;\n\t var filters = options.filters;\n\t\n\t // show advanced search if flag set or if there are filters for advanced search fields\n\t var advanced_search_display = 'none';\n\t if (options.advanced_search) {\n\t advanced_search_display = 'block';\n\t }\n\t\n\t // identify columns with advanced filtering\n\t var show_advanced_search_link = false;\n\t for (var i in options.columns) {\n\t var column = options.columns[i];\n\t if (column.filterable == 'advanced') {\n\t var column_key = column.key;\n\t var f_key = filters[column_key];\n\t var d_key = default_filter_dict[column_key];\n\t if (f_key && d_key && f_key != d_key) {\n\t advanced_search_display = 'block';\n\t }\n\t show_advanced_search_link = true;\n\t }\n\t }\n\t\n\t // hide standard search if advanced is shown\n\t var standard_search_display = 'block';\n\t if (advanced_search_display == 'block') {\n\t standard_search_display = 'none';\n\t }\n\t\n\t //\n\t // standard search\n\t //\n\t var tmpl = '' + '' + '
' + '
';\n\t\n\t //\n\t // advanced search\n\t //\n\t tmpl += '| ' + ' | ' + '
| ';\n\t\n\t // show advanced search link in standard display\n\t if (show_advanced_search_link) {\n\t tmpl += 'Advanced Search';\n\t }\n\t\n\t // finalize standard search display\n\t tmpl += ' | ' + '
' + '' + '
' + '
';\n\t\n\t // return template\n\t return tmpl;\n\t },\n\t\n\t // template\n\t grid_column_filter: function (options, column) {\n\t\n\t // collect parameters\n\t var default_filter_dict = options.default_filter_dict;\n\t var filters = options.filters;\n\t var column_label = column.label;\n\t var column_key = column.key;\n\t if (column.filterable == 'advanced') {\n\t column_label = column_label.toLowerCase();\n\t }\n\t\n\t // start\n\t var tmpl = '| ' + 'Close Advanced Search' + ' | ' + '
' + '
' + '
';\n\t },\n\t\n\t /** Box template */\n\t _templateBox: function (color) {\n\t return '';\n\t },\n\t\n\t /** Main template */\n\t _template: function () {\n\t return '' + '
' + '
' + '
' + 'Select a color
' + '' + '
';\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 37 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function($, _) {/** This class creates/wraps a drill down element. */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(14)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Options) {\n\t\n\t var View = Options.BaseIcons.extend({\n\t initialize: function (options) {\n\t options.type = options.display || 'checkbox';\n\t options.multiple = options.type == 'checkbox';\n\t Options.BaseIcons.prototype.initialize.call(this, options);\n\t },\n\t\n\t /** Set states for selected values */\n\t _setValue: function (new_value) {\n\t Options.BaseIcons.prototype._setValue.call(this, new_value);\n\t if (new_value !== undefined && new_value !== null && this.header_index) {\n\t var self = this;\n\t var values = $.isArray(new_value) ? new_value : [new_value];\n\t _.each(values, function (v) {\n\t var list = self.header_index[v];\n\t _.each(list, function (element) {\n\t self._setState(element, true);\n\t });\n\t });\n\t }\n\t },\n\t\n\t /** Expand/collapse a sub group */\n\t _setState: function (header_id, is_expanded) {\n\t var $button = this.$('.button-' + header_id);\n\t var $subgroup = this.$('.subgroup-' + header_id);\n\t $button.data('is_expanded', is_expanded);\n\t if (is_expanded) {\n\t $subgroup.show();\n\t $button.removeClass('fa-plus-square').addClass('fa-minus-square');\n\t } else {\n\t $subgroup.hide();\n\t $button.removeClass('fa-minus-square').addClass('fa-plus-square');\n\t }\n\t },\n\t\n\t /** Template to create options tree */\n\t _templateOptions: function () {\n\t var self = this;\n\t this.header_index = {};\n\t\n\t // attach event handler\n\t function attach($el, header_id) {\n\t var $button = $el.find('.button-' + header_id);\n\t $button.on('click', function () {\n\t self._setState(header_id, !$button.data('is_expanded'));\n\t });\n\t }\n\t\n\t // recursive function which iterates through options\n\t function iterate($tmpl, options, header) {\n\t header = header || [];\n\t for (var i in options) {\n\t var level = options[i];\n\t var has_options = level.options && level.options.length > 0;\n\t var new_header = header.slice(0);\n\t self.header_index[level.value] = new_header.slice(0);\n\t var $group = $('');\n\t if (has_options) {\n\t var header_id = Utils.uid();\n\t var $button = $('').addClass('button-' + header_id).addClass('ui-drilldown-button fa fa-plus-square');\n\t var $subgroup = $('').addClass('subgroup-' + header_id).addClass('ui-drilldown-subgroup');\n\t $group.append($('').append($button).append(self._templateOption({ label: level.name, value: level.value })));\n\t new_header.push(header_id);\n\t iterate($subgroup, level.options, new_header);\n\t $group.append($subgroup);\n\t attach($group, header_id);\n\t } else {\n\t $group.append(self._templateOption({ label: level.name, value: level.value }));\n\t }\n\t $tmpl.append($group);\n\t }\n\t }\n\t\n\t // iterate through options and create dom\n\t var $tmpl = $('');\n\t iterate($tmpl, this.model.get('data'));\n\t return $tmpl;\n\t },\n\t\n\t /** Template for drill down view */\n\t _template: function () {\n\t return $('').addClass('ui-options-list drilldown-container').attr('id', this.model.id);\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 38 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(5), __webpack_require__(15)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui, Select) {\n\t\n\t /** Batch mode variations */\n\t var Batch = { DISABLED: 'disabled', ENABLED: 'enabled', LINKED: 'linked' };\n\t\n\t /** List of available content selectors options */\n\t var Configurations = {\n\t data: [{ src: 'hda', icon: 'fa-file-o', tooltip: 'Single dataset', multiple: false, batch: Batch.DISABLED }, { src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.LINKED }, { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.LINKED }],\n\t data_multiple: [{ src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.DISABLED }, { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collections', multiple: true, batch: Batch.DISABLED }],\n\t data_collection: [{ src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.DISABLED }],\n\t workflow_data: [{ src: 'hda', icon: 'fa-file-o', tooltip: 'Single dataset', multiple: false, batch: Batch.DISABLED }],\n\t workflow_data_multiple: [{ src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.DISABLED }],\n\t workflow_data_collection: [{ src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.DISABLED }],\n\t module_data: [{ src: 'hda', icon: 'fa-file-o', tooltip: 'Single dataset', multiple: false, batch: Batch.DISABLED }, { src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.ENABLED }],\n\t module_data_collection: [{ src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.DISABLED }, { src: 'hdca', icon: 'fa-folder', tooltip: 'Multiple collections', multiple: true, batch: Batch.ENABLED }]\n\t };\n\t\n\t /** View for hda and hdca content selector ui elements */\n\t var View = Backbone.View.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.model = options && options.model || new Backbone.Model({\n\t src_labels: { 'hda': 'dataset', 'hdca': 'dataset collection' },\n\t pagelimit: 100,\n\t statustimer: 1000\n\t }).set(options);\n\t this.setElement($('').addClass('ui-select-content'));\n\t this.button_product = new Ui.RadioButton.View({\n\t value: 'false',\n\t data: [{ icon: 'fa fa-chain', value: 'false',\n\t tooltip: 'Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads.' }, { icon: 'fa fa-chain-broken', value: 'true',\n\t tooltip: 'Unlinked dataset inputs will be run against *all* other inputs.' }] });\n\t var $batch_div = $('').addClass('ui-form-info').append($('').addClass('fa fa-sitemap')).append($('').html('This is a batch mode input field. Separate jobs will be triggered for each dataset selection.'));\n\t this.$batch = {\n\t linked: $batch_div.clone(),\n\t enabled: $batch_div.clone().append($('').append($('').addClass('ui-form-title').html('Batch options:')).append(this.button_product.$el)).append($('').css('clear', 'both'))\n\t };\n\t\n\t // add drag-drop event handlers\n\t this.$el.on('dragenter', function (e) {\n\t this.lastenter = e.target;self.$el.addClass('ui-dragover');\n\t }).on('dragover', function (e) {\n\t e.preventDefault();\n\t }).on('dragleave', function (e) {\n\t this.lastenter === e.target && self.$el.removeClass('ui-dragover');\n\t }).on('drop', function (e) {\n\t self._handleDrop(e);\n\t });\n\t\n\t // track current history elements\n\t this.history = {};\n\t\n\t // add listeners\n\t this.listenTo(this.model, 'change:data', this._changeData, this);\n\t this.listenTo(this.model, 'change:wait', this._changeWait, this);\n\t this.listenTo(this.model, 'change:current', this._changeCurrent, this);\n\t this.listenTo(this.model, 'change:value', this._changeValue, this);\n\t this.listenTo(this.model, 'change:type change:optional change:multiple change:extensions', this._changeType, this);\n\t this.render();\n\t\n\t // add change event\n\t this.on('change', function () {\n\t options.onchange && options.onchange(self.value());\n\t });\n\t },\n\t\n\t render: function () {\n\t this._changeType();\n\t this._changeValue();\n\t this._changeWait();\n\t },\n\t\n\t /** Indicate that select fields are being updated */\n\t wait: function () {\n\t this.model.set('wait', true);\n\t },\n\t\n\t /** Indicate that the options update has been completed */\n\t unwait: function () {\n\t this.model.set('wait', false);\n\t },\n\t\n\t /** Update data representing selectable options */\n\t update: function (options) {\n\t this.model.set('data', options);\n\t },\n\t\n\t /** Return the currently selected dataset values */\n\t value: function (new_value) {\n\t new_value !== undefined && this.model.set('value', new_value);\n\t var current = this.model.get('current');\n\t if (this.config[current]) {\n\t var id_list = this.fields[current].value();\n\t if (id_list !== null) {\n\t id_list = $.isArray(id_list) ? id_list : [id_list];\n\t if (id_list.length > 0) {\n\t var result = this._batch({ values: [] });\n\t for (var i in id_list) {\n\t var details = this.history[id_list[i] + '_' + this.config[current].src];\n\t if (details) {\n\t result.values.push(details);\n\t } else {\n\t Galaxy.emit.debug('ui-select-content::value()', 'Requested details not found for \\'' + id_list[i] + '\\'.');\n\t return null;\n\t }\n\t }\n\t result.values.sort(function (a, b) {\n\t return a.hid - b.hid;\n\t });\n\t return result;\n\t }\n\t }\n\t } else {\n\t Galaxy.emit.debug('ui-select-content::value()', 'Invalid value/source \\'' + new_value + '\\'.');\n\t }\n\t return null;\n\t },\n\t\n\t /** Change of current select field */\n\t _changeCurrent: function () {\n\t var self = this;\n\t _.each(this.fields, function (field, i) {\n\t if (self.model.get('current') == i) {\n\t field.$el.show();\n\t _.each(self.$batch, function ($batchfield, batchmode) {\n\t $batchfield[self.config[i].batch == batchmode ? 'show' : 'hide']();\n\t });\n\t self.button_type.value(i);\n\t } else {\n\t field.$el.hide();\n\t }\n\t });\n\t },\n\t\n\t /** Change of type */\n\t _changeType: function () {\n\t var self = this;\n\t\n\t // identify selector type identifier i.e. [ flavor ]_[ type ]_[ multiple ]\n\t var config_id = (this.model.get('flavor') ? this.model.get('flavor') + '_' : '') + String(this.model.get('type')) + (this.model.get('multiple') ? '_multiple' : '');\n\t if (Configurations[config_id]) {\n\t this.config = Configurations[config_id];\n\t } else {\n\t this.config = Configurations['data'];\n\t Galaxy.emit.debug('ui-select-content::_changeType()', 'Invalid configuration/type id \\'' + config_id + '\\'.');\n\t }\n\t\n\t // prepare extension component of error message\n\t var data = self.model.get('data');\n\t var extensions = Utils.textify(this.model.get('extensions'));\n\t var src_labels = this.model.get('src_labels');\n\t\n\t // build views\n\t this.fields = [];\n\t this.button_data = [];\n\t _.each(this.config, function (c, i) {\n\t self.button_data.push({\n\t value: i,\n\t icon: c.icon,\n\t tooltip: c.tooltip\n\t });\n\t self.fields.push(new Select.View({\n\t optional: self.model.get('optional'),\n\t multiple: c.multiple,\n\t searchable: !c.multiple || data && data[c.src] && data[c.src].length > self.model.get('pagelimit'),\n\t individual: true,\n\t error_text: 'No ' + (extensions ? extensions + ' ' : '') + (src_labels[c.src] || 'content') + ' available.',\n\t onchange: function () {\n\t self.trigger('change');\n\t }\n\t }));\n\t });\n\t this.button_type = new Ui.RadioButton.View({\n\t value: this.model.get('current'),\n\t data: this.button_data,\n\t onchange: function (value) {\n\t self.model.set('current', value);\n\t self.trigger('change');\n\t }\n\t });\n\t\n\t // append views\n\t this.$el.empty();\n\t var button_width = 0;\n\t if (this.fields.length > 1) {\n\t this.$el.append(this.button_type.$el);\n\t button_width = Math.max(0, this.fields.length * 36) + 'px';\n\t }\n\t _.each(this.fields, function (field) {\n\t self.$el.append(field.$el.css({ 'margin-left': button_width }));\n\t });\n\t _.each(this.$batch, function ($batchfield, batchmode) {\n\t self.$el.append($batchfield.css({ 'margin-left': button_width }));\n\t });\n\t this.model.set('current', 0);\n\t this._changeCurrent();\n\t this._changeData();\n\t },\n\t\n\t /** Change of wait flag */\n\t _changeWait: function () {\n\t var self = this;\n\t _.each(this.fields, function (field) {\n\t field[self.model.get('wait') ? 'wait' : 'unwait']();\n\t });\n\t },\n\t\n\t /** Change of available options */\n\t _changeData: function () {\n\t var options = this.model.get('data');\n\t var self = this;\n\t var select_options = {};\n\t _.each(options, function (items, src) {\n\t select_options[src] = [];\n\t _.each(items, function (item) {\n\t select_options[src].push({\n\t hid: item.hid,\n\t keep: item.keep,\n\t label: item.hid + ': ' + item.name,\n\t value: item.id,\n\t tags: item.tags\n\t });\n\t self.history[item.id + '_' + src] = item;\n\t });\n\t });\n\t _.each(this.config, function (c, i) {\n\t select_options[c.src] && self.fields[i].add(select_options[c.src], function (a, b) {\n\t return b.hid - a.hid;\n\t });\n\t });\n\t },\n\t\n\t /** Change of incoming value */\n\t _changeValue: function () {\n\t var new_value = this.model.get('value');\n\t if (new_value && new_value.values && new_value.values.length > 0) {\n\t // create list with content ids\n\t var list = [];\n\t _.each(new_value.values, function (value) {\n\t list.push(value.id);\n\t });\n\t // sniff first suitable field type from config list\n\t var src = new_value.values[0].src;\n\t var multiple = new_value.values.length > 1;\n\t for (var i = 0; i < this.config.length; i++) {\n\t var field = this.fields[i];\n\t var c = this.config[i];\n\t if (c.src == src && [multiple, true].indexOf(c.multiple) !== -1) {\n\t this.model.set('current', i);\n\t field.value(list);\n\t break;\n\t }\n\t }\n\t } else {\n\t _.each(this.fields, function (field) {\n\t field.value(null);\n\t });\n\t }\n\t },\n\t\n\t /** Handles drop events e.g. from history panel */\n\t _handleDrop: function (ev) {\n\t try {\n\t var data = this.model.get('data');\n\t var current = this.model.get('current');\n\t var config = this.config[current];\n\t var field = this.fields[current];\n\t var drop_data = JSON.parse(ev.originalEvent.dataTransfer.getData('text'))[0];\n\t var new_id = drop_data.id;\n\t var new_src = drop_data.history_content_type == 'dataset' ? 'hda' : 'hdca';\n\t var new_value = { id: new_id, src: new_src };\n\t if (data && _.findWhere(data[new_src], new_value)) {\n\t if (config.src == new_src) {\n\t var current_value = field.value();\n\t if (current_value && config.multiple) {\n\t if (current_value.indexOf(new_id) == -1) {\n\t current_value.push(new_id);\n\t }\n\t } else {\n\t current_value = new_id;\n\t }\n\t field.value(current_value);\n\t } else {\n\t this.model.set('value', { values: [new_value] });\n\t this.model.trigger('change:value');\n\t }\n\t this.trigger('change');\n\t this._handleDropStatus('success');\n\t } else {\n\t this._handleDropStatus('danger');\n\t }\n\t } catch (e) {\n\t this._handleDropStatus('danger');\n\t }\n\t ev.preventDefault();\n\t },\n\t\n\t /** Highlight drag result */\n\t _handleDropStatus: function (status) {\n\t var self = this;\n\t this.$el.removeClass('ui-dragover').addClass('ui-dragover-' + status);\n\t setTimeout(function () {\n\t self.$el.removeClass('ui-dragover-' + status);\n\t }, this.model.get('statustimer'));\n\t },\n\t\n\t /** Assists in identifying the batch mode */\n\t _batch: function (result) {\n\t result['batch'] = false;\n\t var current = this.model.get('current');\n\t var config = this.config[current];\n\t if (config.src == 'hdca' && !config.multiple) {\n\t var hdca = this.history[this.fields[current].value() + '_hdca'];\n\t if (hdca && hdca.map_over_type) {\n\t result['batch'] = true;\n\t }\n\t }\n\t if (config.batch == Batch.LINKED || config.batch == Batch.ENABLED) {\n\t result['batch'] = true;\n\t if (config.batch == Batch.ENABLED && this.button_product.value() === 'true') {\n\t result['product'] = true;\n\t }\n\t }\n\t return result;\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 39 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(13)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, List) {\n\t\n\t /**\n\t * FTP file selector\n\t */\n\t var View = Backbone.View.extend({\n\t // initialize\n\t initialize: function (options) {\n\t // link this\n\t var self = this;\n\t\n\t // create ui-list view to keep track of selected ftp files\n\t this.ftpfile_list = new List.View({\n\t name: 'file',\n\t optional: options.optional,\n\t multiple: options.multiple,\n\t onchange: function () {\n\t options.onchange && options.onchange(self.value());\n\t }\n\t });\n\t\n\t // create elements\n\t this.setElement(this.ftpfile_list.$el);\n\t\n\t // initial fetch of ftps\n\t Utils.get({\n\t url: Galaxy.root + 'api/remote_files',\n\t success: function (response) {\n\t var data = [];\n\t for (var i in response) {\n\t data.push({\n\t value: response[i]['path'],\n\t label: response[i]['path']\n\t });\n\t }\n\t self.ftpfile_list.update(data);\n\t }\n\t });\n\t },\n\t\n\t /** Return/Set currently selected ftp datasets */\n\t value: function (val) {\n\t return this.ftpfile_list.value(val);\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ },\n/* 40 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(5), __webpack_require__(35)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui, GenomespaceBrowser) {\n\t\n\t /**\n\t * GenomeSpace file selector\n\t */\n\t var View = Backbone.View.extend({\n\t // initialize\n\t initialize: function (options) {\n\t\n\t // link this\n\t var self = this;\n\t\n\t // create insert new list element button\n\t this.browse_button = new Ui.ButtonIcon({\n\t title: 'Browse',\n\t icon: 'fa fa-sign-in',\n\t tooltip: 'Browse GenomeSpace',\n\t onclick: function () {\n\t self.browseGenomeSpace();\n\t }\n\t });\n\t\n\t // create genomespace filepath textbox\n\t this.filename_textbox = new Ui.Input();\n\t\n\t // create genomespace token textbox\n\t this.token_textbox = new Ui.Input({\n\t type: 'password'\n\t });\n\t\n\t // create elements\n\t this.setElement(this._template(options));\n\t this.$('.ui-gs-browse-button').append(this.browse_button.$el);\n\t this.$('.ui-gs-filename-textbox').append(this.filename_textbox.$el);\n\t this.$('.ui-gs-token-textbox').append(this.token_textbox.$el);\n\t },\n\t\n\t /** Browse GenomeSpace */\n\t browseGenomeSpace: function (options) {\n\t var self = this;\n\t GenomespaceBrowser.openFileBrowser({\n\t successCallback: function (data) {\n\t self.value(data.destination + \"^\" + data.token);\n\t }\n\t });\n\t },\n\t\n\t /** Main Template */\n\t _template: function (options) {\n\t return '' + '
';\n\t '' + '
';\n\t },\n\t\n\t /** Return/Set currently selected genomespace filename/token */\n\t value: function (new_value) {\n\t // check if new_value is defined\n\t if (new_value !== undefined) {\n\t this._setValue(new_value);\n\t } else {\n\t return this._getValue();\n\t }\n\t },\n\t\n\t // get value\n\t _getValue: function () {\n\t return this.filename_textbox.value() + \"^\" + this.token_textbox.value();\n\t },\n\t\n\t // set value\n\t _setValue: function (new_value) {\n\t if (new_value) {\n\t values = new_value.split(\"^\");\n\t this.filename_textbox.value(values[0]);\n\t this.token_textbox.value(values[1]);\n\t }\n\t }\n\t\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ },\n/* 41 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(5), __webpack_require__(23), __webpack_require__(13)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui, Table, List) {\n\t\n\t // collection of libraries\n\t var Libraries = Backbone.Collection.extend({\n\t url: Galaxy.root + 'api/libraries?deleted=false'\n\t });\n\t\n\t // collection of dataset\n\t var LibraryDatasets = Backbone.Collection.extend({\n\t initialize: function () {\n\t var self = this;\n\t this.config = new Backbone.Model({ library_id: null });\n\t this.config.on('change', function () {\n\t self.fetch({ reset: true });\n\t });\n\t },\n\t url: function () {\n\t return Galaxy.root + 'api/libraries/' + this.config.get('library_id') + '/contents';\n\t }\n\t });\n\t\n\t // hda/hdca content selector ui element\n\t var View = Backbone.View.extend({\n\t // initialize\n\t initialize: function (options) {\n\t // link this\n\t var self = this;\n\t\n\t // collections\n\t this.libraries = new Libraries();\n\t this.datasets = new LibraryDatasets();\n\t\n\t // link app and options\n\t this.options = options;\n\t\n\t // select field for the library\n\t // TODO: Remove this once the library API supports searching for library datasets\n\t this.library_select = new Ui.Select.View({\n\t onchange: function (value) {\n\t self.datasets.config.set('library_id', value);\n\t }\n\t });\n\t\n\t // create ui-list view to keep track of selected data libraries\n\t this.dataset_list = new List.View({\n\t name: 'dataset',\n\t optional: options.optional,\n\t multiple: options.multiple,\n\t onchange: function () {\n\t self.trigger('change');\n\t }\n\t });\n\t\n\t // add reset handler for fetched libraries\n\t this.libraries.on('reset', function () {\n\t var data = [];\n\t self.libraries.each(function (model) {\n\t data.push({\n\t value: model.id,\n\t label: model.get('name')\n\t });\n\t });\n\t self.library_select.update(data);\n\t });\n\t\n\t // add reset handler for fetched library datasets\n\t this.datasets.on('reset', function () {\n\t var data = [];\n\t var library_current = self.library_select.text();\n\t if (library_current !== null) {\n\t self.datasets.each(function (model) {\n\t if (model.get('type') === 'file') {\n\t data.push({\n\t value: model.id,\n\t label: model.get('name')\n\t });\n\t }\n\t });\n\t }\n\t self.dataset_list.update(data);\n\t });\n\t\n\t // add change event. fires on trigger\n\t this.on('change', function () {\n\t options.onchange && options.onchange(self.value());\n\t });\n\t\n\t // create elements\n\t this.setElement(this._template());\n\t this.$('.library-select').append(this.library_select.$el);\n\t this.$el.append(this.dataset_list.$el);\n\t\n\t // initial fetch of libraries\n\t this.libraries.fetch({\n\t reset: true,\n\t success: function () {\n\t self.library_select.trigger('change');\n\t if (self.options.value !== undefined) {\n\t self.value(self.options.value);\n\t }\n\t }\n\t });\n\t },\n\t\n\t /** Return/Set currently selected library datasets */\n\t value: function (val) {\n\t return this.dataset_list.value(val);\n\t },\n\t\n\t /** Template */\n\t _template: function () {\n\t return '' + '' + '' + '
' + '' + '
' + 'Token
' + '' + '' + '
';\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ },\n/* 42 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t var View = Backbone.View.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t min: null,\n\t max: null,\n\t step: null,\n\t precise: false,\n\t split: 10000,\n\t value: null,\n\t onchange: function () {}\n\t }).set(options);\n\t\n\t // create new element\n\t this.setElement(this._template());\n\t this.$el.attr('id', this.model.id);\n\t this.$text = this.$('.ui-form-slider-text');\n\t this.$slider = this.$('.ui-form-slider-element');\n\t\n\t // add text field event\n\t var pressed = [];\n\t this.$text.on('change', function () {\n\t self.value($(this).val());\n\t }).on('keyup', function (e) {\n\t pressed[e.which] = false;\n\t }).on('keydown', function (e) {\n\t var v = e.which;\n\t pressed[v] = true;\n\t if (self.model.get('is_workflow') && pressed[16] && v == 52) {\n\t self.value('$');\n\t event.preventDefault();\n\t } else if (!(v == 8 || v == 9 || v == 13 || v == 37 || v == 39 || v >= 48 && v <= 57 && !pressed[16] || v >= 96 && v <= 105 || (v == 190 || v == 110) && $(this).val().indexOf('.') == -1 && self.model.get('precise') || (v == 189 || v == 109) && $(this).val().indexOf('-') == -1 || self._isParameter($(this).val()) || pressed[91] || pressed[17])) {\n\t event.preventDefault();\n\t }\n\t });\n\t\n\t // build slider, cannot be rebuild in render\n\t var opts = this.model.attributes;\n\t this.has_slider = opts.max !== null && opts.min !== null && opts.max > opts.min;\n\t var step = opts.step;\n\t if (!step) {\n\t if (opts.precise && this.has_slider) {\n\t step = (opts.max - opts.min) / opts.split;\n\t } else {\n\t step = 1.0;\n\t }\n\t }\n\t if (this.has_slider) {\n\t this.$text.addClass('ui-form-slider-left');\n\t this.$slider.slider({ min: opts.min, max: opts.max, step: step }).on('slide', function (event, ui) {\n\t self.value(ui.value);\n\t });\n\t } else {\n\t this.$slider.hide();\n\t }\n\t\n\t // add listeners\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var value = this.model.get('value');\n\t this.has_slider && this.$slider.slider('value', value);\n\t value !== this.$text.val() && this.$text.val(value);\n\t },\n\t\n\t /** Set and return the current value */\n\t value: function (new_val) {\n\t var options = this.model.attributes;\n\t if (new_val !== undefined) {\n\t if (new_val !== null && new_val !== '' && !this._isParameter(new_val)) {\n\t isNaN(new_val) && (new_val = 0);\n\t !options.precise && (new_val = Math.round(new_val));\n\t options.max !== null && (new_val = Math.min(new_val, options.max));\n\t options.min !== null && (new_val = Math.max(new_val, options.min));\n\t }\n\t this.model.set('value', new_val);\n\t this.model.trigger('change');\n\t options.onchange(new_val);\n\t }\n\t return this.model.get('value');\n\t },\n\t\n\t /** Return true if the field contains a workflow parameter i.e. $('name') */\n\t _isParameter: function (value) {\n\t return this.model.get('is_workflow') && String(value).substring(0, 1) === '$';\n\t },\n\t\n\t /** Slider template */\n\t _template: function () {\n\t return '' + 'Select Library' + '' + '
' + '' + '' + '';\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 43 */,\n/* 44 */,\n/* 45 */,\n/* 46 */,\n/* 47 */,\n/* 48 */,\n/* 49 */,\n/* 50 */,\n/* 51 */,\n/* 52 */,\n/* 53 */,\n/* 54 */,\n/* 55 */\n/***/ function(module, exports, __webpack_require__) {\n\n\t/* WEBPACK VAR INJECTION */(function(Backbone) {var jQuery = __webpack_require__(1),\n\t $ = jQuery,\n\t QUERY_STRING = __webpack_require__(26),\n\t Ui = __webpack_require__(5);\n\t\n\tvar Router = Backbone.Router.extend({\n\t // TODO: not many client routes at this point - fill and remove from server.\n\t // since we're at root here, this may be the last to be routed entirely on the client.\n\t initialize: function (page, options) {\n\t this.page = page;\n\t this.options = options;\n\t },\n\t\n\t /** helper to push a new navigation state */\n\t push: function (url, data) {\n\t data = data || {};\n\t data.__identifer = Math.random().toString(36).substr(2);\n\t if (!$.isEmptyObject(data)) {\n\t url += url.indexOf('?') == -1 ? '?' : '&';\n\t url += $.param(data, true);\n\t }\n\t Galaxy.params = {};\n\t this.navigate(url, { 'trigger': true });\n\t },\n\t\n\t /** override to parse query string into obj and send to each route */\n\t execute: function (callback, args, name) {\n\t Galaxy.debug('router execute:', callback, args, name);\n\t var queryObj = QUERY_STRING.parse(args.pop());\n\t args.push(queryObj);\n\t if (callback) {\n\t if (this.authenticate(args, name)) {\n\t callback.apply(this, args);\n\t } else {\n\t this.access_denied();\n\t }\n\t }\n\t },\n\t\n\t authenticate: function (args, name) {\n\t return true;\n\t },\n\t\n\t access_denied: function () {\n\t this.page.display(new Ui.Message({ status: 'danger', message: 'You must be logged in with proper credentials to make this request.', persistent: true }));\n\t }\n\t});\n\t\n\tmodule.exports = Router;\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ },\n/* 56 */,\n/* 57 */,\n/* 58 */,\n/* 59 */,\n/* 60 */,\n/* 61 */,\n/* 62 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/** Generic form view */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(10), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Form, Ui) {\n\t\n\t var View = Backbone.View.extend({\n\t\n\t initialize: function (options) {\n\t this.model = new Backbone.Model(options);\n\t this.url = this.model.get('url');\n\t this.redirect = this.model.get('redirect');\n\t this.setElement('');\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t $.ajax({\n\t url: Galaxy.root + this.url,\n\t type: 'GET'\n\t }).done(function (response) {\n\t var options = $.extend({}, self.model.attributes, response);\n\t var form = new Form({\n\t title: options.title,\n\t message: options.message,\n\t status: options.status || 'warning',\n\t icon: options.icon,\n\t inputs: options.inputs,\n\t buttons: {\n\t 'submit': new Ui.Button({\n\t tooltip: options.submit_tooltip,\n\t title: options.submit_title || 'Save',\n\t icon: options.submit_icon || 'fa-save',\n\t cls: 'btn btn-primary ui-clear-float',\n\t onclick: function () {\n\t self._submit(form);\n\t }\n\t })\n\t }\n\t });\n\t self.$el.empty().append(form.$el);\n\t }).fail(function (response) {\n\t self.$el.empty().append(new Ui.Message({\n\t message: 'Failed to load resource ' + self.url + '.',\n\t status: 'danger',\n\t persistent: true\n\t }).$el);\n\t });\n\t },\n\t\n\t _submit: function (form) {\n\t var self = this;\n\t $.ajax({\n\t url: Galaxy.root + self.url,\n\t data: JSON.stringify(form.data.create()),\n\t type: 'PUT',\n\t contentType: 'application/json'\n\t }).done(function (response) {\n\t var success_message = { message: response.message, status: 'success', persistent: false };\n\t if (self.redirect) {\n\t window.location = Galaxy.root + self.redirect + '?' + $.param(success_message);\n\t } else {\n\t form.data.matchModel(response, function (input, input_id) {\n\t form.field_list[input_id].value(input.value);\n\t });\n\t self._showMessage(form, success_message);\n\t }\n\t }).fail(function (response) {\n\t self._showMessage(form, { message: response.responseJSON.err_msg, status: 'danger', persistent: false });\n\t });\n\t },\n\t\n\t _showMessage: function (form, options) {\n\t var $panel = form.$el.parents().filter(function () {\n\t return ['auto', 'scroll'].indexOf($(this).css('overflow')) != -1;\n\t }).first();\n\t $panel.animate({ scrollTop: 0 }, 500);\n\t form.message.update(options);\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 63 */,\n/* 64 */,\n/* 65 */,\n/* 66 */,\n/* 67 */,\n/* 68 */,\n/* 69 */,\n/* 70 */,\n/* 71 */,\n/* 72 */,\n/* 73 */,\n/* 74 */,\n/* 75 */,\n/* 76 */,\n/* 77 */,\n/* 78 */,\n/* 79 */,\n/* 80 */,\n/* 81 */,\n/* 82 */,\n/* 83 */,\n/* 84 */,\n/* 85 */,\n/* 86 */,\n/* 87 */,\n/* 88 */,\n/* 89 */,\n/* 90 */,\n/* 91 */,\n/* 92 */,\n/* 93 */,\n/* 94 */,\n/* 95 */,\n/* 96 */,\n/* 97 */,\n/* 98 */,\n/* 99 */,\n/* 100 */,\n/* 101 */,\n/* 102 */\n/***/ function(module, exports, __webpack_require__) {\n\n\t/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {var _l = __webpack_require__(6);\n\t\n\tvar AdminPanel = Backbone.View.extend({\n\t initialize: function (page, options) {\n\t var self = this;\n\t this.page = page;\n\t this.root = options.root;\n\t this.config = options.config;\n\t this.settings = options.settings;\n\t this.message = options.message;\n\t this.status = options.status;\n\t this.model = new Backbone.Model({\n\t title: _l('Administration')\n\t });\n\t this.categories = new Backbone.Collection([{\n\t title: 'Server',\n\t items: [{\n\t title: 'Data types registry',\n\t url: 'admin/view_datatypes_registry'\n\t }, {\n\t title: 'Data tables registry',\n\t url: 'admin/view_tool_data_tables'\n\t }, {\n\t title: 'Display applications',\n\t url: 'admin/display_applications'\n\t }, {\n\t title: 'Manage jobs',\n\t url: 'admin/jobs'\n\t }]\n\t }, {\n\t title: 'Tools and Tool Shed',\n\t items: [{\n\t title: 'Search Tool Shed',\n\t url: 'admin_toolshed/browse_tool_sheds',\n\t enabled: self.settings.is_tool_shed_installed\n\t }, {\n\t title: 'Search Tool Shed (Beta)',\n\t url: 'admin_toolshed/browse_toolsheds',\n\t enabled: self.settings.is_tool_shed_installed && self.config.enable_beta_ts_api_install\n\t }, {\n\t title: 'Monitor installing repositories',\n\t url: 'admin_toolshed/monitor_repository_installation?installing_repository_ids=' + self.settings.installing_repository_ids,\n\t enabled: self.settings.installing_repository_ids\n\t }, {\n\t title: 'Manage installed tools',\n\t url: 'admin_toolshed/browse_repositories',\n\t enabled: self.settings.is_repo_installed\n\t }, {\n\t title: 'Reset metadata',\n\t url: 'admin_toolshed/reset_metadata_on_selected_installed_repositories',\n\t enabled: self.settings.is_repo_installed\n\t }, {\n\t title: 'Download local tool',\n\t url: 'admin/package_tool'\n\t }, {\n\t title: 'Tool lineage',\n\t url: 'admin/tool_versions',\n\t target: '__use_router__'\n\t }, {\n\t title: 'Reload a tool\\'s configuration',\n\t url: 'admin/reload_tool'\n\t }, {\n\t title: 'Review tool migration stages',\n\t url: 'admin/review_tool_migration_stages'\n\t }, {\n\t title: 'View Tool Error Logs',\n\t url: 'admin/tool_errors'\n\t }, {\n\t title: 'Manage Display Whitelist',\n\t url: 'admin/sanitize_whitelist'\n\t }, {\n\t title: 'Manage Tool Dependencies',\n\t url: 'admin/manage_tool_dependencies'\n\t }]\n\t }, {\n\t title: 'User Management',\n\t items: [{\n\t title: 'Users',\n\t url: 'admin/users',\n\t target: '__use_router__'\n\t }, {\n\t title: 'Groups',\n\t url: 'admin/groups',\n\t target: '__use_router__'\n\t }, {\n\t title: 'Roles',\n\t url: 'admin/roles',\n\t target: '__use_router__'\n\t }, {\n\t title: 'API keys',\n\t url: 'userskeys/all_users'\n\t }, {\n\t title: 'Impersonate a user',\n\t url: 'admin/impersonate',\n\t enabled: self.config.allow_user_impersonation\n\t }]\n\t }, {\n\t title: 'Data',\n\t items: [{\n\t title: 'Quotas',\n\t url: 'admin/quotas',\n\t target: '__use_router__',\n\t enabled: self.config.enable_quotas\n\t }, {\n\t title: 'Data libraries',\n\t url: 'library_admin/browse_libraries'\n\t }, {\n\t title: 'Roles',\n\t url: 'admin/roles',\n\t target: '__use_router__'\n\t }, {\n\t title: 'Local data',\n\t url: 'data_manager'\n\t }]\n\t }, {\n\t title: 'Form Definitions',\n\t items: [{\n\t title: 'Form definitions',\n\t url: 'forms/browse_form_definitions'\n\t }]\n\t }, {\n\t title: 'Sample Tracking',\n\t items: [{\n\t title: 'Sequencers and external services',\n\t url: 'external_service/browse_external_services'\n\t }, {\n\t title: 'Request types',\n\t url: 'request_type/browse_request_types'\n\t }, {\n\t title: 'Sequencing requests',\n\t url: 'requests_admin/browse_requests'\n\t }, {\n\t title: 'Find samples',\n\t url: 'requests_common/find_samples?cntrller=requests_admin'\n\t }]\n\t }]);\n\t this.setElement(this._template());\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t this.$el.empty();\n\t this.categories.each(function (category) {\n\t var $section = $(self._templateSection(category.attributes));\n\t var $entries = $section.find('.ui-side-section-body');\n\t _.each(category.get('items'), function (item) {\n\t if (item.enabled === undefined || item.enabled) {\n\t var $link = $('').attr({ href: self.root + item.url }).text(_l(item.title));\n\t if (item.target == '__use_router__') {\n\t $link.on('click', function (e) {\n\t e.preventDefault();self.page.router.push(item.url);\n\t });\n\t } else {\n\t $link.attr('target', 'galaxy_main');\n\t }\n\t $entries.append($('').addClass('ui-side-section-body-title').append($link));\n\t }\n\t });\n\t self.$el.append($section);\n\t });\n\t this.page.$('#galaxy_main').prop('src', this.root + 'admin/center?message=' + this.message + '&status=' + this.status);\n\t },\n\t\n\t _templateSection: function (options) {\n\t return ['
', '
' + _l(options.title) + '
', '', '
'].join('');\n\t },\n\t\n\t _template: function () {\n\t return '';\n\t },\n\t\n\t toString: function () {\n\t return 'adminPanel';\n\t }\n\t});\n\t\n\tmodule.exports = AdminPanel;\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ }\n]);\n\n\n/** WEBPACK FOOTER **\n ** admin.bundled.js\n **/","var jQuery = require( 'jquery' ),\n $ = jQuery,\n GalaxyApp = require( 'galaxy' ).GalaxyApp,\n AdminPanel = require( './panels/admin-panel' ),\n FormWrapper = require( 'mvc/form/form-wrapper' ),\n GridView = require( 'mvc/grid/grid-view' ),\n Ui = require( 'mvc/ui/ui-misc' ),\n QueryStringParsing = require( 'utils/query-string-parsing' ),\n Router = require( 'layout/router' ),\n Utils = require( 'utils/utils' ),\n Page = require( 'layout/page' );\n\nwindow.app = function app( options, bootstrapped ){\n window.Galaxy = new GalaxyApp( options, bootstrapped );\n Galaxy.debug( 'admin app' );\n\n /** Routes */\n var AdminRouter = Router.extend({\n routes: {\n '(/)admin(/)users' : 'show_users',\n '(/)admin(/)roles' : 'show_roles',\n '(/)admin(/)groups' : 'show_groups',\n '(/)admin(/)tool_versions' : 'show_tool_versions',\n '(/)admin(/)quotas' : 'show_quotas',\n '(/)admin(/)forms(/)(:form_id)' : 'show_forms'\n },\n\n authenticate: function( args, name ) {\n return Galaxy.user && Galaxy.user.id && Galaxy.user.get( 'is_admin' );\n },\n\n show_users: function() {\n this.page.display( new GridView( { url_base: Galaxy.root + 'admin/users_list', url_data: Galaxy.params, dict_format: true } ) );\n },\n\n show_roles: function() {\n this.page.display( new GridView( { url_base: Galaxy.root + 'admin/roles_list', url_data: Galaxy.params, dict_format: true } ) );\n },\n\n show_groups: function() {\n this.page.display( new GridView( { url_base: Galaxy.root + 'admin/groups_list', url_data: Galaxy.params, dict_format: true } ) );\n },\n\n show_tool_versions: function() {\n this.page.display( new GridView( { url_base: Galaxy.root + 'admin/tool_versions_list', url_data: Galaxy.params, dict_format: true } ) );\n },\n\n show_quotas: function() {\n this.page.display( new GridView( { url_base: Galaxy.root + 'admin/quotas_list', url_data: Galaxy.params, dict_format: true } ) );\n },\n\n show_forms : function( form_id ) {\n var id = '?id=' + QueryStringParsing.get( 'id' );\n var form_defs = {\n reset_user_password: {\n title : 'Reset passwords',\n url : 'admin/reset_user_password' + id,\n icon : 'fa-user',\n submit_title : 'Save new password',\n redirect : 'admin/users'\n },\n manage_roles_and_groups_for_user: {\n url : 'admin/manage_roles_and_groups_for_user' + id,\n icon : 'fa-users',\n redirect : 'admin/users'\n },\n manage_users_and_groups_for_role: {\n url : 'admin/manage_users_and_groups_for_role' + id,\n redirect : 'admin/roles'\n },\n manage_users_and_roles_for_group: {\n url : 'admin/manage_users_and_roles_for_group' + id,\n redirect : 'admin/groups'\n },\n manage_users_and_groups_for_quota: {\n url : 'admin/manage_users_and_groups_for_quota' + id,\n redirect : 'admin/quotas'\n },\n create_role: {\n url : 'admin/create_role',\n redirect : 'admin/roles'\n },\n create_group: {\n url : 'admin/create_group',\n redirect : 'admin/groups'\n },\n create_quota: {\n url : 'admin/create_quota',\n redirect : 'admin/quotas'\n },\n rename_role: {\n url : 'admin/rename_role' + id,\n redirect : 'admin/roles'\n },\n rename_group: {\n url : 'admin/rename_group' + id,\n redirect : 'admin/groups'\n },\n rename_quota: {\n url : 'admin/rename_quota' + id,\n redirect : 'admin/quotas'\n },\n edit_quota: {\n url : 'admin/edit_quota' + id,\n redirect : 'admin/quotas'\n },\n set_quota_default: {\n url : 'admin/set_quota_default' + id,\n redirect : 'admin/quotas'\n },\n };\n this.page.display( new FormWrapper.View ( form_defs[ form_id ] ) );\n }\n });\n\n $(function() {\n _.extend( options.config, { active_view : 'admin' } );\n Utils.setWindowTitle(\"Administration\");\n Galaxy.page = new Page.View( _.extend( options, {\n Left : AdminPanel,\n Router : AdminRouter\n } ) );\n });\n};\n\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/apps/admin.js\n **/","/**\n * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc.\n */\ndefine(['utils/utils',\n 'mvc/ui/ui-select-default',\n 'mvc/ui/ui-slider',\n 'mvc/ui/ui-options',\n 'mvc/ui/ui-drilldown',\n 'mvc/ui/ui-buttons',\n 'mvc/ui/ui-modal'],\n function( Utils, Select, Slider, Options, Drilldown, Buttons, Modal ) {\n\n /** Label wrapper */\n var Label = Backbone.View.extend({\n tagName: 'label',\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model( options );\n this.tagName = options.tagName || this.tagName;\n this.setElement( $( '<' + this.tagName + '/>' ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n title: function( new_title ) {\n this.model.set( 'title', new_title );\n },\n value: function() {\n return this.model.get( 'title' );\n },\n render: function() {\n this.$el.removeClass()\n .addClass( 'ui-label' )\n .addClass( this.model.get( 'cls' ) )\n .html( this.model.get( 'title' ) );\n return this;\n }\n });\n\n /** Displays messages used e.g. in the tool form */\n var Message = Backbone.View.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n message : null,\n status : 'info',\n cls : '',\n persistent : false,\n fade : true\n }).set( options );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n update: function( options ) {\n this.model.set( options );\n },\n render: function() {\n this.$el.removeClass().addClass( 'ui-message' ).addClass( this.model.get( 'cls' ) );\n var status = this.model.get( 'status' );\n if ( this.model.get( 'large' ) ) {\n this.$el.addClass((( status == 'success' && 'done' ) ||\n ( status == 'danger' && 'error' ) ||\n status ) + 'messagelarge' );\n } else {\n this.$el.addClass( 'alert' ).addClass( 'alert-' + status );\n }\n if ( this.model.get( 'message' ) ) {\n this.$el.html( this.messageForDisplay() );\n this.$el[ this.model.get( 'fade' ) ? 'fadeIn' : 'show' ]();\n this.timeout && window.clearTimeout( this.timeout );\n if ( !this.model.get( 'persistent' ) ) {\n var self = this;\n this.timeout = window.setTimeout( function() {\n self.model.set( 'message', '' );\n }, 3000 );\n }\n } else {\n this.$el.fadeOut();\n }\n return this;\n },\n messageForDisplay: function() {\n return _.escape( this.model.get( 'message' ) );\n }\n });\n\n var UnescapedMessage = Message.extend({\n messageForDisplay: function() {\n return this.model.get( 'message' );\n }\n });\n\n /** Renders an input element used e.g. in the tool form */\n var Input = Backbone.View.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n type : 'text',\n placeholder : '',\n disabled : false,\n readonly : false,\n visible : true,\n cls : '',\n area : false,\n color : null,\n style : null\n }).set( options );\n this.tagName = this.model.get( 'area' ) ? 'textarea' : 'input';\n this.setElement( $( '<' + this.tagName + '/>' ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n events: {\n 'input': '_onchange'\n },\n value: function( new_val ) {\n new_val !== undefined && this.model.set( 'value', typeof new_val === 'string' ? new_val : '' );\n return this.model.get( 'value' );\n },\n render: function() {\n var self = this;\n this.$el.removeClass()\n .addClass( 'ui-' + this.tagName )\n .addClass( this.model.get( 'cls' ) )\n .addClass( this.model.get( 'style' ) )\n .attr( 'id', this.model.id )\n .attr( 'type', this.model.get( 'type' ) )\n .attr( 'placeholder', this.model.get( 'placeholder' ) )\n .css( 'color', this.model.get( 'color' ) || '' )\n .css( 'border-color', this.model.get( 'color' ) || '' );\n var datalist = this.model.get( 'datalist' );\n if ( $.isArray( datalist ) && datalist.length > 0 ) {\n this.$el.autocomplete( { source : function( request, response ) { response( self.model.get( 'datalist' ) ) },\n change : function() { self._onchange() } } );\n }\n if ( this.model.get( 'value' ) !== this.$el.val() ) {\n this.$el.val( this.model.get( 'value' ) );\n }\n _.each( [ 'readonly', 'disabled' ], function( attr_name ) {\n self.model.get( attr_name ) ? self.$el.attr( attr_name, true ) : self.$el.removeAttr( attr_name );\n });\n this.$el[ this.model.get( 'visible' ) ? 'show' : 'hide' ]();\n return this;\n },\n _onchange: function() {\n this.value( this.$el.val() );\n this.model.get( 'onchange' ) && this.model.get( 'onchange' )( this.model.get( 'value' ) );\n }\n });\n\n /** Creates a hidden element input field used e.g. in the tool form */\n var Hidden = Backbone.View.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model( options );\n this.setElement( $ ( '' ).append( this.$info = $( '' ) )\n .append( this.$hidden = $( '' ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n value: function( new_val ) {\n new_val !== undefined && this.model.set( 'value', new_val );\n return this.model.get( 'value' );\n },\n render: function() {\n this.$el.attr( 'id', this.model.id );\n this.$hidden.val( this.model.get( 'value' ) );\n this.model.get( 'info' ) ? this.$info.show().text( this.model.get( 'info' ) ) : this.$info.hide();\n return this;\n }\n });\n\n /** Creates a upload element input field */\n var Upload = Backbone.View.extend({\n initialize: function( options ) {\n var self = this;\n this.model = options && options.model || new Backbone.Model( options );\n this.setElement( $ ( '' ).append( this.$info = $( '' ) )\n .append( this.$file = $( '' ).attr( 'type', 'file' ).addClass( 'ui-margin-bottom' ) )\n .append( this.$text = $( '' ).addClass( 'ui-textarea' ).attr( 'disabled', true ) )\n .append( this.$wait = $( '' ).addClass( 'fa fa-spinner fa-spin' ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.$file.on( 'change', function( e ) { self._readFile( e ) } );\n this.render();\n },\n value: function( new_val ) {\n new_val !== undefined && this.model.set( 'value', new_val );\n return this.model.get( 'value' );\n },\n render: function() {\n this.$el.attr( 'id', this.model.id );\n this.model.get( 'info' ) ? this.$info.show().text( this.model.get( 'info' ) ) : this.$info.hide();\n this.model.get( 'value' ) ? this.$text.text( this.model.get( 'value' ) ).show() : this.$text.hide();\n this.model.get( 'wait' ) ? this.$wait.show() : this.$wait.hide();\n return this;\n },\n _readFile: function( e ) {\n var self = this;\n var file = e.target.files && e.target.files[ 0 ];\n if ( file ) {\n var reader = new FileReader();\n reader.onload = function() {\n self.model.set( { wait: false, value: this.result } );\n }\n this.model.set( { wait: true, value: null } );\n reader.readAsText( file );\n }\n }\n });\n\n return {\n Button : Buttons.ButtonDefault,\n ButtonIcon : Buttons.ButtonIcon,\n ButtonCheck : Buttons.ButtonCheck,\n ButtonMenu : Buttons.ButtonMenu,\n ButtonLink : Buttons.ButtonLink,\n Input : Input,\n Label : Label,\n Message : Message,\n UnescapedMessage : UnescapedMessage,\n Upload : Upload,\n Modal : Modal,\n RadioButton : Options.RadioButton,\n Checkbox : Options.Checkbox,\n Radio : Options.Radio,\n Select : Select,\n Hidden : Hidden,\n Slider : Slider,\n Drilldown : Drilldown\n }\n});\n\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/ui/ui-misc.js\n **/","define([ 'utils/utils', 'mvc/ui/ui-misc' ], function( Utils, Ui ) {\nvar View = Backbone.View.extend({\n visible : false,\n initialize : function( options ) {\n var self = this;\n this.model = options && options.model || new Backbone.Model( {\n id : Utils.uid(),\n cls : 'ui-portlet',\n title : '',\n icon : '',\n buttons : null,\n body : null,\n scrollable : true,\n nopadding : false,\n operations : null,\n collapsible : false,\n collapsible_button : false,\n collapsed : false,\n onchange_title : null\n } ).set( options );\n this.setElement( this._template() );\n\n // link all dom elements\n this.$body = this.$( '.portlet-body' );\n this.$title_text = this.$( '.portlet-title-text' );\n this.$title_icon = this.$( '.portlet-title-icon' );\n this.$header = this.$( '.portlet-header' );\n this.$content = this.$( '.portlet-content' );\n this.$backdrop = this.$( '.portlet-backdrop' );\n this.$buttons = this.$( '.portlet-buttons' );\n this.$operations = this.$( '.portlet-operations' );\n\n // add body to component list\n this.model.get( 'body' ) && this.append( this.model.get( 'body' ) );\n\n // add icon for collapsible option\n this.collapsible_button = new Ui.ButtonIcon({\n icon : 'fa-eye',\n tooltip : 'Collapse/Expand',\n cls : 'ui-button-icon-plain',\n onclick : function() { self[ self.collapsed ? 'expand' : 'collapse' ]() }\n });\n this.render();\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n this.$el.removeClass().addClass( options.cls ).attr( 'id', options.id );\n this.$header[ options.title ? 'show' : 'hide' ]();\n this.$title_text.html( options.title );\n _.each( [ this.$content, this.$body ], function( $el ) {\n $el[ options.nopadding ? 'addClass' : 'removeClass' ]( 'no-padding' );\n });\n\n // render title icon\n if ( options.icon ) {\n this.$title_icon.removeClass().addClass( 'portlet-title-icon fa' ).addClass( options.icon ).show();\n } else {\n this.$title_icon.hide();\n }\n\n // make portlet collapsible\n this.$title_text[ options.collapsible ? 'addClass' : 'removeClass' ]( 'no-highlight collapsible' ).off();\n if ( options.collapsible ) {\n this.$title_text.on( 'click', function() { self[ self.collapsed ? 'expand' : 'collapse' ]() } );\n options.collapsed ? this.collapse() : this.expand();\n }\n\n // allow title editing\n this.$title_text.prop( 'disabled', !options.onchange_title );\n options.onchange_title && this.$title_text.make_text_editable({\n on_finish: function( new_title ) {\n options.onchange_title( new_title );\n }\n });\n\n // render buttons\n if ( options.buttons ) {\n this.$buttons.empty().show();\n $.each( this.model.get( 'buttons' ), function( name, item ) {\n item.$el.prop( 'id', name );\n self.$buttons.append( item.$el );\n });\n } else {\n this.$buttons.hide();\n }\n\n // render operations\n this.$operations.empty;\n if ( options.collapsible_button ) {\n this.$operations.append( this.collapsible_button.$el );\n }\n if ( options.operations ) {\n $.each( options.operations, function( name, item ) {\n item.$el.prop( 'id', name );\n self.$operations.append( item.$el );\n });\n }\n return this;\n },\n\n /** Append new doms to body */\n append: function( $el ) {\n this.$body.append( $el );\n },\n\n /** Remove all content */\n empty: function() {\n this.$body.empty();\n },\n\n /** Return header element */\n header: function() {\n return this.$header;\n },\n\n /** Return body element */\n body: function() {\n return this.$body;\n },\n\n /** Show portlet */\n show: function(){\n this.visible = true;\n this.$el.fadeIn( 'fast' );\n },\n\n /** Hide portlet */\n hide: function(){\n this.visible = false;\n this.$el.hide();\n },\n\n /** Enable a particular button */\n enableButton: function( id ) {\n this.$buttons.find( '#' + id ).prop( 'disabled', false );\n },\n\n /** Disable a particular button */\n disableButton: function( id ) {\n this.$buttons.find( '#' + id ).prop( 'disabled', true );\n },\n\n /** Hide a particular operation */\n hideOperation: function( id ) {\n this.$operations.find( '#' + id ).hide();\n },\n\n /** Show a particular operation */\n showOperation: function( id ) {\n this.$operations.find( '#' + id ).show();\n },\n\n /** Replaces the event callback of an existing operation */\n setOperation: function( id, callback ) {\n this.$operations.find( '#' + id ).off( 'click' ).on( 'click', callback );\n },\n\n /** Change title */\n title: function( new_title ) {\n new_title && this.$title_text.html( new_title );\n return this.$title_text.html();\n },\n\n /** Collapse portlet */\n collapse: function() {\n this.collapsed = true;\n this.$content.height( '0%' );\n this.$body.hide();\n this.collapsible_button.setIcon( 'fa-eye-slash' );\n },\n\n /** Expand portlet */\n expand: function() {\n this.collapsed = false;\n this.$content.height( '100%' );\n this.$body.fadeIn( 'fast' );\n this.collapsible_button.setIcon( 'fa-eye' );\n },\n\n /** Disable content access */\n disable: function() {\n this.$backdrop.show();\n },\n\n /** Enable content access */\n enable: function() {\n this.$backdrop.hide();\n },\n\n _template: function() {\n return $( '' ).append( $( '' ).addClass( 'portlet-header' )\n .append( $( '' ).addClass( 'portlet-operations' ) )\n .append( $( '' ).addClass( 'portlet-title' )\n .append( $( '' ).addClass( 'portlet-title-icon' ) )\n .append( $( '' ).addClass( 'portlet-title-text' ) ) ) )\n .append( $( '' ).addClass( 'portlet-content' )\n .append( $( '' ).addClass( 'portlet-body' ) )\n .append( $( '' ).addClass( 'portlet-buttons' ) ) )\n .append( $( '' ).addClass( 'portlet-backdrop' ) );\n }\n});\nreturn {\n View : View\n}\n});\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/ui/ui-portlet.js\n **/","/**\n This is the main class of the form plugin. It is referenced as 'app' in lower level modules.\n*/\ndefine( [ 'utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'mvc/form/form-section', 'mvc/form/form-data' ],\nfunction( Utils, Portlet, Ui, FormSection, FormData ) {\n return Backbone.View.extend({\n initialize: function( options ) {\n this.model = new Backbone.Model({\n initial_errors : false,\n cls : 'ui-portlet-limited',\n icon : null,\n always_refresh : true,\n status : 'warning',\n onchange : function(){}\n }).set( options );\n this.setElement( '' );\n this.render();\n },\n\n /** Update available options */\n update: function( new_model ){\n var self = this;\n this.data.matchModel( new_model, function( node, input_id ) {\n var input = self.input_list[ input_id ];\n if ( input && input.options ) {\n if ( !_.isEqual( input.options, node.options ) ) {\n input.options = node.options;\n var field = self.field_list[ input_id ];\n if ( field.update ) {\n var new_options = [];\n if ( ( [ 'data', 'data_collection', 'drill_down' ] ).indexOf( input.type ) != -1 ) {\n new_options = input.options;\n } else {\n for ( var i in node.options ) {\n var opt = node.options[ i ];\n if ( opt.length > 2 ) {\n new_options.push( { label: opt[ 0 ], value: opt[ 1 ] } );\n }\n }\n }\n field.update( new_options );\n field.trigger( 'change' );\n Galaxy.emit.debug( 'form-view::update()', 'Updating options for ' + input_id );\n }\n }\n }\n });\n },\n\n /** Set form into wait mode */\n wait: function( active ) {\n for ( var i in this.input_list ) {\n var field = this.field_list[ i ];\n var input = this.input_list[ i ];\n if ( input.is_dynamic && field.wait && field.unwait ) {\n field[ active ? 'wait' : 'unwait' ]();\n }\n }\n },\n\n /** Highlight and scroll to input element (currently only used for error notifications) */\n highlight: function ( input_id, message, silent ) {\n var input_element = this.element_list[ input_id ];\n if ( input_element ) {\n input_element.error( message || 'Please verify this parameter.' );\n this.portlet.expand();\n this.trigger( 'expand', input_id );\n if ( !silent ) {\n var $panel = this.$el.parents().filter(function() {\n return [ 'auto', 'scroll' ].indexOf( $( this ).css( 'overflow' ) ) != -1;\n }).first();\n $panel.animate( { scrollTop : $panel.scrollTop() + input_element.$el.offset().top - 120 }, 500 );\n }\n }\n },\n\n /** Highlights errors */\n errors: function( options ) {\n this.trigger( 'reset' );\n if ( options && options.errors ) {\n var error_messages = this.data.matchResponse( options.errors );\n for ( var input_id in this.element_list ) {\n var input = this.element_list[ input_id ];\n if ( error_messages[ input_id ] ) {\n this.highlight( input_id, error_messages[ input_id ], true );\n }\n }\n }\n },\n\n /** Render tool form */\n render: function() {\n var self = this;\n this.off('change');\n this.off('reset');\n // contains the dom field elements as created by the parameter factory i.e. form-parameters\n this.field_list = {};\n // contains input definitions/dictionaries as provided by the parameters to_dict() function through the api\n this.input_list = {};\n // contains the dom elements of each input element i.e. form-input which wraps the actual input field\n this.element_list = {};\n // converts the form into a json data structure\n this.data = new FormData.Manager( this );\n this._renderForm();\n this.data.create();\n this.model.get( 'initial_errors' ) && this.errors( this.model.attributes );\n // add listener which triggers on checksum change, and reset the form input wrappers\n var current_check = this.data.checksum();\n this.on( 'change', function( input_id ) {\n var input = self.input_list[ input_id ];\n if ( !input || input.refresh_on_change || self.model.get( 'always_refresh' ) ) {\n var new_check = self.data.checksum();\n if ( new_check != current_check ) {\n current_check = new_check;\n self.model.get( 'onchange' )();\n }\n }\n });\n this.on('reset', function() {\n _.each( self.element_list, function( input_element ) { input_element.reset() } );\n });\n return this;\n },\n\n /** Renders/appends dom elements of the form */\n _renderForm: function() {\n $( '.tooltip' ).remove();\n var options = this.model.attributes;\n this.message = new Ui.UnescapedMessage();\n this.section = new FormSection.View( this, { inputs: options.inputs } );\n this.portlet = new Portlet.View({\n icon : options.icon,\n title : options.title,\n cls : options.cls,\n operations : options.operations,\n buttons : options.buttons,\n collapsible : options.collapsible,\n collapsed : options.collapsed,\n onchange_title : options.onchange_title\n });\n this.portlet.append( this.message.$el );\n this.portlet.append( this.section.$el );\n this.$el.empty();\n options.inputs && this.$el.append( this.portlet.$el );\n options.message && this.message.update( { persistent: true, status: options.status, message: options.message } );\n Galaxy.emit.debug( 'form-view::initialize()', 'Completed' );\n }\n });\n});\n\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/form/form-view.js\n **/","/** This module contains all button views. */\ndefine( [ 'utils/utils' ], function( Utils ) {\n /** This renders the default button which is used e.g. at the bottom of the upload modal. */\n var ButtonDefault = Backbone.View.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : '',\n icon : '',\n cls : 'btn btn-default',\n wait : false,\n wait_text : 'Sending...',\n wait_cls : 'btn btn-info',\n disabled : false,\n percentage : -1\n }).set( options );\n this.setElement( $( '' ).attr( 'type', 'button' )\n .append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) )\n .append( this.$progress = $( '' ).append( this.$progress_bar = $( '' ) ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( 'ui-button-default' )\n .addClass( options.disabled && 'disabled' )\n .attr( 'id', options.id )\n .attr( 'disabled', options.disabled )\n .off( 'click' ).on( 'click' , function() {\n $( '.tooltip' ).hide();\n options.onclick && !self.disabled && options.onclick();\n })\n .tooltip( { title: options.tooltip, placement: 'bottom' } );\n this.$progress.addClass( 'progress' ).css( 'display', options.percentage !== -1 ? 'block' : 'none' );\n this.$progress_bar.addClass( 'progress-bar' ).css( { width : options.percentage + '%' } );\n this.$icon.removeClass().addClass( 'icon fa' );\n this.$title.removeClass().addClass( 'title' );\n if ( options.wait ) {\n this.$el.addClass( options.wait_cls ).prop( 'disabled', true );\n this.$icon.addClass( 'fa-spinner fa-spin ui-margin-right' );\n this.$title.html( options.wait_text );\n } else {\n this.$el.addClass( options.cls );\n this.$icon.addClass( options.icon );\n this.$title.html( options.title );\n options.icon && options.title && this.$icon.addClass( 'ui-margin-right' );\n }\n },\n\n /** Show button */\n show: function() {\n this.$el.show();\n },\n\n /** Hide button */\n hide: function() {\n this.$el.hide();\n },\n\n /** Disable button */\n disable: function() {\n this.model.set( 'disabled', true );\n },\n\n /** Enable button */\n enable: function() {\n this.model.set( 'disabled', false );\n },\n\n /** Show spinner to indicate that the button is not ready to be clicked */\n wait: function() {\n this.model.set( 'wait', true );\n },\n\n /** Hide spinner to indicate that the button is ready to be clicked */\n unwait: function() {\n this.model.set( 'wait', false );\n },\n\n /** Change icon */\n setIcon: function( icon ) {\n this.model.set( 'icon', icon );\n }\n });\n\n /** This button allows the right-click/open-in-new-tab feature, its used e.g. for panel buttons. */\n var ButtonLink = ButtonDefault.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : '',\n icon : '',\n cls : ''\n }).set( options );\n this.setElement( $( '' ).append( this.$icon = $( '' ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render: function() {\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( options.cls )\n .attr( { id : options.id,\n href : options.href || 'javascript:void(0)',\n title : options.title,\n target : options.target || '_top',\n disabled : options.disabled } )\n .tooltip( { placement: 'bottom' } )\n .off( 'click' ).on( 'click' , function() {\n options.onclick && !options.disabled && options.onclick();\n });\n this.$icon.removeClass().addClass( options.icon );\n }\n });\n\n /** The check button is used in the tool form and allows to distinguish between multiple states e.g. all, partially and nothing selected. */\n var ButtonCheck = Backbone.View.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : 'Select/Unselect all',\n icons : [ 'fa-square-o', 'fa-minus-square-o', 'fa-check-square-o' ],\n value : 0,\n onchange : function(){}\n }).set( options );\n this.setElement( $( '' ).append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render: function( options ) {\n var self = this;\n var options = this.model.attributes;\n this.$el.addClass( 'ui-button-check' )\n .off( 'click' ).on('click', function() {\n self.model.set( 'value', ( self.model.get( 'value' ) === 0 && 2 ) || 0 );\n options.onclick && options.onclick();\n });\n this.$title.html( options.title );\n this.$icon.removeClass()\n .addClass( 'icon fa ui-margin-right' )\n .addClass( options.icons[ options.value ] );\n },\n\n /* Sets a new value and/or returns the value.\n * @param{Integer} new_val - Set a new value 0=unchecked, 1=partial and 2=checked.\n * OR:\n * @param{Integer} new_val - Number of selected options.\n * @param{Integer} total - Total number of available options.\n */\n value: function ( new_val, total ) {\n if ( new_val !== undefined ) {\n if ( total && new_val !== 0 ) {\n new_val = ( new_val !== total ) && 1 || 2;\n }\n this.model.set( 'value', new_val );\n this.model.get( 'onchange' )( this.model.get( 'value' ) );\n }\n return this.model.get( 'value' );\n }\n });\n\n /** This renders a differently styled, more compact button version. */\n var ButtonIcon = ButtonDefault.extend({\n initialize: function( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n title : '',\n icon : '',\n cls : 'ui-button-icon',\n disabled : false\n }).set( options );\n this.setElement( $( '' ).append( this.$button = $( '' ).append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render : function( options ) {\n var self = this;\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( options.cls )\n .addClass( options.disabled && 'disabled' )\n .attr( 'disabled', options.disabled )\n .attr( 'id', options.id )\n .off( 'click' ).on( 'click', function() {\n $( '.tooltip' ).hide();\n !options.disabled && options.onclick && options.onclick();\n });\n this.$button.addClass( 'button' ).tooltip( { title: options.tooltip, placement: 'bottom' } );\n this.$icon.removeClass().addClass( 'icon fa' ).addClass( options.icon );\n this.$title.addClass( 'title' ).html( options.title );\n options.icon && options.title && this.$icon.addClass( 'ui-margin-right' );\n }\n });\n\n /** This class creates a button with dropdown menu. */\n var ButtonMenu = ButtonDefault.extend({\n $menu: null,\n initialize: function ( options ) {\n this.model = options && options.model || new Backbone.Model({\n id : '',\n title : '',\n pull : 'right',\n icon : null,\n onclick : null,\n cls : 'ui-button-icon ui-button-menu',\n tooltip : '',\n target : '',\n href : '',\n onunload : null,\n visible : true,\n tag : ''\n }).set( options );\n this.collection = new Backbone.Collection();\n this.setElement( $( '' ).append( this.$root = $( '' ).append( this.$icon = $( '' ) )\n .append( this.$title = $( '' ) ) ) );\n this.listenTo( this.model, 'change', this.render, this );\n this.listenTo( this.collection, 'change add remove reset', this.render, this );\n this.render();\n },\n\n render: function() {\n var self = this;\n var options = this.model.attributes;\n this.$el.removeClass()\n .addClass( 'dropdown' )\n .addClass( options.cls )\n .attr( 'id', options.id )\n .css( { display : options.visible && this.collection.where( { visible: true } ).length > 0 ? 'block' : 'none' } );\n this.$root.addClass( 'root button dropdown-toggle' )\n .attr( 'data-toggle', 'dropdown' )\n .tooltip( { title: options.tooltip, placement: 'bottom' } )\n .off( 'click' ).on( 'click', function( e ) {\n $( '.tooltip' ).hide();\n e.preventDefault();\n options.onclick && options.onclick();\n } );\n this.$icon.removeClass().addClass( 'icon fa' ).addClass( options.icon );\n this.$title.removeClass().addClass( 'title' ).html( options.title );\n options.icon && options.title && this.$icon.addClass( 'ui-margin-right' );\n this.$menu && this.$menu.remove();\n if ( this.collection.length > 0 ) {\n this.$menu = $( '\n cur_page = self.grid.get('cur_page'),\n text;\n if (page_num === new_page) {\n // Remove link to page since grid will be on this page. It is assumed that\n // this element has a single child, a hyperlink/anchor with text.\n text = $(this).children().text();\n $(this).empty();\n $(this).addClass('inactive-link');\n $(this).text(text);\n }\n else if (page_num === cur_page) {\n // Add hyperlink to this page since grid will no longer be on this page. It is assumed that\n // this element has a single child, a hyperlink/anchor.\n text = $(this).text();\n $(this).empty();\n $(this).removeClass('inactive-link');\n var t = $('' + text + '');\n t.click(function() {\n self.set_page(page_num);\n });\n $(this).append(t);\n }\n });\n\n if (new_page === 'all') {\n this.grid.set('cur_page', new_page);\n } else {\n this.grid.set('cur_page', parseInt(new_page, 10));\n }\n this.execute();\n },\n\n // confirmation/submission of operation request\n submit_operation: function (operation_button, confirmation_text) {\n // identify operation\n var operation_name = $(operation_button).val();\n\n // verify in any item is selected\n var number_of_checked_ids = this.$el.find('input[name=\"id\"]:checked').length;\n if (!number_of_checked_ids > 0) {\n return false;\n }\n\n // Check to see if there's grid confirmation text for this operation\n var operation = _.findWhere(this.grid.attributes.operations, {label: operation_name});\n if (operation && !confirmation_text){\n confirmation_text = operation.confirm || '';\n }\n\n // collect ids\n var item_ids = [];\n this.$el.find('input[name=id]:checked').each(function() {\n item_ids.push( $(this).val() );\n });\n\n // execute operation\n var options = {\n operation : operation_name,\n id : item_ids,\n confirmation_text : confirmation_text\n };\n if ( operation.target == 'top' ) {\n options = _.extend( options, {\n href : operation.href,\n target : operation.target\n });\n }\n this.execute( options );\n return true;\n },\n\n check_all_items: function () {\n var check = this.$('.grid-row-select-checkbox');\n var state = this.$( '#check_all' ).prop( 'checked' );\n _.each( check, function( c ) {\n $( c ).prop( 'checked', state );\n });\n this.init_grid_elements();\n },\n\n // Go back to page one; this is useful when a filter is applied.\n go_page_one: function () {\n // Need to go back to page 1 if not showing all.\n var cur_page = this.grid.get('cur_page');\n if (cur_page !== null && cur_page !== undefined && cur_page !== 'all') {\n this.grid.set('cur_page', 1);\n }\n },\n\n //\n // execute operations and hyperlink requests\n //\n execute: function (options) {\n // get url\n var id = null;\n var href = null;\n var operation = null;\n var confirmation_text = null;\n var target = null;\n\n // check for options\n if (options) {\n // get options\n href = options.href;\n operation = options.operation;\n id = options.id;\n confirmation_text = options.confirmation_text;\n target = options.target;\n\n // check if input contains the operation tag\n if (href !== undefined && href.indexOf('operation=') != -1) {\n // Get operation, id in hyperlink's href.\n var href_parts = href.split(\"?\");\n if (href_parts.length > 1) {\n var href_parms_str = href_parts[1];\n var href_parms = href_parms_str.split(\"&\");\n for (var index = 0; index < href_parms.length; index++) {\n if (href_parms[index].indexOf('operation') != -1) {\n // Found operation parm; get operation value.\n operation = href_parms[index].split('=')[1];\n operation = operation.replace (/\\+/g, ' ');\n } else if (href_parms[index].indexOf('id') != -1) {\n // Found id parm; get id value.\n id = href_parms[index].split('=')[1];\n }\n }\n }\n }\n }\n\n // check for operation details\n if (operation && id) {\n // show confirmation box\n if (confirmation_text && confirmation_text != '' && confirmation_text != 'None' && confirmation_text != 'null')\n if(!confirm(confirmation_text))\n return false;\n\n // use small characters for operation?!\n operation = operation.toLowerCase();\n\n // Update grid.\n this.grid.set({\n operation: operation,\n item_ids: id\n });\n\n // Do operation. If operation cannot be performed asynchronously, redirect to location.\n if ( target == 'top' ) {\n window.top.location = href + '?' + $.param( this.grid.get_url_data() );\n } else if ( this.grid.can_async_op(operation) || this.dict_format ) {\n this.update_grid();\n } else {\n this.go_to(target, href);\n }\n\n // done\n return false;\n }\n\n // refresh grid\n if (href) {\n this.go_to(target, href);\n return false;\n }\n\n // refresh grid\n if (this.grid.get('async') || this.dict_format) {\n this.update_grid();\n } else {\n this.go_to(target, href);\n }\n\n // done\n return false;\n },\n\n // go to url\n go_to: function (target, href) {\n // get aysnc status\n var async = this.grid.get('async');\n this.grid.set('async', false);\n\n // get slide status\n var advanced_search = this.$el.find('#advanced-search').is(':visible');\n this.grid.set('advanced_search', advanced_search);\n\n // get default url\n if(!href) {\n href = this.grid.get('url_base') + '?' + $.param(this.grid.get_url_data());\n }\n\n // clear grid of transient request attributes.\n this.grid.set({\n operation: undefined,\n item_ids: undefined,\n async: async\n });\n switch (target) {\n case 'inbound':\n // this currently assumes that there is only a single grid shown at a time\n var $div = $('.grid-header').closest('.inbound');\n if ($div.length !== 0) {\n $div.load(href);\n return;\n }\n break;\n case 'top':\n window.top.location = href;\n break;\n default:\n window.location = href;\n }\n },\n\n // Update grid.\n update_grid: function () {\n // If there's an operation, do POST; otherwise, do GET.\n var method = (this.grid.get('operation') ? 'POST' : 'GET' );\n\n // Show overlay to indicate loading and prevent user actions.\n this.$el.find('.loading-elt-overlay').show();\n var self = this;\n $.ajax({\n type: method,\n url: self.grid.get('url_base'),\n data: self.grid.get_url_data(),\n error: function(response) { alert( 'Grid refresh failed' );},\n success: function(response_text) {\n\n // backup\n var embedded = self.grid.get('embedded');\n var insert = self.grid.get('insert');\n var advanced_search = self.$el.find('#advanced-search').is(':visible');\n\n // request new configuration\n var json = self.dict_format ? response_text : $.parseJSON(response_text);\n\n // update\n json.embedded = embedded;\n json.insert = insert;\n json.advanced_search = advanced_search;\n\n // Initialize new grid config\n self.init_grid(json);\n\n // Hide loading overlay.\n self.$el.find('.loading-elt-overlay').hide();\n },\n complete: function() {\n // Clear grid of transient request attributes.\n self.grid.set({\n operation: undefined,\n item_ids: undefined\n });\n }\n });\n }\n});\n\n});\n\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/grid/grid-view.js\n **/","// dependencies\ndefine(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc'], function(Utils, Portlet, Ui) {\n\n// ui list element\nvar View = Backbone.View.extend({\n // create portlet to keep track of selected list elements\n initialize : function(options) {\n // link this\n var self = this;\n\n // initialize options\n this.options = options;\n this.name = options.name || 'element';\n this.multiple = options.multiple || false;\n\n // create message handler\n this.message = new Ui.Message();\n\n // create portlet\n this.portlet = new Portlet.View({ cls: 'ui-portlet-section' });\n\n // create select field containing the options which can be inserted into the list\n this.select = new Ui.Select.View({ optional : options.optional });\n\n // create insert new list element button\n this.button = new Ui.ButtonIcon({\n icon : 'fa fa-sign-in',\n tooltip : 'Insert new ' + this.name,\n onclick : function() {\n self.add({\n id : self.select.value(),\n name : self.select.text()\n });\n }\n });\n\n // build main element\n this.setElement(this._template(options));\n this.$('.ui-list-message').append(this.message.$el);\n this.$('.ui-list-portlet').append(this.portlet.$el);\n this.$('.ui-list-button').append(this.button.$el);\n this.$('.ui-list-select').append(this.select.$el);\n },\n\n /** Return/Set currently selected list elements */\n value: function(val) {\n // set new value\n if (val !== undefined) {\n this.portlet.empty();\n if ($.isArray(val)) {\n for (var i in val) {\n var v = val[i];\n var v_id = null;\n var v_name = null;\n if ($.type(v) != 'string') {\n v_id = v.id;\n v_name = v.name;\n } else {\n v_id = v_name = v;\n }\n if (v_id != null) {\n this.add({\n id : v_id,\n name : v_name\n });\n }\n }\n }\n this._refresh();\n }\n // get current value\n var lst = [];\n this.$('.ui-list-id').each(function() {\n lst.push({\n id : $(this).prop('id'),\n name : $(this).find('.ui-list-name').html()\n });\n });\n if (lst.length == 0) {\n return null;\n }\n return lst;\n },\n\n /** Add row */\n add: function(options) {\n var self = this;\n if (this.$('[id=\"' + options.id + '\"]').length === 0) {\n if (!Utils.isEmpty(options.id)) {\n var $el = $(this._templateRow({\n id : options.id,\n name : options.name\n }));\n $el.on('click', function() {\n $el.remove();\n self._refresh();\n });\n $el.on('mouseover', function() {\n $el.addClass('portlet-highlight');\n });\n $el.on('mouseout', function() {\n $el.removeClass('portlet-highlight');\n });\n this.portlet.append($el);\n this._refresh();\n } else {\n this.message.update({ message: 'Please select a valid ' + this.name + '.', status: 'danger' });\n }\n } else {\n this.message.update({ message: 'This ' + this.name + ' is already in the list.' });\n }\n },\n\n /** Update available options */\n update: function(options) {\n this.select.update(options);\n },\n\n /** Refresh view */\n _refresh: function() {\n if (this.$('.ui-list-id').length > 0) {\n !this.multiple && this.button.disable();\n this.$('.ui-list-portlet').show();\n } else {\n this.button.enable();\n this.$('.ui-list-portlet').hide();\n }\n this.options.onchange && this.options.onchange();\n },\n\n /** Main Template */\n _template: function(options) {\n return '
' +\n '
' +\n '
' +\n '' +\n '(no options) ';\n }\n return _.map( options, function( option ){\n if( option.divider ){\n return '';\n } else if( option.header ){\n return [ '', option.html, ' ' ].join( '' );\n }\n var href = option.href || 'javascript:void(0);',\n target = ( option.target )?( ' target=\"' + option.target + '\"' ):( '' ),\n check = ( option.checked )?( '' ):( '' );\n return [\n '',\n check, option.html,\n ' '\n ].join( '' );\n }).join( '' );\n },\n\n // get the absolute position/offset for the menu\n _getShownPosition : function( clickEvent ){\n\n // display menu horiz. centered on click...\n var menuWidth = this.$el.width();\n var x = clickEvent.pageX - menuWidth / 2 ;\n\n // adjust to handle horiz. scroll and window dimensions ( draw entirely on visible screen area )\n x = Math.min( x, $( document ).scrollLeft() + $( window ).width() - menuWidth - 5 );\n x = Math.max( x, $( document ).scrollLeft() + 5 );\n return {\n top: clickEvent.pageY,\n left: x\n };\n },\n\n // bind an event handler to all available frames so that when anything is clicked\n // the menu is removed from the DOM and the event handler unbinds itself\n _setUpCloseBehavior: function(){\n var menu = this;\n//TODO: alternately: focus hack, blocking overlay, jquery.blockui\n\n // function to close popup and unbind itself\n function closePopup( event ){\n $( document ).off( 'click.close_popup' );\n if( window && window.parent !== window ){\n try {\n $( window.parent.document ).off( \"click.close_popup\" );\n } catch( err ){}\n } else {\n try {\n $( 'iframe#galaxy_main' ).contents().off( \"click.close_popup\" );\n } catch( err ){}\n }\n menu.remove();\n }\n\n $( 'html' ).one( \"click.close_popup\", closePopup );\n if( window && window.parent !== window ){\n try {\n $( window.parent.document ).find( 'html' ).one( \"click.close_popup\", closePopup );\n } catch( err ){}\n } else {\n try {\n $( 'iframe#galaxy_main' ).contents().one( \"click.close_popup\", closePopup );\n } catch( err ){}\n }\n },\n\n // add a menu option/item at the given index\n addItem: function( item, index ){\n // append to end if no index\n index = ( index >= 0 ) ? index : this.options.length;\n this.options.splice( index, 0, item );\n return this;\n },\n\n // remove a menu option/item at the given index\n removeItem: function( index ){\n if( index >=0 ){\n this.options.splice( index, 1 );\n }\n return this;\n },\n\n // search for a menu option by its html\n findIndexByHtml: function( html ){\n for( var i = 0; i < this.options.length; i++ ){\n if( _.has( this.options[i], 'html' ) && ( this.options[i].html === html )){\n return i;\n }\n }\n return null;\n },\n\n // search for a menu option by its html\n findItemByHtml: function( html ){\n return this.options[( this.findIndexByHtml( html ))];\n },\n\n // string representation\n toString: function(){\n return 'PopupMenu';\n }\n});\n/** shortcut to new for when you don't need to preserve the ref */\nPopupMenu.create = function _create( $button, options ){\n return new PopupMenu( $button, options );\n};\n\n// -----------------------------------------------------------------------------\n// the following class functions are bridges from the original make_popupmenu and make_popup_menus\n// to the newer backbone.js PopupMenu\n\n/** Create a PopupMenu from simple map initial_options activated by clicking button_element.\n * Converts initial_options to object array used by PopupMenu.\n * @param {jQuery|DOMElement} button_element element which, when clicked, activates menu\n * @param {Object} initial_options map of key -> values, where\n * key is option text, value is fn to call when option is clicked\n * @returns {PopupMenu} the PopupMenu created\n */\nPopupMenu.make_popupmenu = function( button_element, initial_options ){\n var convertedOptions = [];\n _.each( initial_options, function( optionVal, optionKey ){\n var newOption = { html: optionKey };\n\n // keys with null values indicate: header\n if( optionVal === null ){ // !optionVal? (null only?)\n newOption.header = true;\n\n // keys with function values indicate: a menu option\n } else if( jQuery.type( optionVal ) === 'function' ){\n newOption.func = optionVal;\n }\n //TODO:?? any other special optionVals?\n // there was no divider option originally\n convertedOptions.push( newOption );\n });\n return new PopupMenu( $( button_element ), convertedOptions );\n};\n\n/** Find all anchors in $parent (using selector) and covert anchors into a PopupMenu options map.\n * @param {jQuery} $parent the element that contains the links to convert to options\n * @param {String} selector jq selector string to find links\n * @returns {Object[]} the options array to initialize a PopupMenu\n */\n//TODO: lose parent and selector, pass in array of links, use map to return options\nPopupMenu.convertLinksToOptions = function( $parent, selector ){\n $parent = $( $parent );\n selector = selector || 'a';\n var options = [];\n $parent.find( selector ).each( function( elem, i ){\n var option = {}, $link = $( elem );\n\n // convert link text to the option text (html) and the href into the option func\n option.html = $link.text();\n if( $link.attr( 'href' ) ){\n var linkHref = $link.attr( 'href' ),\n linkTarget = $link.attr( 'target' ),\n confirmText = $link.attr( 'confirm' );\n\n option.func = function(){\n // if there's a \"confirm\" attribute, throw up a confirmation dialog, and\n // if the user cancels - do nothing\n if( ( confirmText ) && ( !confirm( confirmText ) ) ){ return; }\n\n // if there's no confirm attribute, or the user accepted the confirm dialog:\n switch( linkTarget ){\n // relocate the center panel\n case '_parent':\n window.parent.location = linkHref;\n break;\n\n // relocate the entire window\n case '_top':\n window.top.location = linkHref;\n break;\n\n // relocate this panel\n default:\n window.location = linkHref;\n }\n };\n }\n options.push( option );\n });\n return options;\n};\n\n/** Create a single popupmenu from existing DOM button and anchor elements\n * @param {jQuery} $buttonElement the element that when clicked will open the menu\n * @param {jQuery} $menuElement the element that contains the anchors to convert into a menu\n * @param {String} menuElementLinkSelector jq selector string used to find anchors to be made into menu options\n * @returns {PopupMenu} the PopupMenu (Backbone View) that can render, control the menu\n */\nPopupMenu.fromExistingDom = function( $buttonElement, $menuElement, menuElementLinkSelector ){\n $buttonElement = $( $buttonElement );\n $menuElement = $( $menuElement );\n var options = PopupMenu.convertLinksToOptions( $menuElement, menuElementLinkSelector );\n // we're done with the menu (having converted it to an options map)\n $menuElement.remove();\n return new PopupMenu( $buttonElement, options );\n};\n\n/** Create all popupmenus within a document or a more specific element\n * @param {DOMElement} parent the DOM element in which to search for popupmenus to build (defaults to document)\n * @param {String} menuSelector jq selector string to find popupmenu menu elements (defaults to \"div[popupmenu]\")\n * @param {Function} buttonSelectorBuildFn the function to build the jq button selector.\n * Will be passed $menuElement, parent.\n * (Defaults to return '#' + $menuElement.attr( 'popupmenu' ); )\n * @returns {PopupMenu[]} array of popupmenus created\n */\nPopupMenu.make_popup_menus = function( parent, menuSelector, buttonSelectorBuildFn ){\n parent = parent || document;\n // orig. Glx popupmenu menus have a (non-std) attribute 'popupmenu'\n // which contains the id of the button that activates the menu\n menuSelector = menuSelector || 'div[popupmenu]';\n // default to (orig. Glx) matching button to menu by using the popupmenu attr of the menu as the id of the button\n buttonSelectorBuildFn = buttonSelectorBuildFn || function( $menuElement, parent ){\n return '#' + $menuElement.attr( 'popupmenu' );\n };\n\n // aggregate and return all PopupMenus\n var popupMenusCreated = [];\n $( parent ).find( menuSelector ).each( function(){\n var $menuElement = $( this ),\n $buttonElement = $( parent ).find( buttonSelectorBuildFn( $menuElement, parent ) );\n popupMenusCreated.push( PopupMenu.fromDom( $buttonElement, $menuElement ) );\n $buttonElement.addClass( 'popup' );\n });\n return popupMenusCreated;\n};\n\n\n// =============================================================================\n return PopupMenu;\n});\n\n\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/ui/popup-menu.js\n **/","/* This class maps the form dom to an api compatible javascript dictionary. */\ndefine([ 'utils/utils' ], function( Utils ) {\n var Manager = Backbone.Model.extend({\n initialize: function( app ) {\n this.app = app;\n },\n\n /** Creates a checksum. */\n checksum: function() {\n var sum = '';\n var self = this;\n this.app.section.$el.find( '.section-row' ).each( function() {\n var id = $(this).attr( 'id' );\n var field = self.app.field_list[ id ];\n if ( field ) {\n sum += id + ':' + JSON.stringify( field.value && field.value() ) + ':' + field.collapsed + ';';\n }\n });\n return sum;\n },\n\n /** Convert dom into a dictionary of flat id/value pairs used e.g. on job submission. */\n create: function() {\n var self = this;\n\n // get raw dictionary from dom\n var dict = {};\n this._iterate( this.app.section.$el, dict );\n\n // add to result dictionary, label elements\n var result_dict = {};\n this.flat_dict = {};\n function add( flat_id, input_id, input_value ) {\n self.flat_dict[ flat_id ] = input_id;\n result_dict[ flat_id ] = input_value;\n self.app.element_list[ input_id ] && self.app.element_list[ input_id ].$el.attr( 'tour_id', flat_id );\n }\n // converter between raw dictionary and job dictionary\n function convert( identifier, head ) {\n for ( var index in head ) {\n var node = head[ index ];\n if ( node.input ) {\n var input = node.input;\n var flat_id = identifier;\n if ( identifier != '' ) {\n flat_id += '|';\n }\n flat_id += input.name;\n switch ( input.type ) {\n case 'repeat':\n var section_label = 'section-';\n var block_indices = [];\n var block_prefix = null;\n for ( var block_label in node ) {\n var pos = block_label.indexOf( section_label );\n if ( pos != -1 ) {\n pos += section_label.length;\n block_indices.push( parseInt( block_label.substr( pos ) ));\n if ( !block_prefix ) {\n block_prefix = block_label.substr( 0, pos );\n }\n }\n }\n block_indices.sort( function( a, b ) { return a - b; });\n var index = 0;\n for ( var i in block_indices ) {\n convert( flat_id + '_' + index++, node[ block_prefix + block_indices[ i ] ]);\n }\n break;\n case 'conditional':\n var value = self.app.field_list[ input.id ].value();\n add( flat_id + '|' + input.test_param.name, input.id, value );\n var selectedCase = matchCase( input, value );\n if ( selectedCase != -1 ) {\n convert( flat_id, head[ input.id + '-section-' + selectedCase ] );\n }\n break;\n case 'section':\n convert( !input.flat && flat_id || '', node );\n break;\n default:\n var field = self.app.field_list[ input.id ];\n if ( field && field.value ) {\n var value = field.value();\n if ( input.ignore === undefined || input.ignore != value ) {\n if ( field.collapsed && input.collapsible_value ) {\n value = input.collapsible_value;\n }\n add( flat_id, input.id, value );\n if ( input.payload ) {\n for ( var p_id in input.payload ) {\n add( p_id, input.id, input.payload[ p_id ] );\n }\n }\n }\n }\n }\n }\n }\n }\n convert( '', dict );\n return result_dict;\n },\n\n /** Matches flat ids to corresponding input element\n * @param{string} flat_id - Flat input id to be looked up.\n */\n match: function ( flat_id ) {\n return this.flat_dict && this.flat_dict[ flat_id ];\n },\n\n /** Match conditional values to selected cases\n */\n matchCase: function( input, value ) {\n return matchCase( input, value );\n },\n\n /** Matches a new tool model to the current input elements e.g. used to update dynamic options\n */\n matchModel: function( model, callback ) {\n var self = this;\n visitInputs( model.inputs, function( input, name ) {\n self.flat_dict[ name ] && callback ( input, self.flat_dict[ name ] );\n });\n },\n\n /** Matches identifier from api response to input elements e.g. used to display validation errors\n */\n matchResponse: function( response ) {\n var result = {};\n var self = this;\n function search ( id, head ) {\n if ( typeof head === 'string' ) {\n var input_id = self.flat_dict[ id ];\n input_id && ( result[ input_id ] = head );\n } else {\n for ( var i in head ) {\n var new_id = i;\n if ( id !== '' ) {\n var separator = '|';\n if ( head instanceof Array ) {\n separator = '_';\n }\n new_id = id + separator + new_id;\n }\n search ( new_id, head[ i ] );\n }\n }\n }\n search( '', response );\n return result;\n },\n\n /** Map dom tree to dictionary tree with input elements.\n */\n _iterate: function( parent, dict ) {\n var self = this;\n var children = $( parent ).children();\n children.each( function() {\n var child = this;\n var id = $( child ).attr( 'id' );\n if ( $( child ).hasClass( 'section-row' ) ) {\n var input = self.app.input_list[ id ];\n dict[ id ] = ( input && { input : input } ) || {};\n self._iterate( child, dict[ id ] );\n } else {\n self._iterate( child, dict );\n }\n });\n }\n });\n\n /** Match conditional values to selected cases\n * @param{dict} input - Definition of conditional input parameter\n * @param{dict} value - Current value\n */\n var matchCase = function( input, value ) {\n if ( input.test_param.type == 'boolean' ) {\n if ( value == 'true' ) {\n value = input.test_param.truevalue || 'true';\n } else {\n value = input.test_param.falsevalue || 'false';\n }\n }\n for ( var i in input.cases ) {\n if ( input.cases[ i ].value == value ) {\n return i;\n }\n }\n return -1;\n };\n\n /** Visits tool inputs\n * @param{dict} inputs - Nested dictionary of input elements\n * @param{dict} callback - Called with the mapped dictionary object and corresponding model node\n */\n var visitInputs = function( inputs, callback, prefix, context ) {\n context = $.extend( true, {}, context );\n _.each( inputs, function ( input ) {\n if ( input && input.type && input.name ) {\n context[ input.name ] = input;\n }\n });\n for ( var key in inputs ) {\n var node = inputs[ key ];\n node.name = node.name || key;\n var name = prefix ? prefix + '|' + node.name : node.name;\n switch ( node.type ) {\n case 'repeat':\n _.each( node.cache, function( cache, j ) {\n visitInputs( cache, callback, name + '_' + j, context );\n });\n break;\n case 'conditional':\n if ( node.test_param ) {\n callback( node.test_param, name + '|' + node.test_param.name, context );\n var selectedCase = matchCase( node, node.test_param.value );\n if ( selectedCase != -1 ) {\n visitInputs( node.cases[ selectedCase ].inputs, callback, name, context );\n } else {\n Galaxy.emit.debug( 'form-data::visitInputs() - Invalid case for ' + name + '.' );\n }\n } else {\n Galaxy.emit.debug( 'form-data::visitInputs() - Conditional test parameter missing for ' + name + '.' );\n }\n break;\n case 'section':\n visitInputs( node.inputs, callback, name, context )\n break;\n default:\n callback( node, name, context );\n }\n }\n };\n\n return {\n Manager : Manager,\n visitInputs : visitInputs\n }\n});\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/form/form-data.js\n **/","/** This class creates a ui table element. */\ndefine( [ 'utils/utils' ], function( Utils ) {\n var View = Backbone.View.extend({\n initialize : function(options) {\n this.options = Utils.merge(options, {\n content : 'No content available.',\n onchange : null,\n ondblclick : null,\n onconfirm : null,\n cls : 'ui-table',\n selectable : true,\n cls_tr : ''\n });\n this.setElement( this._template() );\n this.$thead = this.$('thead');\n this.$tbody = this.$('tbody');\n this.$tmessage = this.$('tmessage');\n this.row = this._row();\n this.row_count = 0;\n },\n\n events : {\n 'click' : '_onclick',\n 'dblclick' : '_ondblclick'\n },\n\n /** Add cell to header row */\n addHeader: function( $el ) {\n this.row.append( $( '
' +\n '
';\n },\n\n /** Row Template */\n _templateRow: function(options) {\n return '' +\n '' +\n '' + options.name + '' +\n '
';\n }\n});\n\nreturn {\n View: View\n}\n\n});\n\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/ui/ui-list.js\n **/","/** Base class for options based ui elements **/\ndefine([ 'utils/utils', 'mvc/ui/ui-buttons' ], function( Utils, Buttons ) {\nvar Base = Backbone.View.extend({\n initialize: function( options ) {\n var self = this;\n this.model = options && options.model || new Backbone.Model({\n visible : true,\n data : [],\n id : Utils.uid(),\n error_text : 'No options available.',\n wait_text : 'Please wait...',\n multiple : false,\n optional : false,\n onchange : function(){}\n }).set( options );\n this.listenTo( this.model, 'change:value', this._changeValue, this );\n this.listenTo( this.model, 'change:wait', this._changeWait, this );\n this.listenTo( this.model, 'change:data', this._changeData, this );\n this.listenTo( this.model, 'change:visible', this._changeVisible, this );\n this.on( 'change', function() { self.model.get( 'onchange' )( self.value() ) } );\n this.render();\n },\n\n render: function() {\n var self = this;\n this.$el.empty()\n .removeClass()\n .addClass( 'ui-options' )\n .append( this.$message = $( '' ) )\n .append( this.$menu = $( '' ).addClass( 'ui-options-menu' ) )\n .append( this.$options = $( this._template() ) );\n\n // add select/unselect all button\n this.all_button = null;\n if ( this.model.get( 'multiple' ) ) {\n this.all_button = new Buttons.ButtonCheck({\n onclick: function() {\n self.$( 'input' ).prop( 'checked', self.all_button.value() !== 0 );\n self.value( self._getValue() );\n self.trigger( 'change' );\n }\n });\n this.$menu.append( this.all_button.$el );\n }\n\n // finalize dom\n this._changeData();\n this._changeWait();\n this._changeVisible();\n },\n\n /** Update available options */\n update: function( options ) {\n this.model.set( 'data', options );\n },\n\n _changeData: function() {\n var self = this;\n this.$options.empty();\n if ( this._templateOptions ) {\n this.$options.append( this._templateOptions( this.model.get( 'data' ) ) );\n } else {\n _.each( this.model.get( 'data' ), function( option ) {\n self.$options.append( $( self._templateOption( option ) )\n .addClass( 'ui-option' )\n .tooltip( { title: option.tooltip, placement: 'bottom' } ) );\n });\n }\n var self = this;\n this.$( 'input' ).on( 'change', function() {\n self.value( self._getValue() );\n self.trigger( 'change' );\n });\n this._changeValue();\n this._changeWait();\n },\n\n _changeVisible: function() {\n this.$el[ this.model.get( 'visible' ) ? 'show' : 'hide' ]();\n },\n\n _changeWait: function() {\n if ( this.model.get( 'wait' ) ) {\n if ( this.length() === 0 ) {\n this._messageShow( this.model.get( 'wait_text' ), 'info' );\n this.$options.hide();\n this.$menu.hide();\n }\n } else {\n if ( this.length() === 0 ) {\n this._messageShow( this.model.get( 'error_text' ), 'danger' );\n this.$options.hide();\n this.$menu.hide();\n } else {\n this.$message.hide();\n this.$options.css( 'display', 'inline-block' );\n this.$menu.show();\n }\n }\n },\n\n _changeValue: function() {\n this._setValue( this.model.get( 'value' ) );\n if ( this._getValue() === null && !this.model.get( 'multiple' ) && !this.model.get( 'optional' ) ) {\n this._setValue( this.first() );\n }\n this.all_button && this.all_button.value( $.isArray( this._getValue() ) ? this._getValue().length : 0, this.length() );\n },\n\n /** Return/Set current selection */\n value: function ( new_value ) {\n new_value !== undefined && this.model.set( 'value', new_value );\n return this._getValue();\n },\n\n /** Return first available option */\n first: function() {\n var options = this.$( 'input' ).first();\n return options.length > 0 ? options.val() : null;\n },\n\n /** Show a spinner indicating that the select options are currently loaded */\n wait: function() {\n this.model.set( 'wait', true );\n },\n\n /** Hide spinner indicating that the request has been completed */\n unwait: function() {\n this.model.set( 'wait', false );\n },\n\n /** Returns the number of options */\n length: function() {\n return this.$( '.ui-option' ).length;\n },\n\n /** Set value to dom */\n _setValue: function( new_value ) {\n var self = this;\n if ( new_value !== undefined ) {\n this.$( 'input' ).prop( 'checked', false );\n if ( new_value !== null ) {\n var values = $.isArray( new_value ) ? new_value : [ new_value ];\n _.each( values, function( v ) {\n self.$( 'input[value=\"' + v + '\"]' ).first().prop( 'checked', true );\n });\n }\n }\n },\n\n /** Return current selection */\n _getValue: function() {\n var selected = [];\n this.$( ':checked' ).each( function() {\n selected.push( $( this ).val() );\n });\n if ( Utils.isEmpty( selected ) ) {\n return null;\n }\n return this.model.get( 'multiple' ) ? selected : selected[ 0 ];\n },\n\n /** Show message instead if options */\n _messageShow: function( text, status ) {\n this.$message.show()\n .removeClass()\n .addClass( 'ui-message alert alert-' + status )\n .html( text );\n },\n\n /** Main template function */\n _template: function() {\n return $( '' ).addClass( 'ui-options-list' );\n }\n});\n\n/** Iconized **/\nvar BaseIcons = Base.extend({\n _templateOption: function( pair ) {\n var id = Utils.uid();\n return $( '' ).addClass( 'ui-option' )\n .append( $( '' ).attr( {\n id : id,\n type : this.model.get( 'type' ),\n name : this.model.id,\n value : pair.value } ) )\n .append( $( '' ).addClass( 'ui-options-label' )\n .attr( 'for', id )\n .html( pair.label ) );\n }\n});\n\n/** Radio button field **/\nvar Radio = {};\nRadio.View = BaseIcons.extend({\n initialize: function( options ) {\n options.type = 'radio';\n BaseIcons.prototype.initialize.call( this, options );\n }\n});\n\n/** Checkbox options field **/\nvar Checkbox = {};\nCheckbox.View = BaseIcons.extend({\n initialize: function( options ) {\n options.type = 'checkbox';\n options.multiple = true;\n BaseIcons.prototype.initialize.call( this, options );\n }\n});\n\n/** Radio button options field styled as classic buttons **/\nvar RadioButton = {};\nRadioButton.View = Base.extend({\n initialize: function( options ) {\n Base.prototype.initialize.call( this, options );\n },\n\n /** Set current value */\n _setValue: function ( new_value ) {\n if ( new_value !== undefined ) {\n this.$( 'input' ).prop( 'checked', false );\n this.$( 'label' ).removeClass( 'active' );\n this.$( '[value=\"' + new_value + '\"]' ).prop( 'checked', true ).closest( 'label' ).addClass( 'active' );\n }\n },\n\n /** Template for a single option */\n _templateOption: function( pair ) {\n var $el = $( '' ).addClass( 'btn btn-default' );\n pair.icon && $el.append( $( '' ).addClass( 'fa' ).addClass( pair.icon ).addClass( !pair.label && 'no-padding' ) );\n $el.append( $( '' ).attr( { type: 'radio', name: this.model.id, value: pair.value } ) );\n pair.label && $el.append( pair.label );\n return $el;\n },\n\n /** Main template function */\n _template: function() {\n return $( '' ).addClass( 'btn-group ui-radiobutton' ).attr( 'data-toggle', 'buttons' );\n }\n});\n\nreturn {\n Base : Base,\n BaseIcons : BaseIcons,\n Radio : Radio,\n RadioButton : RadioButton,\n Checkbox : Checkbox\n};\n\n});\n\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/ui/ui-options.js\n **/","/**\n * This class creates/wraps a default html select field as backbone class.\n */\ndefine([ 'utils/utils', 'mvc/ui/ui-buttons' ], function( Utils, Buttons ) {\nvar View = Backbone.View.extend({\n initialize: function( options ) {\n var self = this;\n this.data = [];\n this.data2 = [];\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n cls : 'ui-select',\n error_text : 'No options available',\n empty_text : 'Nothing selected',\n visible : true,\n wait : false,\n multiple : false,\n searchable : true,\n optional : false,\n disabled : false,\n onchange : function(){},\n value : null,\n individual : false,\n pagesize : 20\n }).set( options );\n this.on( 'change', function() { self.model.get( 'onchange' ) && self.model.get( 'onchange' )( self.value() ) } );\n this.listenTo( this.model, 'change:data', this._changeData, this );\n this.listenTo( this.model, 'change:disabled', this._changeDisabled, this );\n this.listenTo( this.model, 'change:wait', this._changeWait, this );\n this.listenTo( this.model, 'change:visible', this._changeVisible, this );\n this.listenTo( this.model, 'change:value', this._changeValue, this );\n this.listenTo( this.model, 'change:multiple change:searchable change:cls change:id', this.render, this );\n this.render();\n },\n\n render: function() {\n var self = this;\n this.model.get( 'searchable' ) ? this._renderSearchable() : this._renderClassic();\n this.$el.addClass( this.model.get( 'cls' ) )\n .attr( 'id', this.model.get( 'id' ) );\n this.$select.empty().addClass( 'select' )\n .attr( 'id', this.model.get( 'id' ) + '_select' )\n .prop( 'multiple', this.model.get( 'multiple' ) )\n .on( 'change', function() {\n self.value( self._getValue() );\n self.trigger( 'change' );\n });\n this._changeData();\n this._changeWait();\n this._changeVisible();\n this._changeDisabled();\n },\n\n /** Renders the classic selection field */\n _renderClassic: function() {\n var self = this;\n this.$el.addClass( this.model.get( 'multiple' ) ? 'ui-select-multiple' : 'ui-select' )\n .append( this.$select = $( '' ) )\n .append( this.$dropdown = $( '' ) )\n .append( this.$resize = $( '' )\n .append( this.$resize_icon = $( '' ) ) );\n if ( this.model.get( 'multiple' ) ) {\n this.$dropdown.hide();\n this.$resize_icon.addClass( 'fa fa-angle-double-right fa-rotate-45' ).show();\n this.$resize.removeClass()\n .addClass( 'icon-resize' )\n .show()\n .off( 'mousedown' ).on( 'mousedown', function( event ) {\n var currentY = event.pageY;\n var currentHeight = self.$select.height();\n self.minHeight = self.minHeight || currentHeight;\n $( '#dd-helper' ).show().on( 'mousemove', function( event ) {\n self.$select.height( Math.max( currentHeight + ( event.pageY - currentY ), self.minHeight ) );\n }).on( 'mouseup mouseleave', function() {\n $( '#dd-helper' ).hide().off();\n });\n });\n } else {\n this.$dropdown.show();\n this.$resize.hide();\n this.$resize_icon.hide();\n }\n },\n\n /** Renders the default select2 field */\n _renderSearchable: function() {\n var self = this;\n this.$el.append( this.$select = $( '' ) )\n .append( this.$dropdown = $( '' ) );\n this.$dropdown.hide();\n if ( !this.model.get( 'multiple' ) ) {\n this.$dropdown.show().on( 'click', function() {\n self.$select.select2 && self.$select.select2( 'open' );\n });\n }\n this.all_button = null;\n if ( this.model.get( 'multiple' ) && !this.model.get( 'individual' ) ) {\n this.all_button = new Buttons.ButtonCheck({\n onclick: function() {\n var new_value = [];\n self.all_button.value() !== 0 && _.each( self.model.get( 'data' ), function( option ) {\n new_value.push( option.value );\n });\n self.value( new_value );\n self.trigger( 'change' );\n }\n });\n this.$el.prepend( this.all_button.$el );\n }\n },\n\n /** Matches a search term with a given text */\n _match: function( term, text ) {\n return !term || term == '' || String( text ).toUpperCase().indexOf( term.toUpperCase() ) >= 0\n },\n\n /** Updates the selection options */\n _changeData: function() {\n var self = this;\n this.data = [];\n if ( !this.model.get( 'multiple' ) && this.model.get( 'optional' ) ) {\n this.data.push( { value: '__null__', label: self.model.get( 'empty_text' ) } );\n }\n _.each( this.model.get( 'data' ), function( option ) {\n self.data.push( option );\n });\n if ( this.length() == 0 ) {\n this.data.push( { value: '__null__', label: this.model.get( 'error_text' ) } );\n }\n if ( this.model.get( 'searchable' ) ) {\n this.data2 = [];\n _.each( this.data, function( option, index ) {\n self.data2.push( { order: index, id: option.value, text: option.label, tags: option.tags } );\n });\n this.$select.data( 'select2' ) && this.$select.select2( 'destroy' );\n this.matched_tags = {};\n this.$select.select2({\n data : self.data2,\n closeOnSelect : !this.model.get( 'multiple' ),\n multiple : this.model.get( 'multiple' ),\n query : function( q ) {\n self.matched_tags = {};\n var pagesize = self.model.get( 'pagesize' );\n var results = _.filter( self.data2, function ( e ) {\n var found = false;\n _.each( e.tags, function( tag ) {\n if ( self._match( q.term, tag ) ) {\n found = self.matched_tags[ tag ] = true;\n }\n });\n return found || self._match( q.term, e.text );\n });\n q.callback({\n results: results.slice( ( q.page - 1 ) * pagesize, q.page * pagesize ),\n more : results.length >= q.page * pagesize\n });\n },\n formatResult : function( result ) {\n return _.escape( result.text ) +\n '';\n }\n });\n this.$( '.select2-container .select2-search input' ).off( 'blur' );\n } else {\n this.$select.find( 'option' ).remove();\n _.each( this.data, function( option ) {\n self.$select.append( $( '' ).attr( 'value', option.value ).html( _.escape( option.label ) ) );\n });\n }\n this.model.set( 'disabled', this.length() == 0 );\n this._changeValue();\n },\n\n /** Handles field enabling/disabling, usually used when no options are available */\n _changeDisabled: function() {\n if ( this.model.get( 'searchable' ) ) {\n this.$select.select2( this.model.get( 'disabled' ) ? 'disable' : 'enable' );\n } else {\n this.$select.prop( 'disabled', this.model.get( 'disabled' ) );\n }\n },\n\n /** Searchable fields may display a spinner e.g. while waiting for a server response */\n _changeWait: function() {\n this.$dropdown.removeClass()\n .addClass( 'icon-dropdown fa' )\n .addClass( this.model.get( 'wait' ) ? 'fa-spinner fa-spin' : 'fa-caret-down' );\n },\n\n /** Handles field visibility */\n _changeVisible: function() {\n this.$el[ this.model.get( 'visible' ) ? 'show' : 'hide' ]();\n this.$select[ this.model.get( 'visible' ) ? 'show' : 'hide' ]();\n },\n\n /** Synchronizes the model value with the actually selected field value */\n _changeValue: function() {\n this._setValue( this.model.get( 'value' ) );\n if ( this.model.get( 'multiple' ) ) {\n if ( this.all_button ) {\n var value = this._getValue();\n this.all_button.value( $.isArray( value ) ? value.length : 0, this.length() );\n }\n } else if ( this._getValue() === null && !this.model.get( 'optional' ) ) {\n this._setValue( this.first() );\n }\n },\n\n /** Return/Set current selection */\n value: function ( new_value ) {\n new_value !== undefined && this.model.set( 'value', new_value );\n return this._getValue();\n },\n\n /** Return the first select option */\n first: function() {\n return this.data.length > 0 ? this.data[ 0 ].value : null;\n },\n\n /** Check if a value is an existing option */\n exists: function( value ) {\n return _.findWhere( this.data, { value: value } );\n },\n\n /** Return the label/text of the current selection */\n text: function () {\n var v = this._getValue();\n var d = this.exists( $.isArray( v ) ? v[ 0 ] : v );\n return d ? d.label : '';\n },\n\n /** Show the select field */\n show: function() {\n this.model.set( 'visible', true );\n },\n\n /** Hide the select field */\n hide: function() {\n this.model.set( 'visible', false );\n },\n\n /** Show a spinner indicating that the select options are currently loaded */\n wait: function() {\n this.model.set( 'wait', true );\n },\n\n /** Hide spinner indicating that the request has been completed */\n unwait: function() {\n this.model.set( 'wait', false );\n },\n\n /** Returns true if the field is disabled */\n disabled: function() {\n return this.model.get( 'disabled' );\n },\n\n /** Enable the select field */\n enable: function() {\n this.model.set( 'disabled', false );\n },\n\n /** Disable the select field */\n disable: function() {\n this.model.set( 'disabled', true );\n },\n\n /** Update all available options at once */\n add: function( options, sorter ) {\n _.each( this.model.get( 'data' ), function( v ) {\n v.keep && !_.findWhere( options, { value: v.value } ) && options.push( v );\n });\n sorter && options && options.sort( sorter );\n this.model.set( 'data', options );\n },\n\n /** Update available options */\n update: function( options ) {\n this.model.set( 'data', options );\n },\n\n /** Set the custom onchange callback function */\n setOnChange: function( callback ) {\n this.model.set( 'onchange', callback );\n },\n\n /** Number of available options */\n length: function() {\n return $.isArray( this.model.get( 'data' ) ) ? this.model.get( 'data' ).length : 0;\n },\n\n /** Set value to dom */\n _setValue: function( new_value ) {\n var self = this;\n if( new_value === null || new_value === undefined ) {\n new_value = '__null__';\n }\n if ( this.model.get( 'multiple' ) ) {\n new_value = $.isArray( new_value ) ? new_value : [ new_value ];\n } else if ( $.isArray( new_value ) ) {\n if ( new_value.length > 0 ) {\n new_value = new_value[ 0 ];\n } else {\n new_value = '__null__';\n }\n }\n if ( this.model.get( 'searchable' ) ) {\n if ( $.isArray( new_value ) ) {\n var val = [];\n _.each( new_value, function( v ) {\n var d = _.findWhere( self.data2, { id: v } );\n d && val.push( d );\n });\n new_value = val;\n } else {\n var d = _.findWhere( this.data2, { id: new_value } );\n new_value = d;\n }\n this.$select.select2( 'data', new_value );\n } else {\n this.$select.val( new_value );\n }\n },\n\n /** Get value from dom */\n _getValue: function() {\n var val = null;\n if ( this.model.get( 'searchable' ) ) {\n var selected = this.$select.select2( 'data' );\n if ( selected ) {\n if ( $.isArray( selected ) ) {\n val = [];\n selected.sort( function( a, b ) { return a.order - b.order } );\n _.each( selected, function( v ) { val.push( v.id ) } );\n } else {\n val = selected.id;\n }\n }\n } else {\n val = this.$select.val();\n }\n return Utils.isEmpty( val ) ? null : val;\n }\n});\n\nreturn {\n View: View\n}\n\n});\n\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/ui/ui-select-default.js\n **/","define([\n //jquery\n //backbone\n], function(){\n// =============================================================================\n/**\n * view for a popup menu\n */\nvar PopupMenu = Backbone.View.extend({\n//TODO: maybe better as singleton off the Galaxy obj\n /** Cache the desired button element and options, set up the button click handler\n * NOTE: attaches this view as HTML/jQ data on the button for later use.\n */\n initialize: function( $button, options ){\n // default settings\n this.$button = $button;\n if( !this.$button.length ){\n this.$button = $( '' );\n }\n this.options = options || [];\n this.$button.data( 'popupmenu', this );\n\n // set up button click -> open menu behavior\n var menu = this;\n this.$button.click( function( event ){\n // if there's already a menu open, remove it\n $( '.popmenu-wrapper' ).remove();\n menu._renderAndShow( event );\n return false;\n });\n },\n\n // render the menu, append to the page body at the click position, and set up the 'click-away' handlers, show\n _renderAndShow: function( clickEvent ){\n this.render();\n this.$el.appendTo( 'body' ).css( this._getShownPosition( clickEvent )).show();\n this._setUpCloseBehavior();\n },\n\n // render the menu\n // this menu doesn't attach itself to the DOM ( see _renderAndShow )\n render: function(){\n // render the menu body absolute and hidden, fill with template\n this.$el.addClass( 'popmenu-wrapper' ).hide()\n .css({ position : 'absolute' })\n .html( this.template( this.$button.attr( 'id' ), this.options ));\n\n // set up behavior on each link/anchor elem\n if( this.options.length ){\n var menu = this;\n //precondition: there should be one option per li\n this.$el.find( 'li' ).each( function( i, li ){\n var option = menu.options[i];\n\n // if the option has 'func', call that function when the anchor is clicked\n if( option.func ){\n $( this ).children( 'a.popupmenu-option' ).click( function( event ){\n option.func.call( menu, event, option );\n // We must preventDefault otherwise clicking \"cancel\"\n // on a purge or something still navigates and causes\n // the action.\n event.preventDefault();\n // bubble up so that an option click will call the close behavior\n });\n }\n });\n }\n return this;\n },\n\n template : function( id, options ){\n return [\n ''\n ].join( '' );\n },\n\n _templateOptions : function( options ){\n if( !options.length ){\n return '' +\n '' +\n '' +\n '' +\n '
' +\n '' + this.options.content + ' ' +\n '
';\n }\n });\n\n return {\n View: View\n }\n});\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/ui/ui-table.js\n **/","/**\n This class creates a form input element wrapper\n*/\ndefine([], function() {\n return Backbone.View.extend({\n initialize: function( app, options ) {\n this.app = app;\n this.app_options = app.model ? app.model.attributes : {};\n this.field = options && options.field || new Backbone.View();\n this.model = options && options.model || new Backbone.Model({\n text_enable : this.app_options.text_enable || 'Enable',\n text_disable : this.app_options.text_disable || 'Disable',\n cls_enable : this.app_options.cls_enable || 'fa fa-caret-square-o-down',\n cls_disable : this.app_options.cls_disable || 'fa fa-caret-square-o-up',\n always_refresh : this.app_options.always_refresh\n }).set( options );\n\n // set element and link components\n this.setElement( this._template() );\n this.$field = this.$( '.ui-form-field' );\n this.$info = this.$( '.ui-form-info' );\n this.$preview = this.$( '.ui-form-preview' );\n this.$collapsible = this.$( '.ui-form-collapsible' );\n this.$collapsible_text = this.$( '.ui-form-collapsible-text' );\n this.$collapsible_icon = this.$( '.ui-form-collapsible-icon' );\n this.$title = this.$( '.ui-form-title' );\n this.$title_text = this.$( '.ui-form-title-text' );\n this.$error_text = this.$( '.ui-form-error-text' );\n this.$error = this.$( '.ui-form-error' );\n this.$backdrop = this.$( '.ui-form-backdrop' );\n\n // add field element\n this.$field.prepend( this.field.$el );\n\n // decide wether to expand or collapse fields\n var collapsible_value = this.model.get( 'collapsible_value' );\n this.field.collapsed = collapsible_value !== undefined && JSON.stringify( this.model.get( 'value' ) ) == JSON.stringify( collapsible_value );\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n\n // add click handler\n var self = this;\n this.$collapsible.on( 'click', function() {\n self.field.collapsed = !self.field.collapsed;\n app.trigger && app.trigger( 'change' );\n self.render();\n });\n\n // hide error on value change\n if ( this.field.model && !this.model.get( 'always_refresh' ) ) {\n this.listenTo( this.field.model, 'change:value', function() { self.reset() } );\n }\n },\n\n /** Set backdrop for input element */\n backdrop: function() {\n this.model.set( 'backdrop', true );\n },\n\n /** Set error text */\n error: function( text ) {\n this.model.set( 'error_text', text );\n },\n\n /** Reset this view */\n reset: function() {\n !this.model.get( 'fixed' ) && this.model.set( 'error_text', null );\n },\n\n render: function() {\n // render help\n $( '.tooltip' ).hide();\n var help_text = this.model.get( 'help', '' );\n var help_argument = this.model.get( 'argument' );\n if ( help_argument && help_text.indexOf( '(' + help_argument + ')' ) == -1 ) {\n help_text += ' (' + help_argument + ')';\n }\n this.$info.html( help_text );\n // render visibility\n this.$el[ this.model.get( 'hidden' ) ? 'hide' : 'show' ]();\n // render preview view for collapsed fields\n this.$preview[ ( this.field.collapsed && this.model.get( 'collapsible_preview' ) || this.model.get( 'disabled' ) ) ? 'show' : 'hide' ]()\n .html( _.escape( this.model.get( 'text_value' ) ) );\n // render error messages\n var error_text = this.model.get( 'error_text' );\n this.$error[ error_text ? 'show' : 'hide' ]();\n this.$el[ error_text ? 'addClass' : 'removeClass' ]( 'ui-error' );\n this.$error_text.html( error_text );\n // render backdrop\n this.$backdrop[ this.model.get( 'backdrop' ) ? 'show' : 'hide' ]();\n // render input field\n this.field.collapsed || this.model.get( 'disabled' ) ? this.$field.hide() : this.$field.show();\n // render input field color and style\n this.field.model && this.field.model.set( { 'color': this.model.get( 'color' ), 'style': this.model.get( 'style' ) } );\n // render collapsible options\n if ( !this.model.get( 'disabled' ) && this.model.get( 'collapsible_value' ) !== undefined ) {\n var collapsible_state = this.field.collapsed ? 'enable' : 'disable';\n this.$title_text.hide();\n this.$collapsible.show();\n this.$collapsible_text.text( this.model.get( 'label' ) );\n this.$collapsible_icon.removeClass().addClass( 'icon' )\n .addClass( this.model.get( 'cls_' + collapsible_state ) )\n .attr( 'data-original-title', this.model.get( 'text_' + collapsible_state ) )\n .tooltip( { placement: 'bottom' } );\n } else {\n this.$title_text.show().text( this.model.get( 'label' ) );\n this.$collapsible.hide();\n }\n },\n\n _template: function() {\n return $( '' ).addClass( 'ui-form-element' )\n .append( $( '' ).addClass( 'ui-form-error ui-error' )\n .append( $( '' ).addClass( 'fa fa-arrow-down' ) )\n .append( $( '' ).addClass( 'ui-form-error-text' ) )\n )\n .append( $( '' ).addClass( 'ui-form-title' )\n .append( $( '' ).addClass( 'ui-form-collapsible' )\n .append( $( '' ).addClass( 'ui-form-collapsible-icon' ) )\n .append( $( '' ).addClass( 'ui-form-collapsible-text' ) )\n )\n .append( $( '' ).addClass( 'ui-form-title-text' ) )\n )\n .append( $( '' ).addClass( 'ui-form-field' )\n .append( $( '' ).addClass( 'ui-form-info' ) )\n .append( $( '' ).addClass( 'ui-form-backdrop' ) )\n )\n .append( $( '' ).addClass( 'ui-form-preview' ) );\n }\n });\n});\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/form/form-input.js\n **/","/**\n This class creates input elements. New input parameter types should be added to the types dictionary.\n*/\ndefine(['utils/utils',\n 'mvc/ui/ui-misc',\n 'mvc/ui/ui-select-content',\n 'mvc/ui/ui-select-library',\n 'mvc/ui/ui-select-ftp',\n 'mvc/ui/ui-select-genomespace',\n 'mvc/ui/ui-color-picker'],\n function( Utils, Ui, SelectContent, SelectLibrary, SelectFtp, SelectGenomeSpace, ColorPicker ) {\n\n // create form view\n return Backbone.Model.extend({\n /** Available parameter types */\n types: {\n 'text' : '_fieldText',\n 'password' : '_fieldText',\n 'select' : '_fieldSelect',\n 'data_column' : '_fieldSelect',\n 'genomebuild' : '_fieldSelect',\n 'data' : '_fieldData',\n 'data_collection' : '_fieldData',\n 'integer' : '_fieldSlider',\n 'float' : '_fieldSlider',\n 'boolean' : '_fieldBoolean',\n 'drill_down' : '_fieldDrilldown',\n 'color' : '_fieldColor',\n 'hidden' : '_fieldHidden',\n 'hidden_data' : '_fieldHidden',\n 'baseurl' : '_fieldHidden',\n 'library_data' : '_fieldLibrary',\n 'ftpfile' : '_fieldFtp',\n 'upload' : '_fieldUpload',\n 'genomespacefile' : '_fieldGenomeSpace'\n },\n\n /** Returns an input field for a given field type */\n create: function( input_def ) {\n var fieldClass = this.types[ input_def.type ];\n var field = typeof( this[ fieldClass ] ) === 'function' ? this[ fieldClass ].call( this, input_def ) : null;\n if ( !field ) {\n field = input_def.options ? this._fieldSelect( input_def ) : this._fieldText( input_def );\n Galaxy.emit.debug('form-parameters::_addRow()', 'Auto matched field type (' + input_def.type + ').');\n }\n input_def.value === undefined && ( input_def.value = null );\n field.value( input_def.value );\n return field;\n },\n\n /** Data input field */\n _fieldData: function( input_def ) {\n return new SelectContent.View({\n id : 'field-' + input_def.id,\n extensions : input_def.extensions,\n optional : input_def.optional,\n multiple : input_def.multiple,\n type : input_def.type,\n flavor : input_def.flavor,\n data : input_def.options,\n onchange : input_def.onchange\n });\n },\n\n /** Select/Checkbox/Radio options field */\n _fieldSelect: function ( input_def ) {\n // show text field e.g. in workflow editor\n if( input_def.is_workflow ) {\n return this._fieldText( input_def );\n }\n\n // customize properties\n if ( input_def.type == 'data_column' ) {\n input_def.error_text = 'Missing columns in referenced dataset.'\n }\n\n // identify available options\n var data = input_def.data;\n if( !data ) {\n data = [];\n _.each( input_def.options, function( option ) {\n data.push( { label: option[ 0 ], value: option[ 1 ] } );\n });\n }\n\n // identify display type\n var SelectClass = Ui.Select;\n switch ( input_def.display ) {\n case 'checkboxes':\n SelectClass = Ui.Checkbox;\n break;\n case 'radio':\n SelectClass = Ui.Radio;\n break;\n case 'radiobutton':\n SelectClass = Ui.RadioButton;\n break;\n }\n\n // create select field\n return new SelectClass.View({\n id : 'field-' + input_def.id,\n data : data,\n error_text : input_def.error_text || 'No options available',\n multiple : input_def.multiple,\n optional : input_def.optional,\n onchange : input_def.onchange,\n individual : input_def.individual,\n searchable : input_def.flavor !== 'workflow'\n });\n },\n\n /** Drill down options field */\n _fieldDrilldown: function ( input_def ) {\n // show text field e.g. in workflow editor\n if( input_def.is_workflow ) {\n return this._fieldText( input_def );\n }\n\n // create drill down field\n return new Ui.Drilldown.View({\n id : 'field-' + input_def.id,\n data : input_def.options,\n display : input_def.display,\n optional : input_def.optional,\n onchange : input_def.onchange\n });\n },\n\n /** Text input field */\n _fieldText: function( input_def ) {\n // field replaces e.g. a select field\n if ( input_def.options && input_def.data ) {\n input_def.area = input_def.multiple;\n if ( Utils.isEmpty( input_def.value ) ) {\n input_def.value = null;\n } else {\n if ( $.isArray( input_def.value ) ) {\n var str_value = '';\n for ( var i in input_def.value ) {\n str_value += String( input_def.value[ i ] );\n if ( !input_def.multiple ) {\n break;\n }\n str_value += '\\n';\n }\n input_def.value = str_value;\n }\n }\n }\n // create input element\n return new Ui.Input({\n id : 'field-' + input_def.id,\n type : input_def.type,\n area : input_def.area,\n readonly : input_def.readonly,\n placeholder : input_def.placeholder,\n datalist : input_def.datalist,\n onchange : input_def.onchange\n });\n },\n\n /** Slider field */\n _fieldSlider: function( input_def ) {\n return new Ui.Slider.View({\n id : 'field-' + input_def.id,\n precise : input_def.type == 'float',\n is_workflow : input_def.is_workflow,\n min : input_def.min,\n max : input_def.max,\n onchange : input_def.onchange\n });\n },\n\n /** Hidden field */\n _fieldHidden: function( input_def ) {\n return new Ui.Hidden({\n id : 'field-' + input_def.id,\n info : input_def.info\n });\n },\n\n /** Boolean field */\n _fieldBoolean: function( input_def ) {\n return new Ui.RadioButton.View({\n id : 'field-' + input_def.id,\n data : [ { label : 'Yes', value : 'true' },\n { label : 'No', value : 'false' }],\n onchange : input_def.onchange\n });\n },\n\n /** Color picker field */\n _fieldColor: function( input_def ) {\n return new ColorPicker({\n id : 'field-' + input_def.id,\n onchange : input_def.onchange\n });\n },\n\n /** Library dataset field */\n _fieldLibrary: function( input_def ) {\n return new SelectLibrary.View({\n id : 'field-' + input_def.id,\n optional : input_def.optional,\n multiple : input_def.multiple,\n onchange : input_def.onchange\n });\n },\n\n /** FTP file field */\n _fieldFtp: function( input_def ) {\n return new SelectFtp.View({\n id : 'field-' + input_def.id,\n optional : input_def.optional,\n multiple : input_def.multiple,\n onchange : input_def.onchange\n });\n },\n\n /** GenomeSpace file select field\n */\n _fieldGenomeSpace: function( input_def ) {\n var self = this;\n return new SelectGenomeSpace.View({\n id : 'field-' + input_def.id,\n onchange : function() {\n self.app.trigger( 'change' );\n }\n });\n },\n\n /** Upload file field */\n _fieldUpload: function( input_def ) {\n return new Ui.Upload({\n id : 'field-' + input_def.id,\n onchange : input_def.onchange\n });\n }\n });\n\n return {\n View: View\n };\n});\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/form/form-parameters.js\n **/","/** This class creates a ui component which enables the dynamic creation of portlets */\ndefine( [ 'utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc' ],\nfunction( Utils, Portlet, Ui ) {\n var View = Backbone.View.extend({\n initialize: function( options ) {\n this.list = {};\n this.options = Utils.merge( options, {\n title : 'Repeat',\n empty_text : 'Not available.',\n max : null,\n min : null\n });\n this.button_new = new Ui.ButtonIcon({\n icon : 'fa-plus',\n title : 'Insert ' + this.options.title,\n tooltip : 'Add new ' + this.options.title + ' block',\n cls : 'ui-button-icon ui-clear-float form-repeat-add',\n onclick : function() { options.onnew && options.onnew() }\n });\n this.setElement( $( '' ).append( this.$list = $( '' ) )\n .append( $( '' ).append( this.button_new.$el ) ) );\n },\n\n /** Number of repeat blocks */\n size: function() {\n return _.size( this.list );\n },\n\n /** Add new repeat block */\n add: function( options ) {\n if ( !options.id || this.list[ options.id ] ) {\n Galaxy.emit.debug( 'form-repeat::add()', 'Duplicate or invalid repeat block id.' );\n return;\n }\n var button_delete = new Ui.ButtonIcon({\n icon : 'fa-trash-o',\n tooltip : 'Delete this repeat block',\n cls : 'ui-button-icon-plain form-repeat-delete',\n onclick : function() { options.ondel && options.ondel() }\n });\n var portlet = new Portlet.View({\n id : options.id,\n title : 'placeholder',\n cls : options.cls || 'ui-portlet-repeat',\n operations : { button_delete: button_delete }\n });\n portlet.append( options.$el );\n portlet.$el.addClass( 'section-row' ).hide();\n this.list[ options.id ] = portlet;\n this.$list.append( portlet.$el.fadeIn( 'fast' ) );\n this.options.max > 0 && this.size() >= this.options.max && this.button_new.disable();\n this._refresh();\n },\n\n /** Delete repeat block */\n del: function( id ) {\n if ( !this.list[ id ] ) {\n Galaxy.emit.debug( 'form-repeat::del()', 'Invalid repeat block id.' );\n return;\n }\n this.$list.find( '#' + id ).remove();\n delete this.list[ id ];\n this.button_new.enable();\n this._refresh();\n },\n\n /** Remove all */\n delAll: function() {\n for( var id in this.list ) {\n this.del( id );\n }\n },\n\n /** Hides add/del options */\n hideOptions: function() {\n this.button_new.$el.hide();\n _.each( this.list, function( portlet ) { portlet.hideOperation( 'button_delete' ) } );\n _.isEmpty( this.list ) && this.$el.append( $( '' ).addClass( 'ui-form-info' ).html( this.options.empty_text ) );\n },\n\n /** Refresh view */\n _refresh: function() {\n var index = 0;\n for ( var id in this.list ) {\n var portlet = this.list[ id ];\n portlet.title( ++index + ': ' + this.options.title );\n portlet[ this.size() > this.options.min ? 'showOperation' : 'hideOperation' ]( 'button_delete' );\n }\n }\n });\n\n return {\n View : View\n }\n});\n\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/form/form-repeat.js\n **/","/**\n This class creates a form section and populates it with input elements. It also handles repeat blocks and conditionals by recursively creating new sub sections.\n*/\ndefine([ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-portlet', 'mvc/form/form-repeat', 'mvc/form/form-input', 'mvc/form/form-parameters' ],\nfunction( Utils, Ui, Portlet, Repeat, InputElement, Parameters ) {\n var View = Backbone.View.extend({\n initialize: function( app, options ) {\n this.app = app;\n this.inputs = options.inputs;\n this.parameters = new Parameters();\n this.setElement( $( '' ) );\n this.render();\n },\n\n /** Render section view */\n render: function() {\n var self = this;\n this.$el.empty();\n _.each( this.inputs, function( input ) { self.add( input ) } );\n },\n\n /** Add a new input element */\n add: function( input ) {\n var input_def = jQuery.extend( true, {}, input );\n input_def.id = input.id = Utils.uid();\n this.app.input_list[ input_def.id ] = input_def;\n switch( input_def.type ) {\n case 'conditional':\n this._addConditional( input_def );\n break;\n case 'repeat':\n this._addRepeat( input_def );\n break;\n case 'section':\n this._addSection( input_def );\n break;\n default:\n this._addRow( input_def );\n }\n },\n\n /** Add a conditional block */\n _addConditional: function( input_def ) {\n var self = this;\n input_def.test_param.id = input_def.id;\n this.app.model.get( 'sustain_conditionals' ) && ( input_def.test_param.disabled = true );\n var field = this._addRow( input_def.test_param );\n\n // set onchange event for test parameter\n field.model && field.model.set( 'onchange', function( value ) {\n var selectedCase = self.app.data.matchCase( input_def, value );\n for ( var i in input_def.cases ) {\n var case_def = input_def.cases[ i ];\n var section_row = self.$( '#' + input_def.id + '-section-' + i );\n var nonhidden = false;\n for ( var j in case_def.inputs ) {\n if ( !case_def.inputs[ j ].hidden ) {\n nonhidden = true;\n break;\n }\n }\n if ( i == selectedCase && nonhidden ) {\n section_row.fadeIn( 'fast' );\n } else {\n section_row.hide();\n }\n }\n self.app.trigger( 'change' );\n });\n\n // add conditional sub sections\n for ( var i in input_def.cases ) {\n var sub_section = new View( this.app, { inputs: input_def.cases[ i ].inputs } );\n this._append( sub_section.$el.addClass( 'ui-form-section' ), input_def.id + '-section-' + i );\n }\n\n // trigger refresh on conditional input field after all input elements have been created\n field.trigger( 'change' );\n },\n\n /** Add a repeat block */\n _addRepeat: function( input_def ) {\n var self = this;\n var block_index = 0;\n\n // create repeat block element\n var repeat = new Repeat.View({\n title : input_def.title || 'Repeat',\n min : input_def.min,\n max : input_def.max,\n onnew : function() { create( input_def.inputs ); self.app.trigger( 'change' ); }\n });\n\n // helper function to create new repeat blocks\n function create ( inputs ) {\n var sub_section_id = input_def.id + '-section-' + ( block_index++ );\n var sub_section = new View( self.app, { inputs: inputs } );\n repeat.add( { id : sub_section_id,\n $el : sub_section.$el,\n ondel : function() { repeat.del( sub_section_id ); self.app.trigger( 'change' ); } } );\n }\n\n //\n // add parsed/minimum number of repeat blocks\n //\n var n_cache = _.size( input_def.cache );\n for ( var i = 0; i < Math.max( Math.max( n_cache, input_def.min || 0 ), input_def.default || 0 ); i++ ) {\n create( i < n_cache ? input_def.cache[ i ] : input_def.inputs );\n }\n\n // hide options\n this.app.model.get( 'sustain_repeats' ) && repeat.hideOptions();\n\n // create input field wrapper\n var input_element = new InputElement( this.app, {\n label : input_def.title || input_def.name,\n help : input_def.help,\n field : repeat\n });\n this._append( input_element.$el, input_def.id );\n },\n\n /** Add a customized section */\n _addSection: function( input_def ) {\n var portlet = new Portlet.View({\n title : input_def.title || input_def.name,\n cls : 'ui-portlet-section',\n collapsible : true,\n collapsible_button : true,\n collapsed : !input_def.expanded\n });\n portlet.append( new View( this.app, { inputs: input_def.inputs } ).$el );\n portlet.append( $( '' ).addClass( 'ui-form-info' ).html( input_def.help ) );\n this.app.on( 'expand', function( input_id ) { ( portlet.$( '#' + input_id ).length > 0 ) && portlet.expand(); } );\n this._append( portlet.$el, input_def.id );\n },\n\n /** Add a single input field element */\n _addRow: function( input_def ) {\n var self = this;\n var id = input_def.id;\n input_def.onchange = input_def.onchange || function() { self.app.trigger( 'change', id ) };\n var field = this.parameters.create( input_def );\n this.app.field_list[ id ] = field;\n var input_element = new InputElement( this.app, {\n name : input_def.name,\n label : input_def.hide_label ? '' : input_def.label || input_def.name,\n value : input_def.value,\n text_value : input_def.text_value,\n collapsible_value : input_def.collapsible_value,\n collapsible_preview : input_def.collapsible_preview,\n help : input_def.help,\n argument : input_def.argument,\n disabled : input_def.disabled,\n color : input_def.color,\n style : input_def.style,\n backdrop : input_def.backdrop,\n hidden : input_def.hidden,\n fixed : input_def.fixed,\n field : field\n });\n this.app.element_list[ id ] = input_element;\n this._append( input_element.$el, input_def.id );\n return field;\n },\n\n /** Append a new element to the form i.e. input element, repeat block, conditionals etc. */\n _append: function( $el, id ) {\n this.$el.append( $el.addClass( 'section-row' ).attr( 'id', id ) );\n }\n });\n\n return {\n View: View\n };\n});\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/form/form-section.js\n **/","// dependencies\ndefine([], function() {\n\n// grid model\nreturn Backbone.Model.extend({\n defaults: {\n url_base: '',\n async: false,\n async_ops: [],\n categorical_filters: [],\n filters: {},\n sort_key: null,\n show_item_checkboxes: false,\n advanced_search: false,\n cur_page: 1,\n num_pages: 1,\n operation: undefined,\n item_ids: undefined\n },\n\n /**\n * Return true if operation can be done asynchronously.\n */\n can_async_op: function(op) {\n return _.indexOf(this.attributes.async_ops, op) !== -1;\n },\n\n /**\n * Add filtering criterion.\n */\n add_filter: function(key, value, append) {\n // Update URL arg with new condition. \n if (append) {\n // Update or append value.\n var cur_val = this.attributes.filters[key],\n new_val;\n if (cur_val === null || cur_val === undefined) {\n new_val = value;\n } else if (typeof(cur_val) == 'string') {\n if (cur_val == 'All' || cur_val == value) {\n new_val = value;\n } else {\n // Replace string with array.\n var values = [];\n values[0] = cur_val;\n values[1] = value;\n new_val = values;\n }\n } else {\n // Current value is an array.\n new_val = cur_val;\n if ( new_val.indexOf( value ) === -1 ) {\n new_val.push(value);\n }\n }\n this.attributes.filters[key] = new_val;\n } \n else {\n // Replace value.\n this.attributes.filters[key] = value;\n }\n },\n\n /**\n * Remove filtering criterion.\n */\n remove_filter: function(key, condition) {\n var cur_val = this.attributes.filters[key];\n if (cur_val === null || cur_val === undefined) {\n return false; \n }\n\n if (typeof(cur_val) === 'string') {\n // overwrite/remove condition.\n this.attributes.filters[key] = '';\n } else {\n // filter contains an array of conditions.\n var condition_index = _.indexOf(cur_val, condition);\n if (condition_index !== -1) {\n cur_val[condition_index] = '';\n }\n }\n },\n\n /**\n * Returns URL data for obtaining a new grid.\n */\n get_url_data: function() {\n var url_data = {\n async: this.attributes.async,\n sort: this.attributes.sort_key,\n page: this.attributes.cur_page,\n show_item_checkboxes: this.attributes.show_item_checkboxes,\n advanced_search: this.attributes.advanced_search\n };\n\n // Add operation, item_ids only if they have values.\n if (this.attributes.operation) {\n url_data.operation = this.attributes.operation;\n }\n if (this.attributes.item_ids) {\n url_data.id = this.attributes.item_ids;\n }\n\n // Add filter arguments to data, placing \"f-\" in front of all arguments.\n var self = this;\n _.each(_.pairs(self.attributes.filters), function(k) {\n url_data['f-' + k[0]] = k[1];\n });\n return url_data;\n },\n \n // Return URL for obtaining a new grid\n get_url: function (args) {\n return this.get('url_base') + '?' + $.param(this.get_url_data()) + '&' + $.param(args);\n }\n \n});\n\n});\n\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/grid/grid-model.js\n **/","// dependencies\ndefine(['utils/utils'], function(Utils) {\n\n// grid view templates\nreturn {\n // template\n grid: function(options) {\n var tmpl = '';\n if (options.embedded) {\n tmpl = this.grid_header(options) + this.grid_table(options);\n } else {\n tmpl = '' +\n '' +\n '
' +\n this.grid_table(options);\n }\n \n // add info text\n if (options.info_text) {\n tmpl += '
';\n \n // add checkbox\n if (options.show_item_checkboxes) {\n tmpl += '';\n if (options.items.length > 0) {\n tmpl += '' +\n '';\n }\n tmpl += ' ';\n }\n \n // create header elements\n for (var i in options.columns) {\n var column = options.columns[i];\n if (column.visible) {\n tmpl += '';\n if (column.href) {\n tmpl += '' + column.label + '';\n } else {\n tmpl += column.label;\n }\n tmpl += '' + column.extra + '' +\n ' ';\n }\n }\n \n // finalize\n tmpl += ' ';\n \n // return template\n return tmpl;\n },\n \n // template\n body: function(options) {\n // initialize\n var tmpl = '';\n var num_rows_rendered = 0;\n var items_length = options.items.length;\n \n // empty grid?\n if (items_length == 0) {\n // No results.\n tmpl += 'No Items ';\n \n // Link\n if (link) {\n if (options.operations.length != 0) {\n tmpl += ' ';\n }\n }\n tmpl += '';\n num_rows_rendered++;\n }\n return tmpl;\n },\n\n // template\n footer: function(options) {\n \n // create template string\n var tmpl = '';\n \n // paging\n if (options.use_paging && options.num_pages > 1) {\n // get configuration\n var num_page_links = options.num_page_links;\n var cur_page_num = options.cur_page_num;\n var num_pages = options.num_pages;\n \n // First pass on min page.\n var page_link_range = num_page_links / 2;\n var min_page = cur_page_num - page_link_range\n var min_offset = 0;\n if (min_page <= 0) {\n // Min page is too low.\n min_page = 1;\n min_offset = page_link_range - ( cur_page_num - min_page );\n }\n \n // Set max page.\n var max_range = page_link_range + min_offset;\n var max_page = cur_page_num + max_range;\n var max_offset;\n if (max_page <= num_pages) {\n // Max page is fine.\n max_offset = 0;\n } else {\n // Max page is too high.\n max_page = num_pages;\n // +1 to account for the +1 in the loop below.\n max_offset = max_range - ( max_page + 1 - cur_page_num );\n }\n \n // Second and final pass on min page to add any unused\n // offset from max to min.\n if (max_offset != 0) {\n min_page -= max_offset\n if (min_page < 1) {\n min_page = 1\n }\n }\n \n // template header\n tmpl += '';\n if (options.show_item_checkboxes) {\n tmpl += '' +\n '' +\n 'Page:';\n \n if (min_page > 1) {\n tmpl += '1 ...';\n }\n \n // create page urls\n for (var page_index = min_page; page_index < max_page + 1; page_index++) {\n \n if (page_index == options.cur_page_num) {\n tmpl += '' + page_index + '';\n } else {\n tmpl += '' + page_index + '';\n }\n }\n \n // show last page\n if (max_page < num_pages) {\n tmpl += '...' +\n '' + num_pages + '';\n }\n tmpl += '';\n \n // Show all link\n tmpl += ' | Show All' +\n ' ' +\n ' ';\n }\n \n // Grid operations for multiple items.\n if (options.show_item_checkboxes) {\n // start template\n tmpl += '' +\n '' +\n '' +\n 'For selected items: ';\n \n // configure buttons for operations\n for (var i in options.operations) {\n var operation = options.operations[i];\n if (operation.allow_multiple) {\n tmpl += ' ';\n }\n }\n \n // finalize template\n tmpl += ' ' +\n ' ';\n }\n \n // count global operations\n var found_global = false;\n for (i in options.operations) {\n if (options.operations[i].global_operation) {\n found_global = true;\n break;\n }\n }\n \n // add global operations\n if (found_global) {\n tmpl += '' +\n '';\n for (i in options.operations) {\n var operation = options.operations[i];\n if (operation.global_operation) {\n tmpl += '' + operation.label + '';\n }\n }\n tmpl += ' ' +\n ' ';\n }\n \n // add legend\n if (options.legend) {\n tmpl += '' +\n '' + options.legend + ' ' +\n ' ';\n }\n \n // return\n return tmpl;\n },\n \n // template\n message: function(options) {\n var status = options.status == 'success' ? 'done' : options.status;\n return '';\n \n if (column.filterable == 'advanced') {\n tmpl += '' + column_label + ': ';\n }\n tmpl += '';\n if (column.is_text) {\n tmpl += '';\n } else {\n // filter criteria\n tmpl += '';\n \n // add category filters\n var seperator = false;\n for (var cf_label in options.categorical_filters[column_key]) {\n // get category filter\n var cf = options.categorical_filters[column_key][cf_label];\n \n // each filter will have only a single argument, so get that single argument\n var cf_key = '';\n var cf_arg = '';\n for (var key in cf) {\n cf_key = key;\n cf_arg = cf[key];\n }\n \n // add seperator\n if (seperator) {\n tmpl += ' | ';\n }\n seperator = true;\n \n // add category\n var filter = filters[column_key];\n if (filter && cf[column_key] && filter == cf_arg) {\n tmpl += '' + cf_label + '';\n } else {\n tmpl += '' +\n '' + cf_label + '' +\n '';\n }\n }\n tmpl += '';\n }\n tmpl += ' ' +\n ' ';\n \n // return template\n return tmpl;\n },\n \n // template for filter items\n filter_element: function(filter_key, filter_value) {\n filter_value = Utils.sanitize(filter_value);\n return '' + filter_value +\n '' +\n '' +\n '' +\n '';\n\n }\n};\n\n});\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/grid/grid-template.js\n **/","// Provides support for interacting with the GenomeSpace File Browser popup dialogue\ndefine([], function() {\n\n// tool form templates\nreturn {\n openFileBrowser: function( options ) {\n var GS_UI_URL = window.Galaxy.config.genomespace_ui_url;\n var GS_UPLOAD_URL = GS_UI_URL + 'upload/loadUrlToGenomespace.html?getLocation=true'\n\n var newWin = window.open(GS_UPLOAD_URL, \"GenomeSpace File Browser\", \"height=360px,width=600px\");\n \n successCalBack = options['successCallback'];\n window.addEventListener( \"message\", function (e) {\n successCalBack(e.data); \n }, false);\n \n newWin.focus();\n \n if (options['errorCallback'] != null) newWin.setCallbackOnGSUploadError = config['errorCallback']; \n }\n\n};\n\n});\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/tool/tool-genomespace.js\n **/","/** Renders the color picker used e.g. in the tool form **/\ndefine(['utils/utils'], function( Utils ) {\n return Backbone.View.extend({\n colors: {\n standard: ['c00000','ff0000','ffc000','ffff00','92d050','00b050','00b0f0','0070c0','002060','7030a0'],\n base : ['ffffff','000000','eeece1','1f497d','4f81bd','c0504d','9bbb59','8064a2','4bacc6','f79646'],\n theme :[['f2f2f2','7f7f7f','ddd9c3','c6d9f0','dbe5f1','f2dcdb','ebf1dd','e5e0ec','dbeef3','fdeada'],\n ['d8d8d8','595959','c4bd97','8db3e2','b8cce4','e5b9b7','d7e3bc','ccc1d9','b7dde8','fbd5b5'],\n ['bfbfbf','3f3f3f','938953','548dd4','95b3d7','d99694','c3d69b','b2a2c7','92cddc','fac08f'],\n ['a5a5a5','262626','494429','17365d','366092','953734','76923c','5f497a','31859b','e36c09'],\n ['7f7f7e','0c0c0c','1d1b10','0f243e','244061','632423','4f6128','3f3151','205867','974806']]\n },\n\n initialize : function( options ) {\n this.options = Utils.merge( options, {} );\n this.setElement( this._template() );\n this.$panel = this.$( '.ui-color-picker-panel' );\n this.$view = this.$( '.ui-color-picker-view' );\n this.$value = this.$( '.ui-color-picker-value' );\n this.$header = this.$( '.ui-color-picker-header' );\n this._build();\n this.visible = false;\n this.value( this.options.value );\n this.$boxes = this.$( '.ui-color-picker-box' );\n var self = this;\n this.$boxes.on( 'click', function() {\n self.value( $( this ).css( 'background-color' ) );\n self.$header.trigger( 'click' );\n } );\n this.$header.on( 'click', function() {\n self.visible = !self.visible;\n if ( self.visible ) {\n self.$view.fadeIn( 'fast' );\n } else {\n self.$view.fadeOut( 'fast' );\n }\n } );\n },\n\n /** Get/set value */\n value : function ( new_val ) {\n if ( new_val !== undefined && new_val !== null ) {\n this.$value.css( 'background-color', new_val );\n this.$( '.ui-color-picker-box' ).empty();\n this.$( this._getValue() ).html( this._templateCheck() );\n this.options.onchange && this.options.onchange( new_val );\n }\n return this._getValue();\n },\n\n /** Get value from dom */\n _getValue: function() {\n var rgb = this.$value.css( 'background-color' );\n rgb = rgb.match(/^rgb\\((\\d+),\\s*(\\d+),\\s*(\\d+)\\)$/);\n if ( rgb ) {\n function hex( x ) {\n return ( '0' + parseInt( x ).toString( 16 ) ).slice( -2 );\n }\n return '#' + hex( rgb[ 1] ) + hex( rgb[ 2 ] ) + hex( rgb[ 3 ] );\n } else {\n return null;\n }\n },\n\n /** Build color panel */\n _build: function() {\n this._content( { colors : this.colors.base } );\n for ( var i in this.colors.theme ) {\n var line_def = {};\n if ( i == 0 ) {\n line_def[ 'bottom' ] = true;\n } else if ( i != this.colors.theme.length - 1 ) {\n line_def[ 'top' ] = true;\n line_def[ 'bottom' ] = true;\n } else {\n line_def[ 'top' ] = true;\n }\n line_def[ 'colors' ] = this.colors.theme[ i ];\n this._content( line_def );\n }\n this._content( { colors : this.colors.standard } );\n },\n\n /** Create content */\n _content: function( options ) {\n var colors = options.colors;\n var $content = $( this._templateContent() );\n var $line = $content.find( '.line' );\n this.$panel.append( $content );\n for ( var i in colors ) {\n var $box = $( this._templateBox( colors[ i ] ) );\n if ( options.top ) {\n $box.css( 'border-top', 'none' );\n $box.css( 'border-top-left-radius', '0px' );\n $box.css( 'border-top-right-radius', '0px' );\n }\n if ( options.bottom ) {\n $box.css( 'border-bottom', 'none' );\n $box.css( 'border-bottom-left-radius', '0px' );\n $box.css( 'border-bottom-right-radius', '0px' );\n }\n $line.append( $box );\n }\n return $content;\n },\n\n /** Check icon */\n _templateCheck: function() {\n return '';\n },\n\n /** Content template */\n _templateContent: function() {\n return '
| ' +\n this.grid_header(options) +\n ' | ' +\n '' +\n ' | ' +\n ' |
| ' +\n ' | ' +\n ' | ' +\n ' |
' + options.info_text + '
';\n }\n \n // return\n return tmpl;\n },\n \n // template\n grid_table: function(options) {\n return '';\n },\n \n // template\n grid_header: function(options) {\n var tmpl = '';\n if (!options.embedded) {\n tmpl += '
'\n \n // return template\n return tmpl;\n },\n\n // template\n header: function(options) {\n \n // start\n var tmpl = '' + options.title + '
';\n }\n if (options.global_actions) {\n tmpl += '- ';\n var show_popup = (options.global_actions.length >= 3);\n if (show_popup) {\n tmpl += '
- Actions ' +\n '
- ' +\n '' + action.label + '' +\n ' ';\n }\n if (show_popup) {\n tmpl += '
';\n }\n for (var i in options.global_actions) {\n var action = options.global_actions[i];\n tmpl += '
';\n }\n tmpl += '';\n }\n tmpl += '' + value + '';\n if (options.operations.length != 0) {\n tmpl += '
';\n }\n } else {\n tmpl += '';\n }\n tmpl += '' +\n '
' + _.escape( options.message ) + '
' +\n '' +\n '';\n },\n \n // template\n grid_filters: function (options) {\n \n // get filters\n var default_filter_dict = options.default_filter_dict;\n var filters = options.filters;\n\n // show advanced search if flag set or if there are filters for advanced search fields\n var advanced_search_display = 'none';\n if (options.advanced_search) {\n advanced_search_display = 'block';\n }\n \n // identify columns with advanced filtering\n var show_advanced_search_link = false;\n for (var i in options.columns) {\n var column = options.columns[i];\n if (column.filterable == 'advanced') {\n var column_key = column.key;\n var f_key = filters[column_key];\n var d_key = default_filter_dict[column_key];\n if (f_key && d_key && f_key != d_key) {\n advanced_search_display = 'block';\n }\n show_advanced_search_link = true;\n }\n }\n \n // hide standard search if advanced is shown\n var standard_search_display = 'block';\n if (advanced_search_display == 'block') {\n standard_search_display = 'none';\n }\n\n //\n // standard search\n //\n var tmpl = '' +\n '' +\n '
' +\n '
';\n \n //\n // advanced search\n //\n tmpl += '| ' +\n ' | ' +\n '
| ';\n \n // show advanced search link in standard display\n if (show_advanced_search_link) {\n tmpl += 'Advanced Search';\n }\n \n // finalize standard search display\n tmpl += ' | ' +\n '
' +\n '' +\n '
' +\n '
';\n\n // return template\n return tmpl;\n },\n \n // template\n grid_column_filter: function(options, column) {\n \n // collect parameters\n var default_filter_dict = options.default_filter_dict;\n var filters = options.filters;\n var column_label = column.label;\n var column_key = column.key;\n if (column.filterable == 'advanced') {\n column_label = column_label.toLowerCase();\n }\n \n // start\n var tmpl = '| ' +\n 'Close Advanced Search' +\n ' | ' +\n '
' +\n '
' +\n '
';\n },\n\n /** Box template */\n _templateBox: function( color ) {\n return '';\n },\n\n /** Main template */\n _template: function() {\n return '' +\n '
' +\n '
' +\n '
' +\n 'Select a color
' +\n '' +\n '
';\n }\n });\n});\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/ui/ui-color-picker.js\n **/","/** This class creates/wraps a drill down element. */\ndefine([ 'utils/utils', 'mvc/ui/ui-options' ], function( Utils, Options ) {\n\nvar View = Options.BaseIcons.extend({\n initialize: function( options ) {\n options.type = options.display || 'checkbox';\n options.multiple = ( options.type == 'checkbox' );\n Options.BaseIcons.prototype.initialize.call( this, options );\n },\n\n /** Set states for selected values */\n _setValue: function ( new_value ) {\n Options.BaseIcons.prototype._setValue.call( this, new_value );\n if ( new_value !== undefined && new_value !== null && this.header_index ) {\n var self = this;\n var values = $.isArray( new_value ) ? new_value : [ new_value ];\n _.each( values, function( v ) {\n var list = self.header_index[ v ];\n _.each( list, function( element ) {\n self._setState( element, true );\n });\n });\n }\n },\n\n /** Expand/collapse a sub group */\n _setState: function ( header_id, is_expanded ) {\n var $button = this.$( '.button-' + header_id );\n var $subgroup = this.$( '.subgroup-' + header_id );\n $button.data( 'is_expanded', is_expanded );\n if ( is_expanded ) {\n $subgroup.show();\n $button.removeClass( 'fa-plus-square' ).addClass( 'fa-minus-square' );\n } else {\n $subgroup.hide();\n $button.removeClass( 'fa-minus-square' ).addClass( 'fa-plus-square' );\n }\n },\n\n /** Template to create options tree */\n _templateOptions: function() {\n var self = this;\n this.header_index = {};\n\n // attach event handler\n function attach( $el, header_id ) {\n var $button = $el.find( '.button-' + header_id );\n $button.on( 'click', function() {\n self._setState( header_id, !$button.data( 'is_expanded' ) );\n });\n }\n\n // recursive function which iterates through options\n function iterate ( $tmpl, options, header ) {\n header = header || [];\n for (var i in options ) {\n var level = options[ i ];\n var has_options = level.options && level.options.length > 0;\n var new_header = header.slice( 0 );\n self.header_index[ level.value ] = new_header.slice( 0 );\n var $group = $( '' );\n if ( has_options ) {\n var header_id = Utils.uid();\n var $button = $( '' ).addClass( 'button-' + header_id ).addClass( 'ui-drilldown-button fa fa-plus-square' );\n var $subgroup = $( '' ).addClass( 'subgroup-' + header_id ).addClass( 'ui-drilldown-subgroup' );\n $group.append( $( '' )\n .append( $button )\n .append( self._templateOption( { label: level.name, value: level.value } ) ) );\n new_header.push( header_id );\n iterate ( $subgroup, level.options, new_header );\n $group.append( $subgroup );\n attach( $group, header_id );\n } else {\n $group.append( self._templateOption( { label: level.name, value: level.value } ) );\n }\n $tmpl.append( $group );\n }\n }\n\n // iterate through options and create dom\n var $tmpl = $( '' );\n iterate( $tmpl, this.model.get( 'data' ) );\n return $tmpl;\n },\n\n /** Template for drill down view */\n _template: function() {\n return $( '' ).addClass( 'ui-options-list drilldown-container' ).attr( 'id', this.model.id );\n }\n});\n\nreturn {\n View: View\n}\n\n});\n\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/ui/ui-drilldown.js\n **/","define([ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-select-default' ], function( Utils, Ui, Select ) {\n\n/** Batch mode variations */\nvar Batch = { DISABLED: 'disabled', ENABLED: 'enabled', LINKED: 'linked' };\n\n/** List of available content selectors options */\nvar Configurations = {\n data: [\n { src: 'hda', icon: 'fa-file-o', tooltip: 'Single dataset', multiple: false, batch: Batch.DISABLED },\n { src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.LINKED },\n { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.LINKED } ],\n data_multiple: [\n { src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.DISABLED },\n { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collections', multiple: true, batch: Batch.DISABLED } ],\n data_collection: [\n { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.DISABLED } ],\n workflow_data: [\n { src: 'hda', icon: 'fa-file-o', tooltip: 'Single dataset', multiple: false, batch: Batch.DISABLED } ],\n workflow_data_multiple: [\n { src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.DISABLED } ],\n workflow_data_collection: [\n { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.DISABLED } ],\n module_data: [\n { src: 'hda', icon: 'fa-file-o', tooltip: 'Single dataset', multiple: false, batch: Batch.DISABLED },\n { src: 'hda', icon: 'fa-files-o', tooltip: 'Multiple datasets', multiple: true, batch: Batch.ENABLED } ],\n module_data_collection: [\n { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection', multiple: false, batch: Batch.DISABLED },\n { src: 'hdca', icon: 'fa-folder', tooltip: 'Multiple collections', multiple: true, batch: Batch.ENABLED } ]\n};\n\n/** View for hda and hdca content selector ui elements */\nvar View = Backbone.View.extend({\n initialize : function( options ) {\n var self = this;\n this.model = options && options.model || new Backbone.Model({\n src_labels : { 'hda' : 'dataset', 'hdca': 'dataset collection' },\n pagelimit : 100,\n statustimer : 1000\n }).set( options );\n this.setElement( $( '' ).addClass( 'ui-select-content' ) );\n this.button_product = new Ui.RadioButton.View( {\n value : 'false',\n data : [ { icon: 'fa fa-chain', value: 'false',\n tooltip: 'Linked inputs will be run in matched order with other datasets e.g. use this for matching forward and reverse reads.' },\n { icon: 'fa fa-chain-broken', value: 'true',\n tooltip: 'Unlinked dataset inputs will be run against *all* other inputs.' } ] } );\n var $batch_div = $( '' ).addClass( 'ui-form-info' )\n .append( $( '' ).addClass( 'fa fa-sitemap' ) )\n .append( $( '' ).html( 'This is a batch mode input field. Separate jobs will be triggered for each dataset selection.' ) );\n this.$batch = {\n linked : $batch_div.clone(),\n enabled : $batch_div.clone().append( $( '' )\n .append( $( '' ).addClass( 'ui-form-title' ).html( 'Batch options:' ) )\n .append( this.button_product.$el ) )\n .append( $( '' ).css( 'clear', 'both' ) )\n };\n\n // add drag-drop event handlers\n this.$el.on( 'dragenter', function( e ) { this.lastenter = e.target; self.$el.addClass( 'ui-dragover' ); } )\n .on( 'dragover', function( e ) { e.preventDefault(); } )\n .on( 'dragleave', function( e ) { this.lastenter === e.target && self.$el.removeClass( 'ui-dragover' ); } )\n .on( 'drop', function( e ) { self._handleDrop( e ); } );\n\n // track current history elements\n this.history = {};\n\n // add listeners\n this.listenTo( this.model, 'change:data', this._changeData, this );\n this.listenTo( this.model, 'change:wait', this._changeWait, this );\n this.listenTo( this.model, 'change:current', this._changeCurrent, this );\n this.listenTo( this.model, 'change:value', this._changeValue, this );\n this.listenTo( this.model, 'change:type change:optional change:multiple change:extensions', this._changeType, this );\n this.render();\n\n // add change event\n this.on( 'change', function() { options.onchange && options.onchange( self.value() ) } );\n },\n\n render: function() {\n this._changeType();\n this._changeValue();\n this._changeWait();\n },\n\n /** Indicate that select fields are being updated */\n wait: function() {\n this.model.set( 'wait', true );\n },\n\n /** Indicate that the options update has been completed */\n unwait: function() {\n this.model.set( 'wait', false );\n },\n\n /** Update data representing selectable options */\n update: function( options ) {\n this.model.set( 'data', options );\n },\n\n /** Return the currently selected dataset values */\n value: function ( new_value ) {\n new_value !== undefined && this.model.set( 'value', new_value );\n var current = this.model.get( 'current' );\n if ( this.config[ current ] ) {\n var id_list = this.fields[ current ].value();\n if (id_list !== null) {\n id_list = $.isArray( id_list ) ? id_list : [ id_list ];\n if ( id_list.length > 0 ) {\n var result = this._batch( { values: [] } );\n for ( var i in id_list ) {\n var details = this.history[ id_list[ i ] + '_' + this.config[ current ].src ];\n if ( details ) {\n result.values.push( details );\n } else {\n Galaxy.emit.debug( 'ui-select-content::value()', 'Requested details not found for \\'' + id_list[ i ] + '\\'.' );\n return null;\n }\n }\n result.values.sort( function( a, b ) { return a.hid - b.hid } );\n return result;\n }\n }\n } else {\n Galaxy.emit.debug( 'ui-select-content::value()', 'Invalid value/source \\'' + new_value + '\\'.' );\n }\n return null;\n },\n\n /** Change of current select field */\n _changeCurrent: function() {\n var self = this;\n _.each( this.fields, function( field, i ) {\n if ( self.model.get( 'current' ) == i ) {\n field.$el.show();\n _.each( self.$batch, function( $batchfield, batchmode ) {\n $batchfield[ self.config[ i ].batch == batchmode ? 'show' : 'hide' ]();\n });\n self.button_type.value( i );\n } else {\n field.$el.hide();\n }\n });\n },\n\n /** Change of type */\n _changeType: function() {\n var self = this;\n\n // identify selector type identifier i.e. [ flavor ]_[ type ]_[ multiple ]\n var config_id = ( this.model.get( 'flavor' ) ? this.model.get( 'flavor' ) + '_' : '' ) +\n String( this.model.get( 'type' ) ) + ( this.model.get( 'multiple' ) ? '_multiple' : '' );\n if ( Configurations[ config_id ] ) {\n this.config = Configurations[ config_id ];\n } else {\n this.config = Configurations[ 'data' ];\n Galaxy.emit.debug( 'ui-select-content::_changeType()', 'Invalid configuration/type id \\'' + config_id + '\\'.' );\n }\n\n // prepare extension component of error message\n var data = self.model.get( 'data' );\n var extensions = Utils.textify( this.model.get( 'extensions' ) );\n var src_labels = this.model.get( 'src_labels' );\n\n // build views\n this.fields = [];\n this.button_data = [];\n _.each( this.config, function( c, i ) {\n self.button_data.push({\n value : i,\n icon : c.icon,\n tooltip : c.tooltip\n });\n self.fields.push(\n new Select.View({\n optional : self.model.get( 'optional' ),\n multiple : c.multiple,\n searchable : !c.multiple || ( data && data[ c.src ] && data[ c.src ].length > self.model.get( 'pagelimit' ) ),\n individual : true,\n error_text : 'No ' + ( extensions ? extensions + ' ' : '' ) + ( src_labels[ c.src ] || 'content' ) + ' available.',\n onchange : function() {\n self.trigger( 'change' );\n }\n })\n );\n });\n this.button_type = new Ui.RadioButton.View({\n value : this.model.get( 'current' ),\n data : this.button_data,\n onchange: function( value ) {\n self.model.set( 'current', value );\n self.trigger( 'change' );\n }\n });\n\n // append views\n this.$el.empty();\n var button_width = 0;\n if ( this.fields.length > 1 ) {\n this.$el.append( this.button_type.$el );\n button_width = Math.max( 0, this.fields.length * 36 ) + 'px';\n }\n _.each( this.fields, function( field ) {\n self.$el.append( field.$el.css( { 'margin-left': button_width } ) );\n });\n _.each( this.$batch, function( $batchfield, batchmode ) {\n self.$el.append( $batchfield.css( { 'margin-left': button_width } ) );\n });\n this.model.set( 'current', 0 );\n this._changeCurrent();\n this._changeData();\n },\n\n /** Change of wait flag */\n _changeWait: function() {\n var self = this;\n _.each( this.fields, function( field ) { field[ self.model.get( 'wait' ) ? 'wait' : 'unwait' ]() } );\n },\n\n /** Change of available options */\n _changeData: function() {\n var options = this.model.get( 'data' );\n var self = this;\n var select_options = {};\n _.each( options, function( items, src ) {\n select_options[ src ] = [];\n _.each( items, function( item ) {\n select_options[ src ].push({\n hid : item.hid,\n keep : item.keep,\n label: item.hid + ': ' + item.name,\n value: item.id,\n tags : item.tags\n });\n self.history[ item.id + '_' + src ] = item;\n });\n });\n _.each( this.config, function( c, i ) {\n select_options[ c.src ] && self.fields[ i ].add( select_options[ c.src ], function( a, b ) { return b.hid - a.hid } );\n });\n },\n\n /** Change of incoming value */\n _changeValue: function () {\n var new_value = this.model.get( 'value' );\n if ( new_value && new_value.values && new_value.values.length > 0 ) {\n // create list with content ids\n var list = [];\n _.each( new_value.values, function( value ) {\n list.push( value.id );\n });\n // sniff first suitable field type from config list\n var src = new_value.values[ 0 ].src;\n var multiple = new_value.values.length > 1;\n for( var i = 0; i < this.config.length; i++ ) {\n var field = this.fields[ i ];\n var c = this.config[ i ];\n if ( c.src == src && [ multiple, true ].indexOf( c.multiple ) !== -1 ) {\n this.model.set( 'current', i );\n field.value( list );\n break;\n }\n }\n } else {\n _.each( this.fields, function( field ) {\n field.value( null );\n });\n }\n },\n\n /** Handles drop events e.g. from history panel */\n _handleDrop: function( ev ) {\n try {\n var data = this.model.get( 'data' );\n var current = this.model.get( 'current' );\n var config = this.config[ current ];\n var field = this.fields[ current ];\n var drop_data = JSON.parse( ev.originalEvent.dataTransfer.getData( 'text' ) )[ 0 ];\n var new_id = drop_data.id;\n var new_src = drop_data.history_content_type == 'dataset' ? 'hda' : 'hdca';\n var new_value = { id: new_id, src: new_src };\n if ( data && _.findWhere( data[ new_src ], new_value ) ) {\n if ( config.src == new_src ) {\n var current_value = field.value();\n if ( current_value && config.multiple ) {\n if ( current_value.indexOf( new_id ) == -1 ) {\n current_value.push( new_id );\n }\n } else {\n current_value = new_id;\n }\n field.value( current_value );\n } else {\n this.model.set( 'value', { values: [ new_value ] } );\n this.model.trigger( 'change:value' );\n }\n this.trigger( 'change' );\n this._handleDropStatus( 'success' );\n } else {\n this._handleDropStatus( 'danger' );\n }\n } catch( e ) {\n this._handleDropStatus( 'danger' );\n }\n ev.preventDefault();\n },\n\n /** Highlight drag result */\n _handleDropStatus: function( status ) {\n var self = this;\n this.$el.removeClass( 'ui-dragover' ).addClass( 'ui-dragover-' + status );\n setTimeout( function() { self.$el.removeClass( 'ui-dragover-' + status ) }, this.model.get( 'statustimer' ) );\n },\n\n /** Assists in identifying the batch mode */\n _batch: function( result ) {\n result[ 'batch' ] = false;\n var current = this.model.get( 'current' );\n var config = this.config[ current ];\n if ( config.src == 'hdca' && !config.multiple ) {\n var hdca = this.history[ this.fields[ current ].value() + '_hdca' ];\n if ( hdca && hdca.map_over_type ) {\n result[ 'batch' ] = true;\n }\n }\n if ( config.batch == Batch.LINKED || config.batch == Batch.ENABLED ) {\n result[ 'batch' ] = true;\n if ( config.batch == Batch.ENABLED && this.button_product.value() === 'true' ) {\n result[ 'product' ] = true;\n }\n }\n return result;\n }\n});\n\nreturn {\n View: View\n}\n\n});\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/ui/ui-select-content.js\n **/","// dependencies\ndefine(['utils/utils', 'mvc/ui/ui-list'],\n function(Utils, List) {\n\n/**\n * FTP file selector\n */\nvar View = Backbone.View.extend({\n // initialize\n initialize : function(options) {\n // link this\n var self = this;\n\n // create ui-list view to keep track of selected ftp files\n this.ftpfile_list = new List.View({\n name : 'file',\n optional : options.optional,\n multiple : options.multiple,\n onchange : function() {\n options.onchange && options.onchange(self.value());\n }\n });\n\n // create elements\n this.setElement(this.ftpfile_list.$el);\n\n // initial fetch of ftps\n Utils.get({\n url : Galaxy.root + 'api/remote_files',\n success : function(response) {\n var data = [];\n for (var i in response) {\n data.push({\n value : response[i]['path'],\n label : response[i]['path']\n });\n }\n self.ftpfile_list.update(data);\n }\n });\n },\n\n /** Return/Set currently selected ftp datasets */\n value: function(val) {\n return this.ftpfile_list.value(val);\n }\n});\n\nreturn {\n View: View\n}\n\n});\n\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/ui/ui-select-ftp.js\n **/","// dependencies\ndefine(['utils/utils', 'mvc/ui/ui-misc', 'mvc/tool/tool-genomespace'],\n function(Utils, Ui, GenomespaceBrowser) {\n\n/**\n * GenomeSpace file selector\n */\nvar View = Backbone.View.extend({\n // initialize\n initialize : function(options) {\n\n // link this\n var self = this;\n\n // create insert new list element button\n this.browse_button = new Ui.ButtonIcon({\n title : 'Browse',\n icon : 'fa fa-sign-in',\n tooltip : 'Browse GenomeSpace',\n onclick : function() {\n self.browseGenomeSpace();\n }\n });\n\n // create genomespace filepath textbox\n this.filename_textbox = new Ui.Input();\n\n // create genomespace token textbox\n this.token_textbox = new Ui.Input({\n type : 'password' \n });\n\n // create elements\n this.setElement(this._template(options));\n this.$('.ui-gs-browse-button').append(this.browse_button.$el);\n this.$('.ui-gs-filename-textbox').append(this.filename_textbox.$el);\n this.$('.ui-gs-token-textbox').append(this.token_textbox.$el);\n },\n\n /** Browse GenomeSpace */\n browseGenomeSpace: function(options) {\n var self = this;\n GenomespaceBrowser.openFileBrowser({\n successCallback: function(data) {\n self.value(data.destination + \"^\" + data.token);\n }\n });\n },\n \n /** Main Template */\n _template: function(options) {\n return '' +\n '
'\n '' +\n '
';\n },\n \n /** Return/Set currently selected genomespace filename/token */\n value : function (new_value) {\n // check if new_value is defined\n if (new_value !== undefined) {\n this._setValue(new_value);\n }\n else {\n return this._getValue();\n }\n },\n \n // get value\n _getValue: function() {\n return this.filename_textbox.value() +\n \"^\" + this.token_textbox.value();\n },\n \n // set value\n _setValue: function(new_value) {\n if (new_value) {\n values = new_value.split(\"^\");\n this.filename_textbox.value(values[0]);\n this.token_textbox.value(values[1]);\n }\n },\n \n});\n\nreturn {\n View: View\n}\n\n});\n\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/ui/ui-select-genomespace.js\n **/","// dependencies\ndefine(['utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-table', 'mvc/ui/ui-list'],\n function(Utils, Ui, Table, List) {\n\n// collection of libraries\nvar Libraries = Backbone.Collection.extend({\n url: Galaxy.root + 'api/libraries?deleted=false'\n});\n\n// collection of dataset\nvar LibraryDatasets = Backbone.Collection.extend({\n initialize: function() {\n var self = this;\n this.config = new Backbone.Model({ library_id: null });\n this.config.on('change', function() {\n self.fetch({ reset: true });\n });\n },\n url: function() {\n return Galaxy.root + 'api/libraries/' + this.config.get('library_id') + '/contents';\n }\n});\n\n// hda/hdca content selector ui element\nvar View = Backbone.View.extend({\n // initialize\n initialize : function(options) {\n // link this\n var self = this;\n\n // collections\n this.libraries = new Libraries();\n this.datasets = new LibraryDatasets();\n\n // link app and options\n this.options = options;\n\n // select field for the library\n // TODO: Remove this once the library API supports searching for library datasets\n this.library_select = new Ui.Select.View({\n onchange : function(value) {\n self.datasets.config.set('library_id', value);\n }\n });\n\n // create ui-list view to keep track of selected data libraries\n this.dataset_list = new List.View({\n name : 'dataset',\n optional : options.optional,\n multiple : options.multiple,\n onchange : function() {\n self.trigger('change');\n }\n });\n\n // add reset handler for fetched libraries\n this.libraries.on('reset', function() {\n var data = [];\n self.libraries.each(function(model) {\n data.push({\n value : model.id,\n label : model.get('name')\n });\n });\n self.library_select.update(data);\n });\n\n // add reset handler for fetched library datasets\n this.datasets.on('reset', function() {\n var data = [];\n var library_current = self.library_select.text();\n if (library_current !== null) {\n self.datasets.each(function(model) {\n if (model.get('type') === 'file') {\n data.push({\n value : model.id,\n label : model.get('name')\n });\n }\n });\n }\n self.dataset_list.update(data);\n });\n\n // add change event. fires on trigger\n this.on('change', function() {\n options.onchange && options.onchange(self.value());\n });\n\n // create elements\n this.setElement(this._template());\n this.$('.library-select').append(this.library_select.$el);\n this.$el.append(this.dataset_list.$el);\n\n // initial fetch of libraries\n this.libraries.fetch({\n reset: true,\n success: function() {\n self.library_select.trigger('change');\n if (self.options.value !== undefined) {\n self.value(self.options.value);\n }\n }\n });\n },\n\n /** Return/Set currently selected library datasets */\n value: function(val) {\n return this.dataset_list.value(val);\n },\n\n /** Template */\n _template: function() {\n return '' +\n '' +\n '' +\n '
' +\n '' +\n '
' +\n 'Token
' +\n '' +\n '' +\n '
';\n }\n});\n\nreturn {\n View: View\n}\n\n});\n\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/ui/ui-select-library.js\n **/","define([ 'utils/utils' ], function( Utils ) {\n var View = Backbone.View.extend({\n initialize : function( options ) {\n var self = this;\n this.model = options && options.model || new Backbone.Model({\n id : Utils.uid(),\n min : null,\n max : null,\n step : null,\n precise : false,\n split : 10000,\n value : null,\n onchange : function(){}\n }).set( options );\n\n // create new element\n this.setElement( this._template() );\n this.$el.attr( 'id', this.model.id );\n this.$text = this.$( '.ui-form-slider-text' );\n this.$slider = this.$( '.ui-form-slider-element' );\n\n // add text field event\n var pressed = [];\n this.$text.on( 'change', function () {\n self.value( $( this ).val() );\n }).on( 'keyup', function( e ) {\n pressed[e.which] = false;\n }).on( 'keydown', function ( e ) {\n var v = e.which;\n pressed[ v ] = true;\n if ( self.model.get( 'is_workflow' ) && pressed[ 16 ] && v == 52 ) {\n self.value( '$' );\n event.preventDefault();\n } else if (!( v == 8 || v == 9 || v == 13 || v == 37 || v == 39 || ( v >= 48 && v <= 57 && !pressed[ 16 ] ) || ( v >= 96 && v <= 105 )\n || ( ( v == 190 || v == 110 ) && $( this ).val().indexOf( '.' ) == -1 && self.model.get( 'precise' ) )\n || ( ( v == 189 || v == 109 ) && $( this ).val().indexOf( '-' ) == -1 )\n || self._isParameter( $( this ).val() )\n || pressed[ 91 ] || pressed[ 17 ] ) ) {\n event.preventDefault();\n }\n });\n\n // build slider, cannot be rebuild in render\n var opts = this.model.attributes;\n this.has_slider = opts.max !== null && opts.min !== null && opts.max > opts.min;\n var step = opts.step;\n if ( !step ) {\n if ( opts.precise && this.has_slider ) {\n step = ( opts.max - opts.min ) / opts.split;\n } else {\n step = 1.0;\n }\n }\n if ( this.has_slider ) {\n this.$text.addClass( 'ui-form-slider-left' );\n this.$slider.slider( { min: opts.min, max: opts.max, step: step } )\n .on( 'slide', function ( event, ui ) { self.value( ui.value ) } );\n } else {\n this.$slider.hide();\n }\n\n // add listeners\n this.listenTo( this.model, 'change', this.render, this );\n this.render();\n },\n\n render: function() {\n var value = this.model.get( 'value' );\n this.has_slider && this.$slider.slider( 'value', value );\n value !== this.$text.val() && this.$text.val( value );\n },\n\n /** Set and return the current value */\n value : function ( new_val ) {\n var options = this.model.attributes;\n if ( new_val !== undefined ) {\n if ( new_val !== null && new_val !== '' && !this._isParameter( new_val ) ) {\n isNaN( new_val ) && ( new_val = 0 );\n !options.precise && ( new_val = Math.round( new_val ) );\n options.max !== null && ( new_val = Math.min( new_val, options.max ) );\n options.min !== null && ( new_val = Math.max( new_val, options.min ) );\n }\n this.model.set( 'value', new_val );\n this.model.trigger( 'change' );\n options.onchange( new_val );\n }\n return this.model.get( 'value' );\n },\n\n /** Return true if the field contains a workflow parameter i.e. $('name') */\n _isParameter: function( value ) {\n return this.model.get( 'is_workflow' ) && String( value ).substring( 0, 1 ) === '$';\n },\n\n /** Slider template */\n _template: function() {\n return '' +\n 'Select Library' +\n '' +\n '
' +\n '' +\n '' +\n '';\n }\n });\n\n return {\n View : View\n };\n});\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/ui/ui-slider.js\n **/","var jQuery = require( 'jquery' ),\n $ = jQuery,\n QUERY_STRING = require( 'utils/query-string-parsing' ),\n Ui = require( 'mvc/ui/ui-misc' );\n\nvar Router = Backbone.Router.extend({\n // TODO: not many client routes at this point - fill and remove from server.\n // since we're at root here, this may be the last to be routed entirely on the client.\n initialize : function( page, options ){\n this.page = page;\n this.options = options;\n },\n\n /** helper to push a new navigation state */\n push: function( url, data ) {\n data = data || {};\n data.__identifer = Math.random().toString( 36 ).substr( 2 );\n if ( !$.isEmptyObject( data ) ) {\n url += url.indexOf( '?' ) == -1 ? '?' : '&';\n url += $.param( data , true );\n }\n Galaxy.params = {};\n this.navigate( url, { 'trigger': true } );\n },\n\n /** override to parse query string into obj and send to each route */\n execute: function( callback, args, name ){\n Galaxy.debug( 'router execute:', callback, args, name );\n var queryObj = QUERY_STRING.parse( args.pop() );\n args.push( queryObj );\n if( callback ){\n if ( this.authenticate( args, name ) ) {\n callback.apply( this, args );\n } else {\n this.access_denied();\n }\n }\n },\n\n authenticate: function( args, name ) {\n return true;\n },\n\n access_denied: function() {\n this.page.display( new Ui.Message( { status: 'danger', message: 'You must be logged in with proper credentials to make this request.', persistent: true } ) );\n }\n});\n\nmodule.exports = Router\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/layout/router.js\n **/","/** Generic form view */\ndefine( [ 'mvc/form/form-view', 'mvc/ui/ui-misc' ], function( Form, Ui ) {\n\n var View = Backbone.View.extend({\n\n initialize: function( options ) {\n this.model = new Backbone.Model( options );\n this.url = this.model.get( 'url' );\n this.redirect = this.model.get( 'redirect' );\n this.setElement( '' );\n this.render();\n },\n\n render: function() {\n var self = this;\n $.ajax({\n url : Galaxy.root + this.url,\n type : 'GET'\n }).done( function( response ) {\n var options = $.extend( {}, self.model.attributes, response );\n var form = new Form({\n title : options.title,\n message: options.message,\n status : options.status || 'warning',\n icon : options.icon,\n inputs : options.inputs,\n buttons: {\n 'submit': new Ui.Button({\n tooltip : options.submit_tooltip,\n title : options.submit_title || 'Save',\n icon : options.submit_icon || 'fa-save',\n cls : 'btn btn-primary ui-clear-float',\n onclick : function() { self._submit( form ) }\n })\n }\n });\n self.$el.empty().append( form.$el );\n }).fail( function( response ) {\n self.$el.empty().append( new Ui.Message({\n message : 'Failed to load resource ' + self.url + '.',\n status : 'danger',\n persistent : true\n }).$el );\n });\n },\n\n _submit: function( form ) {\n var self = this;\n $.ajax( {\n url : Galaxy.root + self.url,\n data : JSON.stringify( form.data.create() ),\n type : 'PUT',\n contentType : 'application/json'\n }).done( function( response ) {\n var success_message = { message: response.message, status: 'success', persistent: false };\n if ( self.redirect ) {\n window.location = Galaxy.root + self.redirect + '?' + $.param( success_message );\n } else {\n form.data.matchModel( response, function ( input, input_id ) {\n form.field_list[ input_id ].value( input.value );\n });\n self._showMessage( form, success_message );\n }\n }).fail( function( response ) {\n self._showMessage( form, { message: response.responseJSON.err_msg, status: 'danger', persistent: false } );\n });\n },\n\n _showMessage: function( form, options ) {\n var $panel = form.$el.parents().filter(function() {\n return [ 'auto', 'scroll' ].indexOf( $( this ).css( 'overflow' ) ) != -1;\n }).first();\n $panel.animate( { scrollTop : 0 }, 500 );\n form.message.update( options );\n }\n });\n\n return {\n View : View\n };\n});\n\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/mvc/form/form-wrapper.js\n **/","var _l = require( 'utils/localization' );\n\nvar AdminPanel = Backbone.View.extend({\n initialize: function( page, options ) {\n var self = this;\n this.page = page;\n this.root = options.root;\n this.config = options.config;\n this.settings = options.settings;\n this.message = options.message;\n this.status = options.status;\n this.model = new Backbone.Model({\n title : _l( 'Administration' )\n });\n this.categories = new Backbone.Collection([{\n title : 'Server',\n items : [ {\n title : 'Data types registry',\n url : 'admin/view_datatypes_registry'\n },{\n title : 'Data tables registry',\n url : 'admin/view_tool_data_tables'\n },{\n title : 'Display applications',\n url : 'admin/display_applications'\n },{\n title : 'Manage jobs',\n url : 'admin/jobs'\n } ]\n },{\n title : 'Tools and Tool Shed',\n items : [ {\n title : 'Search Tool Shed',\n url : 'admin_toolshed/browse_tool_sheds',\n enabled : self.settings.is_tool_shed_installed\n },{\n title : 'Search Tool Shed (Beta)',\n url : 'admin_toolshed/browse_toolsheds',\n enabled : self.settings.is_tool_shed_installed && self.config.enable_beta_ts_api_install\n },{\n title : 'Monitor installing repositories',\n url : 'admin_toolshed/monitor_repository_installation?installing_repository_ids=' + self.settings.installing_repository_ids,\n enabled : self.settings.installing_repository_ids\n },{\n title : 'Manage installed tools',\n url : 'admin_toolshed/browse_repositories',\n enabled : self.settings.is_repo_installed\n },{\n title : 'Reset metadata',\n url : 'admin_toolshed/reset_metadata_on_selected_installed_repositories',\n enabled : self.settings.is_repo_installed\n },{\n title : 'Download local tool',\n url : 'admin/package_tool'\n },{\n title : 'Tool lineage',\n url : 'admin/tool_versions',\n target : '__use_router__'\n },{\n title : 'Reload a tool\\'s configuration',\n url : 'admin/reload_tool'\n },{\n title : 'Review tool migration stages',\n url : 'admin/review_tool_migration_stages'\n },{\n title : 'View Tool Error Logs',\n url : 'admin/tool_errors'\n },{\n title : 'Manage Display Whitelist',\n url : 'admin/sanitize_whitelist'\n },{\n title : 'Manage Tool Dependencies',\n url : 'admin/manage_tool_dependencies'\n } ]\n },{\n title : 'User Management',\n items : [ {\n title : 'Users',\n url : 'admin/users',\n target : '__use_router__'\n },{\n title : 'Groups',\n url : 'admin/groups',\n target : '__use_router__'\n },{\n title : 'Roles',\n url : 'admin/roles',\n target : '__use_router__'\n },{\n title : 'API keys',\n url : 'userskeys/all_users'\n },{\n title : 'Impersonate a user',\n url : 'admin/impersonate',\n enabled : self.config.allow_user_impersonation\n } ]\n },{\n title : 'Data',\n items : [ {\n title : 'Quotas',\n url : 'admin/quotas',\n target : '__use_router__',\n enabled : self.config.enable_quotas\n },{\n title : 'Data libraries',\n url : 'library_admin/browse_libraries'\n },{\n title : 'Roles',\n url : 'admin/roles',\n target : '__use_router__'\n },{\n title : 'Local data',\n url : 'data_manager'\n } ]\n },{\n title : 'Form Definitions',\n items : [ {\n title : 'Form definitions',\n url : 'forms/browse_form_definitions'\n } ]\n },{\n title : 'Sample Tracking',\n items : [ {\n title : 'Sequencers and external services',\n url : 'external_service/browse_external_services'\n },{\n title : 'Request types',\n url : 'request_type/browse_request_types'\n },{\n title : 'Sequencing requests',\n url : 'requests_admin/browse_requests'\n },{\n title : 'Find samples',\n url : 'requests_common/find_samples?cntrller=requests_admin'\n } ]\n }]);\n this.setElement( this._template() );\n },\n\n render : function() {\n var self = this;\n this.$el.empty();\n this.categories.each( function( category ) {\n var $section = $( self._templateSection( category.attributes ) );\n var $entries = $section.find( '.ui-side-section-body' );\n _.each( category.get( 'items' ), function( item ) {\n if ( item.enabled === undefined || item.enabled ) {\n var $link = $( '' ).attr( { href : self.root + item.url } ).text( _l( item.title ) );\n if ( item.target == '__use_router__' ) {\n $link.on( 'click', function( e ) { e.preventDefault(); self.page.router.push( item.url ); } );\n } else {\n $link.attr( 'target', 'galaxy_main' );\n }\n $entries.append( $( '' ).addClass( 'ui-side-section-body-title' ).append( $link ) );\n }\n });\n self.$el.append( $section );\n });\n this.page.$( '#galaxy_main' ).prop( 'src', this.root + 'admin/center?message=' + this.message + '&status=' + this.status );\n },\n\n _templateSection : function( options ) {\n return [\n '
',\n '
' + _l( options.title ) + '
',\n '',\n '
'\n ].join('');\n },\n\n _template : function() {\n return '';\n },\n\n toString : function() { return 'adminPanel' }\n});\n\nmodule.exports = AdminPanel;\n\n\n/** WEBPACK FOOTER **\n ** ./galaxy/scripts/apps/panels/admin-panel.js\n **/"],"sourceRoot":""}
\ No newline at end of file
diff --git a/static/scripts/bundled/analysis.bundled.js b/static/scripts/bundled/analysis.bundled.js
index def1f96744cd..4cf3a0d72ef0 100644
--- a/static/scripts/bundled/analysis.bundled.js
+++ b/static/scripts/bundled/analysis.bundled.js
@@ -1,18 +1,18 @@
webpackJsonp([3,1],[function(e,t,i){(function(e){var t=i(1),n=t,s=i(52).GalaxyApp,a=i(55),o=i(104),r=i(103),l=i(53),d=i(47),c=i(62),h=i(145),u=i(144),p=i(93),f=i(12),g=i(128),m=i(149),v=i(131),_=i(92),y=i(4),w=i(5),b=i(127),x=i(126);window.app=function(t,i){window.Galaxy=new s(t,i),Galaxy.debug("analysis app");var C=a.extend({routes:{"(/)":"home","(/)root*":"home","(/)tours(/)(:tour_id)":"show_tours","(/)user(/)":"show_user","(/)user(/)(:form_id)":"show_user_form","(/)workflow(/)":"show_workflows","(/)workflow/run(/)":"show_run","(/)pages(/)(:action_id)":"show_pages","(/)visualizations/(:action_id)":"show_visualizations","(/)workflows/list_published(/)":"show_workflows_published","(/)histories(/)(:action_id)":"show_histories","(/)datasets(/)list(/)":"show_datasets","(/)workflow/import_workflow":"show_import_workflow","(/)custom_builds":"show_custom_builds","(/)datasets/edit":"show_dataset_edit_attributes","(/)datasets/error":"show_dataset_error"},require_login:["show_user","show_user_form","show_workflows"],authenticate:function(e,t){return Galaxy.user&&Galaxy.user.id||this.require_login.indexOf(t)==-1},show_tours:function(e){e?p.giveTour(e):this.page.display(new p.ToursView)},show_user:function(){this.page.display(new h.View)},show_user_form:function(e){var t=new h.Model({user_id:Galaxy.params.id});this.page.display(new c.View(t.get(e)))},show_visualizations:function(e){this.page.display(new g.View({action_id:e,plural:"Visualizations",item:"visualization"}))},show_workflows_published:function(){this.page.display(new f({url_base:Galaxy.root+"workflow/list_published",dict_format:!0}))},show_histories:function(e){this.page.display(new v.View({action_id:e}))},show_datasets:function(){this.page.display(new f({url_base:Galaxy.root+"dataset/list",dict_format:!0}))},show_pages:function(e){this.page.display(new g.View({action_id:e,plural:"Pages",item:"page"}))},show_workflows:function(){this.page.display(new m.View)},show_run:function(){this._loadWorkflow()},show_import_workflow:function(){this.page.display(new m.ImportWorkflowView)},show_custom_builds:function(){var e=this,t=this.page.historyPanel.historyView;return t&&t.model&&t.model.id?void this.page.display(new u.View):void window.setTimeout(function(){e.show_custom_builds()},500)},show_dataset_edit_attributes:function(){this.page.display(new x.View)},show_dataset_error:function(){this.page.display(new b.View)},home:function(e){e.tool_id||e.job_id?"upload1"===e.tool_id?(this.page.toolPanel.upload.show(),this._loadCenterIframe("welcome")):this._loadToolForm(e):e.workflow_id?this._loadWorkflow():e.m_c?this._loadCenterIframe(e.m_c+"/"+e.m_a):this._loadCenterIframe("welcome")},_loadToolForm:function(e){e.id=decodeURIComponent(e.tool_id),this.page.display(new d.View(e))},_loadCenterIframe:function(e,t){t=t||Galaxy.root,e=t+e,this.page.$("#galaxy_main").prop("src",e)},_loadWorkflow:function(){var e=this;y.get({url:Galaxy.root+"api/workflows/"+y.getQueryString("id")+"/download",data:{style:"run"},success:function(t){e.page.display(new _.View(t))},error:function(t){var i="Error occurred while loading the resource.",n={message:i,status:"error",persistent:!0,cls:"errormessage"};e.page.display(new w.Message(n))}})}});n(function(){Galaxy.page=new l.View(e.extend(t,{Left:o,Right:r,Router:C}))})}}).call(t,i(3))},,,,,function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(15),i(42),i(14),i(37),i(11),i(8)],s=function(e,t,i,n,s,l,d){var c=a.View.extend({tagName:"label",initialize:function(e){this.model=e&&e.model||new a.Model(e),this.tagName=e.tagName||this.tagName,this.setElement(o("<"+this.tagName+"/>")),this.listenTo(this.model,"change",this.render,this),this.render()},title:function(e){this.model.set("title",e)},value:function(){return this.model.get("title")},render:function(){return this.$el.removeClass().addClass("ui-label").addClass(this.model.get("cls")).html(this.model.get("title")),this}}),h=a.View.extend({initialize:function(e){this.model=e&&e.model||new a.Model({message:null,status:"info",cls:"",persistent:!1,fade:!0}).set(e),this.listenTo(this.model,"change",this.render,this),this.render()},update:function(e){this.model.set(e)},render:function(){this.$el.removeClass().addClass("ui-message").addClass(this.model.get("cls"));var e=this.model.get("status");if(this.model.get("large")?this.$el.addClass(("success"==e&&"done"||"danger"==e&&"error"||e)+"messagelarge"):this.$el.addClass("alert").addClass("alert-"+e),this.model.get("message")){if(this.$el.html(this.messageForDisplay()),this.$el[this.model.get("fade")?"fadeIn":"show"](),this.timeout&&window.clearTimeout(this.timeout),!this.model.get("persistent")){var t=this;this.timeout=window.setTimeout(function(){t.model.set("message","")},3e3)}}else this.$el.fadeOut();return this},messageForDisplay:function(){return r.escape(this.model.get("message"))}}),u=h.extend({messageForDisplay:function(){return this.model.get("message")}}),p=a.View.extend({initialize:function(e){this.model=e&&e.model||new a.Model({type:"text",placeholder:"",disabled:!1,readonly:!1,visible:!0,cls:"",area:!1,color:null,style:null}).set(e),this.tagName=this.model.get("area")?"textarea":"input",this.setElement(o("<"+this.tagName+"/>")),this.listenTo(this.model,"change",this.render,this),this.render()},events:{input:"_onchange"},value:function(e){return void 0!==e&&this.model.set("value","string"==typeof e?e:""),this.model.get("value")},render:function(){var e=this;this.$el.removeClass().addClass("ui-"+this.tagName).addClass(this.model.get("cls")).addClass(this.model.get("style")).attr("id",this.model.id).attr("type",this.model.get("type")).attr("placeholder",this.model.get("placeholder")).css("color",this.model.get("color")||"").css("border-color",this.model.get("color")||"");var t=this.model.get("datalist");return o.isArray(t)&&t.length>0&&this.$el.autocomplete({source:function(t,i){i(e.model.get("datalist"))},change:function(){e._onchange()}}),this.model.get("value")!==this.$el.val()&&this.$el.val(this.model.get("value")),r.each(["readonly","disabled"],function(t){e.model.get(t)?e.$el.attr(t,!0):e.$el.removeAttr(t)}),this.$el[this.model.get("visible")?"show":"hide"](),this},_onchange:function(){this.value(this.$el.val()),this.model.get("onchange")&&this.model.get("onchange")(this.model.get("value"))}}),f=a.View.extend({initialize:function(e){this.model=e&&e.model||new a.Model(e),this.setElement(o("").append(this.$info=o("")).append(this.$hidden=o(""))),this.listenTo(this.model,"change",this.render,this),this.render()},value:function(e){return void 0!==e&&this.model.set("value",e),this.model.get("value")},render:function(){return 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this.$el.attr("id",this.model.id),this.model.get("info")?this.$info.show().text(this.model.get("info")):this.$info.hide(),this.model.get("value")?this.$text.text(this.model.get("value")).show():this.$text.hide(),this.model.get("wait")?this.$wait.show():this.$wait.hide(),this},_readFile:function(e){var t=this,i=e.target.files&&e.target.files[0];if(i){var n=new FileReader;n.onload=function(){t.model.set({wait:!1,value:this.result})},this.model.set({wait:!0,value:null}),n.readAsText(i)}}});return{Button:l.ButtonDefault,ButtonIcon:l.ButtonIcon,ButtonCheck:l.ButtonCheck,ButtonMenu:l.ButtonMenu,ButtonLink:l.ButtonLink,Input:p,Label:c,Message:h,UnescapedMessage:u,Upload:g,Modal:d,RadioButton:n.RadioButton,Checkbox:n.Checkbox,Radio:n.Radio,Select:t,Hidden:f,Slider:i,Drilldown:s}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(3))},,,,function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(5)],s=function(e,t){var i=a.View.extend({visible:!1,initialize:function(i){var n=this;this.model=i&&i.model||new a.Model({id:e.uid(),cls:"ui-portlet",title:"",icon:"",buttons:null,body:null,scrollable:!0,nopadding:!1,operations:null,collapsible:!1,collapsible_button:!1,collapsed:!1,onchange_title:null}).set(i),this.setElement(this._template()),this.$body=this.$(".portlet-body"),this.$title_text=this.$(".portlet-title-text"),this.$title_icon=this.$(".portlet-title-icon"),this.$header=this.$(".portlet-header"),this.$content=this.$(".portlet-content"),this.$backdrop=this.$(".portlet-backdrop"),this.$buttons=this.$(".portlet-buttons"),this.$operations=this.$(".portlet-operations"),this.model.get("body")&&this.append(this.model.get("body")),this.collapsible_button=new t.ButtonIcon({icon:"fa-eye",tooltip:"Collapse/Expand",cls:"ui-button-icon-plain",onclick:function(){n[n.collapsed?"expand":"collapse"]()}}),this.render()},render:function(){var e=this,t=this.model.attributes;return this.$el.removeClass().addClass(t.cls).attr("id",t.id),this.$header[t.title?"show":"hide"](),this.$title_text.html(t.title),o.each([this.$content,this.$body],function(e){e[t.nopadding?"addClass":"removeClass"]("no-padding")}),t.icon?this.$title_icon.removeClass().addClass("portlet-title-icon fa").addClass(t.icon).show():this.$title_icon.hide(),this.$title_text[t.collapsible?"addClass":"removeClass"]("no-highlight collapsible").off(),t.collapsible&&(this.$title_text.on("click",function(){e[e.collapsed?"expand":"collapse"]()}),t.collapsed?this.collapse():this.expand()),this.$title_text.prop("disabled",!t.onchange_title),t.onchange_title&&this.$title_text.make_text_editable({on_finish:function(e){t.onchange_title(e)}}),t.buttons?(this.$buttons.empty().show(),r.each(this.model.get("buttons"),function(t,i){i.$el.prop("id",t),e.$buttons.append(i.$el)})):this.$buttons.hide(),this.$operations.empty,t.collapsible_button&&this.$operations.append(this.collapsible_button.$el),t.operations&&r.each(t.operations,function(t,i){i.$el.prop("id",t),e.$operations.append(i.$el)}),this},append:function(e){this.$body.append(e)},empty:function(){this.$body.empty()},header:function(){return this.$header},body:function(){return this.$body},show:function(){this.visible=!0,this.$el.fadeIn("fast")},hide:function(){this.visible=!1,this.$el.hide()},enableButton:function(e){this.$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.$operations.find("#"+e).show()},setOperation:function(e,t){this.$operations.find("#"+e).off("click").on("click",t)},title:function(e){return e&&this.$title_text.html(e),this.$title_text.html()},collapse:function(){this.collapsed=!0,this.$content.height("0%"),this.$body.hide(),this.collapsible_button.setIcon("fa-eye-slash")},expand:function(){this.collapsed=!1,this.$content.height("100%"),this.$body.fadeIn("fast"),this.collapsible_button.setIcon("fa-eye")},disable:function(){this.$backdrop.show()},enable:function(){this.$backdrop.hide()},_template:function(){return r("").append(r("").addClass("portlet-header").append(r("").addClass("portlet-operations")).append(r("").addClass("portlet-title").append(r("").addClass("portlet-title-icon")).append(r("").addClass("portlet-title-text")))).append(r("").addClass("portlet-content").append(r("").addClass("portlet-body")).append(r("").addClass("portlet-buttons"))).append(r("").addClass("portlet-backdrop"))}});return{View:i}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(3),i(1))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(9),i(5),i(32),i(19)],s=function(e,t,i,n,s){return a.View.extend({initialize:function(e){this.model=new a.Model({initial_errors:!1,cls:"ui-portlet-limited",icon:null,always_refresh:!0,status:"warning",onchange:function(){}}).set(e),this.setElement(""),this.render()},update:function(e){var t=this;this.data.matchModel(e,function(e,i){var n=t.input_list[i];if(n&&n.options&&!o.isEqual(n.options,e.options)){n.options=e.options;var s=t.field_list[i];if(s.update){var a=[];if(["data","data_collection","drill_down"].indexOf(n.type)!=-1)a=n.options;else for(var r in e.options){var l=e.options[r];l.length>2&&a.push({label:l[0],value:l[1]})}s.update(a),s.trigger("change"),Galaxy.emit.debug("form-view::update()","Updating options for "+i)}}})},wait:function(e){for(var t in this.input_list){var i=this.field_list[t],n=this.input_list[t];n.is_dynamic&&i.wait&&i.unwait&&i[e?"wait":"unwait"]()}},highlight:function(e,t,i){var n=this.element_list[e];if(n&&(n.error(t||"Please verify this parameter."),this.portlet.expand(),this.trigger("expand",e),!i)){var s=this.$el.parents().filter(function(){return["auto","scroll"].indexOf(r(this).css("overflow"))!=-1}).first();s.animate({scrollTop:s.scrollTop()+n.$el.offset().top-120},500)}},errors:function(e){if(this.trigger("reset"),e&&e.errors){var t=this.data.matchResponse(e.errors);for(var i in this.element_list){this.element_list[i];t[i]&&this.highlight(i,t[i],!0)}}},render:function(){var e=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new s.Manager(this),this._renderForm(),this.data.create(),this.model.get("initial_errors")&&this.errors(this.model.attributes);var t=this.data.checksum();return this.on("change",function(i){var n=e.input_list[i];if(!n||n.refresh_on_change||e.model.get("always_refresh")){var s=e.data.checksum();s!=t&&(t=s,e.model.get("onchange")())}}),this.on("reset",function(){o.each(e.element_list,function(e){e.reset()})}),this},_renderForm:function(){r(".tooltip").remove();var e=this.model.attributes;this.message=new i.UnescapedMessage,this.section=new n.View(this,{inputs:e.inputs}),this.portlet=new t.View({icon:e.icon,title:e.title,cls:e.cls,operations:e.operations,buttons:e.buttons,collapsible:e.collapsible,collapsed:e.collapsed,onchange_title:e.onchange_title}),this.portlet.append(this.message.$el),this.portlet.append(this.section.$el),this.$el.empty(),e.inputs&&this.$el.append(this.portlet.$el),e.message&&this.message.update({persistent:!0,status:e.status,message:e.message}),Galaxy.emit.debug("form-view::initialize()","Completed")}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(3),i(1))},function(e,t,i){var n,s;(function(a,o){n=[i(4)],s=function(e){var t=a.View.extend({initialize:function(t){this.model=t&&t.model||new a.Model({id:e.uid(),title:"",icon:"",cls:"btn btn-default",wait:!1,wait_text:"Sending...",wait_cls:"btn btn-info",disabled:!1,percentage:-1}).set(t),this.setElement(o("").attr("type","button").append(this.$icon=o("")).append(this.$title=o("")).append(this.$progress=o("").append(this.$progress_bar=o("")))),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var e=this,t=this.model.attributes;this.$el.removeClass().addClass("ui-button-default").addClass(t.disabled&&"disabled").attr("id",t.id).attr("disabled",t.disabled).off("click").on("click",function(){o(".tooltip").hide(),t.onclick&&!e.disabled&&t.onclick()}).tooltip({title:t.tooltip,placement:"bottom"}),this.$progress.addClass("progress").css("display",t.percentage!==-1?"block":"none"),this.$progress_bar.addClass("progress-bar").css({width:t.percentage+"%"}),this.$icon.removeClass().addClass("icon fa"),this.$title.removeClass().addClass("title"),t.wait?(this.$el.addClass(t.wait_cls).prop("disabled",!0),this.$icon.addClass("fa-spinner fa-spin ui-margin-right"),this.$title.html(t.wait_text)):(this.$el.addClass(t.cls),this.$icon.addClass(t.icon),this.$title.html(t.title),t.icon&&t.title&&this.$icon.addClass("ui-margin-right"))},show:function(){this.$el.show()},hide:function(){this.$el.hide()},disable:function(){this.model.set("disabled",!0)},enable:function(){this.model.set("disabled",!1)},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},setIcon:function(e){this.model.set("icon",e)}}),i=t.extend({initialize:function(t){this.model=t&&t.model||new a.Model({id:e.uid(),title:"",icon:"",cls:""}).set(t),this.setElement(o("").append(this.$icon=o(""))),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var e=this.model.attributes;this.$el.removeClass().addClass(e.cls).attr({id:e.id,href:e.href||"javascript:void(0)",title:e.title,target:e.target||"_top",disabled:e.disabled}).tooltip({placement:"bottom"}).off("click").on("click",function(){e.onclick&&!e.disabled&&e.onclick()}),this.$icon.removeClass().addClass(e.icon)}}),n=a.View.extend({initialize:function(t){this.model=t&&t.model||new a.Model({id:e.uid(),title:"Select/Unselect all",icons:["fa-square-o","fa-minus-square-o","fa-check-square-o"],value:0,onchange:function(){}}).set(t),this.setElement(o("").append(this.$icon=o("")).append(this.$title=o(""))),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(e){var t=this,e=this.model.attributes;this.$el.addClass("ui-button-check").off("click").on("click",function(){t.model.set("value",0===t.model.get("value")&&2||0),e.onclick&&e.onclick()}),this.$title.html(e.title),this.$icon.removeClass().addClass("icon fa ui-margin-right").addClass(e.icons[e.value])},value:function(e,t){return void 0!==e&&(t&&0!==e&&(e=e!==t&&1||2),this.model.set("value",e),this.model.get("onchange")(this.model.get("value"))),this.model.get("value")}}),s=t.extend({initialize:function(t){this.model=t&&t.model||new a.Model({id:e.uid(),title:"",icon:"",cls:"ui-button-icon",disabled:!1}).set(t),this.setElement(o("").append(this.$button=o("").append(this.$icon=o("")).append(this.$title=o("")))),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(e){var e=this.model.attributes;this.$el.removeClass().addClass(e.cls).addClass(e.disabled&&"disabled").attr("disabled",e.disabled).attr("id",e.id).off("click").on("click",function(){o(".tooltip").hide(),!e.disabled&&e.onclick&&e.onclick()}),this.$button.addClass("button").tooltip({title:e.tooltip,placement:"bottom"}),this.$icon.removeClass().addClass("icon fa").addClass(e.icon),this.$title.addClass("title").html(e.title),e.icon&&e.title&&this.$icon.addClass("ui-margin-right")}}),r=t.extend({$menu:null,initialize:function(e){this.model=e&&e.model||new a.Model({id:"",title:"",pull:"right",icon:null,onclick:null,cls:"ui-button-icon ui-button-menu",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""}).set(e),this.collection=new a.Collection,this.setElement(o("").append(this.$root=o("").append(this.$icon=o("")).append(this.$title=o("")))),this.listenTo(this.model,"change",this.render,this),this.listenTo(this.collection,"change add remove reset",this.render,this),this.render()},render:function(){var e=this,t=this.model.attributes;this.$el.removeClass().addClass("dropdown").addClass(t.cls).attr("id",t.id).css({display:t.visible&&this.collection.where({visible:!0}).length>0?"block":"none"}),this.$root.addClass("root button dropdown-toggle").attr("data-toggle","dropdown").tooltip({title:t.tooltip,placement:"bottom"}).off("click").on("click",function(e){o(".tooltip").hide(),e.preventDefault(),t.onclick&&t.onclick()}),this.$icon.removeClass().addClass("icon fa").addClass(t.icon),this.$title.removeClass().addClass("title").html(t.title),t.icon&&t.title&&this.$icon.addClass("ui-margin-right"),this.$menu&&this.$menu.remove(),this.collection.length>0&&(this.$menu=o("0?(!this.multiple&&this.button.disable(),this.$(".ui-list-portlet").show()):(this.button.enable(),this.$(".ui-list-portlet").hide()),this.options.onchange&&this.options.onchange()},_template:function(e){return''},_templateRow:function(e){return'").attr("id","loading_indicator"),this.$el.append(this.loading_indicator);var e=r("
").attr({id:"content_table",cellpadding:0});this.$el.append(e);var t=this.model.get_metadata("column_names"),i=r("").appendTo(e),n=r(""+t.join(" ")+" ");else for(var s=1;s<=this.model.get_metadata("columns");s++)n.append(""+s+" ");var a=this,o=this.model.get("first_data_chunk");o?this._renderChunk(o):r.when(a.model.get_next_chunk()).then(function(e){a._renderChunk(e)}),this.scroll_elt.scroll(function(){a.attempt_to_fetch()})},scrolled_to_bottom:function(){return!1},_renderCell:function(e,t,i){var n=r("").text(e),s=this.model.get_metadata("column_types");return void 0!==i?n.attr("colspan",i).addClass("stringalign"):s&&t"),n=this.model.get_metadata("columns");return this.row_count%2!==0&&i.addClass("dark_row"),t.length===n?o.each(t,function(e,t){i.append(this._renderCell(e,t))},this):t.length>n?(o.each(t.slice(0,n-1),function(e,t){i.append(this._renderCell(e,t))},this),i.append(this._renderCell(t.slice(n-1).join("\t"),n-1))):1===t.length?i.append(this._renderCell(e,0,n)):(o.each(t,function(e,t){i.append(this._renderCell(e,t))},this),o.each(o.range(n-t.length),function(){i.append(r(""))})),this.row_count++,i},_renderChunk:function(e){var t=this.$el.find("table");o.each(e.ck_data.split("\n"),function(e,i){""!==e&&t.append(this._renderRow(e))},this)}}),h=c.extend({initialize:function(e){c.prototype.initialize.call(this,e);var t=o.find(this.$el.parents(),function(e){return"auto"===r(e).css("overflow")});t||(t=window),this.scroll_elt=r(t)},scrolled_to_bottom:function(){return this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0}}),u=c.extend({initialize:function(e){c.prototype.initialize.call(this,e),this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:e.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}}),p=a.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,file_ext:null,initialize:function(e){function t(e,t){for(var i=0;i")),this.options=t||[],this.$button.data("popupmenu",this);var i=this;this.$button.click(function(e){return a(".popmenu-wrapper").remove(),i._renderAndShow(e),!1})},_renderAndShow:function(e){this.render(),this.$el.appendTo("body").css(this._getShownPosition(e)).show(),this._setUpCloseBehavior()},render:function(){if(this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options)),this.options.length){var e=this;this.$el.find("li").each(function(t,i){var n=e.options[t];n.func&&a(this).children("a.popupmenu-option").click(function(t){n.func.call(e,t,n),t.preventDefault()})})}return this},template:function(e,t){return['"].join("")},_templateOptions:function(e){return e.length?o.map(e,function(e){if(e.divider)return'';if(e.header)return['',e.html," "].join("");var t=e.href||"javascript:void(0);",i=e.target?' target="'+e.target+'"':"",n=e.checked?'':"";return['",n,e.html," "].join("")}).join(""):"(no options) "},_getShownPosition:function(e){var t=this.$el.width(),i=e.pageX-t/2;return i=Math.min(i,a(document).scrollLeft()+a(window).width()-t-5),i=Math.max(i,a(document).scrollLeft()+5),{top:e.pageY,left:i}},_setUpCloseBehavior:function(){function e(e){if(a(document).off("click.close_popup"),window&&window.parent!==window)try{a(window.parent.document).off("click.close_popup")}catch(e){}else try{a("iframe#galaxy_main").contents().off("click.close_popup")}catch(e){}t.remove()}var t=this;if(a("html").one("click.close_popup",e),window&&window.parent!==window)try{a(window.parent.document).find("html").one("click.close_popup",e)}catch(e){}else try{a("iframe#galaxy_main").contents().one("click.close_popup",e)}catch(e){}},addItem:function(e,t){return t=t>=0?t:this.options.length,this.options.splice(t,0,e),this},removeItem:function(e){return e>=0&&this.options.splice(e,1),this},findIndexByHtml:function(e){for(var t=0;t
'+this.options.content+"
'+e.name+"
"}});return{View:n}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(11)],s=function(e,t){var i=a.View.extend({initialize:function(t){var i=this;this.model=t&&t.model||new a.Model({visible:!0,data:[],id:e.uid(),error_text:"No options available.",wait_text:"Please wait...",
-multiple:!1,optional:!1,onchange:function(){}}).set(t),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:visible",this._changeVisible,this),this.on("change",function(){i.model.get("onchange")(i.value())}),this.render()},render:function(){var e=this;this.$el.empty().removeClass().addClass("ui-options").append(this.$message=o("")).append(this.$menu=o("").addClass("ui-options-menu")).append(this.$options=o(this._template())),this.all_button=null,this.model.get("multiple")&&(this.all_button=new t.ButtonCheck({onclick:function(){e.$("input").prop("checked",0!==e.all_button.value()),e.value(e._getValue()),e.trigger("change")}}),this.$menu.append(this.all_button.$el)),this._changeData(),this._changeWait(),this._changeVisible()},update:function(e){this.model.set("data",e)},_changeData:function(){var e=this;this.$options.empty(),this._templateOptions?this.$options.append(this._templateOptions(this.model.get("data"))):r.each(this.model.get("data"),function(t){e.$options.append(o(e._templateOption(t)).addClass("ui-option").tooltip({title:t.tooltip,placement:"bottom"}))});var e=this;this.$("input").on("change",function(){e.value(e._getValue()),e.trigger("change")}),this._changeValue(),this._changeWait()},_changeVisible:function(){this.$el[this.model.get("visible")?"show":"hide"]()},_changeWait:function(){this.model.get("wait")?0===this.length()&&(this._messageShow(this.model.get("wait_text"),"info"),this.$options.hide(),this.$menu.hide()):0===this.length()?(this._messageShow(this.model.get("error_text"),"danger"),this.$options.hide(),this.$menu.hide()):(this.$message.hide(),this.$options.css("display","inline-block"),this.$menu.show())},_changeValue:function(){this._setValue(this.model.get("value")),null!==this._getValue()||this.model.get("multiple")||this.model.get("optional")||this._setValue(this.first()),this.all_button&&this.all_button.value(o.isArray(this._getValue())?this._getValue().length:0,this.length())},value:function(e){return void 0!==e&&this.model.set("value",e),this._getValue()},first:function(){var e=this.$("input").first();return e.length>0?e.val():null},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},length:function(){return this.$(".ui-option").length},_setValue:function(e){var t=this;if(void 0!==e&&(this.$("input").prop("checked",!1),null!==e)){var i=o.isArray(e)?e:[e];r.each(i,function(e){t.$('input[value="'+e+'"]').first().prop("checked",!0)})}},_getValue:function(){var t=[];return this.$(":checked").each(function(){t.push(o(this).val())}),e.isEmpty(t)?null:this.model.get("multiple")?t:t[0]},_messageShow:function(e,t){this.$message.show().removeClass().addClass("ui-message alert alert-"+t).html(e)},_template:function(){return o("").addClass("ui-options-list")}}),n=i.extend({_templateOption:function(t){var i=e.uid();return o("").addClass("ui-option").append(o("").attr({id:i,type:this.model.get("type"),name:this.model.id,value:t.value})).append(o("").addClass("ui-options-label").attr("for",i).html(t.label))}}),s={};s.View=n.extend({initialize:function(e){e.type="radio",n.prototype.initialize.call(this,e)}});var l={};l.View=n.extend({initialize:function(e){e.type="checkbox",e.multiple=!0,n.prototype.initialize.call(this,e)}});var d={};return d.View=i.extend({initialize:function(e){i.prototype.initialize.call(this,e)},_setValue:function(e){void 0!==e&&(this.$("input").prop("checked",!1),this.$("label").removeClass("active"),this.$('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active"))},_templateOption:function(e){var t=o("").addClass("btn btn-default");return e.icon&&t.append(o("").addClass("fa").addClass(e.icon).addClass(!e.label&&"no-padding")),t.append(o("").attr({type:"radio",name:this.model.id,value:e.value})),e.label&&t.append(e.label),t},_template:function(){return o("").addClass("btn-group ui-radiobutton").attr("data-toggle","buttons")}}),{Base:i,BaseIcons:n,Radio:s,RadioButton:d,Checkbox:l}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(3))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(11)],s=function(e,t){var i=a.View.extend({initialize:function(t){var i=this;this.data=[],this.data2=[],this.model=t&&t.model||new a.Model({id:e.uid(),cls:"ui-select",error_text:"No options available",empty_text:"Nothing selected",visible:!0,wait:!1,multiple:!1,searchable:!0,optional:!1,disabled:!1,onchange:function(){},value:null,individual:!1,pagesize:20}).set(t),this.on("change",function(){i.model.get("onchange")&&i.model.get("onchange")(i.value())}),this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:disabled",this._changeDisabled,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:visible",this._changeVisible,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:multiple change:searchable change:cls change:id",this.render,this),this.render()},render:function(){var e=this;this.model.get("searchable")?this._renderSearchable():this._renderClassic(),this.$el.addClass(this.model.get("cls")).attr("id",this.model.get("id")),this.$select.empty().addClass("select").attr("id",this.model.get("id")+"_select").prop("multiple",this.model.get("multiple")).on("change",function(){e.value(e._getValue()),e.trigger("change")}),this._changeData(),this._changeWait(),this._changeVisible(),this._changeDisabled()},_renderClassic:function(){var e=this;this.$el.addClass(this.model.get("multiple")?"ui-select-multiple":"ui-select").append(this.$select=o("")).append(this.$dropdown=o("")).append(this.$resize=o("").append(this.$resize_icon=o(""))),this.model.get("multiple")?(this.$dropdown.hide(),this.$resize_icon.addClass("fa fa-angle-double-right fa-rotate-45").show(),this.$resize.removeClass().addClass("icon-resize").show().off("mousedown").on("mousedown",function(t){var i=t.pageY,n=e.$select.height();e.minHeight=e.minHeight||n,o("#dd-helper").show().on("mousemove",function(t){e.$select.height(Math.max(n+(t.pageY-i),e.minHeight))}).on("mouseup mouseleave",function(){o("#dd-helper").hide().off()})})):(this.$dropdown.show(),this.$resize.hide(),this.$resize_icon.hide())},_renderSearchable:function(){var e=this;this.$el.append(this.$select=o("")).append(this.$dropdown=o("")),this.$dropdown.hide(),this.model.get("multiple")||this.$dropdown.show().on("click",function(){e.$select.select2&&e.$select.select2("open")}),this.all_button=null,this.model.get("multiple")&&!this.model.get("individual")&&(this.all_button=new t.ButtonCheck({onclick:function(){var t=[];0!==e.all_button.value()&&r.each(e.model.get("data"),function(e){t.push(e.value)}),e.value(t),e.trigger("change")}}),this.$el.prepend(this.all_button.$el))},_match:function(e,t){return!e||""==e||String(t).toUpperCase().indexOf(e.toUpperCase())>=0},_changeData:function(){var e=this;this.data=[],!this.model.get("multiple")&&this.model.get("optional")&&this.data.push({value:"__null__",label:e.model.get("empty_text")}),r.each(this.model.get("data"),function(t){e.data.push(t)}),0==this.length()&&this.data.push({value:"__null__",label:this.model.get("error_text")}),this.model.get("searchable")?(this.data2=[],r.each(this.data,function(t,i){e.data2.push({order:i,id:t.value,text:t.label,tags:t.tags})}),this.$select.data("select2")&&this.$select.select2("destroy"),this.matched_tags={},this.$select.select2({data:e.data2,closeOnSelect:!this.model.get("multiple"),multiple:this.model.get("multiple"),query:function(t){e.matched_tags={};var i=e.model.get("pagesize"),n=r.filter(e.data2,function(i){var n=!1;return r.each(i.tags,function(i){e._match(t.term,i)&&(n=e.matched_tags[i]=!0)}),n||e._match(t.term,i.text)});t.callback({results:n.slice((t.page-1)*i,t.page*i),more:n.length>=t.page*i})},formatResult:function(t){return r.escape(t.text)+'"}}),this.$(".select2-container 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null!==this._getValue()||this.model.get("optional")||this._setValue(this.first())},value:function(e){return void 0!==e&&this.model.set("value",e),this._getValue()},first:function(){return this.data.length>0?this.data[0].value:null},exists:function(e){return r.findWhere(this.data,{value:e})},text:function(){var e=this._getValue(),t=this.exists(o.isArray(e)?e[0]:e);return t?t.label:""},show:function(){this.model.set("visible",!0)},hide:function(){this.model.set("visible",!1)},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},disabled:function(){return this.model.get("disabled")},enable:function(){this.model.set("disabled",!1)},disable:function(){this.model.set("disabled",!0)},add:function(e,t){r.each(this.model.get("data"),function(t){t.keep&&!r.findWhere(e,{value:t.value})&&e.push(t)}),t&&e&&e.sort(t),this.model.set("data",e)},update:function(e){this.model.set("data",e)},setOnChange:function(e){this.model.set("onchange",e)},length:function(){return o.isArray(this.model.get("data"))?this.model.get("data").length:0},_setValue:function(e){var t=this;if(null!==e&&void 0!==e||(e="__null__"),this.model.get("multiple")?e=o.isArray(e)?e:[e]:o.isArray(e)&&(e=e.length>0?e[0]:"__null__"),this.model.get("searchable")){if(o.isArray(e)){var i=[];r.each(e,function(e){var n=r.findWhere(t.data2,{id:e});n&&i.push(n)}),e=i}else{var n=r.findWhere(this.data2,{id:e});e=n}this.$select.select2("data",e)}else this.$select.val(e)},_getValue:function(){var t=null;if(this.model.get("searchable")){var i=this.$select.select2("data");i&&(o.isArray(i)?(t=[],i.sort(function(e,t){return e.order-t.order}),r.each(i,function(e){t.push(e.id)})):t=i.id)}else t=this.$select.val();return e.isEmpty(t)?null:t}});return{View:i}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(3))},function(e,t,i){var n,s;(function(a,o,r){n=[i(8),i(48),i(20)],s=function(e,t,i){var n=a.Model.extend({}),s=a.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this.get("metadata")||this._set_metadata(),this.on("change",this._set_metadata,this)},_set_metadata:function(){var e=new n;o.each(o.keys(this.attributes),function(t){if(0===t.indexOf("metadata_")){var i=t.split("metadata_")[1];e.set(i,this.attributes[t]),delete this.attributes[t]}},this),this.set("metadata",e,{silent:!0})},get_metadata:function(e){return this.attributes.metadata.get(e)},urlRoot:Galaxy.root+"api/datasets"}),l=s.extend({defaults:o.extend({},s.prototype.defaults,{chunk_url:null,first_data_chunk:null,offset:0,at_eof:!1}),initialize:function(e){s.prototype.initialize.call(this),this.attributes.first_data_chunk&&(this.attributes.offset=this.attributes.first_data_chunk.offset),this.attributes.chunk_url=Galaxy.root+"dataset/display?dataset_id="+this.id,this.attributes.url_viz=Galaxy.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof)return null;var e=this,t=r.Deferred();return r.getJSON(this.attributes.chunk_url,{offset:e.attributes.offset}).success(function(i){var n;""!==i.ck_data?(n=i,e.attributes.offset=i.offset):(e.attributes.at_eof=!0,n=null),t.resolve(n)}),t}}),d=a.Collection.extend({model:s}),c=a.View.extend({initialize:function(e){this.row_count=0,this.loading_chunk=!1,new p({model:e.model,$el:this.$el})},expand_to_container:function(){this.$el.height()"}});return{View:t}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1))},function(e,t,i){var n,s,a;!function(o){s=[i(1)],n=o,a="function"==typeof n?n.apply(t,s):n,!(void 0!==a&&(e.exports=a))}(function(e){"use_strict";var t=e;t.fn.make_text_editable=function(e){var i="num_cols"in e?e.num_cols:30,n="num_rows"in e?e.num_rows:4,s="use_textarea"in e&&e.use_textarea,a="on_finish"in e?e.on_finish:null,o="help_text"in e?e.help_text:null,r=t(this);return r.addClass("editable-text").click(function(o){if(!(t(this).children(":input").length>0)){r.removeClass("editable-text");var l,d,c=function(e){r.find(":input").remove(),""!==e?r.text(e):r.html("
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n;(function(s,a){n=function(){function e(e){e+="";for(var t=/(\d+)(\d{3})/;t.test(e);)e=e.replace(t,"$1,$2");return e}var t=function(e){return"promise"in e},i=s.Model.extend({defaults:{ajax_settings:{},interval:1e3,success_fn:function(e){return!0}},go:function(){var e=a.Deferred(),t=this,i=t.get("ajax_settings"),n=t.get("success_fn"),s=t.get("interval"),o=function(){a.ajax(i).success(function(t){n(t)?e.resolve(t):setTimeout(o,s)})};return o(),e}}),n=function(e){e||(e="#ffffff"),"string"==typeof e&&(e=[e]);for(var t=0;t>16,s=(65280&i)>>8,a=255&i,c=p(n,s,a),g=!0,t=0;t>16,l=(65280&o)>>8,d=255&o,h=p(r,l,d),u=f(n,s,a,r,l,d),Math.abs(c-h)<40||u<200){g=!1;break}m++}while(!g&&m<=10);return"#"+(16777216+i).toString(16).substr(1,6)};return{commatize:e,is_deferred:t,ServerStateDeferred:i,get_random_color:n}}.call(t,i,t,e),!(void 0!==n&&(e.exports=n))}).call(t,i(2),i(1))},function(e,t,i){var n,s;(function(a,o){n=[i(56),i(7),i(6)],s=function(e,t,i){e=e||window.BibtexParser;var n="citation",s=a.Model.extend(t.LoggableMixin).extend({_logNamespace:n,defaults:{content:""},initialize:function(){var t;try{t=e(this.attributes.content)}catch(e){return}if(t.errors.length){var i=t.errors.reduce(function(e,t){return e+"; "+t});this.log("Error parsing bibtex: "+i)}if(this._fields={},this.entry=o.first(t.entries),this.entry){var n=this.entry.Fields;for(var s in n){var a=n[s],r=s.toLowerCase();this._fields[r]=a}}},entryType:function(){return this.entry?this.entry.EntryType:void 0},fields:function(){return this._fields}}),r=a.Collection.extend(t.LoggableMixin).extend({_logNamespace:n,urlRoot:Galaxy.root+"api",partial:!0,model:s}),l=r.extend({url:function(){return this.urlRoot+"/histories/"+this.history_id+"/citations"}}),d=r.extend({url:function(){return this.urlRoot+"/tools/"+this.tool_id+"/citations"},partial:!1});return{Citation:s,HistoryCitationCollection:l,ToolCitationCollection:d}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(3))},function(e,t,i){var n,s;(function(i,a,o){n=[],s=function(){return i.View.extend({initialize:function(e,t){this.app=e,this.app_options=e.model?e.model.attributes:{},this.field=t&&t.field||new i.View,this.model=t&&t.model||new i.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(t),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var n=this.model.get("collapsible_value");this.field.collapsed=void 0!==n&&JSON.stringify(this.model.get("value"))==JSON.stringify(n),this.listenTo(this.model,"change",this.render,this),this.render();var s=this;this.$collapsible.on("click",function(){s.field.collapsed=!s.field.collapsed,e.trigger&&e.trigger("change"),s.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){s.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(e){this.model.set("error_text",e)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){a(".tooltip").hide();var e=this.model.get("help",""),t=this.model.get("argument");t&&e.indexOf("("+t+")")==-1&&(e+=" ("+t+")"),this.$info.html(e),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(o.escape(this.model.get("text_value")));var i=this.model.get("error_text");if(this.$error[i?"show":"hide"](),this.$el[i?"addClass":"removeClass"]("ui-error"),this.$error_text.html(i),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var n=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+n)).attr("data-original-title",this.model.get("text_"+n)).tooltip({placement:"bottom"})}},_template:function(){return a("").addClass("ui-form-element").append(a("").addClass("ui-form-error ui-error").append(a("").addClass("fa fa-arrow-down")).append(a("").addClass("ui-form-error-text"))).append(a("").addClass("ui-form-title").append(a("").addClass("ui-form-collapsible").append(a("").addClass("ui-form-collapsible-icon")).append(a("").addClass("ui-form-collapsible-text"))).append(a("").addClass("ui-form-title-text"))).append(a("").addClass("ui-form-field").append(a("").addClass("ui-form-info")).append(a("").addClass("ui-form-backdrop"))).append(a("").addClass("ui-form-preview"))}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(3))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(5),i(38),i(41),i(39),i(40),i(36)],s=function(e,t,i,n,s,l,d){return a.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider",float:"_fieldSlider",boolean:"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(e){var t=this.types[e.type],i="function"==typeof this[t]?this[t].call(this,e):null;return i||(i=e.options?this._fieldSelect(e):this._fieldText(e),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+e.type+").")),void 0===e.value&&(e.value=null),i.value(e.value),i},_fieldData:function(e){return new i.View({id:"field-"+e.id,extensions:e.extensions,optional:e.optional,multiple:e.multiple,type:e.type,flavor:e.flavor,data:e.options,onchange:e.onchange})},_fieldSelect:function(e){if(e.is_workflow)return this._fieldText(e);"data_column"==e.type&&(e.error_text="Missing columns in referenced dataset.");var i=e.data;i||(i=[],o.each(e.options,function(e){i.push({label:e[0],value:e[1]})}));var n=t.Select;switch(e.display){case"checkboxes":n=t.Checkbox;break;case"radio":n=t.Radio;break;case"radiobutton":n=t.RadioButton}return new n.View({id:"field-"+e.id,data:i,error_text:e.error_text||"No options available",multiple:e.multiple,optional:e.optional,onchange:e.onchange,individual:e.individual,searchable:"workflow"!==e.flavor})},_fieldDrilldown:function(e){return e.is_workflow?this._fieldText(e):new t.Drilldown.View({id:"field-"+e.id,data:e.options,display:e.display,optional:e.optional,onchange:e.onchange})},_fieldText:function(i){if(i.options&&i.data)if(i.area=i.multiple,e.isEmpty(i.value))i.value=null;else if(r.isArray(i.value)){var n="";for(var s in i.value){if(n+=String(i.value[s]),!i.multiple)break;n+="\n"}i.value=n}return new t.Input({id:"field-"+i.id,type:i.type,area:i.area,readonly:i.readonly,placeholder:i.placeholder,datalist:i.datalist,onchange:i.onchange})},_fieldSlider:function(e){return new t.Slider.View({id:"field-"+e.id,precise:"float"==e.type,is_workflow:e.is_workflow,min:e.min,max:e.max,onchange:e.onchange})},_fieldHidden:function(e){return new t.Hidden({id:"field-"+e.id,info:e.info})},_fieldBoolean:function(e){return new t.RadioButton.View({id:"field-"+e.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:e.onchange})},_fieldColor:function(e){return new d({id:"field-"+e.id,onchange:e.onchange})},_fieldLibrary:function(e){return new n.View({id:"field-"+e.id,optional:e.optional,multiple:e.multiple,onchange:e.onchange})},_fieldFtp:function(e){return new s.View({id:"field-"+e.id,optional:e.optional,multiple:e.multiple,onchange:e.onchange})},_fieldGenomeSpace:function(e){var t=this;return new l.View({id:"field-"+e.id,onchange:function(){t.app.trigger("change")}})},_fieldUpload:function(e){return new t.Upload({id:"field-"+e.id,onchange:e.onchange})}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(3),i(1))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(9),i(5)],s=function(e,t,i){var n=a.View.extend({initialize:function(t){this.list={},this.options=e.merge(t,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new i.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float 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id.")},delAll:function(){for(var e in this.list)this.del(e)},hideOptions:function(){this.button_new.$el.hide(),r.each(this.list,function(e){e.hideOperation("button_delete")}),r.isEmpty(this.list)&&this.$el.append(o("").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var e=0;for(var t in this.list){var i=this.list[t];i.title(++e+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});return{View:n}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(3))},function(e,t,i){var n,s;(function(a,o,r,l){n=[i(4),i(5),i(9),i(31),i(29),i(30)],s=function(e,t,i,n,s,d){var c=a.View.extend({initialize:function(e,t){this.app=e,this.inputs=t.inputs,this.parameters=new d,this.setElement(o("")),this.render()},render:function(){var e=this;this.$el.empty(),r.each(this.inputs,function(t){e.add(t)})},add:function(t){var i=l.extend(!0,{},t);switch(i.id=t.id=e.uid(),this.app.input_list[i.id]=i,i.type){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(e){var t=this;e.test_param.id=e.id,this.app.model.get("sustain_conditionals")&&(e.test_param.disabled=!0);var i=this._addRow(e.test_param);i.model&&i.model.set("onchange",function(i){var n=t.app.data.matchCase(e,i);for(var s in e.cases){var a=e.cases[s],o=t.$("#"+e.id+"-section-"+s),r=!1;for(var l in a.inputs)if(!a.inputs[l].hidden){r=!0;break}s==n&&r?o.fadeIn("fast"):o.hide()}t.app.trigger("change")});for(var n in e.cases){var s=new c(this.app,{inputs:e.cases[n].inputs});this._append(s.$el.addClass("ui-form-section"),e.id+"-section-"+n)}i.trigger("change")},_addRepeat:function(e){function t(t){var n=e.id+"-section-"+a++,s=new c(i.app,{inputs:t});o.add({id:n,$el:s.$el,ondel:function(){o.del(n),i.app.trigger("change")}})}for(var i=this,a=0,o=new n.View({title:e.title||"Repeat",min:e.min,max:e.max,onnew:function(){t(e.inputs),i.app.trigger("change")}}),l=r.size(e.cache),d=0;d
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","");e.append(E.tool_link(this.model.toJSON()));var t=this.model.get("form_style",null);if("upload1"===this.model.id)e.find("a").on("click",function(e){e.preventDefault(),Galaxy.upload.show()});else if("regular"===t){var i=this;e.find("a").on("click",function(e){e.preventDefault(),Galaxy.router.push("/",{tool_id:i.model.id,version:i.model.get("version")})})}return this.$el.append(e),this}}),b=y.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append(o("").text(this.model.attributes.text)),this}}),x=y.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){y.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(E.panel_section(this.model.toJSON()));var t=this.$el.find(".toolSectionBody");return e.each(this.model.attributes.elems,function(e){if(e instanceof p){var i=new w({model:e,className:"toolTitle"});i.render(),t.append(i.$el)}else if(e instanceof g){var n=new b({model:e});n.render(),t.append(n.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),C=a.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","change :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(E.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),o("#messagebox").is(":visible")&&this.$el.css("top","95px"),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(e){return this.model.attributes.clear_key&&this.model.attributes.clear_key===e.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),$=a.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var e=this,t=new C({model:this.model.get("tool_search")});return t.render(),e.$el.append(t.$el),this.model.get("layout").each(function(t){if(t instanceof m){var i=new x({model:t});i.render(),e.$el.append(i.$el)}else if(t instanceof p){var n=new w({model:t,className:"toolTitleNoSection"});n.render(),e.$el.append(n.$el)}else if(t instanceof g){var s=new b({model:t});s.render(),e.$el.append(s.$el)}}),e.$el.find("a.tool-link").click(function(t){var i=o(this).attr("class").split(/\s+/)[0],n=e.model.get("tools").get(i);e.trigger("tool_link_click",t,n)}),this},handle_search_results:function(){var e=this.model.get("tool_search").get("results");e&&0===e.length?o("#search-no-results").show():o("#search-no-results").hide()}}),k=a.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(E.tool_form(this.model.toJSON()))}}),E=(a.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new $({collection:this.collection}),this.tool_form_view=new k},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var e=this;this.tool_panel_view.on("tool_link_click",function(t,i){t.preventDefault(),e.show_tool(i)})},show_tool:function(e){var t=this;e.fetch().done(function(){t.tool_form_view.model=e,t.tool_form_view.render(),t.tool_form_view.$el.show(),o("#left").width("650px")})}}),{tool_search:e.template(['',' ',''].join("")),panel_section:e.template(['
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'+e.info_text+"
"),t},grid_table:function(e){return''},grid_header:function(e){var t='';if(e.embedded||(t+="
"},header:function(e){var t=""+e.title+"
"),e.global_actions){t+='- ';var i=e.global_actions.length>=3;i&&(t+='
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Separate jobs will be triggered for each dataset selection."));this.$batch={linked:n.clone(),enabled:n.clone().append(o("").append(o("").addClass("ui-form-title").html("Batch options:")).append(this.button_product.$el)).append(o("").css("clear","both"))},this.$el.on("dragenter",function(e){this.lastenter=e.target,i.$el.addClass("ui-dragover")}).on("dragover",function(e){e.preventDefault()}).on("dragleave",function(e){this.lastenter===e.target&&i.$el.removeClass("ui-dragover")}).on("drop",function(e){i._handleDrop(e)}),this.history={},this.listenTo(this.model,"change:data",this._changeData,this),this.listenTo(this.model,"change:wait",this._changeWait,this),this.listenTo(this.model,"change:current",this._changeCurrent,this),this.listenTo(this.model,"change:value",this._changeValue,this),this.listenTo(this.model,"change:type change:optional change:multiple change:extensions",this._changeType,this),this.render(),this.on("change",function(){e.onchange&&e.onchange(i.value())})},render:function(){this._changeType(),this._changeValue(),this._changeWait()},wait:function(){this.model.set("wait",!0)},unwait:function(){this.model.set("wait",!1)},update:function(e){this.model.set("data",e)},value:function(e){void 0!==e&&this.model.set("value",e);var t=this.model.get("current");if(this.config[t]){var i=this.fields[t].value();if(null!==i&&(i=o.isArray(i)?i:[i],i.length>0)){var n=this._batch({values:[]});for(var s in i){var a=this.history[i[s]+"_"+this.config[t].src];if(!a)return Galaxy.emit.debug("ui-select-content::value()","Requested details not found for '"+i[s]+"'."),null;n.values.push(a)}return n.values.sort(function(e,t){return e.hid-t.hid}),n}}else Galaxy.emit.debug("ui-select-content::value()","Invalid value/source '"+e+"'.");return null},_changeCurrent:function(){var e=this;r.each(this.fields,function(t,i){e.model.get("current")==i?(t.$el.show(),r.each(e.$batch,function(t,n){t[e.config[i].batch==n?"show":"hide"]()}),e.button_type.value(i)):t.$el.hide()})},_changeType:function(){var n=this,a=(this.model.get("flavor")?this.model.get("flavor")+"_":"")+String(this.model.get("type"))+(this.model.get("multiple")?"_multiple":"");s[a]?this.config=s[a]:(this.config=s.data,Galaxy.emit.debug("ui-select-content::_changeType()","Invalid configuration/type id '"+a+"'."));var o=n.model.get("data"),l=e.textify(this.model.get("extensions")),d=this.model.get("src_labels");this.fields=[],this.button_data=[],r.each(this.config,function(e,t){n.button_data.push({value:t,icon:e.icon,tooltip:e.tooltip}),n.fields.push(new i.View({optional:n.model.get("optional"),multiple:e.multiple,searchable:!e.multiple||o&&o[e.src]&&o[e.src].length>n.model.get("pagelimit"),individual:!0,error_text:"No "+(l?l+" ":"")+(d[e.src]||"content")+" available.",onchange:function(){n.trigger("change")}}))}),this.button_type=new t.RadioButton.View({value:this.model.get("current"),data:this.button_data,onchange:function(e){n.model.set("current",e),n.trigger("change")}}),this.$el.empty();var c=0;this.fields.length>1&&(this.$el.append(this.button_type.$el),c=Math.max(0,36*this.fields.length)+"px"),r.each(this.fields,function(e){n.$el.append(e.$el.css({"margin-left":c}))}),r.each(this.$batch,function(e,t){n.$el.append(e.css({"margin-left":c}))}),this.model.set("current",0),this._changeCurrent(),this._changeData()},_changeWait:function(){var e=this;r.each(this.fields,function(t){t[e.model.get("wait")?"wait":"unwait"]()})},_changeData:function(){var e=this.model.get("data"),t=this,i={};r.each(e,function(e,n){i[n]=[],r.each(e,function(e){i[n].push({hid:e.hid,keep:e.keep,label:e.hid+": "+e.name,value:e.id,tags:e.tags}),t.history[e.id+"_"+n]=e})}),r.each(this.config,function(e,n){i[e.src]&&t.fields[n].add(i[e.src],function(e,t){return t.hid-e.hid})})},_changeValue:function(){var e=this.model.get("value");if(e&&e.values&&e.values.length>0){var t=[];r.each(e.values,function(e){t.push(e.id)});for(var i=e.values[0].src,n=e.values.length>1,s=0;s
Token
Select Library
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n="citation",s=a.Model.extend(t.LoggableMixin).extend({_logNamespace:n,defaults:{content:""},initialize:function(){var t;try{t=e(this.attributes.content)}catch(i){return}if(t.errors.length){var n=t.errors.reduce(function(e,t){return e+"; "+t});this.log("Error parsing bibtex: "+n)}if(this._fields={},this.entry=o.first(t.entries),this.entry){var s=this.entry.Fields;for(var a in s){var r=s[a],l=a.toLowerCase();this._fields[l]=r}}},entryType:function(){return this.entry?this.entry.EntryType:void 0},fields:function(){return this._fields}}),r=a.Collection.extend(t.LoggableMixin).extend({_logNamespace:n,urlRoot:Galaxy.root+"api",partial:!0,model:s}),l=r.extend({url:function(){return this.urlRoot+"/histories/"+this.history_id+"/citations"}}),d=r.extend({url:function(){return this.urlRoot+"/tools/"+this.tool_id+"/citations"},partial:!1});return{Citation:s,HistoryCitationCollection:l,ToolCitationCollection:d}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(3))},function(e,t,i){var n,s;(function(i,a,o){n=[],s=function(){return i.View.extend({initialize:function(e,t){this.app=e,this.app_options=e.model?e.model.attributes:{},this.field=t&&t.field||new i.View,this.model=t&&t.model||new i.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up",always_refresh:this.app_options.always_refresh}).set(t),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var n=this.model.get("collapsible_value");this.field.collapsed=void 0!==n&&JSON.stringify(this.model.get("value"))==JSON.stringify(n),this.listenTo(this.model,"change",this.render,this),this.render();var s=this;this.$collapsible.on("click",function(){s.field.collapsed=!s.field.collapsed,e.trigger&&e.trigger("change"),s.render()}),this.field.model&&!this.model.get("always_refresh")&&this.listenTo(this.field.model,"change:value",function(){s.reset()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(e){this.model.set("error_text",e)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){a(".tooltip").hide();var e=this.model.get("help",""),t=this.model.get("argument");t&&e.indexOf("("+t+")")==-1&&(e+=" ("+t+")"),this.$info.html(e),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(o.escape(this.model.get("text_value")));var i=this.model.get("error_text");if(this.$error[i?"show":"hide"](),this.$el[i?"addClass":"removeClass"]("ui-error"),this.$error_text.html(i),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var n=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+n)).attr("data-original-title",this.model.get("text_"+n)).tooltip({placement:"bottom"})}},_template:function(){return a("").addClass("ui-form-element").append(a("").addClass("ui-form-error ui-error").append(a("").addClass("fa fa-arrow-down")).append(a("").addClass("ui-form-error-text"))).append(a("").addClass("ui-form-title").append(a("").addClass("ui-form-collapsible").append(a("").addClass("ui-form-collapsible-icon")).append(a("").addClass("ui-form-collapsible-text"))).append(a("").addClass("ui-form-title-text"))).append(a("").addClass("ui-form-field").append(a("").addClass("ui-form-info")).append(a("").addClass("ui-form-backdrop"))).append(a("").addClass("ui-form-preview"))}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(3))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(5),i(38),i(41),i(39),i(40),i(36)],s=function(e,t,i,n,s,l,d){return a.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(e){var t=this.types[e.type],i="function"==typeof this[t]?this[t].call(this,e):null;return i||(i=e.options?this._fieldSelect(e):this._fieldText(e),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+e.type+").")),void 0===e.value&&(e.value=null),i.value(e.value),i},_fieldData:function(e){return new i.View({id:"field-"+e.id,extensions:e.extensions,optional:e.optional,multiple:e.multiple,type:e.type,flavor:e.flavor,data:e.options,onchange:e.onchange})},_fieldSelect:function(e){if(e.is_workflow)return this._fieldText(e);"data_column"==e.type&&(e.error_text="Missing columns in referenced dataset.");var i=e.data;i||(i=[],o.each(e.options,function(e){i.push({label:e[0],value:e[1]})}));var n=t.Select;switch(e.display){case"checkboxes":n=t.Checkbox;break;case"radio":n=t.Radio;break;case"radiobutton":n=t.RadioButton}return new n.View({id:"field-"+e.id,data:i,error_text:e.error_text||"No options available",multiple:e.multiple,optional:e.optional,onchange:e.onchange,individual:e.individual,searchable:"workflow"!==e.flavor})},_fieldDrilldown:function(e){return e.is_workflow?this._fieldText(e):new t.Drilldown.View({id:"field-"+e.id,data:e.options,display:e.display,optional:e.optional,onchange:e.onchange})},_fieldText:function(i){if(i.options&&i.data)if(i.area=i.multiple,e.isEmpty(i.value))i.value=null;else if(r.isArray(i.value)){var n="";for(var s in i.value){if(n+=String(i.value[s]),!i.multiple)break;n+="\n"}i.value=n}return new t.Input({id:"field-"+i.id,type:i.type,area:i.area,readonly:i.readonly,placeholder:i.placeholder,datalist:i.datalist,onchange:i.onchange})},_fieldSlider:function(e){return new t.Slider.View({id:"field-"+e.id,precise:"float"==e.type,is_workflow:e.is_workflow,min:e.min,max:e.max,onchange:e.onchange})},_fieldHidden:function(e){return new t.Hidden({id:"field-"+e.id,info:e.info})},_fieldBoolean:function(e){return new t.RadioButton.View({id:"field-"+e.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:e.onchange})},_fieldColor:function(e){return new d({id:"field-"+e.id,onchange:e.onchange})},_fieldLibrary:function(e){return new n.View({id:"field-"+e.id,optional:e.optional,multiple:e.multiple,onchange:e.onchange})},_fieldFtp:function(e){return new s.View({id:"field-"+e.id,optional:e.optional,multiple:e.multiple,onchange:e.onchange})},_fieldGenomeSpace:function(e){var t=this;return new l.View({id:"field-"+e.id,onchange:function(){t.app.trigger("change")}})},_fieldUpload:function(e){return new t.Upload({id:"field-"+e.id,onchange:e.onchange})}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(3),i(1))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(9),i(5)],s=function(e,t,i){var n=a.View.extend({initialize:function(t){this.list={},this.options=e.merge(t,{title:"Repeat",empty_text:"Not available.",max:null,min:null}),this.button_new=new i.ButtonIcon({icon:"fa-plus",title:"Insert "+this.options.title,tooltip:"Add new "+this.options.title+" block",cls:"ui-button-icon ui-clear-float 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i=l.extend(!0,{},t);switch(i.id=t.id=e.uid(),this.app.input_list[i.id]=i,i.type){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(e){var t=this;e.test_param.id=e.id,this.app.model.get("sustain_conditionals")&&(e.test_param.disabled=!0);var i=this._addRow(e.test_param);i.model&&i.model.set("onchange",function(i){var n=t.app.data.matchCase(e,i);for(var s in e.cases){var a=e.cases[s],o=t.$("#"+e.id+"-section-"+s),r=!1;for(var l in a.inputs)if(!a.inputs[l].hidden){r=!0;break}s==n&&r?o.fadeIn("fast"):o.hide()}t.app.trigger("change")});for(var n in e.cases){var s=new c(this.app,{inputs:e.cases[n].inputs});this._append(s.$el.addClass("ui-form-section"),e.id+"-section-"+n)}i.trigger("change")},_addRepeat:function(e){function t(t){var n=e.id+"-section-"+a++,s=new c(i.app,{inputs:t});o.add({id:n,$el:s.$el,ondel:function(){o.del(n),i.app.trigger("change")}})}for(var i=this,a=0,o=new n.View({title:e.title||"Repeat",min:e.min,max:e.max,onnew:function(){t(e.inputs),i.app.trigger("change")}}),l=r.size(e.cache),d=0;d
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e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):r.when()},toString:function(){var e=this.model?this.model+"":"(no model)";return"DatasetDCEListItemView("+e+")"}});h.prototype.templates=function(){var e=i.wrapTemplate(['"],"element");return a.extend({},t.DatasetListItemView.prototype.templates,{titleBar:e})}();var u=d.extend({className:d.prototype.className+" dataset-collection-element",_swapNewRender:function(e){d.prototype._swapNewRender.call(this,e);var t=this.model.get("state")||"ok";return this.$el.addClass("state-"+t),this.$el},toString:function(){var e=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+e+")"}});return{DCListItemView:d,DCEListItemView:c,DatasetDCEListItemView:h,NestedDCDCEListItemView:u}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(1))},function(e,t,i){var n,s;(function(a,o,r){n=[i(85),i(7),i(6)],s=function(e,t,i){"use strict";var n={defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(e){return a.extend(e,e.object,{element_id:e.id}),delete e.object,e},constructor:function(e,t){e=this._mergeObject(e),this.idAttribute="element_id",o.Model.apply(this,arguments)},parse:function(e,t){var i=e;return i=this._mergeObject(i)}},s=o.Model.extend(t.LoggableMixin).extend(n).extend({_logNamespace:"collections"}),l=o.Collection.extend(t.LoggableMixin).extend({_logNamespace:"collections",model:s,toString:function(){return["DatasetCollectionElementCollection(",this.length,")"].join("")}}),d=e.DatasetAssociation.extend(t.mixin(n,{url:function(){return this.has("history_id")?Galaxy.root+"api/histories/"+this.get("history_id")+"/contents/"+this.get("id"):(console.warn("no endpoint for non-hdas within a collection 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e=this.get("element_identifier");return["DatasetDCE(",e,")"].join("")}})),c=l.extend({model:d,toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),h=o.Model.extend(t.LoggableMixin).extend(t.SearchableModelMixin).extend({_logNamespace:"collections",defaults:{collection_type:null,deleted:!1},collectionClass:l,initialize:function(e,t){this.debug(this+"(DatasetCollection).initialize:",e,t,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){this.debug(this+"._createElementsModel",this.collectionClass,this.get("elements"),this.elements);var e=this.get("elements")||[];this.unset("elements",{silent:!0});var t=this;return a.each(e,function(e,i){a.extend(e,{parent_hdca_id:t.get("id")})}),this.elements=new this.collectionClass(e),this.elements},toJSON:function(){var e=o.Model.prototype.toJSON.call(this);return this.elements&&(e.elements=this.elements.toJSON()),e},inReadyState:function(){var e=this.get("populated");return this.isDeletedOrPurged()||e},hasDetails:function(){return 0!==this.elements.length},getVisibleContents:function(e){return this.elements},parse:function(e,t){var i=o.Model.prototype.parse.call(this,e,t);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},delete:function(e){return this.get("deleted")?r.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},e)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name","tags"],toString:function(){var e=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+e.join(",")+")"}}),u=h.extend({collectionClass:c,toString:function(){return"List"+h.prototype.toString.call(this)}}),p=u.extend({toString:function(){return"Pair"+h.prototype.toString.call(this)}}),f=h.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",e,")"].join("")}})),g=l.extend({model:f,toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),m=p.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedPairDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",e,")"].join("")}})),v=g.extend({model:m,toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),_=h.extend({collectionClass:v,toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}}),y=u.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedListDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedListDCDCE(",e,")"].join("")}})),w=g.extend({model:y,toString:function(){return["NestedListDCDCECollection(",this.length,")"].join("")}}),b=h.extend({collectionClass:w,toString:function(){return["ListOfListsDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:u,PairDatasetCollection:p,ListPairedDatasetCollection:_,ListOfListsDatasetCollection:b}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1))},function(e,t,i){var n,s;(function(a,o,r,l){n=[i(63),i(17),i(7),i(82),i(8),i(100),i(6),i(97)],s=function(e,t,i,n,s,d,c){"use strict";function h(e,t){var i=e.toJSON(),n=m(i,{defaultHideSourceItems:t,creationFn:function(t,i,n){return t=t.map(function(e){return{id:e.id,name:e.name,src:"dataset"===e.history_content_type?"hda":"hdca"}}),e.createHDCA(t,"list",i,n)}});return n}var u="collections",p=a.View.extend(i.LoggableMixin).extend({_logNamespace:u,tagName:"li",className:"collection-element",initialize:function(e){this.element=e.element||{},this.selected=e.selected||!1},render:function(){return this.$el.attr("data-element-id",this.element.id).attr("draggable",!0).html(this.template({element:this.element})),this.selected&&this.$el.addClass("selected"),this},template:o.template(['',"<%- element.name 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'],"dataset");var l={resubmitted:n.wrapTemplate(["<% if( model.resubmitted ){ %>",'","<% } %>"])},d=n.wrapTemplate(["<% _.each( apps, function( app ){ %>",'','<%- app.label %> ','',"<% _.each( app.links, function( link ){ %>",'',"<% print( _l( link.text ) ); %>"," ","<% }); %>","","
","<% }); %>"],"apps");return a.extend({},c.prototype.templates,{warnings:e,details:i,noAccess:o,summaries:r,detailMessages:l,displayApplications:d})}(),{DatasetListItemView:h}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2),i(1))},function(e,t,i){var n,s;(function(a,o){n=[i(10),i(5)],s=function(e,t){var i=a.View.extend({initialize:function(e){this.model=new a.Model(e),this.url=this.model.get("url"),this.redirect=this.model.get("redirect"),this.setElement(""),this.render()},render:function(){var i=this;o.ajax({url:Galaxy.root+this.url,type:"GET"}).done(function(n){var s=o.extend({},i.model.attributes,n),a=new e({title:s.title,message:s.message,status:s.status||"warning",icon:s.icon,inputs:s.inputs,buttons:{submit:new t.Button({tooltip:s.submit_tooltip,title:s.submit_title||"Save",icon:s.submit_icon||"fa-save",cls:"btn btn-primary ui-clear-float",onclick:function(){i._submit(a)}})}});i.$el.empty().append(a.$el)}).fail(function(e){i.$el.empty().append(new t.Message({message:"Failed to load resource "+i.url+".",status:"danger",persistent:!0}).$el)})},_submit:function(e){var t=this;o.ajax({url:Galaxy.root+t.url,data:JSON.stringify(e.data.create()),type:"PUT",contentType:"application/json"}).done(function(i){var n={message:i.message,status:"success",persistent:!1};t.redirect?window.location=Galaxy.root+t.redirect+"?"+o.param(n):(e.data.matchModel(i,function(t,i){e.field_list[i].value(t.value)}),t._showMessage(e,n))}).fail(function(i){t._showMessage(e,{message:i.responseJSON.err_msg,status:"danger",persistent:!1})})},_showMessage:function(e,t){var i=e.$el.parents().filter(function(){return["auto","scroll"].indexOf(o(this).css("overflow"))!=-1}).first();i.animate({scrollTop:0},500),e.message.update(t)}});return{View:i}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1))},function(e,t,i){var n,s;(function(a){n=[i(59),i(90),i(6)],s=function(e,t,i){"use strict";function n(e){return function(t,i){return this.isNew()&&(i=i||{},i.url=this.urlRoot+this.get("history_id")+"/contents",t=t||{},t.type="dataset_collection"),e.call(this,t,i)}}var s=t.HistoryContentMixin,o=e.ListDatasetCollection,r=e.PairDatasetCollection,l=e.ListPairedDatasetCollection,d=e.ListOfListsDatasetCollection,c=o.extend(s).extend({defaults:a.extend(a.clone(o.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list",model_class:"HistoryDatasetCollectionAssociation"}),save:n(o.prototype.save),toString:function(){return"History"+o.prototype.toString.call(this)}}),h=r.extend(s).extend({defaults:a.extend(a.clone(r.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"paired",model_class:"HistoryDatasetCollectionAssociation"}),save:n(r.prototype.save),toString:function(){return"History"+r.prototype.toString.call(this)}}),u=l.extend(s).extend({defaults:a.extend(a.clone(l.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:paired",model_class:"HistoryDatasetCollectionAssociation"}),save:n(l.prototype.save),toString:function(){return"History"+l.prototype.toString.call(this)}}),p=d.extend(s).extend({defaults:a.extend(a.clone(d.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:list",model_class:"HistoryDatasetCollectionAssociation"}),save:n(d.prototype.save),toString:function(){return["HistoryListOfListsDatasetCollection(",this.get("name"),")"].join("")}});return{HistoryListDatasetCollection:c,HistoryPairDatasetCollection:h,HistoryListPairedDatasetCollection:u,HistoryListOfListsDatasetCollection:p}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3))},function(e,t,i){var n,s;(function(a,o,r){n=[i(81),i(88),i(63),i(66),i(7),i(154)],s=function(e,t,i,n,s,l){"use strict";var d=e.PaginatedCollection,c=d.extend(s.LoggableMixin).extend({_logNamespace:"history",model:function(e,n){if("dataset"===e.history_content_type)return new t.HistoryDatasetAssociation(e,n);if("dataset_collection"===e.history_content_type){switch(e.collection_type){case"list":return new i.HistoryListDatasetCollection(e,n);case"paired":return new i.HistoryPairDatasetCollection(e,n);case"list:paired":return new i.HistoryListPairedDatasetCollection(e,n);case"list:list":return new i.HistoryListOfListsDatasetCollection(e,n)}var s="Unknown collection_type: "+e.collection_type;return console.warn(s,e),{validationError:s}}return{validationError:"Unknown history_content_type: "+e.history_content_type}},limitPerPage:500,limitPerProgressiveFetch:500,order:"hid",urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(e,t){t=t||{},d.prototype.initialize.call(this,e,t),this.history=t.history||null,this.setHistoryId(t.historyId||null),this.includeDeleted=t.includeDeleted||this.includeDeleted,this.includeHidden=t.includeHidden||this.includeHidden,this.model.prototype.idAttribute="type_id"},setHistoryId:function(e){this.historyId=e,this._setUpWebStorage()},_setUpWebStorage:function(e){if(this.historyId)return this.storage=new n.HistoryPrefs({id:n.HistoryPrefs.historyStorageKey(this.historyId)}),this.trigger("new-storage",this.storage,this),this.on({"include-deleted":function(e){this.storage.includeDeleted(e)},"include-hidden":function(e){this.storage.includeHidden(e)}}),this.includeDeleted=this.storage.includeDeleted()||!1,this.includeHidden=this.storage.includeHidden()||!1,this},comparators:a.extend(a.clone(d.prototype.comparators),{name:s.buildComparator("name",{ascending:!0}),"name-dsc":s.buildComparator("name",{ascending:!1}),hid:s.buildComparator("hid",{ascending:!1}),"hid-asc":s.buildComparator("hid",{ascending:!0})}),running:function(){return this.filter(function(e){return!e.inReadyState()})},runningAndActive:function(){return this.filter(function(e){return!e.inReadyState()&&e.get("visible")&&!e.get("deleted")})},getByHid:function(e){return this.findWhere({hid:e})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},hidden:function(){return this.filter(function(e){return e.hidden()})},deleted:function(){return this.filter(function(e){return e.get("deleted")})},visibleAndUndeleted:function(){return this.filter(function(e){return e.get("visible")&&!e.get("deleted")})},setIncludeDeleted:function(e,t){if(a.isBoolean(e)&&e!==this.includeDeleted){if(this.includeDeleted=e,a.result(t,"silent"))return;this.trigger("include-deleted",e,this)}},setIncludeHidden:function(e,t){if(a.isBoolean(e)&&e!==this.includeHidden){if(this.includeHidden=e,t=t||{},a.result(t,"silent"))return;this.trigger("include-hidden",e,this)}},fetch:function(e){if(e=e||{},this.historyId&&!e.details){var t=n.HistoryPrefs.get(this.historyId).toJSON();a.isEmpty(t.expandedIds)||(e.details=a.values(t.expandedIds).join(","))}return d.prototype.fetch.call(this,e)},_buildFetchData:function(e){return a.extend(d.prototype._buildFetchData.call(this,e),{v:"dev"})},_fetchParams:d.prototype._fetchParams.concat(["v","details"]),_buildFetchFilters:function(e){var t=d.prototype._buildFetchFilters.call(this,e)||{},i={};return this.includeDeleted||(i.deleted=!1,i.purged=!1),this.includeHidden||(i.visible=!0),a.defaults(t,i)},getTotalItemCount:function(){return this.history.contentsShown()},fetchUpdated:function(e,t){return e&&(t=t||{filters:{}},t.remove=!1,t.filters={"update_time-ge":e.toISOString(),visible:""}),this.fetch(t)},fetchDeleted:function(e){e=e||{};var t=this;return e.filters=a.extend(e.filters,{deleted:!0,purged:void 0}),e.remove=!1,t.trigger("fetching-deleted",t),t.fetch(e).always(function(){t.trigger("fetching-deleted-done",t)})},fetchHidden:function(e){e=e||{};var t=this;return e.filters=a.extend(e.filters,{visible:!1}),e.remove=!1,t.trigger("fetching-hidden",t),t.fetch(e).always(function(){t.trigger("fetching-hidden-done",t)})},fetchAllDetails:function(e){e=e||{};var t={details:"all"};return e.data=a.extend(e.data||{},t),this.fetch(e)},fetchCollectionCounts:function(e){return e=e||{},e.keys=["type_id","element_count"].join(","),e.filters=a.extend(e.filters||{},{history_content_type:"dataset_collection"}),e.remove=!1,this.fetch(e)},_filterAndUpdate:function(e,t){var i=this,n=i.model.prototype.idAttribute,s=[t];return i.fetch({filters:e,remove:!1}).then(function(e){return e=e.reduce(function(e,t,s){var a=i.get(t[n]);return a?e.concat(a):e},[]),i.ajaxQueue("save",s,e)})},ajaxQueue:function(e,t,i){return i=i||this.models,new l.AjaxQueue(i.slice().reverse().map(function(i,n){var s=a.isString(e)?i[e]:e;return function(){return s.apply(i,t)}})).deferred},progressivelyFetchDetails:function(e){function i(t){t=t||0;var o=a.extend(a.clone(e),{view:"summary",keys:d,limit:r,offset:t,reset:0===t,remove:!1});a.defer(function(){s.fetch.call(s,o).fail(n.reject).done(function(e){n.notify(e,r,t),e.length!==r?(s.allFetched=!0,n.resolve(e,r,t)):i(t+r)})})}e=e||{};var n=o.Deferred(),s=this,r=e.limitPerCall||s.limitPerProgressiveFetch,l=t.HistoryDatasetAssociation.prototype.searchAttributes,d=l.join(",");return i(),n},isCopyable:function(e){var t=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return a.isObject(e)&&e.id&&a.contains(t,e.model_class)},copy:function(e){var t,i,n;a.isString(e)?(t=e,n="hda",i="dataset"):(t=e.id,n={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[e.model_class]||"hda",i="hdca"===n?"dataset_collection":"dataset");var s=this,r=o.ajax(this.url(),{method:"POST",contentType:"application/json",data:JSON.stringify({content:t,source:n,type:i})}).done(function(e){s.add([e],{parse:!0})}).fail(function(e,a,o){s.trigger("error",s,r,{},"Error copying contents",{type:i,id:t,source:n})});return r},createHDCA:function(e,t,i,n,s){var a=this.model({history_content_type:"dataset_collection",collection_type:t,history_id:this.historyId,name:i,hide_source_items:n||!1,element_identifiers:e});return a.save(s)},haveSearchDetails:function(){return this.allFetched&&this.all(function(e){return a.has(e.attributes,"annotation")})},matches:function(e){return this.filter(function(t){return t.matches(e)})},clone:function(){var e=r.Collection.prototype.clone.call(this);return e.historyId=this.historyId,e},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});return{HistoryContents:c}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(a,o,r,l){n=[i(64),i(66),i(81),i(4),i(7),i(6)],s=function(e,t,i,n,s,d){"use strict";var c=a.Model.extend(s.LoggableMixin).extend(s.mixin(s.SearchableModelMixin,{_logNamespace:"history",UPDATE_DELAY:4e3,defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",deleted:!1,contents_active:{},contents_states:{}},urlRoot:Galaxy.root+"api/histories",contentsClass:e.HistoryContents,searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},initialize:function(e,t){t=t||{},this.logger=t.logger||null,this.log(this+".initialize:",e,t),this.contents=new this.contentsClass([],{history:this,historyId:this.get("id"),order:t.order}),this._setUpListeners(),this._setUpCollectionListeners(),this.updateTimeoutId=null},_setUpListeners:function(){return this.on({error:function(e,t,i,n,s){this.clearUpdateTimeout()},"change:id":function(e,t){this.contents&&(this.contents.historyId=t)}})},_setUpCollectionListeners:function(){return this.contents?this.listenTo(this.contents,{error:function(){this.trigger.apply(this,o.makeArray(arguments))}}):this},contentsShown:function(){var e=this.get("contents_active"),t=e.active||0;return t+=this.contents.includeDeleted?e.deleted:0,t+=this.contents.includeHidden?e.hidden:0},nice_size:function(){var e=this.get("size");return e?n.bytesToString(e,!0,2):d("(empty)")},toJSON:function(){return r.extend(a.Model.prototype.toJSON.call(this),{nice_size:this.nice_size()})},get:function(e){return"nice_size"===e?this.nice_size():a.Model.prototype.get.apply(this,arguments)},ownedByCurrUser:function(){return!(!Galaxy||!Galaxy.user)&&(!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.get("user_id"))},numOfUnfinishedJobs:function(){var e=this.get("non_ready_jobs");return e?e.length:0},numOfUnfinishedShownContents:function(){return this.contents.runningAndActive().length||0},_fetchContentRelatedAttributes:function(){var e=["size","non_ready_jobs","contents_active","hid_counter"];return this.fetch({data:l.param({keys:e.join(",")})})},refresh:function(e){e=e||{};var t=this,i=t.lastUpdateTime;this.contents.allFetched=!1;var n=0!==t.contents.currentPage?function(){return t.contents.fetchPage(t.contents.currentPage)}:function(){return t.contents.fetchUpdated(i)};return n().done(function(i,n,s){var a;try{a=new Date(s.getResponseHeader("Date"))}catch(e){}t.lastUpdateTime=a||new Date,t.checkForUpdates(e)})},checkForUpdates:function(e){function t(){n.clearUpdateTimeout(),n.updateTimeoutId=setTimeout(function(){n.refresh(e)},i)}e=e||{};var i=this.UPDATE_DELAY,n=this;if(n.id){var s=this.numOfUnfinishedShownContents();s>0?t():n._fetchContentRelatedAttributes().done(function(e){n.numOfUnfinishedJobs()>0?t():n.trigger("ready")})}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},parse:function(e,t){var i=a.Model.prototype.parse.call(this,e,t);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},fetchWithContents:function(e,t){e=e||{};var i=this;return e.view="dev-detailed",this.fetch(e).then(function(e){return i.contents.history=i,i.contents.setHistoryId(e.id),i.fetchContents(t)})},fetchContents:function(e){e=e||{};var t=this;return t.lastUpdateTime=new Date,t.contents.fetchCurrentPage(e)},_delete:function(e){return this.get("deleted")?o.when():this.save({deleted:!0},e)},purge:function(e){return this.get("purged")?o.when():this.save({deleted:!0,purged:!0},e)},undelete:function(e){return this.get("deleted")?this.save({deleted:!1},e):o.when()},copy:function(e,t,i){if(e=void 0===e||e,!this.id)throw new Error("You must set the history ID before copying it.");var n={history_id:this.id};e&&(n.current=!0),t&&(n.name=t),i||(n.all_datasets=!1),n.view="dev-detailed";var s=this,a=o.post(this.urlRoot,n);return e?a.then(function(e){var t=new c(e);return t.setAsCurrent().done(function(){s.trigger("copied",s,e)})}):a.done(function(e){s.trigger("copied",s,e)})},setAsCurrent:function(){var e=this,t=o.getJSON(Galaxy.root+"history/set_as_current?id="+this.id);return t.done(function(){e.trigger("set-as-current",e)}),t},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}})),h=i.InfinitelyScrollingCollection,u=h.extend(s.LoggableMixin).extend({_logNamespace:"history",model:c,order:"update_time",limitOnFirstFetch:10,limitPerFetch:10,initialize:function(e,t){t=t||{},this.log("HistoryCollection.initialize",e,t),h.prototype.initialize.call(this,e,t),this.includeDeleted=t.includeDeleted||!1,this.currentHistoryId=t.currentHistoryId,this.setUpListeners()},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot},setUpListeners:function(){return this.on({"change:deleted":function(e){this.debug("change:deleted",this.includeDeleted,e.get("deleted")),!this.includeDeleted&&e.get("deleted")&&this.remove(e)},copied:function(e,t){this.setCurrent(new c(t,[]))},"set-as-current":function(e){var t=this.currentHistoryId;this.trigger("no-longer-current",t),this.currentHistoryId=e.id}})},_buildFetchData:function(e){return r.extend(h.prototype._buildFetchData.call(this,e),{view:"dev-detailed"})},_buildFetchFilters:function(e){var t=h.prototype._buildFetchFilters.call(this,e)||{},i={};return this.includeDeleted?i.deleted=null:(i.deleted=!1,i.purged=!1),r.defaults(t,i)},fetchFirst:function(e){var t=this,i=l.when();return this.currentHistoryId&&(i=h.prototype.fetchFirst.call(t,{silent:!0,limit:1,filters:{purged:"",deleted:"","encoded_id-in":this.currentHistoryId}})),i.then(function(){return e=e||{},e.offset=0,t.fetchMore(e)})},comparators:r.extend(r.clone(h.prototype.comparators),{name:s.buildComparator("name",{ascending:!0}),"name-dsc":s.buildComparator("name",{ascending:!1}),size:s.buildComparator("size",{ascending:!1}),"size-asc":s.buildComparator("size",{ascending:!0})}),sort:function(e){e=e||{};var t=e.silent,i=this.remove(this.get(this.currentHistoryId));return h.prototype.sort.call(this,r.defaults({silent:!0},e)),this.unshift(i,{silent:!0}),t||this.trigger("sort",this,e),this},create:function(e,t,i,n){var s=this,a=o.getJSON(Galaxy.root+"history/create_new_current");return a.done(function(e){s.setCurrent(new c(e,[],i||{}))})},setCurrent:function(e,t){return t=t||{},this.unshift(e,t),this.currentHistoryId=e.get("id"),t.silent||this.trigger("new-current",e,this),this},toString:function(){return"HistoryCollection("+this.length+",current:"+this.currentHistoryId+")"}});return{History:c,HistoryCollection:u}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(3),i(1))},function(e,t,i){var n,s;(function(a){n=[i(7)],s=function(e){"use strict";var t=e.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:!1,show_hidden:!1},addExpanded:function(e){var t=this.get("expandedIds");t[e.id]=e.get("id"),this.save("expandedIds",t)},removeExpanded:function(e){var t=this.get("expandedIds");delete t[e.id],this.save("expandedIds",t)},isExpanded:function(e){return a.result(this.get("expandedIds"),e,!1)},allExpanded:function(){return a.values(this.get("expandedIds"))},clearExpanded:function(){this.set("expandedIds",{})},includeDeleted:function(e){return a.isUndefined(e)||this.set("show_deleted",e),this.get("show_deleted")},includeHidden:function(e){return a.isUndefined(e)||this.set("show_hidden",e),this.get("show_hidden")},toString:function(){return"HistoryPrefs("+this.id+")"}},{storageKeyPrefix:"history:",historyStorageKey:function(e){if(!e)throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+e);return t.storageKeyPrefix+e},get:function(e){return new t({id:t.historyStorageKey(e)})},clearAll:function(e){for(var i in sessionStorage)0===i.indexOf(t.storageKeyPrefix)&&sessionStorage.removeItem(i)}});return{HistoryPrefs:t}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3))},function(e,t,i){var n,s;(function(a,o,r,l){n=[i(7),i(6)],s=function(e,t){"use strict";var i="list",n=a.View.extend(e.LoggableMixin).extend({_logNamespace:i,initialize:function(e){this.expanded=e.expanded||!1,this.log("\t expanded:",this.expanded),this.fxSpeed=void 0!==e.fxSpeed?e.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(e){var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){var e=o(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(e).replaceWith(this._renderDetails().show()),e},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;0===t?(i._swapNewRender(e),i.trigger("rendered",i)):o(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",r.isFunction(this.className)?this.className():this.className).append(e.children())},_setUpBehaviors:function(e){e=e||this.$el,e.find("[title]").tooltip({placement:"bottom"})},$details:function(e){return e=e||this.$el,e.find("> .details")},_renderDetails:function(){var e=o(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(e),e},toggleExpanded:function(e){return e=void 0===e?!this.expanded:e,e?this.expand():this.collapse(),this},expand:function(){var e=this;return e._fetchModelDetails().always(function(){e._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?l.when():this.model.fetch()},_expand:function(){var e=this,t=e._renderDetails();e.$details().replaceWith(t),e.expanded=!0,e.$details().slideDown(e.fxSpeed,function(){e.trigger("expanded",e)})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var e=this;e.expanded=!1,this.$details().slideUp(e.fxSpeed,function(){e.trigger("collapsed",e)})}}),s=n.extend(e.mixin(e.SelectableViewMixin,e.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(t){n.prototype.initialize.call(this,t),e.SelectableViewMixin.initialize.call(this,t),e.DraggableViewMixin.initialize.call(this,t),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(e){e?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var e=n.prototype._buildNewRender.call(this);return e.children(".warnings").replaceWith(this._renderWarnings()),e.children(".title-bar").replaceWith(this._renderTitleBar()),e.children(".primary-actions").append(this._renderPrimaryActions()),e.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),e},_swapNewRender:function(e){return n.prototype._swapNewRender.call(this,e),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var e=this,t=o(''),i=e.model.toJSON();return r.each(e.templates.warnings,function(n){t.append(o(n(i,e)))}),t},_renderTitleBar:function(){return o(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return o(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(e){e.stopPropagation(),e.altKey?(this.toggleSelect(e),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(e){var t=32,i=13;return!e||"keydown"!==e.type||e.keyCode!==t&&e.keyCode!==i||(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){var e=this.model?this.model+"":"(no model)";return"ListItemView("+e+")"}}));s.prototype.templates=function(){var t=e.wrapTemplate(['','','
"]),i={},n=e.wrapTemplate(['"],"element"),s=e.wrapTemplate(['']),a=e.wrapTemplate(['']);return{el:t,warnings:i,titleBar:n,subtitle:s,details:a}}();var d=s.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(e){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=e.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=e.foldoutPanelClass||this.foldoutPanelClass,s.prototype.initialize.call(this,e),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return o();var e=s.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,e)},_createFoldoutPanel:function(){var e=this.model,t=this._getFoldoutPanelClass(e),i=this._getFoldoutPanelOptions(e),n=new t(r.extend(i,{model:e}));return n},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(e,t){return t=t||this.$("> .details"),this.foldout=e.render(0),e.$("> .controls").hide(),t.append(e.$el)},expand:function(){var e=this;return e._fetchModelDetails().always(function(){"foldout"===e.foldoutStyle?e._expand():"drilldown"===e.foldoutStyle&&e._expandByDrilldown()})},_expandByDrilldown:function(){var e=this;e.listenTo(e.foldout,"close",function(){e.trigger("collapsed:drilldown",e,e.foldout)}),e.trigger("expanded:drilldown",e,e.foldout)}});return d.prototype.templates=function(){var t=e.wrapTemplate(['','',"
",'','','',"',"
"],"collection");return r.extend({},s.prototype.templates,{
-details:t})}(),{ExpandableView:n,ListItemView:s,FoldoutListItemView:d}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(3),i(1))},function(e,t,i){var n,s;(function(a,o){n=[i(3),i(27),i(16),i(47)],s=function(e,t,i,n){"use strict";var s={hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}},r=a.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(e){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new r(this.toJSON())},set_value:function(e){this.set("value",e||"")}}),l=a.Collection.extend({model:r}),d=r.extend({}),c=r.extend({set_value:function(e){this.set("value",parseInt(e,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),h=c.extend({set_value:function(e){this.set("value",parseFloat(e))}}),u=r.extend({get_samples:function(){return e.map(this.get("options"),function(e){return e[0]})}});r.subModelTypes={integer:c,float:h,data:d,select:u};var p=a.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:Galaxy.root+"api/tools",initialize:function(t){this.set("inputs",new l(e.map(t.inputs,function(e){var t=r.subModelTypes[e.type]||r;return new t(e)})))},toJSON:function(){var e=a.Model.prototype.toJSON.call(this);return e.inputs=this.get("inputs").map(function(e){return e.toJSON()}),e},remove_inputs:function(e){var t=this,i=t.get("inputs").filter(function(t){return e.indexOf(t.get("type"))!==-1});t.get("inputs").remove(i)},copy:function(e){var t=new p(this.toJSON());if(e){var i=new a.Collection;t.get("inputs").each(function(e){e.get_samples()&&i.push(e)}),t.set("inputs",i)}return t},apply_search_results:function(t){return e.indexOf(t,this.attributes.id)!==-1?this.show():this.hide(),this.is_visible()},set_input_value:function(e,t){this.get("inputs").find(function(t){return t.get("name")===e}).set("value",t)},set_input_values:function(t){var i=this;e.each(e.keys(t),function(e){i.set_input_value(e,t[e])})},run:function(){return this._run()},rerun:function(e,t){return this._run({action:"rerun",target_dataset_id:e.id,regions:t})},get_inputs_dict:function(){var e={};return this.get("inputs").each(function(t){e[t.get("name")]=t.get("value")}),e},_run:function(n){var s=e.extend({tool_id:this.id,inputs:this.get_inputs_dict()},n),a=o.Deferred(),r=new t.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(s),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(e){return"pending"!==e}});return o.when(r.go()).then(function(e){a.resolve(new i.DatasetCollection(e))}),a}});e.extend(p.prototype,s);var f=(a.View.extend({}),a.Collection.extend({model:p})),g=a.Model.extend(s),m=a.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){e.each(this.attributes.elems,function(e){e.show()}),this.show(),this.set("open",!1)},apply_search_results:function(t){var i,n=!0;e.each(this.attributes.elems,function(e){e instanceof g?(i=e,i.hide()):e instanceof p&&e.apply_search_results(t)&&(n=!1,i&&i.show())}),n?this.hide():(this.show(),this.set("open",!0))}});e.extend(m.prototype,s);var v=a.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,clear_btn_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:Galaxy.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var e=this.attributes.query;if(e.length','<%- name %>',"
",'