' +
@@ -543,12 +517,10 @@ var TracksterView = Backbone.View.extend(
},
// create
- create_browser : function(name, dbkey)
- {
+ create_browser : function(name, dbkey) {
$(document).trigger("convert_to_values");
- view = ui.create_visualization (
- {
+ view = ui.create_visualization ({
container: $("#center .unified-panel-body"),
name: name,
dbkey: dbkey
@@ -562,8 +534,7 @@ var TracksterView = Backbone.View.extend(
},
// initialization for editor-specific functions.
- init_editor : function ()
- {
+ init_editor : function () {
// set title
$("#center .unified-panel-title").text(view.config.get_value('name') + " (" + view.dbkey + ")");
@@ -577,8 +548,7 @@ var TracksterView = Backbone.View.extend(
});
// initialize icons
- $("#add-bookmark-button").click(function()
- {
+ $("#add-bookmark-button").click(function() {
// add new bookmark.
var position = view.chrom + ":" + view.low + "-" + view.high,
annotation = "Bookmark description";
diff --git a/static/maps/viz/trackster.js.map b/static/maps/viz/trackster.js.map
index fb8866b39a3..57c103d149b 100644
--- a/static/maps/viz/trackster.js.map
+++ b/static/maps/viz/trackster.js.map
@@ -1 +1 @@
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\ No newline at end of file
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diff --git a/static/scripts/bundled/analysis.bundled.js b/static/scripts/bundled/analysis.bundled.js
index 0ce03fe5614..703a9e77a2f 100644
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").addClass("fa fa-spinner fa-spin"))),this.listenTo(this.model,"change",this.render,this),this.$file.on("change",function(e){t._readFile(e)}),this.render()},value:function(e){return void 0!==e&&this.model.set("value",e),this.model.get("value")},render:function(){return 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.$wait.hide(),this},_readFile:function(e){var t=this,i=e.target.files&&e.target.files[0];if(i){var n=new FileReader;n.onload=function(){t.model.set({wait:!1,value:this.result})},this.model.set({wait:!0,value:null}),n.readAsText(i)}}});return{Button:l.ButtonDefault,ButtonIcon:l.ButtonIcon,ButtonCheck:l.ButtonCheck,ButtonMenu:l.ButtonMenu,ButtonLink:l.ButtonLink,Input:p,Label:d,Message:h,UnescapedMessage:u,Upload:g,Modal:c,RadioButton:n.RadioButton,Checkbox:n.Checkbox,Radio:n.Radio,Select:t,Hidden:f,Slider:i,Drilldown:s}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},,function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(7)],s=function(e,t){var i=a.View.extend({visible:!1,initialize:function(i){var n=this;this.model=i&&i.model||new a.Model({id:e.uid(),cls:"ui-portlet",title:"",icon:"",buttons:null,body:null,scrollable:!0,nopadding:!1,operations:null,collapsible:!1,collapsible_button:!1,collapsed:!1,onchange_title:null}).set(i),this.setElement(this._template()),this.$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("
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").append(this.$button=o("
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"),this.render()},update:function(e){var t=this;this.data.matchModel(e,function(e,i){var n=t.input_list[i];if(n&&n.options&&!o.isEqual(n.options,e.options)){n.options=e.options;var s=t.field_list[i];if(s.update){var a=[];if(["data","data_collection","drill_down"].indexOf(n.type)!=-1)a=n.options;else for(var r in e.options){var l=e.options[r];l.length>2&&a.push({label:l[0],value:l[1]})}s.update(a),s.trigger("change"),Galaxy.emit.debug("form-view::update()","Updating options for "+i)}}})},wait:function(e){for(var t in this.input_list){var i=this.field_list[t],n=this.input_list[t];n.is_dynamic&&i.wait&&i.unwait&&i[e?"wait":"unwait"]()}},highlight:function(e,t,i){var n=this.element_list[e];if(n&&(n.error(t||"Please verify this parameter."),this.portlet.expand(),this.trigger("expand",e),!i)){var s=this.$el.parents().filter(function(){return["auto","scroll"].indexOf(r(this).css("overflow"))!=-1}).first();s.animate({scrollTop:s.scrollTop()+n.$el.offset().top-120},500)}},errors:function(e){if(this.trigger("reset"),e&&e.errors){var t=this.data.matchResponse(e.errors);for(var i in this.element_list){this.element_list[i];t[i]&&this.highlight(i,t[i],!0)}}},render:function(){var e=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new s.Manager(this),this._renderForm(),this.data.create(),this.model.get("initial_errors")&&this.errors(this.model.attributes);var t=this.data.checksum();return this.on("change",function(i){var n=e.input_list[i];if(!n||n.refresh_on_change||e.model.get("always_refresh")){var s=e.data.checksum();s!=t&&(t=s,e.model.get("onchange")&&e.model.get("onchange")())}}),this.on("reset",function(){o.each(e.element_list,function(e){e.reset()})}),this},_renderForm:function(){r(".tooltip").remove();var e=this.model.attributes;this.message=new i.UnescapedMessage,this.section=new n.View(this,{inputs:e.inputs}),this.portlet=new t.View({icon:e.icon,title:e.title,cls:e.cls,operations:e.operations,buttons:e.buttons,collapsible:e.collapsible,collapsed:e.collapsed,onchange_title:e.onchange_title}),this.portlet.append(this.message.$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.message_status,message:e.message}),Galaxy.emit.debug("form-view::initialize()","Completed")}})}.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){a.ajaxSettings.traditional=!0,n=[i(4),i(48),i(49),i(22)],s=function(e,t,i,n){return o.View.extend({grid:null,initialize:function(t){this.dict_format=t.dict_format;var i=this;window.add_tag_to_grid_filter=function(e,t){var n=e+(void 0!==t&&""!==t?":"+t:""),s=r("#advanced-search").is(":visible");s||(r("#standard-search").slideToggle("fast"),r("#advanced-search").slideToggle("fast")),i.add_filter_condition("tags",n)},this.dict_format?(this.setElement("
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").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(3),i(1),i(2))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(7),i(59),i(61),i(60),i(57)],s=function(e,t,i,n,s,l){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"},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,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 l({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})},_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(3),i(2),i(1))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(9),i(7)],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",floating:"clear",cls:"ui-button-icon form-repeat-add",onclick:function(){t.onnew&&t.onnew()}}),this.setElement(o("
").append(this.$list=o("
")).append(o("
").append(this.button_new.$el)))},size:function(){return r.size(this.list)},add:function(e){if(!e.id||this.list[e.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var n=new i.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){e.ondel&&e.ondel()}}),s=new t.View({id:e.id,title:"placeholder",cls:e.cls||"ui-portlet-repeat",operations:{button_delete:n}});s.append(e.$el),s.$el.addClass("section-row").hide(),this.list[e.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(e){return this.list[e]?(this.$list.find("#"+e).remove(),delete this.list[e],this.button_new.enable(),void this._refresh()):void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.")},delAll:function(){for(var e in this.list)this.del(e)},hideOptions:function(){this.button_new.$el.hide(),r.each(this.list,function(e){e.hideOperation("button_delete")}),r.isEmpty(this.list)&&this.$el.append(o("
").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var e=0;for(var t in this.list){var i=this.list[t];i.title(++e+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});return{View:n}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(a,o,r,l){n=[i(4),i(7),i(9),i(46),i(44),i(45)],s=function(e,t,i,n,s,c){var d=a.View.extend({initialize:function(e,t){this.app=e,this.inputs=t.inputs,this.parameters=new c,this.setElement(o("
")),this.render()},render:function(){var e=this;this.$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.$("#"+e.id+"-section-"+s),r=!1;for(var l in a.inputs)if(!a.inputs[l].hidden){r=!0;break}s==n&&r?o.fadeIn("fast"):o.hide()}t.app.trigger("change")});for(var n in e.cases){var s=new d(this.app,{inputs:e.cases[n].inputs});this._append(s.$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 d(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),c=0;c
").addClass("ui-form-info").html(e.help)),this.app.on("expand",function(e){t.$("#"+e).length>0&&t.expand()}),this._append(t.$el,e.id)},_addRow:function(e){var t=this,i=e.id;e.onchange=e.onchange||function(){t.app.trigger("change",i)};var n=this.parameters.create(e);this.app.field_list[i]=n;var a=new s(this.app,{name:e.name,label:e.hide_label?"":e.label||e.name,value:e.value,text_value:e.text_value,collapsible_value:e.collapsible_value,collapsible_preview:e.collapsible_preview,help:e.help,argument:e.argument,disabled:e.disabled,color:e.color,style:e.style,backdrop:e.backdrop,hidden:e.hidden,fixed:e.fixed,field:n});return this.app.element_list[i]=a,this._append(a.$el,e.id),n},_append:function(e,t){this.$el.append(e.addClass("section-row").attr("id",t))}});return{View:d}}.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(i,a,o){n=[],s=function(){return i.Model.extend({defaults:{url_base:"",async:!1,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:!1,advanced_search:!1,cur_page:1,num_pages:1,operation:void 0,item_ids:void 0},can_async_op:function(e){return a.indexOf(this.attributes.async_ops,e)!==-1},add_filter:function(e,t,i){if(i){var n,s=this.attributes.filters[e];if(null===s||void 0===s)n=t;else if("string"==typeof s)if("All"==s)n=t;else{var a=[];a[0]=s,a[1]=t,n=a}else n=s,n.push(t);this.attributes.filters[e]=n}else this.attributes.filters[e]=t},remove_filter:function(e,t){var i=this.attributes.filters[e];if(null===i||void 0===i)return!1;if("string"==typeof i)this.attributes.filters[e]="";else{var n=a.indexOf(i,t);n!==-1&&(i[n]="")}},get_url_data:function(){var e={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};this.attributes.operation&&(e.operation=this.attributes.operation),this.attributes.item_ids&&(e.id=this.attributes.item_ids);var t=this;return a.each(a.pairs(t.attributes.filters),function(t){e["f-"+t[0]]=t[1]}),e},get_url:function(e){return this.get("url_base")+"?"+o.param(this.get_url_data())+"&"+o.param(e)}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1))},function(e,t,n){var s,a;(function(o){s=[n(4)],a=function(e){return{grid:function(e){var t="";return t=e.embedded?this.grid_header(e)+this.grid_table(e):'
'+this.grid_table(e),e.info_text&&(t+='
'+e.info_text+"
"),t},grid_table:function(e){return'
'},grid_header:function(e){var t='"},header:function(e){var t="
";e.show_item_checkboxes&&(t+="",e.items.length>0&&(t+=' ");for(var i in e.columns){var n=e.columns[i];n.visible&&(t+='")}return t+=" "},body:function(e){var t="",i=0,n=e.items.length;0==n&&(t+='
No Items ',i=1);for(var s in e.items){var a=e.items[s],r=a.encode_id;t+="
",e.show_item_checkboxes&&(t+='",h?(0!=e.operations.length&&(t+=''),t+='",0!=e.operations.length&&(t+="
")):t+=''+(u||"")+"
",t+=" "}}t+=" ",i++}return t},footer:function(e){var t="";if(e.use_paging&&e.num_pages>1){var n=e.num_page_links,s=e.cur_page_num,a=e.num_pages,o=n/2,r=s-o,l=0;r<=0&&(r=1,l=o-(s-r));var c=o+l,d=s+c;d<=a?max_offset=0:(d=a,max_offset=c-(d+1-s)),0!=max_offset&&(r-=max_offset,r<1&&(r=1)),t+='
',e.show_item_checkboxes&&(t+="Page:',r>1&&(t+='1 '+h+" ":''+h+" '+a+" "),t+="",t+=' | Show All '}if(e.show_item_checkboxes){t+='
For "}var p=!1;for(i in e.operations)if(e.operations[i].global_operation){p=!0;break}if(p){t+='
';for(i in e.operations){var u=e.operations[i];u.global_operation&&(t+=''+u.label+" ")}t+=" "}return e.legend&&(t+='
'+e.legend+" "),t},message:function(e){return'
'+e.message+'
'},grid_filters:function(e){var t=e.default_filter_dict,i=e.filters,n="none";e.advanced_search&&(n="block");var s=!1;for(var a in e.columns){var o=e.columns[a];if("advanced"==o.filterable){var r=o.key,l=i[r],c=t[r];l&&c&&l!=c&&(n="block"),s=!0}}var d="block";"block"==n&&(d="none");var h='
';for(var a in e.columns){var o=e.columns[a];"standard"==o.filterable&&(h+=this.grid_column_filter(e,o))}h+="
",s&&(h+='Advanced Search '),h+="
",h+='
Close Advanced Search
"},grid_column_filter:function(e,t){var i=(e.default_filter_dict,e.filters),n=t.label,s=t.key;"advanced"==t.filterable&&(n=n.toLowerCase());var a="
";if("advanced"==t.filterable&&(a+=''+n+": "),a+='',t.is_text){a+=''}else{a+='';var m=!1;for(cf_label in e.categorical_filters[s]){var v=e.categorical_filters[s][cf_label],_="",y="";for(key in v)_=key,y=v[key];m&&(a+=" | "),m=!0;var u=i[s];a+=u&&v[s]&&u==y?''+cf_label+" ":''+cf_label+" "}return a+=" "},filter_element:function(t,i){return i=e.sanitize(i),'
'+i+' '}}}.apply(t,s),!(void 0!==a&&(e.exports=a))}).call(t,n(1))},function(e,t,i){var n,s;(function(a){n=[i(41),i(86),i(5)],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,c=e.ListOfListsDatasetCollection,d=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=c.extend(s).extend({defaults:a.extend(a.clone(c.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:list",model_class:"HistoryDatasetCollectionAssociation"}),save:n(c.prototype.save),toString:function(){return["HistoryListOfListsDatasetCollection(",this.get("name"),")"].join("")}});return{HistoryListDatasetCollection:d,HistoryPairDatasetCollection:h,HistoryListPairedDatasetCollection:u,HistoryListOfListsDatasetCollection:p}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(a,o,r){n=[i(77),i(84),i(50),i(53),i(6),i(147)],s=function(e,t,i,n,s,l){"use strict";var c=e.PaginatedCollection,d=c.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||{},c.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(c.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 c.prototype.fetch.call(this,e)},_buildFetchData:function(e){return a.extend(c.prototype._buildFetchData.call(this,e),{v:"dev"})},_fetchParams:c.prototype._fetchParams.concat(["v","details"]),_buildFetchFilters:function(e){var t=c.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:c,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,c=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:d}}.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(51),i(53),i(77),i(4),i(6),i(5)],s=function(e,t,i,n,s,c){"use strict";var d=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):c("(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 d(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:d,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 d(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 d(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:d,HistoryCollection:u}}.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){n=[i(6)],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(2))},function(e,t,i){var n,s;(function(a,o,r,l){n=[i(6),i(5)],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.$el},_renderWarnings:function(){var e=this,t=o('
'),i=e.model.toJSON();return r.each(e.templates.warnings,function(n){t.append(o(n(i,e)))}),t},_renderTitleBar:function(){return o(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return o(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(e){e.stopPropagation(),e.altKey?(this.toggleSelect(e),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(e){var t=32,i=13;return!e||"keydown"!==e.type||e.keyCode!==t&&e.keyCode!==i||(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){var e=this.model?this.model+"":"(no model)";return"ListItemView("+e+")"}}));s.prototype.templates=function(){var t=e.wrapTemplate(['
"]),i={},n=e.wrapTemplate(['
','
','
','<%- element.name %> ',"
",'
',"
"],"element"),s=e.wrapTemplate(['
']),a=e.wrapTemplate(['
']);return{el:t,warnings:i,titleBar:n,subtitle:s,details:a}}();var c=s.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(e){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=e.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=e.foldoutPanelClass||this.foldoutPanelClass,s.prototype.initialize.call(this,e),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return o();var e=s.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,e)},_createFoldoutPanel:function(){var e=this.model,t=this._getFoldoutPanelClass(e),i=this._getFoldoutPanelOptions(e),n=new t(r.extend(i,{model:e}));return n},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(e,t){return t=t||this.$("> .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 c.prototype.templates=function(){var t=e.wrapTemplate(['
',"
"],"collection");return r.extend({},s.prototype.templates,{details:t})}(),{ExpandableView:n,ListItemView:s,FoldoutListItemView:c}}.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(6),i(5)],s=function(e,t){var i=a.View.extend(e.LoggableMixin).extend(e.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",initialize:function(e){e.usePrompt===!1?this.label="":this.label='
'+t("Tags")+" ",this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.$el.html(this._template()),this.$input().select2({placeholder:"Add tags",width:"100%",tags:function(){return e._getTagsUsed()}}),this._setUpBehaviors(),this},_hashToName:function(e){return e.startsWith("#")?"name:"+e.slice(1):e},_nameToHash:function(e){return e.startsWith("name:")&&(e="#"+e.slice(5)),e},_template:function(){return[this.label,'
'].join("")},tagsToCSV:function(){var e=this,t=this.model.get("tags");return!o.isArray(t)||o.isEmpty(t)?"":t.map(function(t){return o.escape(e._nameToHash(t))}).sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){var e=this;return o.map(Galaxy.user.get("tags_used"),e._nameToHash)},_setUpBehaviors:function(){var e=this;this.$input().on("change",function(t){t.val=o.map(t.val,e._hashToName),e.model.save({tags:t.val}),t.added&&e._addNewTagToTagsUsed(t.added.text+"")})},_addNewTagToTagsUsed:function(e){var t=Galaxy.user.get("tags_used");o.contains(t,e)||(t.push(e),t.sort(),Galaxy.user.set("tags_used",t))},remove:function(){this.$input.off(),this.stopListening(this.model),a.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",this.model+"",")"].join("")}});return{TagsEditor:i}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2))},function(e,t,i){var n,s;(function(a,o){n=[i(2),i(19),i(10),i(30)],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}),c=r.extend({}),d=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=d.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:d,float:h,data:c,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
");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.$el.append(o(" ','','
',"
"].join("")),tool_link:e.template(['
',"<% _.each( labels, function( label ){ %>",'',"<%- label %>"," ","<% }); %>"," ",'
',"<%- name %>"," "," <%- description %>"].join("")),tool_form:e.template(['
<%- tool.name %> (version <%- tool.version %>)
','
',"<% _.each( tool.inputs, function( input ){ %>",'
","<% }); %>","
",'
','
",'
"].join(""),{variable:"tool"})});return{ToolParameter:r,IntegerToolParameter:d,SelectToolParameter:u,Tool:p,ToolCollection:f,ToolSearch:v,ToolPanel:_,ToolPanelView:$,ToolFormView:k}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1))},function(e,t,i){var n,s;(function(a,o){n=[i(4)],s=function(e){return a.View.extend({
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").addClass("button-"+p).addClass("ui-drilldown-button fa fa-plus-square"),g=o("
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");return n(a,this.model.get("data")),a},_template:function(){return o("
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").addClass("ui-form-info").append(o("
").addClass("fa fa-sitemap")).append(o("
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").addClass("ui-form-title").html("Batch options:")).append(this.button_product.$el)).append(o("
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Select Library
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").addClass("ui-tabs tabbable tabs-left").append(o("
").addClass("tab-navigation nav nav-tabs")).append(o("
").addClass("tab-content"))},_template_tab:function(e){var t=o("
").addClass("tab-element").attr("id","tab-"+e.id).append(o("
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'+r.escape(t.path)+' '+e.bytesToString(t.size)+' '+t.ctime+" "},_templateTable:function(){return'
Available files: '},_templateInfo:function(){return'
Your FTP directory does not contain any files.
'},_template:function(){return'
This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at '+this.options.ftp_upload_site+' using your Galaxy credentials (email address and password).
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").addClass("upload-settings")),this.$el.append(o("
").addClass("upload-settings-cover")),this.$el.append(o("
").addClass("upload-settings-table ui-table-striped").append("
")),this.$cover=this.$(".upload-settings-cover"),this.$table=this.$(".upload-settings-table > tbody"),this.listenTo(this.model,"change",this.render,this),this.model.trigger("change")},render:function(){var e=this;this.$table.empty(),r.each(this.options.parameters,function(t){var i=o("
").addClass("upload-"+t.id+" upload-icon-button fa").addClass(e.model.get(t.id)&&e.options.class_check||e.options.class_uncheck).on("click",function(){e.model.get("enabled")&&e.model.set(t.id,!e.model.get(t.id))});e.$table.append(o("
").append(o("
").append(i)).append(o("
").append(t.title)))}),this.$cover[this.model.get("enabled")&&"hide"||"show"]()}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},,,function(e,t,i){(function(e,t){!function(i){e.event.props.push("dataTransfer"),i.uploadpost=function(t){var n=i.extend({},{data:{},success:function(){},error:function(){},progress:function(){},url:null,maxfilesize:2048,error_filesize:"File exceeds 2GB. Please use a FTP client.",error_default:"Please make sure the file is available.",error_server:"Upload request failed.",error_login:"Uploads require you to log in."},t),s=n.data;if(s.error_message)return void n.error(s.error_message);var a=new FormData;for(var o in s.payload)a.append(o,s.payload[o]);var r=0;for(var o in s.files){var l=s.files[o];a.append(l.name,l.file,l.file.name),r+=l.file.size}return r>1048576*n.maxfilesize?void n.error(n.error_filesize):(xhr=new XMLHttpRequest,xhr.open("POST",n.url,!0),xhr.setRequestHeader("Accept","application/json"),xhr.setRequestHeader("Cache-Control","no-cache"),xhr.setRequestHeader("X-Requested-With","XMLHttpRequest"),xhr.onreadystatechange=function(){if(xhr.readyState==xhr.DONE){var t=null;if(xhr.responseText)try{t=e.parseJSON(xhr.responseText)}catch(e){t=xhr.responseText}if(xhr.status<200||xhr.status>299){var i=xhr.statusText;403==xhr.status?i=n.error_login:0==xhr.status?i=n.error_server:i||(i=n.error_default),n.error(i+" ("+xhr.status+")")}else n.success(t)}},xhr.upload.addEventListener("progress",function(e){e.lengthComputable&&n.progress(Math.round(100*e.loaded/e.total))},!1),Galaxy.emit.debug("uploadbox::uploadpost()","Posting following data.",n),void xhr.send(a))},i.fn.uploadinput=function(e){var t=this,n=i.extend({},{ondragover:function(){},ondragleave:function(){},onchange:function(){},multiple:!1},e),s=i('
");return t.append(s.change(function(e){n.onchange(e.target.files),i(this).val("")})),t.on("drop",function(e){n.ondragleave(e),e.dataTransfer&&(n.onchange(e.dataTransfer.files),e.preventDefault())}),t.on("dragover",function(e){e.preventDefault(),n.ondragover(e)}),t.on("dragleave",function(e){e.stopPropagation(),n.ondragleave(e)}),{dialog:function(){s.trigger("click")}}},i.fn.uploadbox=function(e){function n(e){if(e&&e.length&&!m){var i=f;return t.each(e,function(e,i){"new"!==e.mode&&t.filter(p,function(t){return t.name===e.name&&t.size===e.size}).length&&(e.duplicate=!0)}),t.each(e,function(e){if(!e.duplicate){var t=String(f++);p[t]=e,u.announce(t,p[t]),g++}}),i}}function s(e){p[e]&&(delete p[e],g--)}function a(){if(0==g||v)return v=!1,m=!1,void u.complete();m=!0;var e=-1;for(var t in p){e=t;break}p[e];s(e),i.uploadpost({url:u.url,data:u.initialize(e),success:function(t){u.success(e,t),a()},error:function(t){u.error(e,t),a()},progress:function(t){u.progress(e,t)}})}function o(){_.dialog()}function r(e){for(e in p)s(e)}function l(){m||(m=!0,a())}function c(){v=!0}function d(e){return u=i.extend({},u,e)}function h(){return window.File&&window.FormData&&window.XMLHttpRequest&&window.FileList}var u=i.extend({},{dragover:function(){},dragleave:function(){},announce:function(e){},initialize:function(e){},progress:function(e,t){},success:function(e,t){},error:function(e,t){alert(t)},complete:function(){}},e),p={},f=0,g=0,m=!1,v=!1,_=i(this).uploadinput({multiple:!0,onchange:function(e){n(e)},ondragover:e.ondragover,ondragleave:e.ondragleave});return{select:o,add:n,remove:s,start:l,stop:c,reset:r,configure:d,compatible:h}}}(e)}).call(t,i(1),i(2))},,,,,,,,function(e,t,i){var n,s;(function(a,o){n=[i(6),i(5),i(17)],s=function(e,t){var i=a.View.extend(e.LoggableMixin).extend(e.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(e){e=e||{},this.tooltipConfig=e.tooltipConfig||{placement:"bottom"},this.listenTo(this.model,"change:annotation",function(){this.render()}),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.$el.html(this._template()),this.$annotation().make_text_editable({use_textarea:!0,on_finish:function(t){e.$annotation().text(t),e.model.save({annotation:t},{silent:!0}).fail(function(){e.$annotation().text(e.model.previous("annotation"))})}}),this},_template:function(){var e=this.model.get("annotation");return['
',t("Annotation")," ",'
',o.escape(e),"
"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off(),this.stopListening(this.model),a.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}});return{AnnotationEditor:i}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2))},function(e,t,i){var n,s;(function(a){n=[i(2),i(3),i(6)],s=function(e,t,i){"use strict";var n=t.Collection.extend({initialize:function(e,i){t.Collection.prototype.initialize.call(this,e,i),this.setOrder(i.order||this.order,{silent:!0})},_setUpListeners:function(){return this.on({"changed-order":this.sort})},fetch:function(e){return e=this._buildFetchOptions(e),t.Collection.prototype.fetch.call(this,e)},_buildFetchOptions:function(t){t=e.clone(t)||{};var i=this;t.traditional=!0,t.data=t.data||i._buildFetchData(t);var n=this._buildFetchFilters(t);return e.isEmpty(n)||e.extend(t.data,this._fetchFiltersToAjaxData(n)),t},_buildFetchData:function(t){var i={};return this.order&&(i.order=this.order),e.defaults(e.pick(t,this._fetchParams),i)},_fetchParams:["order","limit","offset","view","keys"],_buildFetchFilters:function(t){return e.clone(t.filters||{})},_fetchFiltersToAjaxData:function(t){var i={q:[],qv:[]};return e.each(t,function(e,t){void 0!==e&&""!==e&&(e===!0&&(e="True"),e===!1&&(e="False"),null===e&&(e="None"),i.q.push(t),i.qv.push(e))}),i},reset:function(e,i){return this.allFetched=!1,t.Collection.prototype.reset.call(this,e,i)},order:null,comparators:{update_time:i.buildComparator("update_time",{ascending:!1}),"update_time-asc":i.buildComparator("update_time",{ascending:!0}),create_time:i.buildComparator("create_time",{ascending:!1}),"create_time-asc":i.buildComparator("create_time",{ascending:!0})},setOrder:function(t,i){i=i||{};var n=this,s=n.comparators[t];if(e.isUndefined(s))throw new Error("unknown order: "+t);if(s!==n.comparator){n.order;return n.order=t,n.comparator=s,i.silent||n.trigger("changed-order",i),n}}}),s=n.extend({limitPerPage:500,initialize:function(e,t){n.prototype.initialize.call(this,e,t),this.currentPage=t.currentPage||0},getTotalItemCount:function(){return this.length},shouldPaginate:function(){return this.getTotalItemCount()>=this.limitPerPage},getLastPage:function(){return Math.floor(this.getTotalItemCount()/this.limitPerPage)},getPageCount:function(){return this.getLastPage()+1},getPageLimitOffset:function(e){return e=this.constrainPageNum(e),{limit:this.limitPerPage,offset:e*this.limitPerPage}},constrainPageNum:function(e){return Math.max(0,Math.min(e,this.getLastPage()))},fetchPage:function(t,i){var n=this;return t=n.constrainPageNum(t),n.currentPage=t,i=e.defaults(i||{},n.getPageLimitOffset(t)),n.trigger("fetching-more"),n.fetch(i).always(function(){n.trigger("fetching-more-done")})},fetchCurrentPage:function(e){return this.fetchPage(this.currentPage,e)},fetchPrevPage:function(e){return this.fetchPage(this.currentPage-1,e)},fetchNextPage:function(e){return this.fetchPage(this.currentPage+1,e)}}),o=n.extend({limitOnFirstFetch:null,limitPerFetch:100,initialize:function(e,t){n.prototype.initialize.call(this,e,t),this.limitOnFirstFetch=t.limitOnFirstFetch||this.limitOnFirstFetch,this.limitPerFetch=t.limitPerFetch||this.limitPerFetch,this.allFetched=!1,this.lastFetched=t.lastFetched||0},_buildFetchOptions:function(e){return e.remove=e.remove||!1,n.prototype._buildFetchOptions.call(this,e)},fetchFirst:function(t){return t=t?e.clone(t):{},this.allFetched=!1,this.lastFetched=0,this.fetchMore(e.defaults(t,{
-reset:!0,limit:this.limitOnFirstFetch}))},fetchMore:function(t){t=e.clone(t||{});var i=this;if(!t.reset&&i.allFetched)return a.when();t.offset=t.reset?0:t.offset||i.lastFetched;var n=t.limit=t.limit||i.limitPerFetch||null;return i.trigger("fetching-more"),i.fetch(t).always(function(){i.trigger("fetching-more-done")}).done(function(t){var s=e.isArray(t)?t.length:0;i.lastFetched+=s,(!n||s
','
',''].join(""))}};return{CollectionCreatorMixin:e}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(a){n=[i(87),i(41),i(40),i(6),i(5)],s=function(e,t,i,n,s){"use strict";var o="collections",r=e.ModelListPanel,l=r.extend({_logNamespace:o,className:r.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:i.DatasetDCEListItemView,NestedDCDCEViewClass:i.NestedDCDCEListItemView,modelCollectionKey:"elements",initialize:function(e){r.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,this.panelStack=[],this.parentName=e.parentName,this.foldoutStyle=e.foldoutStyle||"foldout",this.downloadUrl=this.model.attributes.url+"/download"},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;i.log("_queueNewRender:",e,t),i._swapNewRender(e),i.trigger("rendered",i)},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(e){switch(e.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",e.get("element_type"))},_getItemViewOptions:function(e){var t=r.prototype._getItemViewOptions.call(this,e);return a.extend(t,{linkTarget:this.linkTarget,hasUser:this.hasUser,foldoutStyle:this.foldoutStyle})},_setUpItemViewListeners:function(e){var t=this;return r.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}}),this},_expandDrilldownPanel:function(e){this.panelStack.push(e),this.$("> .controls").add(this.$list()).hide(),e.parentName=this.model.get("name"),this.$el.append(e.render().$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.render()},events:{"click .navigation .back":"close"},close:function(e){this.remove(),this.trigger("close")},toString:function(){return"CollectionView("+(this.model?this.model.get("name"):"")+")"}});l.prototype.templates=function(){var e=n.wrapTemplate(['
','
",'
','
<%- collection.name || collection.element_identifier %>
','
','<% if( collection.collection_type === "list" ){ %>',s("a list of datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',s("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',s("a list of paired datasets"),'<% } else if( collection.collection_type === "list:list" ){ %>',s("a list of dataset lists"),"<% } %>","
","
",'
','
","
"],"collection");return a.extend(a.clone(r.prototype.templates),{controls:e})}();var c=l.extend({DatasetDCEViewClass:i.DatasetDCEListItemView,toString:function(){return"ListCollectionView("+(this.model?this.model.get("name"):"")+")"}}),d=c.extend({toString:function(){return"PairCollectionView("+(this.model?this.model.get("name"):"")+")"}}),h=l.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemView.extend({foldoutPanelClass:d}),toString:function(){return"ListOfPairsCollectionView("+(this.model?this.model.get("name"):"")+")"}}),u=l.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemView.extend({foldoutPanelClass:d}),toString:function(){return"ListOfListsCollectionView("+(this.model?this.model.get("name"):"")+")"}});return{CollectionView:l,ListCollectionView:c,PairCollectionView:d,ListOfPairsCollectionView:h,ListOfListsCollectionView:u}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(a,o){n=[i(11),i(43),i(55),i(76),i(18),i(6),i(5)],s=function(e,t,i,n,s,r,l){"use strict";var c=t.DatasetListItemView,d=c.extend({initialize:function(e){c.prototype.initialize.call(this,e),this.hasUser=e.hasUser,this.purgeAllowed=e.purgeAllowed||!1,this.tagsEditorShown=e.tagsEditorShown||!1,this.annotationEditorShown=e.annotationEditorShown||!1},_renderPrimaryActions:function(){var t=c.prototype._renderPrimaryActions.call(this);return this.model.get("state")===e.NOT_VIEWABLE?t:c.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===e.DISCARDED||!this.model.get("accessible"))return null;var t=this.model.get("purged"),i=this.model.get("deleted"),n={title:l("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return i||t?(n.disabled=!0,t?n.title=l("Cannot edit attributes of datasets removed from disk"):i&&(n.title=l("Undelete dataset to edit attributes"))):a.contains([e.UPLOAD,e.NEW],this.model.get("state"))&&(n.disabled=!0,n.title=l("This dataset is not yet editable")),s(n)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var e=this,t=this.model.isDeletedOrPurged();return s({title:l(t?"Dataset is already deleted":"Delete"),disabled:t,faIcon:"fa-times",classes:"delete-btn",onclick:function(){e.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},_renderDetails:function(){var t=c.prototype._renderDetails.call(this),i=this.model.get("state");return!this.model.isDeletedOrPurged()&&a.contains([e.OK,e.FAILED_METADATA],i)&&(this._renderTags(t),this._renderAnnotation(t),this._makeDbkeyEditLink(t)),this._setUpBehaviors(t),t},_renderToolHelpButton:function(){var e=this.model.attributes.dataset_id,t=this.model.attributes.creating_job,i=this,n=function(t){var n='
';t.name&&t.help?(n+="Tool help for "+t.name+"
Tool help is unavailable for this dataset. ",i.$el.find(".details").append(o.parseHTML(n))},a=function(e){o.ajax({url:Galaxy.root+"api/tools/"+e.tool_id+"/build"}).done(function(e){n(e)}).fail(function(){n({})})};return null===Galaxy.user.id?null:s({title:"Tool Help",classes:"icon-btn",href:"#",faIcon:"fa-question",onclick:function(){i.$el.find(".toolhelp").length>0?i.$el.find(".toolhelp").toggle():o.ajax({url:Galaxy.root+"api/jobs/"+t}).done(function(e){a(e)}).fail(function(){console.log('Failed at recovering job information from the Galaxy API for job id "'+t+'".')})}})},_renderSecondaryActions:function(){var t=c.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case e.UPLOAD:case e.NOT_VIEWABLE:return t;case e.ERROR:return t.unshift(this._renderErrButton()),t.concat([this._renderRerunButton(),this._renderToolHelpButton()]);case e.OK:case e.FAILED_METADATA:return t.concat([this._renderRerunButton(),this._renderVisualizationsButton(),this._renderToolHelpButton()])}return t.concat([this._renderRerunButton(),this._renderToolHelpButton()])},_renderErrButton:function(){return s({title:l("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){var e=this.model.get("creating_job");if(this.model.get("rerunnable"))return s({title:l("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(t){t.preventDefault(),Galaxy.router.push("/",{job_id:e})}})},_renderVisualizationsButton:function(){var e=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||a.isEmpty(e))return null;if(!a.isObject(e[0]))return this.warn("Visualizations have been switched off"),null;var t=o(this.templates.visualizations(e,this));return t.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(t.find(".visualization-link").addBack(".visualization-link")),t},_addScratchBookFn:function(e){e.click(function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",url:o(this).attr("href")}),e.preventDefault(),e.stopPropagation())})},_renderTags:function(e){if(this.hasUser){var t=this;this.tagsEditor=new i.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.tagsEditorShown=!0},onhide:function(){t.tagsEditorShown=!1},$activator:s({title:l("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(e){if(this.hasUser){var t=this;this.annotationEditor=new n.AnnotationEditor({model:this.model,el:e.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.annotationEditorShown=!0},onhide:function(){t.annotationEditorShown=!1},$activator:s({title:l("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(e){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var t=o('
? ').attr("href",this.model.urls.edit).attr("target",this.linkTarget);e.find(".dbkey .value").replaceWith(t)}},events:a.extend(a.clone(c.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(e){this.trigger("edit",this,e)},"click .delete-btn":function(e){this.trigger("delete",this,e)},"click .rerun-btn":function(e){this.trigger("rerun",this,e)},"click .report-err-btn":function(e){this.trigger("report-err",this,e)},"click .visualization-btn":function(e){this.trigger("visualize",this,e)},"click .dbkey a":function(e){this.trigger("edit",this,e)}}),_clickUndeleteLink:function(e){return this.model.undelete(),!1},_clickPurgeLink:function(e){return confirm(l("This will permanently remove the data in your dataset. Are you sure?"))&&this.model.purge(),!1},toString:function(){var e=this.model?this.model+"":"(no model)";return"HDAEditView("+e+")"}});return d.prototype.templates=function(){var e=a.extend({},c.prototype.templates.warnings,{failed_metadata:r.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
","<% } %>"],"dataset"),deleted:r.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
',l("This dataset has been deleted"),'
',l("Undelete it")," ","<% if( view.purgeAllowed ){ %>",'
',l("Permanently remove it from disk")," ","<% } %>","
","<% } %>"],"dataset")}),t=r.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'
">',' ","<% } else { %>",'
","<% } %>"],"visualizations");return a.extend({},c.prototype.templates,{warnings:e,visualizations:t})}(),{DatasetListItemEdit:d}}.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(11),i(6),i(5)],s=function(e,t,i){"use strict";var n="dataset",s=t.SearchableModelMixin,l=a.Model.extend(t.LoggableMixin).extend(t.mixin(s,{_logNamespace:n,defaults:{state:e.NEW,deleted:!1,purged:!1,name:"(unnamed dataset)",accessible:!0,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(t,i){this.debug(this+"(Dataset).initialize",t,i),
+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(c.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 c.prototype.fetch.call(this,e)},_buildFetchData:function(e){return a.extend(c.prototype._buildFetchData.call(this,e),{v:"dev"})},_fetchParams:c.prototype._fetchParams.concat(["v","details"]),_buildFetchFilters:function(e){var t=c.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:c,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,c=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:d}}.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(51),i(53),i(77),i(4),i(6),i(5)],s=function(e,t,i,n,s,c){"use strict";var d=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):c("(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 d(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:d,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 d(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 d(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:d,HistoryCollection:u}}.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){n=[i(6)],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(2))},function(e,t,i){var n,s;(function(a,o,r,l){n=[i(6),i(5)],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.$el},_renderWarnings:function(){var e=this,t=o('
'),i=e.model.toJSON();return r.each(e.templates.warnings,function(n){t.append(o(n(i,e)))}),t},_renderTitleBar:function(){return o(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return o(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(e){e.stopPropagation(),e.altKey?(this.toggleSelect(e),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(e){var t=32,i=13;return!e||"keydown"!==e.type||e.keyCode!==t&&e.keyCode!==i||(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){var e=this.model?this.model+"":"(no model)";return"ListItemView("+e+")"}}));s.prototype.templates=function(){var t=e.wrapTemplate(['
"]),i={},n=e.wrapTemplate(['
','
','
','<%- element.name %> ',"
",'
',"
"],"element"),s=e.wrapTemplate(['
']),a=e.wrapTemplate(['
']);return{el:t,warnings:i,titleBar:n,subtitle:s,details:a}}();var c=s.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(e){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=e.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=e.foldoutPanelClass||this.foldoutPanelClass,s.prototype.initialize.call(this,e),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return o();var e=s.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,e)},_createFoldoutPanel:function(){var e=this.model,t=this._getFoldoutPanelClass(e),i=this._getFoldoutPanelOptions(e),n=new t(r.extend(i,{model:e}));return n},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(e,t){return t=t||this.$("> .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 c.prototype.templates=function(){var t=e.wrapTemplate(['
',"
"],"collection");return r.extend({},s.prototype.templates,{details:t})}(),{ExpandableView:n,ListItemView:s,FoldoutListItemView:c}}.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(6),i(5)],s=function(e,t){var i=a.View.extend(e.LoggableMixin).extend(e.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",initialize:function(e){e.usePrompt===!1?this.label="":this.label='
'+t("Tags")+" ",this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.$el.html(this._template()),this.$input().select2({placeholder:"Add tags",width:"100%",tags:function(){return e._getTagsUsed()}}),this._setUpBehaviors(),this},_hashToName:function(e){return e.startsWith("#")?"name:"+e.slice(1):e},_nameToHash:function(e){return e.startsWith("name:")&&(e="#"+e.slice(5)),e},_template:function(){return[this.label,'
'].join("")},tagsToCSV:function(){var e=this,t=this.model.get("tags");return!o.isArray(t)||o.isEmpty(t)?"":t.map(function(t){return o.escape(e._nameToHash(t))}).sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){var e=this;return o.map(Galaxy.user.get("tags_used"),e._nameToHash)},_setUpBehaviors:function(){var e=this;this.$input().on("change",function(t){t.val=o.map(t.val,e._hashToName),e.model.save({tags:t.val}),t.added&&e._addNewTagToTagsUsed(t.added.text+"")})},_addNewTagToTagsUsed:function(e){var t=Galaxy.user.get("tags_used");o.contains(t,e)||(t.push(e),t.sort(),Galaxy.user.set("tags_used",t))},remove:function(){this.$input.off(),this.stopListening(this.model),a.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",this.model+"",")"].join("")}});return{TagsEditor:i}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2))},function(e,t,i){var n,s;(function(a,o){n=[i(2),i(20),i(10),i(30)],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}),c=r.extend({}),d=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=d.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:d,float:h,data:c,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
");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.$el.append(o(" ','','
',"
"].join("")),tool_link:e.template(['
',"<% _.each( labels, function( label ){ %>",'',"<%- label %>"," ","<% }); %>"," ",'
',"<%- name %>"," "," <%- description %>"].join("")),tool_form:e.template(['
<%- tool.name %> (version <%- tool.version %>)
','
',"<% _.each( tool.inputs, function( input ){ %>",'
","<% }); %>","
",'
','
",'
"].join(""),{variable:"tool"})});return{ToolParameter:r,IntegerToolParameter:d,SelectToolParameter:u,Tool:p,ToolCollection:f,ToolSearch:v,ToolPanel:_,ToolPanelView:$,ToolFormView:k}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1))},function(e,t,i){var n,s;(function(a,o){n=[i(4)],s=function(e){return a.View.extend({
+colors:{standard:["c00000","ff0000","ffc000","ffff00","92d050","00b050","00b0f0","0070c0","002060","7030a0"],base:["ffffff","000000","eeece1","1f497d","4f81bd","c0504d","9bbb59","8064a2","4bacc6","f79646"],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"]]},initialize:function(t){this.options=e.merge(t,{}),this.setElement(this._template()),this.$panel=this.$(".ui-color-picker-panel"),this.$view=this.$(".ui-color-picker-view"),this.$value=this.$(".ui-color-picker-value"),this.$header=this.$(".ui-color-picker-header"),this._build(),this.visible=!1,this.value(this.options.value),this.$boxes=this.$(".ui-color-picker-box");var i=this;this.$boxes.on("click",function(){i.value(o(this).css("background-color")),i.$header.trigger("click")}),this.$header.on("click",function(){i.visible=!i.visible,i.visible?i.$view.fadeIn("fast"):i.$view.fadeOut("fast")})},value:function(e){return void 0!==e&&null!==e&&(this.$value.css("background-color",e),this.$(".ui-color-picker-box").empty(),this.$(this._getValue()).html(this._templateCheck()),this.options.onchange&&this.options.onchange(e)),this._getValue()},_getValue:function(){function e(e){return("0"+parseInt(e).toString(16)).slice(-2)}var t=this.$value.css("background-color");return t=t.match(/^rgb\((\d+),\s*(\d+),\s*(\d+)\)$/),t?"#"+e(t[1])+e(t[2])+e(t[3]):null},_build:function(){this._content({colors:this.colors.base});for(var e in this.colors.theme){var t={};0==e?t.bottom=!0:e!=this.colors.theme.length-1?(t.top=!0,t.bottom=!0):t.top=!0,t.colors=this.colors.theme[e],this._content(t)}this._content({colors:this.colors.standard})},_content:function(e){var t=e.colors,i=o(this._templateContent()),n=i.find(".line");this.$panel.append(i);for(var s in t){var a=o(this._templateBox(t[s]));e.top&&(a.css("border-top","none"),a.css("border-top-left-radius","0px"),a.css("border-top-right-radius","0px")),e.bottom&&(a.css("border-bottom","none"),a.css("border-bottom-left-radius","0px"),a.css("border-bottom-right-radius","0px")),n.append(a)}return i},_templateCheck:function(){return'
'},_templateContent:function(){return'
'},_templateBox:function(e){return'
'},_template:function(){return'
'}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1))},function(e,t,n){var s,a;(function(o,r){s=[n(4),n(24)],a=function(e,t){var n=t.BaseIcons.extend({initialize:function(e){e.type=e.display||"checkbox",e.multiple="checkbox"==e.type,t.BaseIcons.prototype.initialize.call(this,e)},_setValue:function(e){if(t.BaseIcons.prototype._setValue.call(this,e),void 0!==e&&null!==e&&this.header_index){var i=this,n=o.isArray(e)?e:[e];r.each(n,function(e){var t=i.header_index[e];r.each(t,function(e){i._setState(e,!0)})})}},_setState:function(e,t){var i=this.$(".button-"+e),n=this.$(".subgroup-"+e);i.data("is_expanded",t),t?(n.show(),i.removeClass("fa-plus-square").addClass("fa-minus-square")):(n.hide(),i.removeClass("fa-minus-square").addClass("fa-plus-square"))},_templateOptions:function(){function t(e,t){var i=e.find(".button-"+t);i.on("click",function(){s._setState(t,!i.data("is_expanded"))})}function n(a,r,l){l=l||[];for(i in r){var c=r[i],d=c.options&&c.options.length>0,h=l.slice(0);s.header_index[c.value]=h.slice(0);var u=o("
");if(d){var p=e.uid(),f=o("
").addClass("button-"+p).addClass("ui-drilldown-button fa fa-plus-square"),g=o("
").addClass("subgroup-"+p).addClass("ui-drilldown-subgroup");u.append(o("
").append(f).append(s._templateOption({label:c.name,value:c.value}))),h.push(p),n(g,c.options,h),u.append(g),t(u,p)}else u.append(s._templateOption({label:c.name,value:c.value}));a.append(u)}}var s=this;this.header_index={};var a=o("
");return n(a,this.model.get("data")),a},_template:function(){return o("
").addClass("ui-options-list drilldown-container").attr("id",this.model.id)}});return{View:n}}.apply(t,s),!(void 0!==a&&(e.exports=a))}).call(t,n(1),n(2))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(7),i(25)],s=function(e,t,i){var n={DISABLED:"disabled",ENABLED:"enabled",LINKED:"linked"},s={data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:n.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:n.LINKED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:n.LINKED}],data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:n.DISABLED},{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collections",multiple:!0,batch:n.DISABLED}],data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:n.DISABLED}],workflow_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:n.DISABLED}],workflow_data_multiple:[{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:n.DISABLED}],workflow_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:n.DISABLED}],module_data:[{src:"hda",icon:"fa-file-o",tooltip:"Single dataset",multiple:!1,batch:n.DISABLED},{src:"hda",icon:"fa-files-o",tooltip:"Multiple datasets",multiple:!0,batch:n.ENABLED}],module_data_collection:[{src:"hdca",icon:"fa-folder-o",tooltip:"Dataset collection",multiple:!1,batch:n.DISABLED},{src:"hdca",icon:"fa-folder",tooltip:"Multiple collections",multiple:!0,batch:n.ENABLED}]},l=a.View.extend({initialize:function(e){var i=this;this.model=e&&e.model||new a.Model({src_labels:{hda:"dataset",hdca:"dataset collection"},pagelimit:100,statustimer:1e3}).set(e),this.setElement(o("
").addClass("ui-select-content")),this.button_product=new t.RadioButton.View({value:"false",data:[{icon:"fa fa-chain",value:"false",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",tooltip:"Unlinked dataset inputs will be run against *all* other inputs."}]});var n=o("
").addClass("ui-form-info").append(o("
").addClass("fa fa-sitemap")).append(o("
").html("This is a batch mode input field. 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")),c=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"),selectall:!1,error_text:"No "+(l?l+" ":"")+(c[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.$el.empty();var d=0;this.fields.length>1&&(this.$el.append(this.button_type.$el),d=Math.max(0,36*this.fields.length)+"px"),r.each(this.fields,function(e){n.$el.append(e.$el.css({"margin-left":d}))}),r.each(this.$batch,function(e,t){n.$el.append(e.css({"margin-left":d}))}),this.model.set("current",0),this._changeCurrent(),this._changeData()},_changeWait:function(){var e=this;r.each(this.fields,function(t){t[e.model.get("wait")?"wait":"unwait"]()})},_changeData:function(){var e=this.model.get("data"),t=this,i={};r.each(e,function(e,n){i[n]=[],r.each(e,function(e){i[n].push({hid:e.hid,keep:e.keep,label:e.hid+": "+e.name,value:e.id,tags:e.tags}),t.history[e.id+"_"+n]=e})}),r.each(this.config,function(e,n){i[e.src]&&t.fields[n].add(i[e.src],function(e,t){return t.hid-e.hid})})},_changeValue:function(){var e=this.model.get("value");if(e&&e.values&&e.values.length>0){var t=[];r.each(e.values,function(e){t.push(e.id)});for(var i=e.values[0].src,n=e.values.length>1,s=0;s
Select Library
'}});return{View:r}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3))},function(e,t,i){var n,s;(function(a,o){n=[i(4)],s=function(e){var t=a.View.extend({initialize:function(t){var i=this;this.model=t&&t.model||new a.Model({id:e.uid(),min:null,max:null,step:null,precise:!1,split:1e4,value:null,onchange:function(){}}).set(t),this.setElement(this._template()),this.$el.attr("id",this.model.id),this.$text=this.$(".ui-form-slider-text"),this.$slider=this.$(".ui-form-slider-element");var n=[];this.$text.on("change",function(){i.value(o(this).val())}).on("keyup",function(e){n[e.which]=!1}).on("keydown",function(e){var t=e.which;n[t]=!0,i.model.get("is_workflow")&&n[16]&&52==t?(i.value("$"),event.preventDefault()):8==t||9==t||13==t||37==t||39==t||t>=48&&t<=57&&!n[16]||t>=96&&t<=105||(190==t||110==t)&&o(this).val().indexOf(".")==-1&&i.model.get("precise")||(189==t||109==t)&&o(this).val().indexOf("-")==-1||i._isParameter(o(this).val())||n[91]||n[17]||event.preventDefault()});var s=this.model.attributes;this.has_slider=null!==s.max&&null!==s.min&&s.max>s.min;var r=s.step;r||(r=s.precise&&this.has_slider?(s.max-s.min)/s.split:1),this.has_slider?(this.$text.addClass("ui-form-slider-left"),this.$slider.slider({min:s.min,max:s.max,step:r}).on("slide",function(e,t){i.value(t.value)})):this.$slider.hide(),this.listenTo(this.model,"change",this.render,this),this.render()},render:function(){var e=this.model.get("value");this.has_slider&&this.$slider.slider("value",e),e!==this.$text.val()&&this.$text.val(e)},value:function(e){var t=this.model.attributes;return void 0!==e&&(null===e||""===e||this._isParameter(e)||(isNaN(e)&&(e=0),!t.precise&&(e=Math.round(e)),null!==t.max&&(e=Math.min(e,t.max)),null!==t.min&&(e=Math.max(e,t.min))),this.model.set("value",e),this.model.trigger("change"),t.onchange(e)),this.model.get("value")},_isParameter:function(e){return this.model.get("is_workflow")&&"$"===String(e).substring(0,1)},_template:function(){return'
'}});return{View:t}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1))},function(e,t,i){var n,s;(function(a,o){n=[i(4)],s=function(e){var t=a.View.extend({initialize:function(e){this.collection=new a.Collection,this.model=e&&e.model||new a.Model({onchange:null,visible:!0}).set(e),this.setElement(o(this._template())),this.$nav=this.$(".tab-navigation"),this.$content=this.$(".tab-content"),this.$el.on("click",function(){o(".tooltip").hide()}),this.render(),this.listenTo(this.model,"change",this.render,this),this.listenTo(this.collection,"add",this._add,this),this.listenTo(this.collection,"remove",this._remove,this),this.listenTo(this.collection,"change",this._change,this),this.listenTo(this.collection,"reset",this._reset,this),this.listenTo(this.collection,"add remove reset",this.render,this)},render:function(){var e=this.model.get("current");e=this.$("#"+e).length>0?e:this.first(),e&&(this.$nav.children().removeClass("active"),this.$content.children().removeClass("active"),this.$("#tab-"+e).addClass("active"),this.$("#"+e).addClass("active")),this.$el[this.model.get("visible")?"fadeIn":"fadeOut"]("fast"),this.$nav[this.size()>1?"show":"hide"]()},current:function(){return this.model.get("current")},show:function(e){e&&(this.model.set({current:e,visible:!0}),this.model.get("onchange")&&this.model.get("onchange")(e))},hide:function(){this.model.set("visible",!1)},first:function(){var e=this.collection.first();return e&&e.id},size:function(){return this.collection.length},add:function(e){this.collection.add(e)},del:function(e){this.collection.remove(e)},delAll:function(){this.collection.reset()},showTab:function(e){this.collection.get(e).set("hidden",!1)},hideTab:function(e){this.collection.get(e).set("hidden",!0)},_add:function(e){var t=this,i=e.attributes;this.$content.append(o("
").attr("id",i.id).addClass("tab-pane").append(i.$el)),this.$nav.append(o(this._template_tab(i)).show().tooltip({title:i.tooltip,placement:"bottom",container:t.$el}).on("click",function(e){e.preventDefault(),t.show(i.id)})),1==this.size()&&this.show(i.id)},_remove:function(e){this.$("#tab-"+e.id).remove(),this.$("#"+e.id).remove()},_reset:function(){this.$nav.empty(),this.$content.empty()},_change:function(e){this.$("#tab-"+e.id)[e.get("hidden")?"hide":"show"]()},_template:function(){return o("
").addClass("ui-tabs tabbable tabs-left").append(o("
").addClass("tab-navigation nav nav-tabs")).append(o("
").addClass("tab-content"))},_template_tab:function(e){var t=o("
").addClass("tab-element").attr("id","tab-"+e.id).append(o("
").attr("id","tab-title-link-"+e.id)),i=t.find("a");return e.icon&&i.append(o("
").addClass("tab-icon fa").addClass(e.icon)),i.append(o("
").attr("id","tab-title-text-"+e.id).addClass("tab-title-text").append(e.title)),t}});return{View:t}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4)],s=function(e){return a.View.extend({initialize:function(t){var i=this;this.options=e.merge(t,{class_add:"upload-icon-button fa fa-square-o",class_remove:"upload-icon-button fa fa-check-square-o",class_partial:"upload-icon-button fa fa-minus-square-o",collection:null,onchange:function(){},onadd:function(){},onremove:function(){}}),this.collection=this.options.collection,this.setElement(this._template()),this.rows=[],e.get({url:Galaxy.root+"api/remote_files",success:function(e){i._fill(e)},error:function(){i._fill()}})},_fill:function(t){if(t&&t.length>0){this.$(".upload-ftp-content").html(o(this._templateTable()));var i=0;for(index in t)this.rows.push(this._add(t[index])),i+=t[index].size;if(this.$(".upload-ftp-number").html(t.length+" files"),this.$(".upload-ftp-disk").html(e.bytesToString(i,!0)),this.collection){var n=this;this.$("._has_collection").show(),this.$select_all=this.$(".upload-selectall").addClass(this.options.class_add),this.$select_all.on("click",function(){var e=n.$select_all.hasClass(n.options.class_add);for(index in t){var i=t[index],s=n._find(i);(!s&&e||s&&!e)&&n.rows[index].trigger("click")}}),this._refresh()}}else this.$(".upload-ftp-content").html(o(this._templateInfo()));this.$(".upload-ftp-wait").hide()},_add:function(e){var t=this,i=o(this._templateRow(e)),n=i.find(".icon");return this.$("tbody").append(i),this.collection?(n.addClass(this._find(e)?this.options.class_remove:this.options.class_add),i.on("click",function(){var i=t._find(e);n.removeClass(),i?(t.options.onremove(i),n.addClass(t.options.class_add)):(t.options.onadd(e),n.addClass(t.options.class_remove)),t._refresh()})):i.on("click",function(){t.options.onchange(e)}),i},_refresh:function(){var e=this.collection.where({file_mode:"ftp",enabled:!0});this.$select_all.removeClass(),0==e.length?this.$select_all.addClass(this.options.class_add):this.$select_all.addClass(e.length==this.rows.length?this.options.class_remove:this.options.class_partial)},_find:function(e){var t=this.collection.findWhere({file_path:e.path,file_mode:"ftp",enabled:!0});return t&&t.get("id")},_templateRow:function(t){return'
'+r.escape(t.path)+' '+e.bytesToString(t.size)+' '+t.ctime+" "},_templateTable:function(){return'
Available files: '},_templateInfo:function(){return'
Your FTP directory does not contain any files.
'},_template:function(){return'
This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at '+this.options.ftp_upload_site+' using your Galaxy credentials (email address and password).
'}})}.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){n=[i(4)],s=function(e){return a.View.extend({options:{class_check:"fa-check-square-o",class_uncheck:"fa-square-o",parameters:[{id:"space_to_tab",title:"Convert spaces to tabs"},{id:"to_posix_lines",title:"Use POSIX standard"}]},initialize:function(e){this.model=e.model,this.setElement(o("
").addClass("upload-settings")),this.$el.append(o("
").addClass("upload-settings-cover")),this.$el.append(o("
").addClass("upload-settings-table ui-table-striped").append("
")),this.$cover=this.$(".upload-settings-cover"),this.$table=this.$(".upload-settings-table > tbody"),this.listenTo(this.model,"change",this.render,this),this.model.trigger("change")},render:function(){var e=this;this.$table.empty(),r.each(this.options.parameters,function(t){var i=o("
").addClass("upload-"+t.id+" upload-icon-button fa").addClass(e.model.get(t.id)&&e.options.class_check||e.options.class_uncheck).on("click",function(){e.model.get("enabled")&&e.model.set(t.id,!e.model.get(t.id))});e.$table.append(o("
").append(o("
").append(i)).append(o("
").append(t.title)))}),this.$cover[this.model.get("enabled")&&"hide"||"show"]()}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},,,function(e,t,i){(function(e,t){!function(i){e.event.props.push("dataTransfer"),i.uploadpost=function(t){var n=i.extend({},{data:{},success:function(){},error:function(){},progress:function(){},url:null,maxfilesize:2048,error_filesize:"File exceeds 2GB. Please use a FTP client.",error_default:"Please make sure the file is available.",error_server:"Upload request failed.",error_login:"Uploads require you to log in."},t),s=n.data;if(s.error_message)return void n.error(s.error_message);var a=new FormData;for(var o in s.payload)a.append(o,s.payload[o]);var r=0;for(var o in s.files){var l=s.files[o];a.append(l.name,l.file,l.file.name),r+=l.file.size}return r>1048576*n.maxfilesize?void n.error(n.error_filesize):(xhr=new XMLHttpRequest,xhr.open("POST",n.url,!0),xhr.setRequestHeader("Accept","application/json"),xhr.setRequestHeader("Cache-Control","no-cache"),xhr.setRequestHeader("X-Requested-With","XMLHttpRequest"),xhr.onreadystatechange=function(){if(xhr.readyState==xhr.DONE){var t=null;if(xhr.responseText)try{t=e.parseJSON(xhr.responseText)}catch(e){t=xhr.responseText}if(xhr.status<200||xhr.status>299){var i=xhr.statusText;403==xhr.status?i=n.error_login:0==xhr.status?i=n.error_server:i||(i=n.error_default),n.error(i+" ("+xhr.status+")")}else n.success(t)}},xhr.upload.addEventListener("progress",function(e){e.lengthComputable&&n.progress(Math.round(100*e.loaded/e.total))},!1),Galaxy.emit.debug("uploadbox::uploadpost()","Posting following data.",n),void xhr.send(a))},i.fn.uploadinput=function(e){var t=this,n=i.extend({},{ondragover:function(){},ondragleave:function(){},onchange:function(){},multiple:!1},e),s=i('
");return t.append(s.change(function(e){n.onchange(e.target.files),i(this).val("")})),t.on("drop",function(e){n.ondragleave(e),e.dataTransfer&&(n.onchange(e.dataTransfer.files),e.preventDefault())}),t.on("dragover",function(e){e.preventDefault(),n.ondragover(e)}),t.on("dragleave",function(e){e.stopPropagation(),n.ondragleave(e)}),{dialog:function(){s.trigger("click")}}},i.fn.uploadbox=function(e){function n(e){if(e&&e.length&&!m){var i=f;return t.each(e,function(e,i){"new"!==e.mode&&t.filter(p,function(t){return t.name===e.name&&t.size===e.size}).length&&(e.duplicate=!0)}),t.each(e,function(e){if(!e.duplicate){var t=String(f++);p[t]=e,u.announce(t,p[t]),g++}}),i}}function s(e){p[e]&&(delete p[e],g--)}function a(){if(0==g||v)return v=!1,m=!1,void u.complete();m=!0;var e=-1;for(var t in p){e=t;break}p[e];s(e),i.uploadpost({url:u.url,data:u.initialize(e),success:function(t){u.success(e,t),a()},error:function(t){u.error(e,t),a()},progress:function(t){u.progress(e,t)}})}function o(){_.dialog()}function r(e){for(e in p)s(e)}function l(){m||(m=!0,a())}function c(){v=!0}function d(e){return u=i.extend({},u,e)}function h(){return window.File&&window.FormData&&window.XMLHttpRequest&&window.FileList}var u=i.extend({},{dragover:function(){},dragleave:function(){},announce:function(e){},initialize:function(e){},progress:function(e,t){},success:function(e,t){},error:function(e,t){alert(t)},complete:function(){}},e),p={},f=0,g=0,m=!1,v=!1,_=i(this).uploadinput({multiple:!0,onchange:function(e){n(e)},ondragover:e.ondragover,ondragleave:e.ondragleave});return{select:o,add:n,remove:s,start:l,stop:c,reset:r,configure:d,compatible:h}}}(e)}).call(t,i(1),i(2))},,,,,,,,function(e,t,i){var n,s;(function(a,o){n=[i(6),i(5),i(18)],s=function(e,t){var i=a.View.extend(e.LoggableMixin).extend(e.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(e){e=e||{},this.tooltipConfig=e.tooltipConfig||{placement:"bottom"},this.listenTo(this.model,"change:annotation",function(){this.render()}),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.$el.html(this._template()),this.$annotation().make_text_editable({use_textarea:!0,on_finish:function(t){e.$annotation().text(t),e.model.save({annotation:t},{silent:!0}).fail(function(){e.$annotation().text(e.model.previous("annotation"))})}}),this},_template:function(){var e=this.model.get("annotation");return['
',t("Annotation")," ",'
',o.escape(e),"
"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off(),this.stopListening(this.model),a.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}});return{AnnotationEditor:i}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2))},function(e,t,i){var n,s;(function(a){n=[i(2),i(3),i(6)],s=function(e,t,i){"use strict";var n=t.Collection.extend({initialize:function(e,i){t.Collection.prototype.initialize.call(this,e,i),this.setOrder(i.order||this.order,{silent:!0})},_setUpListeners:function(){return this.on({"changed-order":this.sort})},fetch:function(e){return e=this._buildFetchOptions(e),t.Collection.prototype.fetch.call(this,e)},_buildFetchOptions:function(t){t=e.clone(t)||{};var i=this;t.traditional=!0,t.data=t.data||i._buildFetchData(t);var n=this._buildFetchFilters(t);return e.isEmpty(n)||e.extend(t.data,this._fetchFiltersToAjaxData(n)),t},_buildFetchData:function(t){var i={};return this.order&&(i.order=this.order),e.defaults(e.pick(t,this._fetchParams),i)},_fetchParams:["order","limit","offset","view","keys"],_buildFetchFilters:function(t){return e.clone(t.filters||{})},_fetchFiltersToAjaxData:function(t){var i={q:[],qv:[]};return e.each(t,function(e,t){void 0!==e&&""!==e&&(e===!0&&(e="True"),e===!1&&(e="False"),null===e&&(e="None"),i.q.push(t),i.qv.push(e))}),i},reset:function(e,i){return this.allFetched=!1,t.Collection.prototype.reset.call(this,e,i)},order:null,comparators:{update_time:i.buildComparator("update_time",{ascending:!1}),"update_time-asc":i.buildComparator("update_time",{ascending:!0}),create_time:i.buildComparator("create_time",{ascending:!1}),"create_time-asc":i.buildComparator("create_time",{ascending:!0})},setOrder:function(t,i){i=i||{};var n=this,s=n.comparators[t];if(e.isUndefined(s))throw new Error("unknown order: "+t);if(s!==n.comparator){n.order;return n.order=t,n.comparator=s,i.silent||n.trigger("changed-order",i),n}}}),s=n.extend({limitPerPage:500,initialize:function(e,t){n.prototype.initialize.call(this,e,t),this.currentPage=t.currentPage||0},getTotalItemCount:function(){return this.length},shouldPaginate:function(){return this.getTotalItemCount()>=this.limitPerPage},getLastPage:function(){return Math.floor(this.getTotalItemCount()/this.limitPerPage)},getPageCount:function(){return this.getLastPage()+1},getPageLimitOffset:function(e){return e=this.constrainPageNum(e),{limit:this.limitPerPage,offset:e*this.limitPerPage}},constrainPageNum:function(e){return Math.max(0,Math.min(e,this.getLastPage()))},fetchPage:function(t,i){var n=this;return t=n.constrainPageNum(t),n.currentPage=t,i=e.defaults(i||{},n.getPageLimitOffset(t)),n.trigger("fetching-more"),n.fetch(i).always(function(){n.trigger("fetching-more-done")})},fetchCurrentPage:function(e){return this.fetchPage(this.currentPage,e)},fetchPrevPage:function(e){return this.fetchPage(this.currentPage-1,e)},fetchNextPage:function(e){return this.fetchPage(this.currentPage+1,e)}}),o=n.extend({limitOnFirstFetch:null,limitPerFetch:100,initialize:function(e,t){n.prototype.initialize.call(this,e,t),this.limitOnFirstFetch=t.limitOnFirstFetch||this.limitOnFirstFetch,this.limitPerFetch=t.limitPerFetch||this.limitPerFetch,this.allFetched=!1,this.lastFetched=t.lastFetched||0},_buildFetchOptions:function(e){return e.remove=e.remove||!1,n.prototype._buildFetchOptions.call(this,e)},fetchFirst:function(t){return t=t?e.clone(t):{},this.allFetched=!1,this.lastFetched=0,this.fetchMore(e.defaults(t,{
+reset:!0,limit:this.limitOnFirstFetch}))},fetchMore:function(t){t=e.clone(t||{});var i=this;if(!t.reset&&i.allFetched)return a.when();t.offset=t.reset?0:t.offset||i.lastFetched;var n=t.limit=t.limit||i.limitPerFetch||null;return i.trigger("fetching-more"),i.fetch(t).always(function(){i.trigger("fetching-more-done")}).done(function(t){var s=e.isArray(t)?t.length:0;i.lastFetched+=s,(!n||s
','
',''].join(""))}};return{CollectionCreatorMixin:e}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(a){n=[i(87),i(41),i(40),i(6),i(5)],s=function(e,t,i,n,s){"use strict";var o="collections",r=e.ModelListPanel,l=r.extend({_logNamespace:o,className:r.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:i.DatasetDCEListItemView,NestedDCDCEViewClass:i.NestedDCDCEListItemView,modelCollectionKey:"elements",initialize:function(e){r.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,this.panelStack=[],this.parentName=e.parentName,this.foldoutStyle=e.foldoutStyle||"foldout",this.downloadUrl=this.model.attributes.url+"/download"},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;i.log("_queueNewRender:",e,t),i._swapNewRender(e),i.trigger("rendered",i)},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(e){switch(e.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",e.get("element_type"))},_getItemViewOptions:function(e){var t=r.prototype._getItemViewOptions.call(this,e);return a.extend(t,{linkTarget:this.linkTarget,hasUser:this.hasUser,foldoutStyle:this.foldoutStyle})},_setUpItemViewListeners:function(e){var t=this;return r.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}}),this},_expandDrilldownPanel:function(e){this.panelStack.push(e),this.$("> .controls").add(this.$list()).hide(),e.parentName=this.model.get("name"),this.$el.append(e.render().$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.render()},events:{"click .navigation .back":"close"},close:function(e){this.remove(),this.trigger("close")},toString:function(){return"CollectionView("+(this.model?this.model.get("name"):"")+")"}});l.prototype.templates=function(){var e=n.wrapTemplate(['
','
",'
','
<%- collection.name || collection.element_identifier %>
','
','<% if( collection.collection_type === "list" ){ %>',s("a list of datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',s("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',s("a list of paired datasets"),'<% } else if( collection.collection_type === "list:list" ){ %>',s("a list of dataset lists"),"<% } %>","
","
",'
','
","
"],"collection");return a.extend(a.clone(r.prototype.templates),{controls:e})}();var c=l.extend({DatasetDCEViewClass:i.DatasetDCEListItemView,toString:function(){return"ListCollectionView("+(this.model?this.model.get("name"):"")+")"}}),d=c.extend({toString:function(){return"PairCollectionView("+(this.model?this.model.get("name"):"")+")"}}),h=l.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemView.extend({foldoutPanelClass:d}),toString:function(){return"ListOfPairsCollectionView("+(this.model?this.model.get("name"):"")+")"}}),u=l.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemView.extend({foldoutPanelClass:d}),toString:function(){return"ListOfListsCollectionView("+(this.model?this.model.get("name"):"")+")"}});return{CollectionView:l,ListCollectionView:c,PairCollectionView:d,ListOfPairsCollectionView:h,ListOfListsCollectionView:u}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(a,o){n=[i(11),i(43),i(55),i(76),i(19),i(6),i(5)],s=function(e,t,i,n,s,r,l){"use strict";var c=t.DatasetListItemView,d=c.extend({initialize:function(e){c.prototype.initialize.call(this,e),this.hasUser=e.hasUser,this.purgeAllowed=e.purgeAllowed||!1,this.tagsEditorShown=e.tagsEditorShown||!1,this.annotationEditorShown=e.annotationEditorShown||!1},_renderPrimaryActions:function(){var t=c.prototype._renderPrimaryActions.call(this);return this.model.get("state")===e.NOT_VIEWABLE?t:c.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===e.DISCARDED||!this.model.get("accessible"))return null;var t=this.model.get("purged"),i=this.model.get("deleted"),n={title:l("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return i||t?(n.disabled=!0,t?n.title=l("Cannot edit attributes of datasets removed from disk"):i&&(n.title=l("Undelete dataset to edit attributes"))):a.contains([e.UPLOAD,e.NEW],this.model.get("state"))&&(n.disabled=!0,n.title=l("This dataset is not yet editable")),s(n)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var e=this,t=this.model.isDeletedOrPurged();return s({title:l(t?"Dataset is already deleted":"Delete"),disabled:t,faIcon:"fa-times",classes:"delete-btn",onclick:function(){e.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},_renderDetails:function(){var t=c.prototype._renderDetails.call(this),i=this.model.get("state");return!this.model.isDeletedOrPurged()&&a.contains([e.OK,e.FAILED_METADATA],i)&&(this._renderTags(t),this._renderAnnotation(t),this._makeDbkeyEditLink(t)),this._setUpBehaviors(t),t},_renderToolHelpButton:function(){var e=this.model.attributes.dataset_id,t=this.model.attributes.creating_job,i=this,n=function(t){var n='
';t.name&&t.help?(n+="Tool help for "+t.name+"
Tool help is unavailable for this dataset. ",i.$el.find(".details").append(o.parseHTML(n))},a=function(e){o.ajax({url:Galaxy.root+"api/tools/"+e.tool_id+"/build"}).done(function(e){n(e)}).fail(function(){n({})})};return null===Galaxy.user.id?null:s({title:"Tool Help",classes:"icon-btn",href:"#",faIcon:"fa-question",onclick:function(){i.$el.find(".toolhelp").length>0?i.$el.find(".toolhelp").toggle():o.ajax({url:Galaxy.root+"api/jobs/"+t}).done(function(e){a(e)}).fail(function(){console.log('Failed at recovering job information from the Galaxy API for job id "'+t+'".')})}})},_renderSecondaryActions:function(){var t=c.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case e.UPLOAD:case e.NOT_VIEWABLE:return t;case e.ERROR:return t.unshift(this._renderErrButton()),t.concat([this._renderRerunButton(),this._renderToolHelpButton()]);case e.OK:case e.FAILED_METADATA:return t.concat([this._renderRerunButton(),this._renderVisualizationsButton(),this._renderToolHelpButton()])}return t.concat([this._renderRerunButton(),this._renderToolHelpButton()])},_renderErrButton:function(){return s({title:l("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){var e=this.model.get("creating_job");if(this.model.get("rerunnable"))return s({title:l("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(t){t.preventDefault(),Galaxy.router.push("/",{job_id:e})}})},_renderVisualizationsButton:function(){var e=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||a.isEmpty(e))return null;if(!a.isObject(e[0]))return this.warn("Visualizations have been switched off"),null;var t=o(this.templates.visualizations(e,this));return t.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(t.find(".visualization-link").addBack(".visualization-link")),t},_addScratchBookFn:function(e){e.click(function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",url:o(this).attr("href")}),e.preventDefault(),e.stopPropagation())})},_renderTags:function(e){if(this.hasUser){var t=this;this.tagsEditor=new i.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.tagsEditorShown=!0},onhide:function(){t.tagsEditorShown=!1},$activator:s({title:l("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(e){if(this.hasUser){var t=this;this.annotationEditor=new n.AnnotationEditor({model:this.model,el:e.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.annotationEditorShown=!0},onhide:function(){t.annotationEditorShown=!1},$activator:s({title:l("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(e){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var t=o('
? ').attr("href",this.model.urls.edit).attr("target",this.linkTarget);e.find(".dbkey .value").replaceWith(t)}},events:a.extend(a.clone(c.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(e){this.trigger("edit",this,e)},"click .delete-btn":function(e){this.trigger("delete",this,e)},"click .rerun-btn":function(e){this.trigger("rerun",this,e)},"click .report-err-btn":function(e){this.trigger("report-err",this,e)},"click .visualization-btn":function(e){this.trigger("visualize",this,e)},"click .dbkey a":function(e){this.trigger("edit",this,e)}}),_clickUndeleteLink:function(e){return this.model.undelete(),!1},_clickPurgeLink:function(e){return confirm(l("This will permanently remove the data in your dataset. Are you sure?"))&&this.model.purge(),!1},toString:function(){var e=this.model?this.model+"":"(no model)";return"HDAEditView("+e+")"}});return d.prototype.templates=function(){var e=a.extend({},c.prototype.templates.warnings,{failed_metadata:r.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
","<% } %>"],"dataset"),deleted:r.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
',l("This dataset has been deleted"),'
',l("Undelete it")," ","<% if( view.purgeAllowed ){ %>",'
',l("Permanently remove it from disk")," ","<% } %>","
","<% } %>"],"dataset")}),t=r.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'
">',' ","<% } else { %>",'
","<% } %>"],"visualizations");return a.extend({},c.prototype.templates,{warnings:e,visualizations:t})}(),{DatasetListItemEdit:d}}.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(11),i(6),i(5)],s=function(e,t,i){"use strict";var n="dataset",s=t.SearchableModelMixin,l=a.Model.extend(t.LoggableMixin).extend(t.mixin(s,{_logNamespace:n,defaults:{state:e.NEW,deleted:!1,purged:!1,name:"(unnamed dataset)",accessible:!0,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(t,i){this.debug(this+"(Dataset).initialize",t,i),
//!! this state is not in trans.app.model.Dataset.states - set it here -
this.get("accessible")||this.set("state",e.NOT_VIEWABLE),this.urls=this._generateUrls(),this._setUpListeners()},_generateUrls:function(){var e=this.get("id");if(!e)return{};var t={purge:"datasets/"+e+"/purge_async",display:"datasets/"+e+"/display/?preview=True",edit:"datasets/"+e+"/edit",download:"datasets/"+e+"/display"+this._downloadQueryParameters(),report_error:"dataset/errors?id="+e,rerun:"tool_runner/rerun?id="+e,show_params:"datasets/"+e+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+e+"&metadata_name="};return o.each(t,function(e,i){t[i]=Galaxy.root+e}),this.urls=t,t},_downloadQueryParameters:function(){return"?to_ext="+this.get("file_ext")},_setUpListeners:function(){this.on("change:state",function(e,t){this.log(this+" has changed state:",e,t),this.inReadyState()&&this.trigger("state:ready",e,t,this.previous("state"))}),this.on("change:id change:file_ext",function(e){this._generateUrls()})},toJSON:function(){var e=a.Model.prototype.toJSON.call(this);return o.extend(e,{urls:this.urls})},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},inReadyState:function(){var t=o.contains(e.READY_STATES,this.get("state"));return this.isDeletedOrPurged()||t},hasDetails:function(){return!this.get("accessible")||this.has("annotation")},hasData:function(){return this.get("file_size")>0},fetch:function(e){var t=this;return a.Model.prototype.fetch.call(this,e).always(function(){t._generateUrls()})},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},save:function(e,t){return t=t||{},t.wait=!!o.isUndefined(t.wait)||t.wait,a.Model.prototype.save.call(this,e,t)},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)},purge:function(e){if(this.get("purged"))return r.when();e=e||{},e.url=this.urls.purge;var t=this,n=r.ajax(e);return n.done(function(e,i,n){t.set({deleted:!0,purged:!0})}),n.fail(function(n,s,a){var o=i("Unable to purge dataset"),r="Removal of datasets by users is not allowed in this Galaxy instance";n.responseJSON&&n.responseJSON.error?o=n.responseJSON.error:n.responseText.indexOf(r)!==-1&&(o=r),n.responseText=o,t.trigger("error",t,n,e,i(o),{error:o})}),n},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var e=this.get("id")||"";return this.get("name")&&(e='"'+this.get("name")+'",'+e),"Dataset("+e+")"}})),c=a.Collection.extend(t.LoggableMixin).extend({_logNamespace:n,model:l,urlRoot:Galaxy.root+"api/datasets",url:function(){return this.urlRoot},ids:function(){return this.map(function(e){return e.get("id")})},notReady:function(){return this.filter(function(e){return!e.inReadyState()})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},ajaxQueue:function(e,t){var i=r.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var a=this.chain().reverse().map(function(o,r){return function(){var l=e.call(o,t);l.done(function(e){i.notify({curr:r,total:n,response:e,model:o})}),l.always(function(e){s.push(e),a.length?a.shift()():i.resolve(s)})}}).value();return a.shift()(),i},matches:function(e){return this.filter(function(t){return t.matches(e)})},toString:function(){return["DatasetAssociationCollection(",this.length,")"].join("")}});return{DatasetAssociation:l,DatasetAssociationCollection:c}}.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){n=[i(8),i(90),i(5)],s=function(e,t,i){"use strict";var n={defaultName:a.template("Copy of '<%- name %>'"),title:a.template(i("Copying history")+' "<%- name %>"'),submitLabel:i("Copy"),errorMessage:i("History could not be copied."),progressive:i("Copying history"),activeLabel:i("Copy only the active, non-deleted datasets"),allLabel:i("Copy all datasets including deleted ones"),anonWarning:i("As an anonymous user, unless you login or register, you will lose your current history ")+i("after copying this history. "),_template:a.template(["<% if( isAnon ){ %>",'
',"<%- anonWarning %>",i("You can"),'
',i("login here")," ",i("or")," ",'
',i("register here")," .","
","<% } %>","
"].join("")),_showAjaxIndicator:function(){var e='
";this.modal.$(".modal-body").empty().append(e).css({"margin-top":"8px"})},dialog:function(e,n,s){function l(){var i=e.$("#copy-modal-title").val();if(!i)return void e.$(".invalid-title").show();var s="copy-all"===e.$('input[name="copy-what"]:checked').val();e.$("button").prop("disabled",!0),c._showAjaxIndicator(),n.copy(!0,i,s).done(function(e){d.resolve(e)}).fail(function(e,a,o){var r={name:i,copyAllDatasets:s};t.ajaxErrorModal(n,e,r,c.errorMessage),d.rejectWith(d,arguments)}).done(function(){g&&e.hide()})}s=s||{};var c=this,d=o.Deferred(),h=s.nameFn||this.defaultName,u=h({name:n.get("name")}),p=s.allDatasets?"copy-all":"copy-non-deleted",f=!!a.isUndefined(s.allowAll)||s.allowAll,g=!!a.isUndefined(s.autoClose)||s.autoClose;this.modal=e;var m=s.closing_callback;return e.show(a.extend(s,{title:this.title({name:n.get("name")}),body:r(c._template({name:u,isAnon:Galaxy.user.isAnonymous(),allowAll:f,copyWhat:p,activeLabel:this.activeLabel,allLabel:this.allLabel,anonWarning:this.anonWarning})),buttons:a.object([[i("Cancel"),function(){e.hide()}],[this.submitLabel,l]]),height:"auto",closing_events:!0,closing_callback:function(e){e&&d.reject({cancelled:!0}),m&&m(e)}})),e.$("#copy-modal-title").focus().select(),e.$("#copy-modal-title").on("keydown",function(e){13===e.keyCode&&(e.preventDefault(),l())}),d}},s=a.extend({},n,{defaultName:a.template("imported: <%- name %>"),title:a.template(i("Importing history")+' "<%- name %>"'),submitLabel:i("Import"),errorMessage:i("History could not be imported."),progressive:i("Importing history"),activeLabel:i("Import only the active, non-deleted datasets"),allLabel:i("Import all datasets including deleted ones"),anonWarning:i("As an anonymous user, unless you login or register, you will lose your current history ")+i("after importing this history. ")}),l=function(t,i){i=i||{};var a=window.parent.Galaxy.modal||new e.View({});return i.useImport?s.dialog(a,t,i):n.dialog(a,t,i)};return l}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(1))},function(e,t,i){var n,s;(function(a){n=[i(43),i(6),i(5)],s=function(e,t,i){"use strict";var n=e.DatasetListItemView,s=n.extend({className:n.prototype.className+" history-content",initialize:function(e,t){n.prototype.initialize.call(this,e,t)},toString:function(){var e=this.model?this.model+"":"(no model)";return"HDAListItemView("+e+")"}});return s.prototype.templates=function(){var e=t.wrapTemplate(['
','
','
','<%- dataset.hid %> ','<%- dataset.name %> ',"
","",'
',"<% _.each(_.sortBy(_.uniq(dataset.tags), function(x) { return x }), function(tag){ %>",'<% if (tag.indexOf("name:") == 0){ %>','<%- tag.slice(5) %> ',"<% } %>","<% }); %>"," ","
"],"dataset"),s=a.extend({},n.prototype.templates.warnings,{hidden:t.wrapTemplate(["<% if( !dataset.visible ){ %>",'
',i("This dataset has been hidden"),"
","<% } %>"],"dataset")});return a.extend({},n.prototype.templates,{titleBar:e,warnings:s})}(),{HDAListItemView:s}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(a){n=[i(81),i(86),i(6),i(5)],s=function(e,t,i,n){"use strict";var s=e.DatasetAssociation,o=t.HistoryContentMixin,r=s.extend(i.mixin(o,{defaults:a.extend({},s.prototype.defaults,o.defaults,{history_content_type:"dataset",model_class:"HistoryDatasetAssociation"})}));return{HistoryDatasetAssociation:r}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(a){n=[i(11),i(40),i(79),i(6),i(5)],s=function(e,t,i,n,s){"use strict";var o=t.DCListItemView,r=o.extend({className:o.prototype.className+" history-content",_setUpListeners:function(){o.prototype._setUpListeners.call(this),this.listenTo(this.model,{"change:tags change:populated change:visible":function(e,t){this.render()}})},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return i.ListCollectionView;case"paired":return i.PairCollectionView;case"list:paired":return i.ListOfPairsCollectionView;case"list:list":return i.ListOfListsCollectionView}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(t){o.prototype._swapNewRender.call(this,t);var i=this.model.get("populated")?e.OK:e.RUNNING;return this.$el.addClass("state-"+i),this.$el},toString:function(){var e=this.model?this.model+"":"(no model)";return"HDCAListItemView("+e+")"}});return r.prototype.templates=function(){var e=a.extend({},o.prototype.templates.warnings,{hidden:n.wrapTemplate(["<% if( !collection.visible ){ %>",'
',s("This collection has been hidden"),"
","<% } %>"],"collection")}),t=n.wrapTemplate(['
','
','
','<%- collection.hid %> ','<%- collection.name %> ',"
",'
','
',"<% _.each(_.sortBy(_.uniq(collection.tags), function(x) { return x }), function(tag){ %>",'<% if (tag.indexOf("name:") == 0){ %>','<%- tag.slice(5) %> ',"<% } %>","<% }); %>"," ","
"],"collection");return a.extend({},o.prototype.templates,{warnings:e,titleBar:t})}(),{HDCAListItemView:r}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(a){n=[i(11),i(6),i(5)],s=function(e,t,i){"use strict";var n={defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",hidden:function(){return!this.get("visible")},isVisible:function(e,t){var i=!0;return e||!this.get("deleted")&&!this.get("purged")||(i=!1),t||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var e=this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id");return e},hide:function(e){return this.get("visible")?this.save({visible:!1},e):a.when()},unhide:function(e){return this.get("visible")?a.when():this.save({visible:!0},e)},toString:function(){return[this.get("type_id"),this.get("hid"),this.get("name")].join(":")}};return{HistoryContentMixin:n}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1))},function(e,t,i){var n,s;(function(a,o,r){n=[i(54),i(145),i(6),i(5),i(94)],s=function(e,t,i,n){"use strict";var s="list",l=a.View.extend(i.LoggableMixin).extend({_logNamespace:s,viewClass:e.ListItemView,collectionClass:a.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:n("This list is empty"),noneFoundMsg:n("No matching items found"),searchPlaceholder:n("search"),initialize:function(e,t){e=e||{},e.logger&&(this.logger=e.logger),this.log(this+".initialize:",e),this.fxSpeed=o.has(e,"fxSpeed")?e.fxSpeed:this.fxSpeed,this.filters=[],this.searchFor=e.searchFor||"",this.selecting=void 0===e.selecting||e.selecting,this.selected=e.selected||[],this.lastSelected=null,this.dragItems=e.dragItems||!1,this.viewClass=e.viewClass||this.viewClass,this.views=[],this.collection=e.collection||this._createDefaultCollection(),this.filters=e.filters||[],this.$scrollContainer=e.$scrollContainer||this.$scrollContainer,this.title=e.title||"",this.subtitle=e.subtitle||"",this._setUpListeners()},_setUpListeners:function(){return this.off(),this.on({error:function(e,t,i,n,s){console.error(e,t,i,n,s)},loading:function(){this._showLoadingIndicator("loading...",40)},"loading-done":function(){this._hideLoadingIndicator(40)}}),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this._setUpCollectionListeners(),this._setUpViewListeners(),this},_createDefaultCollection:function(){return new this.collectionClass([])},_setUpCollectionListeners:function(){return this.log(this+"._setUpCollectionListeners",this.collection),this.stopListening(this.collection),this.listenTo(this.collection,{error:function(e,t,i,n,s){this.trigger("error",e,t,i,n,s)},update:function(e,t){var i=t.changes;return t.renderAll||i.added.length+i.removed.length>1?this.renderItems():1===i.added.length?this.addItemView(o.first(i.added),e,t):1===i.removed.length?this.removeItemView(o.first(i.removed),e,t):void 0}}),this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners"),this.on({"view:selected":function(e,t){if(t&&t.shiftKey&&this.lastSelected){var i=this.viewFromModelId(this.lastSelected);i&&this.selectRange(e,i)}else t&&t.altKey&&!this.selecting&&this.showSelectors();this.selected.push(e.model.id),this.lastSelected=e.model.id},"view:de-selected":function(e,t){this.selected=o.without(this.selected,e.model.id)}})},render:function(e){this.log(this+".render",e);var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var e=r(this.templates.el({},this));return this._renderControls(e),this._renderTitle(e),this._renderSubtitle(e),this._renderSearch(e),this.renderItems(e),e},_renderControls:function(e){this.debug(this+"(ListPanel)._renderControls");var t=r(this.templates.controls({},this));return e.find(".controls").replaceWith(t),t},_renderTitle:function(e){},_renderSubtitle:function(e){},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;i.log("_queueNewRender:",e,t),r(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",this.className).append(e.children()),this.selecting&&this.showSelectors(0),this},_setUpBehaviors:function(e){return e=e||this.$el,this.$controls(e).find("[title]").tooltip(),this._renderMultiselectActionMenu(e),this},_renderMultiselectActionMenu:function(e){e=e||this.$el;var t=e.find(".list-action-menu"),i=this.multiselectActions();if(!i.length)return t.empty();var s=r(['"].join("")),a=i.map(function(e){var t=['
',e.html," "].join("");return r(t).click(function(t){return t.preventDefault(),e.func(t)})});return s.find("ul").append(a),t.replaceWith(s),s},multiselectActions:function(){return[]},$scrollContainer:function(e){return(e||this.$el).parent().parent()},$controls:function(e){return(e||this.$el).find("> .controls")},$list:function(e){return(e||this.$el).find("> .list-items")},$messages:function(e){return(e||this.$el).find("> .controls .messages")},$emptyMessage:function(e){return(e||this.$el).find("> .empty-message")},renderItems:function(e){e=e||this.$el;var t=this;t.log(this+".renderItems",e);var i=t.$list(e);t.freeViews();var n=t._filterCollection();return t.views=n.map(function(e){var i=t._createItemView(e);return i}),i.empty(),t.views.length&&t._attachItems(e),t._renderEmptyMessage(e).toggle(!t.views.length),t.trigger("views:ready",t.views),t.views},_filterCollection:function(){var e=this;return e.collection.filter(o.bind(e._filterItem,e))},_filterItem:function(e){var t=this;return o.every(t.filters.map(function(t){return t.call(e)}))&&(!t.searchFor||e.matchesAll(t.searchFor))},_createItemView:function(e){var t=this._getItemViewClass(e),i=o.extend(this._getItemViewOptions(e),{model:e}),n=new t(i);return this._setUpItemViewListeners(n),n},_destroyItemView:function(e){this.stopListening(e),this.views=o.without(this.views,e)},_destroyItemViews:function(e){var t=this;return t.views.forEach(function(e){t.stopListening(e)}),t.views=[],t},freeViews:function(){return this._destroyItemViews()},_getItemViewClass:function(e){return this.viewClass},_getItemViewOptions:function(e){return{fxSpeed:this.fxSpeed,expanded:!1,selectable:this.selecting,selected:o.contains(this.selected,e.id),draggable:this.dragItems}},_setUpItemViewListeners:function(e){var t=this;return this.listenTo(e,"all",function(){var e=Array.prototype.slice.call(arguments,0);e[0]="view:"+e[0],t.trigger.apply(t,e)}),this.listenTo(e,"draggable:dragstart",function(e,t){var i={},n=this.getSelectedModels();i=n.length?n.toJSON():[t.model.toJSON()],e.dataTransfer.setData("text",JSON.stringify(i))},this),t},_attachItems:function(e){var t=this;return this.$list(e).append(this.views.map(function(e){return t._renderItemView$el(e)})),this},_renderItemView$el:function(e){return e.render(0).$el},_renderEmptyMessage:function(e){this.debug("_renderEmptyMessage",e,this.searchFor);var t=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(e).text(t)},expandAll:function(){o.each(this.views,function(e){e.expand()})},collapseAll:function(){o.each(this.views,function(e){e.collapse()})},addItemView:function(e,t,i){var n=this,s=n._filterCollection().indexOf(e);if(s!==-1){var a=n._createItemView(e);return r(a).queue("fx",[function(e){n.$emptyMessage().is(":visible")?n.$emptyMessage().fadeOut(n.fxSpeed,e):e()},function(e){n._attachView(a,s),e()}]),a}},_attachView:function(e,t,i){i=!!o.isUndefined(i)||i,t=t||0;var n=this;return n.views.splice(t,0,e),n._insertIntoListAt(t,n._renderItemView$el(e).hide()),n.trigger("view:attached",e),i?e.$el.slideDown(n.fxSpeed,function(){n.trigger("view:attached:rendered")}):(e.$el.show(),n.trigger("view:attached:rendered")),e},_insertIntoListAt:function(e,t){var i=this.$list();return 0===e?i.prepend(t):i.children().eq(e-1).after(t),t},removeItemView:function(e,t,i){var n=this,s=o.find(n.views,function(t){return t.model===e});if(s)return n.views=o.without(n.views,s),n.trigger("view:removed",s),r({}).queue("fx",[function(e){s.$el.fadeOut(n.fxSpeed,e)},function(e){s.remove(),n.trigger("view:removed:rendered"),n.views.length?e():n._renderEmptyMessage().fadeIn(n.fxSpeed,e)}]),s},viewFromModelId:function(e){return o.find(this.views,function(t){return t.model.id===e})},viewFromModel:function(e){return e?this.viewFromModelId(e.id):void 0},viewsWhereModel:function(e){return this.views.filter(function(t){return o.isMatch(t.model.attributes,e)})},viewRange:function(e,t){if(e===t)return e?[e]:[];var i=this.views.indexOf(e),n=this.views.indexOf(t);return i===-1||n===-1?i===n?[]:i===-1?[t]:[e]:i
.controls .search-query");return i.val()!==e&&i.val(e),this},clearSearch:function(e){return this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.renderItems(),this},THROTTLE_SELECTOR_FX_AT:20,showSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!0,this.$(".list-actions").slideDown(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,o.each(this.views,function(t){t.showSelector(e)})},hideSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!1,this.$(".list-actions").slideUp(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,o.each(this.views,function(t){t.hideSelector(e)}),this.selected=[],this.lastSelected=null},toggleSelectors:function(){this.selecting?this.hideSelectors():this.showSelectors()},selectAll:function(e){o.each(this.views,function(t){t.select(e)})},deselectAll:function(e){this.lastSelected=null,o.each(this.views,function(t){t.deselect(e)})},selectRange:function(e,t){var i=this.viewRange(e,t);return o.each(i,function(e){e.select()}),i},getSelectedViews:function(){return o.filter(this.views,function(e){return e.selected})},getSelectedModels:function(){return new this.collection.constructor(o.map(this.getSelectedViews(),function(e){return e.model}))},_showLoadingIndicator:function(e,i,n){this.debug("_showLoadingIndicator",this.indicator,e,i,n),i=void 0!==i?i:this.fxSpeed,this.indicator||(this.indicator=new t(this.$el),this.debug("\t created",this.indicator)),this.$el.is(":visible")?(this.$el.fadeOut(i),this.indicator.show(e,i,n)):this.indicator.show(0,n)},_hideLoadingIndicator:function(e,t){this.debug("_hideLoadingIndicator",this.indicator,e,t),e=void 0!==e?e:this.fxSpeed,this.indicator&&this.indicator.hide(e,t)},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(e,t){return t=t||0,this.$scrollContainer().animate({scrollTop:e},t),this},scrollToTop:function(e){return this.scrollTo(0,e)},scrollToItem:function(e,t){return e?this:this},scrollToId:function(e,t){return this.scrollToItem(this.viewFromModelId(e),t)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});l.prototype.templates=function(){var e=i.wrapTemplate([""]),t=i.wrapTemplate(['','
",'
<%- view.subtitle %>
','
','
','
",'
','
','',n("All")," ",'',n("None")," ","
",'","
","
','
",'
<%- view.subtitle %>
','
','
','
",'
','
','',n("All")," ",'',n("None")," ","
",'","
","
").addClass("ui-form-composite").append(this.$message=o("
")).append(this.$header=o("
")).append(this.$steps=o("
"))),o("body").append(this.$el),this._configure(),this.render(),o(window).resize(function(){i._refresh()})},_refresh:function(e){var t=r.reduce(this.$el.children(),function(e,t){return e+o(t).outerHeight()},0)-this.$steps.height()+90;this.$steps.css("height",o(window).height()-t)},_configure:function(){function t(e,t){for(var s=/\$\{(.+?)\}/g;match=s.exec(String(e));){var a=match[1];t(i.wp_inputs[a]=i.wp_inputs[a]||{label:a,name:a,type:"text",color:"hsl( "+100*++n+", 70%, 30% )",style:"ui-form-wp-source",links:[]})}}var i=this;this.forms=[],this.steps=[],this.links=[],this.parms=[],r.each(this.model.get("steps"),function(t,n){Galaxy.emit.debug("tool-form-composite::initialize()",n+" : Preparing workflow step.");var s=h[t.step_type],a=parseInt(n+1)+": "+(t.step_label||t.step_name);t.annotation&&(a+=" - "+t.annotation),t.step_version&&(a+=" (Galaxy Version "+t.step_version+")"),t=e.merge({index:n,title:r.escape(a),icon:s||"",help:null,citations:null,collapsible:!0,collapsed:n>0&&!i._isDataStep(t),sustain_version:!0,sustain_repeats:!0,sustain_conditionals:!0,narrow:!0,text_enable:"Edit",text_disable:"Undo",cls_enable:"fa fa-edit",cls_disable:"fa fa-undo",errors:t.messages,initial_errors:!0,cls:"ui-portlet-narrow",hide_operations:!0,needs_refresh:!1,always_refresh:"tool"!=t.step_type},t),i.steps[n]=t,i.links[n]=[],i.parms[n]={}}),r.each(this.steps,function(e,t){s.visitInputs(e.inputs,function(e,n){i.parms[t][n]=e})}),r.each(this.steps,function(e,t){r.each(e.output_connections,function(e){r.each(i.steps,function(n,s){n.step_index===e.input_step_index&&i.links[t].push(n)})})}),r.each(this.steps,function(e,t){r.each(i.steps,function(n,s){var a={};r.each(e.output_connections,function(e){n.step_index===e.input_step_index&&(a[e.input_name]=e)}),r.each(i.parms[s],function(i,n){var s=a[n];s&&(i.type="hidden",i.help=i.step_linked?i.help+", ":"",i.help+="Output dataset '"+s.output_name+"' from step "+(parseInt(t)+1),i.step_linked=i.step_linked||[],i.step_linked.push(e))})})});var n=0;this.wp_inputs={},r.each(this.steps,function(e,n){r.each(i.parms[n],function(i,n){t(i.value,function(t){t.links.push(e),i.wp_linked=!0,i.type="text",i.backdrop=!0,i.style="ui-form-wp-target"})}),r.each(e.post_job_actions,function(e){r.each(e.action_arguments,function(e){t(e,function(){})})})}),r.each(this.steps,function(t,n){if("tool"==t.step_type){var a=!0;s.visitInputs(t.inputs,function(n,s,o){var r=n.value&&"RuntimeValue"==n.value.__class__,l=["data","data_collection"].indexOf(n.type)!=-1,c=o[n.data_ref];n.step_linked&&!i._isDataStep(n.step_linked)&&(a=!1),n.options&&(0==n.options.length&&!a||n.wp_linked)&&(n.is_workflow=!0),c&&(n.is_workflow=c.step_linked&&!i._isDataStep(c.step_linked)||n.wp_linked),(l||n.value&&"RuntimeValue"==n.value.__class__&&!n.step_linked)&&(t.collapsed=!1),r&&(n.value=n.default_value),n.flavor="workflow",r||l||"hidden"===n.type||n.wp_linked||(n.optional||!e.isEmpty(n.value)&&""!==n.value)&&(n.collapsible_value=n.value,n.collapsible_preview=!0)})}})},render:function(){var e=this;this.deferred.reset(),this._renderHeader(),this._renderMessage(),this._renderParameters(),this._renderHistory(),r.each(this.steps,function(t){e._renderStep(t)})},_renderHeader:function(){var e=this;this.execute_btn=new i.Button({icon:"fa-check",title:"Run workflow",cls:"btn btn-primary",onclick:function(){e._execute()}}),this.$header.addClass("ui-form-header").empty().append(new i.Label({title:"Workflow: "+this.model.get("name")}).$el).append(this.execute_btn.$el)},_renderMessage:function(){this.$message.empty(),this.model.get("has_upgrade_messages")&&this.$message.append(new i.Message({message:"Some tools in this workflow may have changed since it was last saved or some errors were found. The workflow may still run, but any new options will have default values. Please review the messages below to make a decision about whether the changes will affect your analysis.",status:"warning",persistent:!0,fade:!1}).$el);var e=this.model.get("step_version_changes");e&&e.length>0&&this.$message.append(new i.Message({message:"Some tools are being executed with different versions compared to those available when this workflow was last saved because the other versions are not or no longer available on this Galaxy instance. To upgrade your workflow and dismiss this message simply edit the workflow and re-save it.",status:"warning",persistent:!0,fade:!1}).$el)},_renderParameters:function(){var e=this;this.wp_form=null,r.isEmpty(this.wp_inputs)||(this.wp_form=new n({title:"Workflow Parameters ",inputs:this.wp_inputs,cls:"ui-portlet-narrow",onchange:function(){r.each(e.wp_form.input_list,function(t,i){r.each(t.links,function(t){e._refreshStep(t)})})}}),this._append(this.$steps.empty(),this.wp_form.$el))},_renderHistory:function(){this.history_form=new n({cls:"ui-portlet-narrow",title:"History Options ",inputs:[{type:"conditional",name:"new_history",test_param:{name:"check",label:"Send results to a new history",type:"boolean",value:"false",help:""},cases:[{value:"true",inputs:[{name:"name",label:"History name",type:"text",value:this.model.get("name")}]}]}]}),this._append(this.$steps,this.history_form.$el)},_renderStep:function(t){var i=this,s=null;this.deferred.execute(function(a){if(i.$steps.addClass("ui-steps"),"tool"==t.step_type)t.postchange=function(i,n){var s={tool_id:t.id,tool_version:t.version,inputs:o.extend(!0,{},n.data.create())};n.wait(!0),Galaxy.emit.debug("tool-form-composite::postchange()","Sending current state.",s),e.request({type:"POST",url:Galaxy.root+"api/tools/"+t.id+"/build",data:s,success:function(e){n.update(e),n.wait(!1),Galaxy.emit.debug("tool-form-composite::postchange()","Received new model.",e),i.resolve()},error:function(e){Galaxy.emit.debug("tool-form-composite::postchange()","Refresh request failed.",e),
-i.reject()}})},s=new l(t),t.post_job_actions&&t.post_job_actions.length&&s.portlet.append(o("
").addClass("ui-form-element-disabled").append(o("
").addClass("ui-form-title").html("Job Post Actions ")).append(o("
").addClass("ui-form-preview").html(r.reduce(t.post_job_actions,function(e,t){return e+" "+t.short_str},""))));else{var c=["data_input","data_collection_input"].indexOf(t.step_type)!=-1;r.each(t.inputs,function(e){e.flavor="module",e.hide_label=c}),s=new n(e.merge({title:t.title,onchange:function(){r.each(i.links[t.index],function(e){i._refreshStep(e)})},inputs:t.inputs&&t.inputs.length>0?t.inputs:[{type:"hidden",name:"No options available.",ignore:null}]},t))}i.forms[t.index]=s,i._append(i.$steps,s.$el),i._refresh(),t.needs_refresh&&i._refreshStep(t),s.portlet[i.show_progress?"disable":"enable"](),i.show_progress&&i.execute_btn.model.set({wait:!0,wait_text:"Preparing...",percentage:100*(t.index+1)/i.steps.length}),Galaxy.emit.debug("tool-form-composite::initialize()",t.index+" : Workflow step state ready.",t),setTimeout(function(){a.resolve()},0)})},_refreshStep:function(e){var t=this,i=this.forms[e.index];i?(r.each(t.parms[e.index],function(e,n){if(e.step_linked||e.wp_linked){var s=i.field_list[i.data.match(n)];if(s){var a=void 0;if(e.step_linked)a={values:[]},r.each(e.step_linked,function(e){t._isDataStep(e)&&(value=t.forms[e.index].data.create().input,value&&r.each(value.values,function(e){a.values.push(e)}))}),!e.multiple&&a.values.length>0&&(a={values:[a.values[0]]});else if(e.wp_linked){a=e.value;for(var o=/\$\{(.+?)\}/g;match=o.exec(e.value);){var l=t.wp_form.field_list[t.wp_form.data.match(match[1])],c=l&&l.value();c&&(a=a.split(match[0]).join(c))}}void 0!==a&&s.value(a)}}}),i.trigger("change")):e.needs_refresh=!0},_refreshHistory:function(){var e=this,t=parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.model;this._refresh_history&&clearTimeout(this._refresh_history),t&&t.refresh().success(function(){0===t.numOfUnfinishedShownContents()&&(e._refresh_history=setTimeout(function(){e._refreshHistory()},t.UPDATE_DELAY))})},_execute:function(){var e=this;this.show_progress=!0,this._enabled(!1),this.deferred.execute(function(t){setTimeout(function(){t.resolve(),e._submit()},0)})},_submit:function(){var t=this,i=this.history_form.data.create(),n={new_history_name:i["new_history|name"]?i["new_history|name"]:null,history_id:i["new_history|name"]?null:this.model.get("history_id"),replacement_params:this.wp_form?this.wp_form.data.create():{},parameters:{},parameters_normalized:!0,batch:!0},s=!0;for(var a in this.forms){var r=this.forms[a],l=r.data.create(),c=t.steps[a],h=c.step_index;r.trigger("reset");for(var u in l){var p=l[u],f=r.data.match(u),g=(r.field_list[f],r.input_list[f]);if(!g.step_linked){if(s=this._isDataStep(c)?p&&p.values&&p.values.length>0:g.optional||g.is_workflow&&""!==p||!g.is_workflow&&null!==p,!s){r.highlight(f);break}n.parameters[h]=n.parameters[h]||{},n.parameters[h][u]=l[u]}}if(!s)break}s?(Galaxy.emit.debug("tool-form-composite::submit()","Validation complete.",n),e.request({type:"POST",url:Galaxy.root+"api/workflows/"+this.model.id+"/invocations",data:n,success:function(e){if(Galaxy.emit.debug("tool-form-composite::submit","Submission successful.",e),t.$el.children().hide(),t.$el.append(t._templateSuccess(e)),o.isArray(e)&&e.length>0){t.$el.append(o("
",{id:"webhook-view"}));new d.WebhookView({urlRoot:Galaxy.root+"api/webhooks/workflow",toolId:n.tool_id,toolVersion:n.tool_version})}t._refreshHistory()},error:function(e){Galaxy.emit.debug("tool-form-composite::submit","Submission failed.",e);var i=!1;if(e&&e.err_data)for(var s in t.forms){var a=t.forms[s],o=e.err_data[a.model.get("step_index")];if(o){var r=a.data.matchResponse(o);for(var l in r){a.highlight(l,r[l]),i=!0;break}}}i||t.modal.show({title:"Workflow submission failed",body:t._templateError(n,e&&e.err_msg),buttons:{Close:function(){t.modal.hide()}}})},complete:function(){t._enabled(!0)}})):(t._enabled(!0),Galaxy.emit.debug("tool-form-composite::submit()","Validation failed.",n))},_append:function(e,t){e.append("
").append(t)},_enabled:function(e){this.execute_btn.model.set({wait:!e,wait_text:"Sending...",percentage:-1}),this.wp_form&&this.wp_form.portlet[e?"enable":"disable"](),this.history_form&&this.history_form.portlet[e?"enable":"disable"](),r.each(this.forms,function(t){t&&t.portlet[e?"enable":"disable"]()})},_isDataStep:function(e){lst=o.isArray(e)?e:[e];for(var t=0;t0?o("
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e=this;this.tool_panel.get("layout").size()>0&&(this.$el.prepend(this.tool_panel_view.$el),this.tool_panel_view.render()),e.$("#internal-workflows").append(e._templateAllWorkflow({title:o("All workflows"),href:"workflow"})),n.each(this.stored_workflow_menu_entries,function(t){e.$("#internal-workflows").append(e._templateWorkflowLink({title:t.stored_workflow.name,href:"workflow/run?id="+t.encoded_stored_workflow_id}))})},_templateTool:function(e){return['"].join("")},_templateAllWorkflow:function(e){return['"].join("")},_templateWorkflowLink:function(e){return['"].join("")},_template:function(){return['"].join("")},toString:function(){return"toolPanel"}}));e.exports=r}).call(t,i(3),i(2))},,,,,,,,,,,,,,,,,function(e,t,i){var n,s;(function(a,o){n=[i(40),i(80),i(6),i(5)],s=function(e,t,i,n){"use strict";var s=e.DCListItemView,r=s.extend({initialize:function(e){s.prototype.initialize.call(this,e)},toString:function(){var e=this.model?this.model+"":"(no 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n=t.model.get("name");e&&e!==n?(t.$el.find(i).text(e),t.model.save({name:e}).fail(function(){t.$el.find(i).text(t.model.previous("name"))})):t.$el.find(i).text(n)}}),this.tagsEditor=new s.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},usePrompt:!1}),this.tagsEditor.toggle(!0)}},toString:function(){return"CollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),c=l.extend({DatasetDCEViewClass:i.DatasetDCEListItemEdit,toString:function(){return"ListCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),d=c.extend({toString:function(){return"PairCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),h=d.extend({_setUpBehaviors:function(e){r.prototype._setUpBehaviors.call(this,e)},toString:function(){return"NestedPairCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),u=l.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemEdit.extend({foldoutPanelClass:h}),toString:function(){return"ListOfPairsCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}}),p=l.extend({NestedDCDCEViewClass:i.NestedDCDCEListItemEdit.extend({foldoutPanelClass:h}),toString:function(){return"ListOfListsCollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}});return{CollectionViewEdit:l,ListCollectionViewEdit:c,PairCollectionViewEdit:d,ListOfPairsCollectionViewEdit:u,ListOfListsCollectionViewEdit:p}}.apply(t,n),!(void 0!==s&&(e.exports=s))},function(e,t,i){var n,s;(function(a,o,r,l){n=[i(149),i(96),i(78),i(6),i(5),i(93)],s=function(e,t,i,n,s){"use strict";function c(e){function t(){return i.length||(i=[new RegExp(this.filters[0]),new RegExp(this.filters[1])]),i}e=e||{},e.createPair=e.createPair||function(e){e=e||{};var t=e.listA.splice(e.indexA,1)[0],i=e.listB.splice(e.indexB,1)[0],n=e.listB.indexOf(t),s=e.listA.indexOf(i);return n!==-1&&e.listB.splice(n,1),s!==-1&&e.listA.splice(s,1),this._pair(t,i,{silent:!0})};var i=[];return e.preprocessMatch=e.preprocessMatch||function(e){var i=t.call(this);return o.extend(e,{matchTo:e.matchTo.name.replace(i[0],""),possible:e.possible.name.replace(i[1],"")})},function(t){this.debug("autopair _strategy ---------------------------"),t=t||{};var i,n=t.listA,s=t.listB,a=0,o={score:0,index:null},r=[];for(this.debug("starting list lens:",n.length,s.length),this.debug("bestMatch (starting):",JSON.stringify(o,null," "));a=d?r.push(e.createPair.call(this,{listA:n,indexA:a,listB:s,indexB:o.index})):a+=1,!n.length||!s.length)return r}return this.debug("paired:",JSON.stringify(r,null," ")),this.debug("autopair _strategy ---------------------------"),r}}function d(e,t){var i=e.toJSON();return f(i,{historyId:e.historyId,defaultHideSourceItems:t})}var h="collections",u=a.View.extend(n.LoggableMixin).extend({_logNamespace:h,tagName:"li",className:"dataset paired",initialize:function(e){this.pair=e.pair||{}},template:o.template(['<%- pair.forward.name %> ','','<%- pair.name %> '," ",'<%- pair.reverse.name %> '].join("")),render:function(){return this.$el.attr("draggable",!0).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container"),this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(e){e.currentTarget.style.opacity="0.4",e.originalEvent&&(e=e.originalEvent),e.dataTransfer.effectAllowed="move",e.dataTransfer.setData("text/plain",JSON.stringify(this.pair)),this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(e){e.currentTarget.style.opacity="1.0",this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(e){this.$el.parent().trigger(e)},toString:function(){return"PairView("+this.pair.name+")"}}),p=a.View.extend(n.LoggableMixin).extend(i.CollectionCreatorMixin).extend({_logNamespace:h,className:"list-of-pairs-collection-creator collection-creator 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e.sort(function(e,i){return t(e.name,i.name)}),e},_ensureIds:function(){return this.initialList.forEach(function(e){e.hasOwnProperty("id")||(e.id=o.uniqueId())}),this.initialList},_splitByFilters:function(){function e(e,t){return t.test(e.name)}var t=this.filters.map(function(e){return new RegExp(e)}),i=[[],[]];return this.unpaired.forEach(function(n){t.forEach(function(t,s){e(n,t)&&i[s].push(n)})}),i},_addToUnpaired:function(e){var i=function(n,s){if(n===s)return n;var a=Math.floor((s-n)/2)+n,o=t(e.name,this.unpaired[a].name);if(o<0)return i(n,a);if(o>0)return i(a+1,s);for(;this.unpaired[a]&&this.unpaired[a].name===e.name;)a++;return a}.bind(this);this.unpaired.splice(i(0,this.unpaired.length),0,e)},autoPair:function(e){var t=this._splitByFilters(),i=[];return this.twoPassAutopairing&&(i=this.autopairSimple({listA:t[0],listB:t[1]}),t=this._splitByFilters()),e=e||this.strategy,t=this._splitByFilters(),i=i.concat(this[e].call(this,{listA:t[0],listB:t[1]}))},autopairSimple:c({scoreThreshold:function(){return 1},match:function(e){return e=e||{},e.matchTo===e.possible?{index:e.index,score:1}:e.bestMatch}}),autopairLevenshtein:c({scoreThreshold:function(){return this.matchPercentage},match:function(t){t=t||{};var i=e(t.matchTo,t.possible),n=1-i/Math.max(t.matchTo.length,t.possible.length);return n>t.bestMatch.score?{index:t.index,score:n}:t.bestMatch}}),autopairLCS:c({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var t=this._naiveStartingAndEndingLCS(e.matchTo,e.possible).length,i=t/Math.max(e.matchTo.length,e.possible.length);return i>e.bestMatch.score?{index:e.index,score:i}:e.bestMatch}}),_naiveStartingAndEndingLCS:function(e,t){for(var i="",n="",s=0,a=0;s=0&&a>=0&&e[s]===t[a];)n=[e[s],n].join(""),s-=1,a-=1;return i+n},_pair:function(e,t,i){i=i||{},this.debug("_pair:",e,t);var n=this._createPair(e,t,i.name);return this.paired.push(n),this.unpaired=o.without(this.unpaired,e,t),i.silent||this.trigger("pair:new",n),n},_createPair:function(e,t,i){if(!e||!t||e===t)throw new Error("Bad pairing: "+[JSON.stringify(e),JSON.stringify(t)]);return i=i||this._guessNameForPair(e,t),{forward:e,name:i,reverse:t}},_guessNameForPair:function(e,t,i){i=void 0!==i?i:this.removeExtensions;var n=e.name,s=t.name,a=this._naiveStartingAndEndingLCS(n.replace(new RegExp(this.filters[0]),""),s.replace(new RegExp(this.filters[1]),""));if(i){var o=a.lastIndexOf(".");if(o>0){var r=a.slice(o,a.length);a=a.replace(r,""),n=n.replace(r,""),s=s.replace(r,"")}}return a||n+" & "+s},_unpair:function(e,t){if(t=t||{},!e)throw new Error("Bad pair: "+JSON.stringify(e));return this.paired=o.without(this.paired,e),this._addToUnpaired(e.forward),this._addToUnpaired(e.reverse),t.silent||this.trigger("pair:unpair",[e]),e},unpairAll:function(){for(var e=[];this.paired.length;)e.push(this._unpair(this.paired[0],{silent:!0}));this.trigger("pair:unpair",e)},_pairToJSON:function(e,t){return t=t||"hda",{collection_type:"paired",src:"new_collection",name:e.name,element_identifiers:[{name:"forward",id:e.forward.id,src:t},{name:"reverse",id:e.reverse.id,src:t}]}},createList:function(e){var t=this,i=Galaxy.root+"api/histories/"+this.historyId+"/contents/dataset_collections",n={type:"dataset_collection",collection_type:"list:paired",hide_source_items:t.hideOriginals||!1,name:o.escape(e||t.$(".collection-name").val()),element_identifiers:t.paired.map(function(e){return t._pairToJSON(e)})};return t.blocking=!0,r.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(n)}).always(function(){t.blocking=!1}).fail(function(e,i,n){t._ajaxErrHandler(e,i,n)}).done(function(e,i,n){t.trigger("collection:created",e,i,n),t.metric("collection:created",e),"function"==typeof t.oncreate&&t.oncreate.call(this,e,i,n)})},_ajaxErrHandler:function(e,t,i){this.error(e,t,i);var n=s("An error occurred while creating this collection");e&&(n+=0===e.readyState&&0===e.status?": "+s("Galaxy could not be reached and may be updating.")+s(" Try again in a few minutes."):e.responseJSON?""+JSON.stringify(e.responseJSON)+" ":": "+i),creator._showAlert(n,"alert-danger")},render:function(e,t){return this.$el.empty().html(this.templates.main()),this._renderHeader(e),this._renderMiddle(e),this._renderFooter(e),this._addPluginComponents(),this.trigger("rendered",this),this},_renderHeader:function(e,t){var i=this.$(".header").empty().html(this.templates.header()).find(".help-content").prepend(l(this.templates.helpContent()));return this._renderFilters(),i},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(e,t){var i=this.$(".middle").empty().html(this.templates.middle());return this.unpairedPanelHidden?this.$(".unpaired-columns").hide():this.pairedPanelHidden&&this.$(".paired-columns").hide(),this._renderUnpaired(),this._renderPaired(),i},_renderUnpaired:function(e,t){var i,n,a=this,o=[],r=this._splitByFilters();return this.$(".forward-column .title").text([r[0].length,s("unpaired forward")].join(" ")),this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-r[0].length)),this.$(".reverse-column .title").text([r[1].length,s("unpaired reverse")].join(" ")),this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-r[1].length)),this.$(".unpaired-columns .column-datasets").empty(),this.$(".autopair-link").toggle(0!==this.unpaired.length),0===this.unpaired.length?void this._renderUnpairedEmpty():(n=r[1].map(function(e,t){return void 0!==r[0][t]&&r[0][t]!==e&&o.push(a._renderPairButton()),a._renderUnpairedDataset(e)}),i=r[0].map(function(e){return a._renderUnpairedDataset(e)}),i.length||n.length?(this.$(".unpaired-columns .forward-column .column-datasets").append(i).add(this.$(".unpaired-columns .paired-column .column-datasets").append(o)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(n)),void this._adjUnpairedOnScrollbar()):void this._renderUnpairedNotShown())},_renderUnpairedDisplayStr:function(e){return["(",e," ",s("filtered out"),")"].join("")},_renderUnpairedDataset:function(e){return l("
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"],"history");return a.extend(a.clone(l.prototype.templates),{quotaMsg:e})}(),{CurrentHistoryView:c}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(1))},function(e,t,i){var n,s;(function(a,o,r){n=[i(126),i(51),i(11),i(84),i(121),i(122),i(55),i(76),i(42),i(120),i(119),i(18),i(22),i(6),i(5),i(17)],
-s=function(e,t,i,n,s,l,c,d,h,u,p,f,g,m,v){"use strict";var _=e.HistoryView,y=_.extend({HDAViewClass:s.HDAListItemEdit,HDCAViewClass:l.HDCAListItemEdit,initialize:function(e){e=e||{},_.prototype.initialize.call(this,e),this.tagsEditor=null,this.dragItems=!0,this.annotationEditor=null,this.purgeAllowed=e.purgeAllowed||!1,this.annotationEditorShown=e.annotationEditorShown||!1,this.tagsEditorShown=e.tagsEditorShown||!1},_setUpListeners:function(){return _.prototype._setUpListeners.call(this),this.on({"droptarget:drop":function(e,t){this.dataDropped(t),this.dropTargetOff()},"view:attached view:removed":function(){this._renderCounts()},"search:loading-progress":this._renderSearchProgress,"search:searching":this._renderSearchFindings})},_setUpModelListeners:function(){return _.prototype._setUpModelListeners.call(this),this.listenTo(this.model,"change:size",this.updateHistoryDiskSize),this},_setUpCollectionListeners:function(){return _.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"change:deleted":this._handleItemDeletedChange,"change:visible":this._handleItemVisibleChange,"change:purged":function(e){this.model.fetch()},"fetching-deleted":function(e){this.$("> .controls .deleted-count").html(""+v("loading...")+" ")},"fetching-hidden":function(e){this.$("> .controls .hidden-count").html(""+v("loading...")+" ")},"fetching-deleted-done fetching-hidden-done":this._renderCounts}),this},_buildNewRender:function(){var e=_.prototype._buildNewRender.call(this);return this.model?(Galaxy&&Galaxy.user&&Galaxy.user.id&&Galaxy.user.id===this.model.get("user_id")&&(this._renderTags(e),this._renderAnnotation(e)),e):e},updateHistoryDiskSize:function(){this.$(".history-size").text(this.model.get("nice_size"))},renderItems:function(e){var t=_.prototype.renderItems.call(this,e);return this.searchFor||this._renderCounts(e),t},_renderCounts:function(e){e=e instanceof a?e:this.$el;var t=this.templates.counts(this.model.toJSON(),this);return e.find("> .controls .subtitle").html(t)},_renderTags:function(e){var t=this;this.tagsEditor=new c.TagsEditor({model:this.model,el:e.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDATagEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDATagEditors(!1,t.fxSpeed)},$activator:f({title:v("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".controls .actions"))})},_renderAnnotation:function(e){var t=this;this.annotationEditor=new d.AnnotationEditor({model:this.model,el:e.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDAAnnotationEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDAAnnotationEditors(!1,t.fxSpeed)},$activator:f({title:v("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".controls .actions"))})},_setUpBehaviors:function(e){if(e=e||this.$el,_.prototype._setUpBehaviors.call(this,e),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.model.get("user_id")){var t=this,i="> .controls .name";e.find(i).attr("title",v("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(e){var n=t.model.get("name");e&&e!==n?(t.$el.find(i).text(e),t.model.save({name:e}).fail(function(){t.$el.find(i).text(t.model.previous("name"))})):t.$el.find(i).text(n)}})}},multiselectActions:function(){var e=this,t=[{html:v("Hide datasets"),func:function(){var t=n.HistoryDatasetAssociation.prototype.hide;e.getSelectedModels().ajaxQueue(t)}},{html:v("Unhide datasets"),func:function(){var t=n.HistoryDatasetAssociation.prototype.unhide;e.getSelectedModels().ajaxQueue(t)}},{html:v("Delete datasets"),func:function(){var t=n.HistoryDatasetAssociation.prototype.delete;e.getSelectedModels().ajaxQueue(t)}},{html:v("Undelete datasets"),func:function(){var t=n.HistoryDatasetAssociation.prototype.undelete;e.getSelectedModels().ajaxQueue(t)}}];return e.purgeAllowed&&t.push({html:v("Permanently delete datasets"),func:function(){if(confirm(v("This will permanently remove the data in your datasets. Are you sure?"))){var t=n.HistoryDatasetAssociation.prototype.purge;e.getSelectedModels().ajaxQueue(t)}}}),t=t.concat(e._collectionActions())},_collectionActions:function(){var e=this;return[{html:v("Build Dataset List"),func:function(){e.buildCollection("list")}},{html:v("Build Dataset Pair"),func:function(){e.buildCollection("paired")}},{html:v("Build List of Dataset Pairs"),func:function(){e.buildCollection("list:paired")}}]},buildCollection:function(e,t,i){var n,s=this,t=t||s.getSelectedModels(),i=i||!1;"list"==e?n=h.createListCollection:"paired"==e?n=u.createPairCollection:"list:paired"==e?n=p.createListOfPairsCollection:console.warn("Unknown collectionType encountered "+e),n(t,i).done(function(){s.model.refresh()})},_getItemViewOptions:function(e){var t=_.prototype._getItemViewOptions.call(this,e);return o.extend(t,{purgeAllowed:this.purgeAllowed,tagsEditorShown:this.tagsEditor&&!this.tagsEditor.hidden,annotationEditorShown:this.annotationEditor&&!this.annotationEditor.hidden}),t},_handleItemDeletedChange:function(e){e.get("deleted")?this._handleItemDeletion(e):this._handleItemUndeletion(e),this._renderCounts()},_handleItemDeletion:function(e){var t=this.model.get("contents_active");t.deleted+=1,t.active-=1,this.model.contents.includeDeleted||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUndeletion:function(e){var t=this.model.get("contents_active");t.deleted-=1,this.model.contents.includeDeleted||(t.active-=1),this.model.set("contents_active",t)},_handleItemVisibleChange:function(e){e.hidden()?this._handleItemHidden(e):this._handleItemUnhidden(e),this._renderCounts()},_handleItemHidden:function(e){var t=this.model.get("contents_active");t.hidden+=1,t.active-=1,this.model.contents.includeHidden||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUnhidden:function(e){var t=this.model.get("contents_active");t.hidden-=1,this.model.contents.includeHidden||(t.active-=1),this.model.set("contents_active",t)},toggleHDATagEditors:function(e,t){o.each(this.views,function(i){i.tagsEditor&&i.tagsEditor.toggle(e,t)})},toggleHDAAnnotationEditors:function(e,t){o.each(this.views,function(i){i.annotationEditor&&i.annotationEditor.toggle(e,t)})},events:o.extend(o.clone(_.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(e){this.toggleShowDeleted()},"click .toggle-hidden-link":function(e){this.toggleShowHidden()}}),_renderSearchProgress:function(e,t){var i=e+t;return this.$("> .controls .subtitle").html(["",v("Searching "),i,"/",this.model.contentsShown()," "].join(""))},_renderSearchFindings:function(){return this.$("> .controls .subtitle").html([v("Found"),this.views.length].join(" ")),this},dropTargetOn:function(){if(this.dropTarget)return this;this.dropTarget=!0;var e={dragenter:o.bind(this.dragenter,this),dragover:o.bind(this.dragover,this),dragleave:o.bind(this.dragleave,this),drop:o.bind(this.drop,this)},t=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),t]);for(var i in e)e.hasOwnProperty(i)&&t.on(i,e[i]);return this},_renderDropTarget:function(){return this.$(".history-drop-target").remove(),r("
").addClass("history-drop-target")},_renderDropTargetHelp:function(){return this.$(".history-drop-target-help").remove(),r("
").addClass("history-drop-target-help").text(v("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget)return this;this.dropTarget=!1;var e=this.$(".history-drop-target").get(0);for(var t in this._dropHandlers)this._dropHandlers.hasOwnProperty(t)&&e.off(t,this._dropHandlers[t]);return this.$(".history-drop-target").remove(),this.$(".history-drop-target-help").remove(),this},dropTargetToggle:function(){return this.dropTarget?this.dropTargetOff():this.dropTargetOn(),this},dragenter:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","2px solid black")},dragover:function(e){e.preventDefault(),e.stopPropagation()},dragleave:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","1px dashed black")},drop:function(e){e.preventDefault();var t=this,i=e.originalEvent.dataTransfer,n=i.getData("text");i.dropEffect="move";try{n=JSON.parse(n)}catch(e){t.warn("error parsing JSON from drop:",n)}return t.trigger("droptarget:drop",e,n,t),!1},dataDropped:function(e){var t=this;return o.isObject(e)&&"HistoryDatasetAssociation"===e.model_class&&e.id?0!==t.contents.currentPage?t.contents.fetchPage(0).then(function(){return t.model.contents.copy(e.id)}):t.model.contents.copy(e.id):a.when()},toString:function(){return"HistoryViewEdit("+(this.model?this.model.get("name"):"")+")"}});return y.prototype.templates=function(){var e=m.wrapTemplate(["<% var shown = Math.max( view.views.length, history.contents_active.active ) %>","<% if( shown ){ %>",'',"<%- shown %> ",v("shown")," ","<% } %>","<% if( history.contents_active.deleted ){ %>",'',"<% if( view.model.contents.includeDeleted ){ %>",'',v("hide deleted")," ","<% } else { %>","<%- history.contents_active.deleted %> ",'',v("deleted")," ","<% } %>"," ","<% } %>","<% if( history.contents_active.hidden ){ %>",'',"<% if( view.model.contents.includeHidden ){ %>",'',v("hide hidden")," ","<% } else { %>","<%- history.contents_active.hidden %> ",'',v("hidden")," ","<% } %>"," ","<% } %>"],"history");return o.extend(o.clone(_.prototype.templates),{counts:e})}(),{HistoryViewEdit:y}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1),i(2),i(1))},function(e,t,i){var n,s;(function(a,o){n=[i(87),i(52),i(51),i(53),i(83),i(85),i(91),i(90),i(18),i(6),i(5),i(94)],s=function(e,t,i,n,s,r,l,c,d,h,u){"use strict";var p=e.ModelListPanel,f=p.extend({_logNamespace:"history",HDAViewClass:s.HDAListItemView,HDCAViewClass:r.HDCAListItemView,collectionClass:i.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:p.prototype.className+" history-panel",emptyMsg:u("This history is empty"),noneFoundMsg:u("No matching datasets found"),searchPlaceholder:u("search datasets"),FETCH_COLLECTION_COUNTS_DELAY:2e3,initialize:function(e){p.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_createDefaultCollection:function(){return new this.collectionClass([],{history:this.model})},freeModel:function(){return p.prototype.freeModel.call(this),this.model&&this.model.clearUpdateTimeout(),this},_setUpListeners:function(){p.prototype._setUpListeners.call(this),this.on({error:function(e,t,i,n,s){this.errorHandler(e,t,i,n,s)},"loading-done":function(){var e=this;a.delay(function(){e.model.contents.fetchCollectionCounts()},e.FETCH_COLLECTION_COUNTS_DELAY)},"views:ready view:attached view:removed":function(e){this._renderSelectButton()},"view:attached":function(e){this.scrollTo(0)}})},loadHistory:function(e,i,n){n=a.extend(n||{silent:!0}),this.info("loadHistory:",e,i,n);var s=this;return s.setModel(new t.History({id:e})),n.silent=!0,s.trigger("loading"),s.model.fetchWithContents(i,n).always(function(){s.render(),s.trigger("loading-done")})},refreshContents:function(e){return this.model?this.model.refresh(e):o.when()},_setUpCollectionListeners:function(){return p.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"fetching-more":function(){this._toggleContentsLoadingIndicator(!0),this.$emptyMessage().hide()},"fetching-more-done":function(){this._toggleContentsLoadingIndicator(!1)}})},_showLoadingIndicator:function(e,t,i){var n=o('
');this.$el.html(n.text(e).slideDown(a.isUndefined(t)?this.fxSpeed:t))},_hideLoadingIndicator:function(e){this.$(".loading-indicator").slideUp(a.isUndefined(e)?this.fxSpeed+200:e,function(){o(this).remove()})},_buildNewRender:function(){var e=p.prototype._buildNewRender.call(this);return this._renderSelectButton(e),e},_renderSelectButton:function(e){if(e=e||this.$el,!this.multiselectActions().length)return null;if(!this.views.length)return this.hideSelectors(),e.find(".controls .actions .show-selectors-btn").remove(),null;var t=e.find(".controls .actions .show-selectors-btn");return t.length?t:d({title:u("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"}).prependTo(e.find(".controls .actions"))},_renderEmptyMessage:function(e){var t=this,i=t.$emptyMessage(e),n=t.model.get("contents_active").active<=0;return n?i.empty().append(t.emptyMsg).show():t.searchFor&&t.model.contents.haveSearchDetails()&&!t.views.length?i.empty().append(t.noneFoundMsg).show():(i.hide(),o())},$scrollContainer:function(e){return this.$list(e)},_toggleContentsLoadingIndicator:function(e){e?this.$list().html('
'):this.$list().find(".contents-loading-indicator").remove()},renderItems:function(e){e=e||this.$el;var t=this,i=t.$list(e);o(".tooltip").remove(),i.empty(),t.views=[];var n=t._filterCollection();return n.length?(t._renderPagination(e),t.views=t._renderSomeItems(n,i)):e.find("> .controls .list-pagination").empty(),t._renderEmptyMessage(e).toggle(!n.length),t.trigger("views:ready",t.views),t.views},_renderPagination:function(e){var t=e.find("> .controls .list-pagination");return this.searchFor||!this.model.contents.shouldPaginate()?t.empty():(t.html(this.templates.pagination({current:this.model.contents.currentPage+1,last:this.model.contents.getLastPage()+1},this)),t.find("select.pages").tooltip(),t)},_renderSomeItems:function(e,t){var i=this,n=[];return t.append(e.map(function(e){var t=i._createItemView(e);return n.push(t),i._renderItemView$el(t)})),n},_filterItem:function(e){var t=this,i=t.model.contents;return(i.includeHidden||!e.hidden())&&(i.includeDeleted||!e.isDeletedOrPurged())&&p.prototype._filterItem.call(t,e)},_getItemViewClass:function(e){var t=e.get("history_content_type");switch(t){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+t)},_getItemViewOptions:function(e){var t=p.prototype._getItemViewOptions.call(this,e);return a.extend(t,{linkTarget:this.linkTarget,expanded:this.model.contents.storage.isExpanded(e.id),hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(e){var t=this;return p.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{expanded:function(e){t.model.contents.storage.addExpanded(e.model)},collapsed:function(e){t.model.contents.storage.removeExpanded(e.model)}})},collapseAll:function(){this.model.contents.storage.clearExpanded(),p.prototype.collapseAll.call(this)},getSelectedModels:function(){var e=p.prototype.getSelectedModels.call(this);return e.historyId=this.collection.historyId,e},events:a.extend(a.clone(p.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click > .controls .prev":"_clickPrevPage","click > .controls .next":"_clickNextPage","change > .controls .pages":"_changePageSelect","click .messages [class$=message]":"clearMessages"}),_clickPrevPage:function(e){this.model.clearUpdateTimeout(),this.model.contents.fetchPrevPage()},_clickNextPage:function(e){this.model.clearUpdateTimeout(),this.model.contents.fetchNextPage()},_changePageSelect:function(e){this.model.clearUpdateTimeout();var t=o(e.currentTarget).val();this.model.contents.fetchPage(t)},toggleShowDeleted:function(e,t){e=void 0!==e?e:!this.model.contents.includeDeleted;var i=this,n=i.model.contents;return n.setIncludeDeleted(e,t),i.trigger("show-deleted",e),n.fetchCurrentPage({renderAll:!0}),e},toggleShowHidden:function(e,t,i){e=void 0!==e?e:!this.model.contents.includeHidden;var n=this,s=n.model.contents;return s.setIncludeHidden(e,i),n.trigger("show-hidden",e),s.fetchCurrentPage({renderAll:!0}),e},_firstSearch:function(e){var t=this,i="> .controls .search-input";if(this.log("onFirstSearch",e),t.model.contents.haveSearchDetails())return void t.searchItems(e);t.$(i).searchInput("toggle-loading"),t.searchFor=e;t.model.contents.progressivelyFetchDetails({silent:!0}).progress(function(e,i,n){t.renderItems(),t.trigger("search:loading-progress",i,n)}).always(function(){t.$el.find(i).searchInput("toggle-loading")}).done(function(){t.searchItems(e,"force")})},clearSearch:function(e){var t=this;return t.searchFor?(t.searchFor="",t.trigger("search:clear",t),t.$("> .controls .search-query").val(""),t.model.contents.fetchCurrentPage({silent:!0}).done(function(){t.renderItems()}),t):t},errorHandler:function(e,t,i){if(!t||0!==t.status||0!==t.readyState){if(this.error(e,t,i),a.isString(e)&&a.isString(t)){var n=e,s=t;return c.errorModal(n,s,i)}return t&&502===t.status?c.badGatewayErrorModal():c.ajaxErrorModal(e,t,i)}},clearMessages:function(e){var t=a.isUndefined(e)?this.$messages().children('[class$="message"]'):o(e.currentTarget);return t.fadeOut(this.fxSpeed,function(){o(this).remove()}),this},scrollToHid:function(e){return this.scrollToItem(a.first(this.viewsWhereModel({hid:e})))},ordinalIndicator:function(e){var t=e+"";switch(t.charAt(t.length-1)){case"1":return t+"st";case"2":return t+"nd";case"3":return t+"rd";default:return t+"th"}},toString:function(){return"HistoryView("+(this.model?this.model.get("name"):"")+")"}});return f.prototype.templates=function(){var e=h.wrapTemplate([""]),t=h.wrapTemplate(['','
','
<%- history.name %>
',"
",'
','
<%- history.nice_size %>
','
','
',"<% if( history.deleted && history.purged ){ %>",'
',u("This history has been purged and deleted"),"
","<% } else if( history.deleted ){ %>",'
',u("This history has been deleted"),"
","<% } else if( history.purged ){ %>",'
',u("This history has been purged"),"
","<% } %>","<% if( history.message ){ %>",'
messagesmall">',"<%= history.message.text %>","
","<% } %>","
",'
','
','
",'
','
','',u("All")," ",'',u("None")," ","
",'","
",'',"
>previous ','',"<% _.range( 1, pages.last + 1 ).forEach( function( i ){ %>",'>',"<%- view.ordinalIndicator( i ) %> of <%- pages.last %> pages"," ","<% }); %>"," ",'>next '],"pages");return a.extend(a.clone(p.prototype.templates),{el:e,controls:t,pagination:i})}(),{HistoryView:f}}.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){n=[i(22),i(82),i(6),i(5),i(27)],s=function(e,t,i,n,s){"use strict";function r(e,t,i){return o.clone(l).filter(function(n){return!(e&&!n.anon)&&(!(!t&&n.purge)&&(n.href&&(n.href=i+n.href,n.target=n.target||"galaxy_main"),n.confirm&&(n.func=function(){confirm(n.confirm)&&(galaxy_main.location=n.href)}),!0))})}var l=[{html:n("History Lists"),header:!0},{html:n("Saved Histories"),href:"histories/list",target:"_top"},{html:n("Histories Shared with Me"),href:"histories/list_shared",target:"_top"},{html:n("Current History"),header:!0,anon:!0},{html:n("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:n("Copy History"),func:function(){t(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:n("Share or Publish"),href:"history/sharing"},{html:n("Show Structure"),href:"history/display_structured",anon:!0},{html:n("Extract Workflow"),href:"workflow/build_from_current_history"},{html:n("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really delete the current history?"))&&(galaxy_main.window.location.href="history/delete?id="+Galaxy.currHistoryPanel.model.id)}},{html:n("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really delete the current history permanently? This cannot be undone."))&&(galaxy_main.window.location.href="history/delete?purge=True&id="+Galaxy.currHistoryPanel.model.id)}},{html:n("Dataset Actions"),header:!0,anon:!0},{html:n("Copy Datasets"),href:"dataset/copy_datasets"},{html:n("Dataset Security"),href:"root/history_set_default_permissions"},{html:n("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:n("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:n("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really unhide all hidden datasets?"))&&a.post(Galaxy.root+"history/adjust_hidden",{user_action:"unhide"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:n("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really delete all hidden datasets?"))&&a.post(Galaxy.root+"history/adjust_hidden",{user_action:"delete"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:n("Purge Deleted Datasets"),confirm:n("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:n("Downloads"),header:!0},{html:n("Export Tool Citations"),href:"history/citations",anon:!0},{html:n("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:n("Other Actions"),header:!0},{html:n("Import from File"),href:"history/import_archive"}];s.add({url:"api/webhooks/history-menu/all",async:!1,callback:function(e){var t=[];a.each(e.models,function(e,i){var s=i.toJSON();s.activate&&t.push({html:n(s.config.title),anon:!0})}),t.length>0&&(t.unshift({html:n("Webhooks"),header:!0}),a.merge(l,t))}});var c=function(t,i){i=i||{};var n=void 0===i.anonymous||i.anonymous,s=i.purgeAllowed||!1,a=r(n,s,Galaxy.root);return new e(t,a)};return c}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1),i(2))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(21)],s=function(e,t){var i=a.View.extend({initialize:function(t){var i=this;this.setElement(o("
")),this.model=new a.Model,e.get({url:Galaxy.root+"page/list",success:function(e){e.dict_format=!0,i.model.set(e),i.render()}})},render:function(){var e=new t(this.model.attributes);this.$el.empty().append(e.$el),this.$el.append(this._templateShared())},_templateShared:function(){var e=o("
Pages shared with you by others "),t=this.model.attributes;if(t.shared_by_others&&t.shared_by_others.length>0){var i=o('');r.each(t.shared_by_others,function(e,t){var n=Galaxy.root+"page/display_by_username_and_slug?username="+e.username+"&slug="+e.slug;i.append(''+r.escape(e.title)+" "+r.escape(e.username)+" Failed: "+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));this.$progress_bar.css({width:e+"%"}),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[e]),this.model.set("enabled","init"==e);var t=this.model.get("enabled");this.$text_content.attr("disabled",!t),"success"==e&&(this.$el.addClass("success"),this.$percentage.html("100%")),"error"==e&&(this.$el.addClass("danger"),this.$info_progress.hide())},_refreshFileSize:function(){this.$size.html(e.bytesToString(this.model.get("file_size")))},_removeRow:function(){["init","success","error"].indexOf(this.model.get("status"))!==-1&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new i(this).$el),this.settings.show())},_template:function(e){return'
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"].join("")),helpContent:o.template(["",n(["Pair collections are permanent collections containing two datasets: one forward and one reverse. ","Often these are forward and reverse reads. The pair collections can be passed to tools and ","workflows in order to have analyses done on both datasets. This interface allows ","you to create a pair, name it, and swap which is forward and which reverse."].join("")),"
","","",n(['Click the "Swap" link to make your forward dataset the reverse ',"and the reverse dataset forward."].join(""))," ","",n(['Click the "Cancel" button to exit the interface.'].join(""))," "," ",n(['Once your collection is complete, enter a name and ','click "Create list" .'].join("")),"
"].join("")),invalidInitial:o.template(['",'"].join(""))}),toString:function(){return"PairCollectionCreator"}}),u=function(t,i){return i=i||{},i.title=n("Create a collection from a pair of datasets"),e.collectionCreatorModal(t,i,h)};return{PairCollectionCreator:h,pairCollectionCreatorModal:u,createPairCollection:s}}.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){n=[i(80),i(83),i(6),i(5)],s=function(e,t,i,n){"use strict";var s=e.DatasetListItemEdit,r=s.extend({className:s.prototype.className+" history-content",_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):e.model.has("rerunnable")?a.when():e.model.fetch({silent:!0,data:{keys:["rerunnable","creating_job"].join(",")}})},events:o.extend(o.clone(s.prototype.events),{"click .unhide-link":function(e){return this.model.unhide(),!1}}),toString:function(){var e=this.model?this.model+"":"(no model)";return"HDAListItemEdit("+e+")"}});return r.prototype.templates=function(){var e=o.extend({},s.prototype.templates.warnings,{hidden:i.wrapTemplate(["<% if( !dataset.visible ){ %>",'","<% } %>"],"dataset")});return o.extend({},s.prototype.templates,{titleBar:t.HDAListItemView.prototype.templates.titleBar,warnings:e})}(),{HDAListItemEdit:r}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1),i(2))},function(e,t,i){var n,s;n=[i(85),i(118),i(19),i(5)],s=function(e,t,i,n){"use strict";var s=e.HDCAListItemView,a=s.extend({_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return t.ListCollectionViewEdit;case"paired":return t.PairCollectionViewEdit;case"list:paired":return t.ListOfPairsCollectionViewEdit;case"list:list":return t.ListOfListsCollectionViewEdit}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_renderPrimaryActions:function(){return this.log(this+"._renderPrimaryActions"),s.prototype._renderPrimaryActions.call(this).concat([this._renderDeleteButton()])},_renderDeleteButton:function(){var e=this,t=this.model.get("deleted");return i({title:n(t?"Dataset collection is already deleted":"Delete"),classes:"delete-btn",faIcon:"fa-times",disabled:t,onclick:function(){e.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},toString:function(){var e=this.model?this.model+"":"(no model)";return"HDCAListItemEdit("+e+")"}});return{HDCAListItemEdit:a}}.apply(t,n),!(void 0!==s&&(e.exports=s))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(14),i(52),i(82)],s=function(e,t,i,n){var s=a.View.extend({initialize:function(t){var i=this;this.setElement(o("
")),this.model=new a.Model,e.get({url:Galaxy.root+"history/"+t.action_id,success:function(e){e.dict_format=!0,r.each(e.operations,function(e){"Copy"==e.label&&(e.onclick=function(e){i._showCopyDialog(e)})}),i.model.set(e),i.render()}})},render:function(){var e=new t(this.model.attributes);this.$el.empty().append(e.$el)},_showCopyDialog:function(e){var t=new i.History({id:e});t.fetch().fail(function(){alert("History could not be fetched. Please contact an administrator")}).done(function(){n(t,{}).done(function(){window.parent&&window.parent.Galaxy&&window.parent.Galaxy.currHistoryPanel&&window.parent.Galaxy.currHistoryPanel.loadCurrentHistory(),window.location.reload(!0)})})}});return{View:s}}.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){n=[i(52),i(125),i(6),i(5)],s=function(e,t,i,n){"use strict";var s=i.SessionStorageModel.extend({defaults:{tagsEditorShown:!1,annotationEditorShown:!1,scrollPosition:0},toString:function(){return"HistoryViewPrefs("+JSON.stringify(this.toJSON())+")"}});s.storageKey=function(){return"history-panel"};var l=t.HistoryViewEdit,c=l.extend({className:l.prototype.className+" current-history-panel",HDCAViewClass:l.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),emptyMsg:[n("This history is empty"),". ",n("You can "),'',n("load your own data")," ",n(" or "),'',n("get data from an external source")," "].join(""),initialize:function(e){e=e||{},this.preferences=new s(a.extend({id:s.storageKey()},a.pick(e,a.keys(s.prototype.defaults)))),l.prototype.initialize.call(this,e),this.panelStack=[],this.currentContentId=e.currentContentId||null},_setUpListeners:function(){l.prototype._setUpListeners.call(this);var e=this;this.on("new-model",function(){e.preferences.set("scrollPosition",0)})},loadCurrentHistory:function(){return this.loadHistory(null,{url:Galaxy.root+"history/current_history_json"})},switchToHistory:function(e,t){return Galaxy.user.isAnonymous()?(this.trigger("error",n("You must be logged in to switch histories"),n("Anonymous user")),o.when()):this.loadHistory(e,{url:Galaxy.root+"history/set_as_current?id="+e})},createNewHistory:function(e){return Galaxy.user.isAnonymous()?(this.trigger("error",n("You must be logged in to create histories"),n("Anonymous user")),o.when()):this.loadHistory(null,{url:Galaxy.root+"history/create_new_current"})},setModel:function(e,t,i){return l.prototype.setModel.call(this,e,t,i),this.model&&this.model.id&&(this.log("checking for updates"),this.model.checkForUpdates()),this},_setUpModelListeners:function(){return l.prototype._setUpModelListeners.call(this),this.listenTo(this.model,{"change:nice_size change:size":function(){this.trigger("history-size-change",this,this.model,arguments)},"change:id":function(){this.once("loading-done",function(){this.model.checkForUpdates()})}})},_setUpCollectionListeners:function(){l.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,"state:ready",function(e,t,i){e.get("visible")||this.collection.storage.includeHidden()||this.removeItemView(e)})},_setUpBehaviors:function(e){e=e||this.$el;var t=this;return l.prototype._setUpBehaviors.call(t,e),this._debouncedScrollCaptureHandler||(this._debouncedScrollCaptureHandler=a.debounce(function(){t.$el.is(":visible")&&t.preferences.set("scrollPosition",o(this).scrollTop())},40)),t.$scrollContainer(e).off("scroll",this._debouncedScrollCaptureHandler).on("scroll",this._debouncedScrollCaptureHandler),t},_buildNewRender:function(){if(!this.model)return o();var e=l.prototype._buildNewRender.call(this);return e.find(".search").prependTo(e.find("> .controls")),this._renderQuotaMessage(e),e},_renderQuotaMessage:function(e){return e=e||this.$el,o(this.templates.quotaMsg({},this)).prependTo(e.find(".messages"))},_renderTags:function(e){var t=this;l.prototype._renderTags.call(t,e),t.preferences.get("tagsEditorShown")&&t.tagsEditor.toggle(!0),t.listenTo(t.tagsEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(e){t.preferences.set("tagsEditorShown",e.hidden)})},_renderAnnotation:function(e){var t=this;l.prototype._renderAnnotation.call(t,e),t.preferences.get("annotationEditorShown")&&t.annotationEditor.toggle(!0),t.listenTo(t.annotationEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(e){t.preferences.set("annotationEditorShown",e.hidden)})},_swapNewRender:function(e){l.prototype._swapNewRender.call(this,e);var t=this;return a.delay(function(){var e=t.preferences.get("scrollPosition");e&&t.scrollTo(e,0)},10),this},_attachItems:function(e){l.prototype._attachItems.call(this,e);var t=this;return t.currentContentId&&t._setCurrentContentById(t.currentContentId),this},addItemView:function(e,t,i){var n=l.prototype.addItemView.call(this,e,t,i);return n&&this.panelStack.length?this._collapseDrilldownPanel():n},_setUpItemViewListeners:function(e){var t=this;return l.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}})},setCurrentContent:function(e){this.$(".history-content.current-content").removeClass("current-content"),e?(e.$el.addClass("current-content"),this.currentContentId=e.model.id):this.currentContentId=null},_setCurrentContentById:function(e){var t=this.viewFromModelId(e)||null;this.setCurrentContent(t)},_expandDrilldownPanel:function(e){this.panelStack.push(e),this.$controls().add(this.$list()).hide(),e.parentName=this.model.get("name"),e.delegateEvents().render().$el.appendTo(this.$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.$controls().add(this.$list()).show()},events:a.extend(a.clone(l.prototype.events),{"click .uploader-link":function(e){Galaxy.upload.show(e)},"click .get-data-link":function(e){var t=o(".toolMenuContainer");t.parent().scrollTop(0),t.find('span:contains("Get Data")').click()}}),listenToGalaxy:function(e){this.listenTo(e,{"center-frame:load":function(e){var t=e.fullpath,i=null,n={display:/datasets\/([a-f0-9]+)\/display/,edit:/datasets\/([a-f0-9]+)\/edit/,report_error:/dataset\/errors\?id=([a-f0-9]+)/,rerun:/tool_runner\/rerun\?id=([a-f0-9]+)/,show_params:/datasets\/([a-f0-9]+)\/show_params/};a.find(n,function(e,n){return i=a.result(t.match(e),1)}),this._setCurrentContentById(i?"dataset-"+i:null)},"center-panel:load":function(e){this._setCurrentContentById()}})},connectToQuotaMeter:function(e){return e?(this.listenTo(e,"quota:over",this.showQuotaMessage),this.listenTo(e,"quota:under",this.hideQuotaMessage),this.on("rendered rendered:initial",function(){e&&e.isOverQuota()&&this.showQuotaMessage()}),this):this},clearMessages:function(e){var t=a.isUndefined(e)?this.$messages().children('[class$="message"]'):o(e.currentTarget);return t=t.not(".quota-message"),t.fadeOut(this.fxSpeed,function(){o(this).remove()}),this},showQuotaMessage:function(){var e=this.$(".quota-message");e.is(":hidden")&&e.slideDown(this.fxSpeed)},hideQuotaMessage:function(){var e=this.$(".quota-message");e.is(":hidden")||e.slideUp(this.fxSpeed)},unhideHidden:function(){var e=this;return confirm(n("Really unhide all hidden datasets?"))?e.model.contents._filterAndUpdate({visible:!1,deleted:"",purged:""},{visible:!0}).done(function(){e.model.contents.includeHidden||e.renderItems()}):r.when()},deleteHidden:function(){var e=this;return confirm(n("Really delete all hidden datasets?"))?e.model.contents._filterAndUpdate({visible:!1,deleted:"",purged:""},{deleted:!0,visible:!0}):r.when()},toString:function(){return"CurrentHistoryView("+(this.model?this.model.get("name"):"")+")"}});return c.prototype.templates=function(){var e=i.wrapTemplate(['',n("You are over your disk quota"),". ",n("Tool execution is on hold until your disk usage drops below your allocated quota"),".","
"],"history");return a.extend(a.clone(l.prototype.templates),{quotaMsg:e})}(),{CurrentHistoryView:c}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(1))},function(e,t,i){var n,s;(function(a,o,r){n=[i(126),i(51),i(11),i(84),i(121),i(122),i(55),i(76),i(42),i(120),i(119),i(19),i(22),i(6),i(5),i(18)],
+s=function(e,t,i,n,s,l,c,d,h,u,p,f,g,m,v){"use strict";var _=e.HistoryView,y=_.extend({HDAViewClass:s.HDAListItemEdit,HDCAViewClass:l.HDCAListItemEdit,initialize:function(e){e=e||{},_.prototype.initialize.call(this,e),this.tagsEditor=null,this.dragItems=!0,this.annotationEditor=null,this.purgeAllowed=e.purgeAllowed||!1,this.annotationEditorShown=e.annotationEditorShown||!1,this.tagsEditorShown=e.tagsEditorShown||!1},_setUpListeners:function(){return _.prototype._setUpListeners.call(this),this.on({"droptarget:drop":function(e,t){this.dataDropped(t),this.dropTargetOff()},"view:attached view:removed":function(){this._renderCounts()},"search:loading-progress":this._renderSearchProgress,"search:searching":this._renderSearchFindings})},_setUpModelListeners:function(){return _.prototype._setUpModelListeners.call(this),this.listenTo(this.model,"change:size",this.updateHistoryDiskSize),this},_setUpCollectionListeners:function(){return _.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"change:deleted":this._handleItemDeletedChange,"change:visible":this._handleItemVisibleChange,"change:purged":function(e){this.model.fetch()},"fetching-deleted":function(e){this.$("> .controls .deleted-count").html(""+v("loading...")+" ")},"fetching-hidden":function(e){this.$("> .controls .hidden-count").html(""+v("loading...")+" ")},"fetching-deleted-done fetching-hidden-done":this._renderCounts}),this},_buildNewRender:function(){var e=_.prototype._buildNewRender.call(this);return this.model?(Galaxy&&Galaxy.user&&Galaxy.user.id&&Galaxy.user.id===this.model.get("user_id")&&(this._renderTags(e),this._renderAnnotation(e)),e):e},updateHistoryDiskSize:function(){this.$(".history-size").text(this.model.get("nice_size"))},renderItems:function(e){var t=_.prototype.renderItems.call(this,e);return this.searchFor||this._renderCounts(e),t},_renderCounts:function(e){e=e instanceof a?e:this.$el;var t=this.templates.counts(this.model.toJSON(),this);return e.find("> .controls .subtitle").html(t)},_renderTags:function(e){var t=this;this.tagsEditor=new c.TagsEditor({model:this.model,el:e.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDATagEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDATagEditors(!1,t.fxSpeed)},$activator:f({title:v("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".controls .actions"))})},_renderAnnotation:function(e){var t=this;this.annotationEditor=new d.AnnotationEditor({model:this.model,el:e.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDAAnnotationEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDAAnnotationEditors(!1,t.fxSpeed)},$activator:f({title:v("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".controls .actions"))})},_setUpBehaviors:function(e){if(e=e||this.$el,_.prototype._setUpBehaviors.call(this,e),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.model.get("user_id")){var t=this,i="> .controls .name";e.find(i).attr("title",v("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(e){var n=t.model.get("name");e&&e!==n?(t.$el.find(i).text(e),t.model.save({name:e}).fail(function(){t.$el.find(i).text(t.model.previous("name"))})):t.$el.find(i).text(n)}})}},multiselectActions:function(){var e=this,t=[{html:v("Hide datasets"),func:function(){var t=n.HistoryDatasetAssociation.prototype.hide;e.getSelectedModels().ajaxQueue(t)}},{html:v("Unhide datasets"),func:function(){var t=n.HistoryDatasetAssociation.prototype.unhide;e.getSelectedModels().ajaxQueue(t)}},{html:v("Delete datasets"),func:function(){var t=n.HistoryDatasetAssociation.prototype.delete;e.getSelectedModels().ajaxQueue(t)}},{html:v("Undelete datasets"),func:function(){var t=n.HistoryDatasetAssociation.prototype.undelete;e.getSelectedModels().ajaxQueue(t)}}];return e.purgeAllowed&&t.push({html:v("Permanently delete datasets"),func:function(){if(confirm(v("This will permanently remove the data in your datasets. Are you sure?"))){var t=n.HistoryDatasetAssociation.prototype.purge;e.getSelectedModels().ajaxQueue(t)}}}),t=t.concat(e._collectionActions())},_collectionActions:function(){var e=this;return[{html:v("Build Dataset List"),func:function(){e.buildCollection("list")}},{html:v("Build Dataset Pair"),func:function(){e.buildCollection("paired")}},{html:v("Build List of Dataset Pairs"),func:function(){e.buildCollection("list:paired")}}]},buildCollection:function(e,t,i){var n,s=this,t=t||s.getSelectedModels(),i=i||!1;"list"==e?n=h.createListCollection:"paired"==e?n=u.createPairCollection:"list:paired"==e?n=p.createListOfPairsCollection:console.warn("Unknown collectionType encountered "+e),n(t,i).done(function(){s.model.refresh()})},_getItemViewOptions:function(e){var t=_.prototype._getItemViewOptions.call(this,e);return o.extend(t,{purgeAllowed:this.purgeAllowed,tagsEditorShown:this.tagsEditor&&!this.tagsEditor.hidden,annotationEditorShown:this.annotationEditor&&!this.annotationEditor.hidden}),t},_handleItemDeletedChange:function(e){e.get("deleted")?this._handleItemDeletion(e):this._handleItemUndeletion(e),this._renderCounts()},_handleItemDeletion:function(e){var t=this.model.get("contents_active");t.deleted+=1,t.active-=1,this.model.contents.includeDeleted||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUndeletion:function(e){var t=this.model.get("contents_active");t.deleted-=1,this.model.contents.includeDeleted||(t.active-=1),this.model.set("contents_active",t)},_handleItemVisibleChange:function(e){e.hidden()?this._handleItemHidden(e):this._handleItemUnhidden(e),this._renderCounts()},_handleItemHidden:function(e){var t=this.model.get("contents_active");t.hidden+=1,t.active-=1,this.model.contents.includeHidden||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUnhidden:function(e){var t=this.model.get("contents_active");t.hidden-=1,this.model.contents.includeHidden||(t.active-=1),this.model.set("contents_active",t)},toggleHDATagEditors:function(e,t){o.each(this.views,function(i){i.tagsEditor&&i.tagsEditor.toggle(e,t)})},toggleHDAAnnotationEditors:function(e,t){o.each(this.views,function(i){i.annotationEditor&&i.annotationEditor.toggle(e,t)})},events:o.extend(o.clone(_.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(e){this.toggleShowDeleted()},"click .toggle-hidden-link":function(e){this.toggleShowHidden()}}),_renderSearchProgress:function(e,t){var i=e+t;return this.$("> .controls .subtitle").html(["",v("Searching "),i,"/",this.model.contentsShown()," "].join(""))},_renderSearchFindings:function(){return this.$("> .controls .subtitle").html([v("Found"),this.views.length].join(" ")),this},dropTargetOn:function(){if(this.dropTarget)return this;this.dropTarget=!0;var e={dragenter:o.bind(this.dragenter,this),dragover:o.bind(this.dragover,this),dragleave:o.bind(this.dragleave,this),drop:o.bind(this.drop,this)},t=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),t]);for(var i in e)e.hasOwnProperty(i)&&t.on(i,e[i]);return this},_renderDropTarget:function(){return this.$(".history-drop-target").remove(),r("
").addClass("history-drop-target")},_renderDropTargetHelp:function(){return this.$(".history-drop-target-help").remove(),r("
").addClass("history-drop-target-help").text(v("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget)return this;this.dropTarget=!1;var e=this.$(".history-drop-target").get(0);for(var t in this._dropHandlers)this._dropHandlers.hasOwnProperty(t)&&e.off(t,this._dropHandlers[t]);return this.$(".history-drop-target").remove(),this.$(".history-drop-target-help").remove(),this},dropTargetToggle:function(){return this.dropTarget?this.dropTargetOff():this.dropTargetOn(),this},dragenter:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","2px solid black")},dragover:function(e){e.preventDefault(),e.stopPropagation()},dragleave:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","1px dashed black")},drop:function(e){e.preventDefault();var t=this,i=e.originalEvent.dataTransfer,n=i.getData("text");i.dropEffect="move";try{n=JSON.parse(n)}catch(e){t.warn("error parsing JSON from drop:",n)}return t.trigger("droptarget:drop",e,n,t),!1},dataDropped:function(e){var t=this;return o.isObject(e)&&"HistoryDatasetAssociation"===e.model_class&&e.id?0!==t.contents.currentPage?t.contents.fetchPage(0).then(function(){return t.model.contents.copy(e.id)}):t.model.contents.copy(e.id):a.when()},toString:function(){return"HistoryViewEdit("+(this.model?this.model.get("name"):"")+")"}});return y.prototype.templates=function(){var e=m.wrapTemplate(["<% var shown = Math.max( view.views.length, history.contents_active.active ) %>","<% if( shown ){ %>",'',"<%- shown %> ",v("shown")," ","<% } %>","<% if( history.contents_active.deleted ){ %>",'',"<% if( view.model.contents.includeDeleted ){ %>",'',v("hide deleted")," ","<% } else { %>","<%- history.contents_active.deleted %> ",'',v("deleted")," ","<% } %>"," ","<% } %>","<% if( history.contents_active.hidden ){ %>",'',"<% if( view.model.contents.includeHidden ){ %>",'',v("hide hidden")," ","<% } else { %>","<%- history.contents_active.hidden %> ",'',v("hidden")," ","<% } %>"," ","<% } %>"],"history");return o.extend(o.clone(_.prototype.templates),{counts:e})}(),{HistoryViewEdit:y}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1),i(2),i(1))},function(e,t,i){var n,s;(function(a,o){n=[i(87),i(52),i(51),i(53),i(83),i(85),i(91),i(90),i(19),i(6),i(5),i(94)],s=function(e,t,i,n,s,r,l,c,d,h,u){"use strict";var p=e.ModelListPanel,f=p.extend({_logNamespace:"history",HDAViewClass:s.HDAListItemView,HDCAViewClass:r.HDCAListItemView,collectionClass:i.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:p.prototype.className+" history-panel",emptyMsg:u("This history is empty"),noneFoundMsg:u("No matching datasets found"),searchPlaceholder:u("search datasets"),FETCH_COLLECTION_COUNTS_DELAY:2e3,initialize:function(e){p.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_createDefaultCollection:function(){return new this.collectionClass([],{history:this.model})},freeModel:function(){return p.prototype.freeModel.call(this),this.model&&this.model.clearUpdateTimeout(),this},_setUpListeners:function(){p.prototype._setUpListeners.call(this),this.on({error:function(e,t,i,n,s){this.errorHandler(e,t,i,n,s)},"loading-done":function(){var e=this;a.delay(function(){e.model.contents.fetchCollectionCounts()},e.FETCH_COLLECTION_COUNTS_DELAY)},"views:ready view:attached view:removed":function(e){this._renderSelectButton()},"view:attached":function(e){this.scrollTo(0)}})},loadHistory:function(e,i,n){n=a.extend(n||{silent:!0}),this.info("loadHistory:",e,i,n);var s=this;return s.setModel(new t.History({id:e})),n.silent=!0,s.trigger("loading"),s.model.fetchWithContents(i,n).always(function(){s.render(),s.trigger("loading-done")})},refreshContents:function(e){return this.model?this.model.refresh(e):o.when()},_setUpCollectionListeners:function(){return p.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"fetching-more":function(){this._toggleContentsLoadingIndicator(!0),this.$emptyMessage().hide()},"fetching-more-done":function(){this._toggleContentsLoadingIndicator(!1)}})},_showLoadingIndicator:function(e,t,i){var n=o('
');this.$el.html(n.text(e).slideDown(a.isUndefined(t)?this.fxSpeed:t))},_hideLoadingIndicator:function(e){this.$(".loading-indicator").slideUp(a.isUndefined(e)?this.fxSpeed+200:e,function(){o(this).remove()})},_buildNewRender:function(){var e=p.prototype._buildNewRender.call(this);return this._renderSelectButton(e),e},_renderSelectButton:function(e){if(e=e||this.$el,!this.multiselectActions().length)return null;if(!this.views.length)return this.hideSelectors(),e.find(".controls .actions .show-selectors-btn").remove(),null;var t=e.find(".controls .actions .show-selectors-btn");return t.length?t:d({title:u("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"}).prependTo(e.find(".controls .actions"))},_renderEmptyMessage:function(e){var t=this,i=t.$emptyMessage(e),n=t.model.get("contents_active").active<=0;return n?i.empty().append(t.emptyMsg).show():t.searchFor&&t.model.contents.haveSearchDetails()&&!t.views.length?i.empty().append(t.noneFoundMsg).show():(i.hide(),o())},$scrollContainer:function(e){return this.$list(e)},_toggleContentsLoadingIndicator:function(e){e?this.$list().html('
'):this.$list().find(".contents-loading-indicator").remove()},renderItems:function(e){e=e||this.$el;var t=this,i=t.$list(e);o(".tooltip").remove(),i.empty(),t.views=[];var n=t._filterCollection();return n.length?(t._renderPagination(e),t.views=t._renderSomeItems(n,i)):e.find("> .controls .list-pagination").empty(),t._renderEmptyMessage(e).toggle(!n.length),t.trigger("views:ready",t.views),t.views},_renderPagination:function(e){var t=e.find("> .controls .list-pagination");return this.searchFor||!this.model.contents.shouldPaginate()?t.empty():(t.html(this.templates.pagination({current:this.model.contents.currentPage+1,last:this.model.contents.getLastPage()+1},this)),t.find("select.pages").tooltip(),t)},_renderSomeItems:function(e,t){var i=this,n=[];return t.append(e.map(function(e){var t=i._createItemView(e);return n.push(t),i._renderItemView$el(t)})),n},_filterItem:function(e){var t=this,i=t.model.contents;return(i.includeHidden||!e.hidden())&&(i.includeDeleted||!e.isDeletedOrPurged())&&p.prototype._filterItem.call(t,e)},_getItemViewClass:function(e){var t=e.get("history_content_type");switch(t){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+t)},_getItemViewOptions:function(e){var t=p.prototype._getItemViewOptions.call(this,e);return a.extend(t,{linkTarget:this.linkTarget,expanded:this.model.contents.storage.isExpanded(e.id),hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(e){var t=this;return p.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{expanded:function(e){t.model.contents.storage.addExpanded(e.model)},collapsed:function(e){t.model.contents.storage.removeExpanded(e.model)}})},collapseAll:function(){this.model.contents.storage.clearExpanded(),p.prototype.collapseAll.call(this)},getSelectedModels:function(){var e=p.prototype.getSelectedModels.call(this);return e.historyId=this.collection.historyId,e},events:a.extend(a.clone(p.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click > .controls .prev":"_clickPrevPage","click > .controls .next":"_clickNextPage","change > .controls .pages":"_changePageSelect","click .messages [class$=message]":"clearMessages"}),_clickPrevPage:function(e){this.model.clearUpdateTimeout(),this.model.contents.fetchPrevPage()},_clickNextPage:function(e){this.model.clearUpdateTimeout(),this.model.contents.fetchNextPage()},_changePageSelect:function(e){this.model.clearUpdateTimeout();var t=o(e.currentTarget).val();this.model.contents.fetchPage(t)},toggleShowDeleted:function(e,t){e=void 0!==e?e:!this.model.contents.includeDeleted;var i=this,n=i.model.contents;return n.setIncludeDeleted(e,t),i.trigger("show-deleted",e),n.fetchCurrentPage({renderAll:!0}),e},toggleShowHidden:function(e,t,i){e=void 0!==e?e:!this.model.contents.includeHidden;var n=this,s=n.model.contents;return s.setIncludeHidden(e,i),n.trigger("show-hidden",e),s.fetchCurrentPage({renderAll:!0}),e},_firstSearch:function(e){var t=this,i="> .controls .search-input";if(this.log("onFirstSearch",e),t.model.contents.haveSearchDetails())return void t.searchItems(e);t.$(i).searchInput("toggle-loading"),t.searchFor=e;t.model.contents.progressivelyFetchDetails({silent:!0}).progress(function(e,i,n){t.renderItems(),t.trigger("search:loading-progress",i,n)}).always(function(){t.$el.find(i).searchInput("toggle-loading")}).done(function(){t.searchItems(e,"force")})},clearSearch:function(e){var t=this;return t.searchFor?(t.searchFor="",t.trigger("search:clear",t),t.$("> .controls .search-query").val(""),t.model.contents.fetchCurrentPage({silent:!0}).done(function(){t.renderItems()}),t):t},errorHandler:function(e,t,i){if(!t||0!==t.status||0!==t.readyState){if(this.error(e,t,i),a.isString(e)&&a.isString(t)){var n=e,s=t;return c.errorModal(n,s,i)}return t&&502===t.status?c.badGatewayErrorModal():c.ajaxErrorModal(e,t,i)}},clearMessages:function(e){var t=a.isUndefined(e)?this.$messages().children('[class$="message"]'):o(e.currentTarget);return t.fadeOut(this.fxSpeed,function(){o(this).remove()}),this},scrollToHid:function(e){return this.scrollToItem(a.first(this.viewsWhereModel({hid:e})))},ordinalIndicator:function(e){var t=e+"";switch(t.charAt(t.length-1)){case"1":return t+"st";case"2":return t+"nd";case"3":return t+"rd";default:return t+"th"}},toString:function(){return"HistoryView("+(this.model?this.model.get("name"):"")+")"}});return f.prototype.templates=function(){var e=h.wrapTemplate([""]),t=h.wrapTemplate(['','
','
<%- history.name %>
',"
",'
','
<%- history.nice_size %>
','
','
',"<% if( history.deleted && history.purged ){ %>",'
',u("This history has been purged and deleted"),"
","<% } else if( history.deleted ){ %>",'
',u("This history has been deleted"),"
","<% } else if( history.purged ){ %>",'
',u("This history has been purged"),"
","<% } %>","<% if( history.message ){ %>",'
messagesmall">',"<%= history.message.text %>","
","<% } %>","
",'
','
','
",'
','
','',u("All")," ",'',u("None")," ","
",'","
",'',"
>previous ','',"<% _.range( 1, pages.last + 1 ).forEach( function( i ){ %>",'>',"<%- view.ordinalIndicator( i ) %> of <%- pages.last %> pages"," ","<% }); %>"," ",'>next '],"pages");return a.extend(a.clone(p.prototype.templates),{el:e,controls:t,pagination:i})}(),{HistoryView:f}}.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){n=[i(22),i(82),i(6),i(5),i(27)],s=function(e,t,i,n,s){"use strict";function r(e,t,i){return o.clone(l).filter(function(n){return!(e&&!n.anon)&&(!(!t&&n.purge)&&(n.href&&(n.href=i+n.href,n.target=n.target||"galaxy_main"),n.confirm&&(n.func=function(){confirm(n.confirm)&&(galaxy_main.location=n.href)}),!0))})}var l=[{html:n("History Lists"),header:!0},{html:n("Saved Histories"),href:"histories/list",target:"_top"},{html:n("Histories Shared with Me"),href:"histories/list_shared",target:"_top"},{html:n("Current History"),header:!0,anon:!0},{html:n("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:n("Copy History"),func:function(){t(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:n("Share or Publish"),href:"history/sharing"},{html:n("Show Structure"),href:"history/display_structured",anon:!0},{html:n("Extract Workflow"),href:"workflow/build_from_current_history"},{html:n("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really delete the current history?"))&&(galaxy_main.window.location.href="history/delete?id="+Galaxy.currHistoryPanel.model.id)}},{html:n("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really delete the current history permanently? This cannot be undone."))&&(galaxy_main.window.location.href="history/delete?purge=True&id="+Galaxy.currHistoryPanel.model.id)}},{html:n("Dataset Actions"),header:!0,anon:!0},{html:n("Copy Datasets"),href:"dataset/copy_datasets"},{html:n("Dataset Security"),href:"root/history_set_default_permissions"},{html:n("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:n("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:n("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really unhide all hidden datasets?"))&&a.post(Galaxy.root+"history/adjust_hidden",{user_action:"unhide"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:n("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(n("Really delete all hidden datasets?"))&&a.post(Galaxy.root+"history/adjust_hidden",{user_action:"delete"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:n("Purge Deleted Datasets"),confirm:n("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:n("Downloads"),header:!0},{html:n("Export Tool Citations"),href:"history/citations",anon:!0},{html:n("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:n("Other Actions"),header:!0},{html:n("Import from File"),href:"history/import_archive"}];s.add({url:"api/webhooks/history-menu/all",async:!1,callback:function(e){var t=[];a.each(e.models,function(e,i){var s=i.toJSON();s.activate&&t.push({html:n(s.config.title),anon:!0})}),t.length>0&&(t.unshift({html:n("Webhooks"),header:!0}),a.merge(l,t))}});var c=function(t,i){i=i||{};var n=void 0===i.anonymous||i.anonymous,s=i.purgeAllowed||!1,a=r(n,s,Galaxy.root);return new e(t,a)};return c}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1),i(2))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(14)],s=function(e,t){var i=a.View.extend({initialize:function(t){var i=this;this.setElement(o("
")),this.model=new a.Model,e.get({url:Galaxy.root+"page/list",success:function(e){e.dict_format=!0,i.model.set(e),i.render()}})},render:function(){var e=new t(this.model.attributes);this.$el.empty().append(e.$el),this.$el.append(this._templateShared())},_templateShared:function(){var e=o("
Pages shared with you by others "),t=this.model.attributes;if(t.shared_by_others&&t.shared_by_others.length>0){var i=o('');r.each(t.shared_by_others,function(e,t){var n=Galaxy.root+"page/display_by_username_and_slug?username="+e.username+"&slug="+e.slug;i.append(''+r.escape(e.title)+" "+r.escape(e.username)+" Failed: "+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));this.$progress_bar.css({width:e+"%"}),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[e]),this.model.set("enabled","init"==e);var t=this.model.get("enabled");this.$text_content.attr("disabled",!t),"success"==e&&(this.$el.addClass("success"),this.$percentage.html("100%")),"error"==e&&(this.$el.addClass("danger"),this.$info_progress.hide())},_refreshFileSize:function(){this.$size.html(e.bytesToString(this.model.get("file_size")))},_removeRow:function(){["init","success","error"].indexOf(this.model.get("status"))!==-1&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new i(this).$el),this.settings.show())},_template:function(e){return'
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
read more )'),t}return"There is no description available for this file extension."},_template:function(){return''}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1))},function(e,t,i){var n,s;(function(a,o,r){n=[i(4),i(65),i(64),i(16),i(7),i(17),i(68)],s=function(e,t,i,n,s,l){return a.View.extend({status_classes:{init:"upload-mode fa fa-exclamation text-primary",ready:"upload-mode fa fa-check text-success",running:"upload-mode fa fa-spinner fa-spin",success:"upload-mode fa fa-check",error:"upload-mode fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template()),this.$source=this.$(".upload-source"),this.$settings=this.$(".upload-settings"),this.$status=this.$(".upload-status"),this.$text=this.$(".upload-text"),this.$text_content=this.$(".upload-text-content"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$file_name=this.$(".upload-file-name"),this.$file_desc=this.$(".upload-file-desc"),this.$file_size=this.$(".upload-file-size"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.uploadinput=this.$el.uploadinput({ondragover:function(){i.model.get("enabled")&&i.$el.addClass("warning")},ondragleave:function(){i.$el.removeClass("warning")},onchange:function(e){"running"!=i.model.get("status")&&e&&e.length>0&&(i.model.reset({file_data:e[0],file_name:e[0].name,file_size:e[0].size,file_mode:e[0].mode||"local"}),i._refreshReady())}}),this.button_menu=new s.ButtonMenu({icon:"fa-caret-down",title:"Select",pull:"left"}),this.$source.append(this.button_menu.$el),this.button_menu.addMenu({icon:"fa-laptop",title:"Choose local file",onclick:function(){i.uploadinput.dialog()}}),this.app.ftp_upload_site&&this.button_menu.addMenu({icon:"fa-folder-open-o",title:"Choose FTP file",onclick:function(){i._showFtp()}}),this.button_menu.addMenu({icon:"fa-edit",title:"Paste/Fetch data",onclick:function(){i.model.reset({file_mode:"new",file_name:"New File"})}}),this.ftp=new n.View({title:"Choose FTP file:",container:this.$source.find(".ui-button-menu"),placement:"right"}),this.settings=new n.View({title:"Upload configuration",container:this.$settings,placement:"bottom"}),this.$text_content.on("change input",function(e){i.model.set({url_paste:o(e.target).val(),file_size:o(e.target).val().length}),i._refreshReady()}),this.$settings.on("click",function(e){i._showSettings()}).on("mousedown",function(e){e.preventDefault()}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:file_name",function(){i._refreshFileName()}),this.listenTo(this.model,"change:file_mode",function(){i._refreshMode()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()}),this.listenTo(this.model,"remove",function(){i.remove()}),this.app.collection.on("reset",function(){i.remove()})},render:function(){this.$el.attr("id","upload-row-"+this.model.id),this.$file_name.html(r.escape(this.model.get("file_name")||"-")),this.$file_desc.html(this.model.get("file_desc")||"Unavailable"),this.$file_size.html(e.bytesToString(this.model.get("file_size"))),this.$status.removeClass().addClass(this.status_classes.init)},remove:function(){a.View.prototype.remove.apply(this)},_refreshReady:function(){this.app.collection.each(function(e){e.set("status",e.get("file_size")>0&&"ready"||"init")})},_refreshMode:function(){var e=this.model.get("file_mode");"new"==e?(this.height=this.$el.height(),this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$text_content.val("").trigger("keyup")):(this.$el.height(this.height),this.$text.hide())},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("Failed: "+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));0!=e?this.$progress_bar.css({width:e+"%"}):(this.$progress_bar.addClass("no-transition"),this.$progress_bar.css({width:"0%"}),this.$progress_bar[0].offsetHeight,this.$progress_bar.removeClass("no-transition")),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$status.removeClass().addClass(this.status_classes[e]),this.model.set("enabled","running"!=e),this.$text_content.attr("disabled",!this.model.get("enabled")),this.$el.removeClass("success danger warning"),"running"!=e&&"ready"!=e||this.model.set("percentage",0),this.$source.find(".button")["running"==e?"addClass":"removeClass"]("disabled"),"success"==e&&(this.$el.addClass("success"),this.model.set("percentage",100),this.$percentage.html("100%")),"error"==e?(this.$el.addClass("danger"),this.model.set("percentage",0),this.$info_progress.hide(),this.$info_text.show()):(this.$info_progress.show(),this.$info_text.hide())},_refreshFileName:function(){this.$file_name.html(this.model.get("file_name")||"-")},_refreshFileSize:function(){this.$file_size.html(e.bytesToString(this.model.get("file_size")))},_showFtp:function(){if(this.ftp.visible)this.ftp.hide();else{var e=this;this.ftp.empty(),this.ftp.append(new i({ftp_upload_site:this.app.ftp_upload_site,onchange:function(t){e.ftp.hide(),"running"!=e.model.get("status")&&t&&(e.model.reset({file_mode:"ftp",file_name:t.path,file_size:t.size,file_path:t.path}),e._refreshReady())}}).$el),this.ftp.show()}},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new t(this).$el),this.settings.show())},_template:function(){return'
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
read more )'),t}return"There is no description available for this file extension."},_template:function(){return'Description Name Size Settings Status
Failed: "+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));this.$progress_bar.css({width:e+"%"}),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[e]),this.model.set("enabled","init"==e);var t=this.model.get("enabled");this.$text_content.attr("disabled",!t),t?(this.select_genome.enable(),this.select_extension.enable()):(this.select_genome.disable(),this.select_extension.disable()),"success"==e&&(this.$el.addClass("success"),this.$percentage.html("100%")),"error"==e&&(this.$el.addClass("danger"),this.$info_progress.hide())},_refreshFileSize:function(){this.$size.html(e.bytesToString(this.model.get("file_size")))},_removeRow:function(){["init","success","error"].indexOf(this.model.get("status"))!==-1&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new i(this).$el),this.settings.show())},_template:function(e){return'
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
read more )'),t}return"There is no description available for this file extension."},_template:function(){return'
Name Size Type Genome Settings Status
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chrom/contig length of chrom/contig For example, the first few entries of mm9.len are as follows:
chr1 197195432\nchr2 181748087\nchr3 159599783\nchr4 155630120\nchr5 152537259 Trackster uses this information to populate the select box for chrom/contig, andto set the maximum basepair of the track browser. You may either upload a .len fileof this format (Len File option), or directly enter the information into the box (Len Entry option).
"},_templateFasta:function(){return"FASTA format This is a multi-fasta file from your current history that provides the genomesequences for each chromosome/contig in your build.
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In Galaxy, datasets are associated with a history, so\n\t * this object is also known as a HistoryDatasetAssociation.\n\t */\n\t var Dataset = Backbone.Model.extend({\n\t defaults: {\n\t id: '',\n\t type: '',\n\t name: '',\n\t hda_ldda: 'hda',\n\t metadata: null\n\t },\n\t\n\t initialize: function () {\n\t // Metadata can be passed in as a model or a set of attributes; if it's\n\t // already a model, there's no need to set metadata.\n\t if (!this.get('metadata')) {\n\t this._set_metadata();\n\t }\n\t\n\t // Update metadata on change.\n\t this.on('change', this._set_metadata, this);\n\t },\n\t\n\t _set_metadata: function () {\n\t var metadata = new DatasetMetadata();\n\t\n\t // Move metadata from dataset attributes to metadata object.\n\t _.each(_.keys(this.attributes), function (k) {\n\t if (k.indexOf('metadata_') === 0) {\n\t // Found metadata.\n\t var new_key = k.split('metadata_')[1];\n\t metadata.set(new_key, this.attributes[k]);\n\t delete this.attributes[k];\n\t }\n\t }, this);\n\t\n\t // Because this is an internal change, silence it.\n\t this.set('metadata', metadata, { 'silent': true });\n\t },\n\t\n\t /**\n\t * Returns dataset metadata for a given attribute.\n\t */\n\t get_metadata: function (attribute) {\n\t return this.attributes.metadata.get(attribute);\n\t },\n\t\n\t urlRoot: Galaxy.root + \"api/datasets\"\n\t });\n\t\n\t /**\n\t * A tabular dataset. This object extends dataset to provide incremental chunked data.\n\t */\n\t var TabularDataset = Dataset.extend({\n\t defaults: _.extend({}, Dataset.prototype.defaults, {\n\t chunk_url: null,\n\t first_data_chunk: null,\n\t offset: 0,\n\t at_eof: false\n\t }),\n\t\n\t initialize: function (options) {\n\t Dataset.prototype.initialize.call(this);\n\t\n\t // If first data chunk is available, next chunk is 1.\n\t if (this.attributes.first_data_chunk) {\n\t this.attributes.offset = this.attributes.first_data_chunk.offset;\n\t }\n\t this.attributes.chunk_url = Galaxy.root + 'dataset/display?dataset_id=' + this.id;\n\t this.attributes.url_viz = Galaxy.root + 'visualization';\n\t },\n\t\n\t /**\n\t * Returns a jQuery Deferred object that resolves to the next data chunk or null if at EOF.\n\t */\n\t get_next_chunk: function () {\n\t // If already at end of file, do nothing.\n\t if (this.attributes.at_eof) {\n\t return null;\n\t }\n\t\n\t // Get next chunk.\n\t var self = this,\n\t next_chunk = $.Deferred();\n\t $.getJSON(this.attributes.chunk_url, {\n\t offset: self.attributes.offset\n\t }).success(function (chunk) {\n\t var rval;\n\t if (chunk.ck_data !== '') {\n\t // Found chunk.\n\t rval = chunk;\n\t self.attributes.offset = chunk.offset;\n\t } else {\n\t // At EOF.\n\t self.attributes.at_eof = true;\n\t rval = null;\n\t }\n\t next_chunk.resolve(rval);\n\t });\n\t\n\t return next_chunk;\n\t }\n\t });\n\t\n\t var DatasetCollection = Backbone.Collection.extend({\n\t model: Dataset\n\t });\n\t\n\t /**\n\t * Provides a base for table-based, dynamic view of a tabular dataset.\n\t * Do not instantiate directly; use either TopLevelTabularDatasetChunkedView\n\t * or EmbeddedTabularDatasetChunkedView.\n\t */\n\t var TabularDatasetChunkedView = Backbone.View.extend({\n\t\n\t /**\n\t * Initialize view and, importantly, set a scroll element.\n\t */\n\t initialize: function (options) {\n\t // Row count for rendering.\n\t this.row_count = 0;\n\t this.loading_chunk = false;\n\t\n\t // load trackster button\n\t new TabularButtonTracksterView({\n\t model: options.model,\n\t $el: this.$el\n\t });\n\t },\n\t\n\t expand_to_container: function () {\n\t if (this.$el.height() < this.scroll_elt.height()) {\n\t this.attempt_to_fetch();\n\t }\n\t },\n\t\n\t attempt_to_fetch: function (func) {\n\t var self = this;\n\t if (!this.loading_chunk && this.scrolled_to_bottom()) {\n\t this.loading_chunk = true;\n\t this.loading_indicator.show();\n\t $.when(self.model.get_next_chunk()).then(function (result) {\n\t if (result) {\n\t self._renderChunk(result);\n\t self.loading_chunk = false;\n\t }\n\t self.loading_indicator.hide();\n\t self.expand_to_container();\n\t });\n\t }\n\t },\n\t\n\t render: function () {\n\t // Add loading indicator.\n\t this.loading_indicator = $('
').attr('id', 'loading_indicator');\n\t this.$el.append(this.loading_indicator);\n\t\n\t // Add data table and header.\n\t var data_table = $('').attr({\n\t id: 'content_table',\n\t cellpadding: 0\n\t });\n\t this.$el.append(data_table);\n\t var column_names = this.model.get_metadata('column_names'),\n\t header_container = $('' + column_names.join(' ') + ' ');\n\t } else {\n\t for (var j = 1; j <= this.model.get_metadata('columns'); j++) {\n\t header_row.append('' + j + ' ');\n\t }\n\t }\n\t\n\t // Render first chunk.\n\t var self = this,\n\t first_chunk = this.model.get('first_data_chunk');\n\t if (first_chunk) {\n\t // First chunk is bootstrapped, so render now.\n\t this._renderChunk(first_chunk);\n\t } else {\n\t // No bootstrapping, so get first chunk and then render.\n\t $.when(self.model.get_next_chunk()).then(function (result) {\n\t self._renderChunk(result);\n\t });\n\t }\n\t\n\t // -- Show new chunks during scrolling. --\n\t\n\t // Set up chunk loading when scrolling using the scrolling element.\n\t this.scroll_elt.scroll(function () {\n\t self.attempt_to_fetch();\n\t });\n\t },\n\t\n\t /**\n\t * Returns true if user has scrolled to the bottom of the view.\n\t */\n\t scrolled_to_bottom: function () {\n\t return false;\n\t },\n\t\n\t // -- Helper functions. --\n\t\n\t _renderCell: function (cell_contents, index, colspan) {\n\t var $cell = $('').text(cell_contents);\n\t var column_types = this.model.get_metadata('column_types');\n\t if (colspan !== undefined) {\n\t $cell.attr('colspan', colspan).addClass('stringalign');\n\t } else if (column_types) {\n\t if (index < column_types.length) {\n\t if (column_types[index] === 'str' || column_types[index] === 'list') {\n\t /* Left align all str columns, right align the rest */\n\t $cell.addClass('stringalign');\n\t }\n\t }\n\t }\n\t return $cell;\n\t },\n\t\n\t _renderRow: function (line) {\n\t // Check length of cells to ensure this is a complete row.\n\t var cells = line.split('\\t'),\n\t row = $(' '),\n\t num_columns = this.model.get_metadata('columns');\n\t\n\t if (this.row_count % 2 !== 0) {\n\t row.addClass('dark_row');\n\t }\n\t\n\t if (cells.length === num_columns) {\n\t _.each(cells, function (cell_contents, index) {\n\t row.append(this._renderCell(cell_contents, index));\n\t }, this);\n\t } else if (cells.length > num_columns) {\n\t // SAM file or like format with optional metadata included.\n\t _.each(cells.slice(0, num_columns - 1), function (cell_contents, index) {\n\t row.append(this._renderCell(cell_contents, index));\n\t }, this);\n\t row.append(this._renderCell(cells.slice(num_columns - 1).join('\\t'), num_columns - 1));\n\t } else if (cells.length === 1) {\n\t // Comment line, just return the one cell.\n\t row.append(this._renderCell(line, 0, num_columns));\n\t } else {\n\t // cells.length is greater than one, but less than num_columns. Render cells and pad tds.\n\t // Possibly a SAM file or like format with optional metadata missing.\n\t // Could also be a tabular file with a line with missing columns.\n\t _.each(cells, function (cell_contents, index) {\n\t row.append(this._renderCell(cell_contents, index));\n\t }, this);\n\t _.each(_.range(num_columns - cells.length), function () {\n\t row.append($(''));\n\t });\n\t }\n\t\n\t this.row_count++;\n\t return row;\n\t },\n\t\n\t _renderChunk: function (chunk) {\n\t var data_table = this.$el.find('table');\n\t _.each(chunk.ck_data.split('\\n'), function (line, index) {\n\t if (line !== '') {\n\t data_table.append(this._renderRow(line));\n\t }\n\t }, this);\n\t }\n\t });\n\t\n\t /**\n\t * Tabular view that is placed at the top level of page. Scrolling occurs\n\t * view top-level elements outside of view.\n\t */\n\t var TopLevelTabularDatasetChunkedView = TabularDatasetChunkedView.extend({\n\t\n\t initialize: function (options) {\n\t TabularDatasetChunkedView.prototype.initialize.call(this, options);\n\t\n\t // Scrolling happens in top-level elements.\n\t scroll_elt = _.find(this.$el.parents(), function (p) {\n\t return $(p).css('overflow') === 'auto';\n\t });\n\t\n\t // If no scrolling element found, use window.\n\t if (!scroll_elt) {\n\t scroll_elt = window;\n\t }\n\t\n\t // Wrap scrolling element for easy access.\n\t this.scroll_elt = $(scroll_elt);\n\t },\n\t\n\t /**\n\t * Returns true if user has scrolled to the bottom of the view.\n\t */\n\t scrolled_to_bottom: function () {\n\t return this.$el.height() - this.scroll_elt.scrollTop() - this.scroll_elt.height() <= 0;\n\t }\n\t\n\t });\n\t\n\t /**\n\t * Tabular view tnat is embedded in a page. Scrolling occurs in view's el.\n\t */\n\t var EmbeddedTabularDatasetChunkedView = TabularDatasetChunkedView.extend({\n\t\n\t initialize: function (options) {\n\t TabularDatasetChunkedView.prototype.initialize.call(this, options);\n\t\n\t // Because view is embedded, set up div to do scrolling.\n\t this.scroll_elt = this.$el.css({\n\t position: 'relative',\n\t overflow: 'scroll',\n\t height: options.height || '500px'\n\t });\n\t },\n\t\n\t /**\n\t * Returns true if user has scrolled to the bottom of the view.\n\t */\n\t scrolled_to_bottom: function () {\n\t return this.$el.scrollTop() + this.$el.innerHeight() >= this.el.scrollHeight;\n\t }\n\t\n\t });\n\t\n\t /** Button for trackster visualization */\n\t var TabularButtonTracksterView = Backbone.View.extend({\n\t\n\t // gene region columns\n\t col: {\n\t chrom: null,\n\t start: null,\n\t end: null\n\t },\n\t\n\t // url for trackster\n\t url_viz: null,\n\t\n\t // dataset id\n\t dataset_id: null,\n\t\n\t // database key\n\t genome_build: null,\n\t\n\t // data type\n\t file_ext: null,\n\t\n\t // backbone initialize\n\t initialize: function (options) {\n\t // check if environment is available\n\t var Galaxy = parent.Galaxy;\n\t\n\t // link galaxy modal or create one\n\t if (Galaxy && Galaxy.modal) {\n\t this.modal = Galaxy.modal;\n\t }\n\t\n\t // link galaxy frames\n\t if (Galaxy && Galaxy.frame) {\n\t this.frame = Galaxy.frame;\n\t }\n\t\n\t // check\n\t if (!this.modal || !this.frame) {\n\t return;\n\t }\n\t\n\t // model/metadata\n\t var model = options.model;\n\t var metadata = model.get('metadata');\n\t\n\t // check for datatype\n\t if (!model.get('file_ext')) {\n\t return;\n\t }\n\t\n\t // get data type\n\t this.file_ext = model.get('file_ext');\n\t\n\t // check for bed-file format\n\t if (this.file_ext == 'bed') {\n\t // verify that metadata exists\n\t if (metadata.get('chromCol') && metadata.get('startCol') && metadata.get('endCol')) {\n\t // read in columns\n\t this.col.chrom = metadata.get('chromCol') - 1;\n\t this.col.start = metadata.get('startCol') - 1;\n\t this.col.end = metadata.get('endCol') - 1;\n\t } else {\n\t console.log('TabularButtonTrackster : Bed-file metadata incomplete.');\n\t return;\n\t }\n\t }\n\t\n\t // check for vcf-file format\n\t if (this.file_ext == 'vcf') {\n\t // search array\n\t function search(str, array) {\n\t for (var j = 0; j < array.length; j++) if (array[j].match(str)) return j;\n\t return -1;\n\t };\n\t\n\t // load\n\t this.col.chrom = search('Chrom', metadata.get('column_names'));\n\t this.col.start = search('Pos', metadata.get('column_names'));\n\t this.col.end = null;\n\t\n\t // verify that metadata exists\n\t if (this.col.chrom == -1 || this.col.start == -1) {\n\t console.log('TabularButtonTrackster : VCF-file metadata incomplete.');\n\t return;\n\t }\n\t }\n\t\n\t // check\n\t if (this.col.chrom === undefined) {\n\t return;\n\t }\n\t\n\t // get dataset id\n\t if (model.id) {\n\t this.dataset_id = model.id;\n\t } else {\n\t console.log('TabularButtonTrackster : Dataset identification is missing.');\n\t return;\n\t }\n\t\n\t // get url\n\t if (model.get('url_viz')) {\n\t this.url_viz = model.get('url_viz');\n\t } else {\n\t console.log('TabularButtonTrackster : Url for visualization controller is missing.');\n\t return;\n\t }\n\t\n\t // get genome_build / database key\n\t if (model.get('genome_build')) {\n\t this.genome_build = model.get('genome_build');\n\t }\n\t\n\t // create the icon\n\t var btn_viz = new mod_icon_btn.IconButtonView({\n\t model: new mod_icon_btn.IconButton({\n\t title: 'Visualize',\n\t icon_class: 'chart_curve',\n\t id: 'btn_viz'\n\t })\n\t });\n\t\n\t // set element\n\t this.setElement(options.$el);\n\t\n\t // add to element\n\t this.$el.append(btn_viz.render().$el);\n\t\n\t // hide the button\n\t this.hide();\n\t },\n\t\n\t /** Add event handlers */\n\t events: {\n\t 'mouseover tr': 'show',\n\t 'mouseleave': 'hide'\n\t },\n\t\n\t // show button\n\t show: function (e) {\n\t var self = this;\n\t\n\t // is numeric\n\t function is_numeric(n) {\n\t return !isNaN(parseFloat(n)) && isFinite(n);\n\t };\n\t\n\t // check\n\t if (this.col.chrom === null) return;\n\t\n\t // get selected data line\n\t var row = $(e.target).parent();\n\t\n\t // verify that location has been found\n\t var chrom = row.children().eq(this.col.chrom).html();\n\t var start = row.children().eq(this.col.start).html();\n\t\n\t // end is optional\n\t var end = this.col.end ? row.children().eq(this.col.end).html() : start;\n\t\n\t // double check location\n\t if (!chrom.match(\"^#\") && chrom !== \"\" && is_numeric(start)) {\n\t\n\t // get target gene region\n\t var btn_viz_pars = {\n\t dataset_id: this.dataset_id,\n\t gene_region: chrom + \":\" + start + \"-\" + end\n\t };\n\t\n\t // get button position\n\t var offset = row.offset();\n\t var left = offset.left - 10;\n\t var top = offset.top - $(window).scrollTop() + 3;\n\t\n\t // update css\n\t $('#btn_viz').css({ 'position': 'fixed', 'top': top + 'px', 'left': left + 'px' });\n\t $('#btn_viz').off('click');\n\t $('#btn_viz').click(function () {\n\t self.frame.add({\n\t title: 'Trackster',\n\t url: self.url_viz + '/trackster?' + $.param(btn_viz_pars)\n\t });\n\t });\n\t\n\t // show the button\n\t $('#btn_viz').show();\n\t } else {\n\t // hide the button\n\t $('#btn_viz').hide();\n\t }\n\t },\n\t\n\t /** hide button */\n\t hide: function () {\n\t this.$('#btn_viz').hide();\n\t }\n\t });\n\t\n\t // -- Utility functions. --\n\t\n\t /**\n\t * Create a model, attach it to a view, render view, and attach it to a parent element.\n\t */\n\t var createModelAndView = function (model, view, model_config, parent_elt) {\n\t // Create model, view.\n\t var a_view = new view({\n\t model: new model(model_config)\n\t });\n\t\n\t // Render view and add to parent element.\n\t a_view.render();\n\t if (parent_elt) {\n\t parent_elt.append(a_view.$el);\n\t }\n\t\n\t return a_view;\n\t };\n\t\n\t /**\n\t * Create a tabular dataset chunked view (and requisite tabular dataset model)\n\t * and appends to parent_elt.\n\t */\n\t var createTabularDatasetChunkedView = function (options) {\n\t // If no model, create and set model from dataset config.\n\t if (!options.model) {\n\t options.model = new TabularDataset(options.dataset_config);\n\t }\n\t\n\t var parent_elt = options.parent_elt;\n\t var embedded = options.embedded;\n\t\n\t // Clean up options so that only needed options are passed to view.\n\t delete options.embedded;\n\t delete options.parent_elt;\n\t delete options.dataset_config;\n\t\n\t // Create and set up view.\n\t var view = embedded ? new EmbeddedTabularDatasetChunkedView(options) : new TopLevelTabularDatasetChunkedView(options);\n\t view.render();\n\t\n\t if (parent_elt) {\n\t parent_elt.append(view.$el);\n\t // If we're sticking this in another element, once it's appended check\n\t // to make sure we've filled enough space.\n\t // Without this, the scroll elements don't work.\n\t view.expand_to_container();\n\t }\n\t\n\t return view;\n\t };\n\t\n\t return {\n\t Dataset: Dataset,\n\t TabularDataset: TabularDataset,\n\t DatasetCollection: DatasetCollection,\n\t TabularDatasetChunkedView: TabularDatasetChunkedView,\n\t createTabularDatasetChunkedView: createTabularDatasetChunkedView\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__(3), __webpack_require__(2), __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_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t\n\t 'use strict';\n\t //==============================================================================\n\t /** Map of possible HDA/collection/job states to their string equivalents.\n\t * A port of galaxy.model.Dataset.states.\n\t */\n\t\n\t var STATES = {\n\t // NOT ready states\n\t /** is uploading and not ready */\n\t UPLOAD: 'upload',\n\t /** the job that will produce the dataset queued in the runner */\n\t QUEUED: 'queued',\n\t /** the job that will produce the dataset is running */\n\t RUNNING: 'running',\n\t /** metadata for the dataset is being discovered/set */\n\t SETTING_METADATA: 'setting_metadata',\n\t\n\t // ready states\n\t /** was created without a tool */\n\t NEW: 'new',\n\t /** has no data */\n\t EMPTY: 'empty',\n\t /** has successfully completed running */\n\t OK: 'ok',\n\t\n\t /** the job that will produce the dataset paused */\n\t PAUSED: 'paused',\n\t /** metadata discovery/setting failed or errored (but otherwise ok) */\n\t FAILED_METADATA: 'failed_metadata',\n\t //TODO: not in trans.app.model.Dataset.states - is in database\n\t /** not accessible to the current user (i.e. due to permissions) */\n\t NOT_VIEWABLE: 'noPermission',\n\t /** deleted while uploading */\n\t DISCARDED: 'discarded',\n\t /** the tool producing this dataset failed */\n\t ERROR: 'error'\n\t };\n\t\n\t STATES.READY_STATES = [STATES.OK, STATES.EMPTY, STATES.PAUSED, STATES.FAILED_METADATA, STATES.NOT_VIEWABLE, STATES.DISCARDED, STATES.ERROR];\n\t\n\t STATES.NOT_READY_STATES = [STATES.UPLOAD, STATES.QUEUED, STATES.RUNNING, STATES.SETTING_METADATA, STATES.NEW];\n\t\n\t //==============================================================================\n\t return STATES;\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\n/***/ },\n/* 12 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/** This module contains all button views. */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t /** This renders the default button which is used e.g. at the bottom of the upload modal. */\n\t var ButtonDefault = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t title: '',\n\t floating: 'right',\n\t icon: '',\n\t cls: 'btn btn-default',\n\t wait: false,\n\t wait_text: 'Sending...',\n\t wait_cls: 'btn btn-info',\n\t disabled: false,\n\t percentage: -1\n\t }).set(options);\n\t this.setElement($('
').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).css('float', options.floating).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 = $('
').append(this.$button = $('
').append(this.$icon = $('
').append(this.$root = $('
').append(this.$icon = $('
');\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') && 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.message_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__(3), __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, _, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [\n\t //jquery\n\t //backbone\n\t], __WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t //=============================================================================\n\t /**\n\t * backbone model for icon buttons\n\t */\n\t var IconButton = Backbone.Model.extend({\n\t defaults: {\n\t title: \"\",\n\t icon_class: \"\",\n\t on_click: null,\n\t menu_options: null,\n\t is_menu_button: true,\n\t id: null,\n\t href: null,\n\t target: null,\n\t enabled: true,\n\t visible: true,\n\t tooltip_config: {}\n\t }\n\t });\n\t\n\t /**\n\t * backbone view for icon buttons\n\t */\n\t var IconButtonView = Backbone.View.extend({\n\t\n\t initialize: function () {\n\t // better rendering this way\n\t this.model.attributes.tooltip_config = { placement: 'bottom' };\n\t this.model.bind('change', this.render, this);\n\t },\n\t\n\t render: function () {\n\t // hide tooltip\n\t this.$el.tooltip('hide');\n\t\n\t var new_elem = this.template(this.model.toJSON());\n\t // configure tooltip\n\t new_elem.tooltip(this.model.get('tooltip_config'));\n\t this.$el.replaceWith(new_elem);\n\t this.setElement(new_elem);\n\t return this;\n\t },\n\t\n\t events: {\n\t 'click': 'click'\n\t },\n\t\n\t click: function (event) {\n\t // if on_click pass to that function\n\t if (_.isFunction(this.model.get('on_click'))) {\n\t this.model.get('on_click')(event);\n\t return false;\n\t }\n\t // otherwise, bubble up ( to href or whatever )\n\t return true;\n\t },\n\t\n\t // generate html element\n\t template: function (options) {\n\t var buffer = 'title=\"' + options.title + '\" class=\"icon-button';\n\t\n\t if (options.is_menu_button) {\n\t buffer += ' menu-button';\n\t }\n\t\n\t buffer += ' ' + options.icon_class;\n\t\n\t if (!options.enabled) {\n\t buffer += '_disabled';\n\t }\n\t\n\t // close class tag\n\t buffer += '\"';\n\t\n\t if (options.id) {\n\t buffer += ' id=\"' + options.id + '\"';\n\t }\n\t\n\t buffer += ' href=\"' + options.href + '\"';\n\t // add target for href\n\t if (options.target) {\n\t buffer += ' target=\"' + options.target + '\"';\n\t }\n\t // set visibility\n\t if (!options.visible) {\n\t buffer += ' style=\"display: none;\"';\n\t }\n\t\n\t // enabled/disabled\n\t if (options.enabled) {\n\t buffer = '' + '
' + '
' + '
' + '
' + '
';\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__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 16 */\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_AMD_DEFINE_RESULT__ = function (Utils) {\n\t\n\t /**\n\t * A plugin for initializing select2 input items.\n\t * Make sure the select2 library itself is loaded beforehand.\n\t * Also the element to which select2 will be appended has to \n\t * be created before select2 initialization (and passed as option).\n\t */\n\t var View = Backbone.View.extend({\n\t // options\n\t optionsDefault: {\n\t css: '',\n\t placeholder: 'No data available',\n\t data: [],\n\t value: null,\n\t multiple: false,\n\t minimumInputLength: 0,\n\t // example format of initial data: \"id:name,55:anotherrole@role.com,27:role@role.com\"\n\t initialData: ''\n\t },\n\t\n\t // initialize\n\t initialize: function (options) {\n\t // configure options\n\t this.options = Utils.merge(options, this.optionsDefault);\n\t\n\t // create new element\n\t this.setElement(this._template(this.options));\n\t\n\t // check if container exists\n\t if (!this.options.container) {\n\t console.log('ui-select::initialize() : container not specified.');\n\t return;\n\t }\n\t\n\t // add to dom\n\t this.options.container.append(this.$el);\n\t\n\t // link selection dictionary\n\t this.select_data = this.options.data;\n\t\n\t // refresh\n\t this._refresh();\n\t\n\t if (!this.options.multiple) {\n\t // initial value\n\t if (this.options.value) {\n\t this._setValue(this.options.value);\n\t }\n\t\n\t // add change event\n\t var self = this;\n\t if (this.options.onchange) {\n\t this.$el.on('change', function () {\n\t self.options.onchange(self.value());\n\t });\n\t }\n\t }\n\t },\n\t\n\t // value\n\t value: function (new_value) {\n\t // get current id/value\n\t var before = this._getValue();\n\t\n\t // check if new_value is defined\n\t if (new_value !== undefined) {\n\t this._setValue(new_value);\n\t }\n\t\n\t // get current id/value\n\t var after = this._getValue();\n\t\n\t // fire onchange\n\t if (after != before && this.options.onchange) {\n\t this.options.onchange(after);\n\t }\n\t\n\t // return current value\n\t return after;\n\t },\n\t\n\t // label\n\t text: function () {\n\t return this.$el.select2('data').text;\n\t },\n\t\n\t // disabled\n\t disabled: function () {\n\t return !this.$el.select2('enable');\n\t },\n\t\n\t // enable\n\t enable: function () {\n\t this.$el.select2('enable', true);\n\t },\n\t\n\t // disable\n\t disable: function () {\n\t this.$el.select2('enable', false);\n\t },\n\t\n\t // add\n\t add: function (options) {\n\t // add options\n\t this.select_data.push({\n\t id: options.id,\n\t text: options.text\n\t });\n\t\n\t // refresh\n\t this._refresh();\n\t },\n\t\n\t // remove\n\t del: function (id) {\n\t // search option\n\t var index = this._getIndex(id);\n\t\n\t // check if found\n\t if (index != -1) {\n\t // remove options\n\t this.select_data.splice(index, 1);\n\t\n\t // refresh\n\t this._refresh();\n\t }\n\t },\n\t\n\t // remove\n\t remove: function () {\n\t this.$el.select2('destroy');\n\t },\n\t\n\t // update\n\t update: function (options) {\n\t // copy options\n\t this.select_data = [];\n\t for (var key in options.data) {\n\t this.select_data.push(options.data[key]);\n\t }\n\t\n\t // refresh\n\t this._refresh();\n\t },\n\t\n\t // refresh\n\t _refresh: function () {\n\t // add select2 data based on type of input\n\t if (!this.options.multiple) {\n\t var selected = this._getValue();\n\t var select_opt = {\n\t data: this.select_data,\n\t containerCssClass: this.options.css,\n\t placeholder: this.options.placeholder,\n\t dropdownAutoWidth: true\n\t };\n\t this.$el.select2(select_opt);\n\t // select previous value (if exists)\n\t this._setValue(selected);\n\t } else {\n\t var select_opt = {\n\t multiple: this.options.multiple,\n\t containerCssClass: this.options.css,\n\t placeholder: this.options.placeholder,\n\t minimumInputLength: this.options.minimumInputLength,\n\t ajax: this.options.ajax,\n\t dropdownCssClass: this.options.dropdownCssClass,\n\t escapeMarkup: this.options.escapeMarkup,\n\t formatResult: this.options.formatResult,\n\t formatSelection: this.options.formatSelection,\n\t initSelection: this.options.initSelection,\n\t initialData: this.options.initialData\n\t };\n\t this.$el.select2(select_opt);\n\t }\n\t },\n\t\n\t // get index\n\t _getIndex: function (value) {\n\t // returns the index of the searched value\n\t _.findIndex(this.select_data, { id: value });\n\t },\n\t\n\t // get value\n\t _getValue: function () {\n\t return this.$el.select2('val');\n\t },\n\t\n\t // set value\n\t _setValue: function (new_value) {\n\t var index = this._getIndex(new_value);\n\t if (index == -1) {\n\t if (this.select_data.length > 0) {\n\t new_value = this.select_data[0].id;\n\t }\n\t }\n\t this.$el.select2('val', new_value);\n\t },\n\t\n\t // element\n\t _template: function (options) {\n\t return '
';\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__(3), __webpack_require__(2)))\n\n/***/ },\n/* 17 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_FACTORY__, __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;// from: https://raw.githubusercontent.com/umdjs/umd/master/jqueryPlugin.js\n\t// Uses AMD or browser globals to create a jQuery plugin.\n\t(function (factory) {\n\t if (true) {\n\t //TODO: So...this turns out to be an all or nothing thing. If I load jQuery in the define below, it will\n\t // (of course) wipe the old jquery *and all the plugins loaded into it*. So the define below *is still\n\t // relying on jquery being loaded globally* in order to preserve plugins.\n\t !(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(1)], __WEBPACK_AMD_DEFINE_FACTORY__ = (factory), __WEBPACK_AMD_DEFINE_RESULT__ = (typeof __WEBPACK_AMD_DEFINE_FACTORY__ === 'function' ? (__WEBPACK_AMD_DEFINE_FACTORY__.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__)) : __WEBPACK_AMD_DEFINE_FACTORY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t } else {\n\t // Browser globals\n\t factory(jQuery);\n\t }\n\t})(function (jQuery) {\n\t 'use_strict';\n\t\n\t var $ = jQuery;\n\t\n\t // ============================================================================\n\t /**\n\t * Make an element with text editable: (a) when user clicks on text, a textbox/area\n\t * is provided for editing; (b) when enter key pressed, element's text is set and on_finish\n\t * is called.\n\t */\n\t $.fn.make_text_editable = function (config_dict) {\n\t // Get config options.\n\t var num_cols = \"num_cols\" in config_dict ? config_dict.num_cols : 30,\n\t num_rows = \"num_rows\" in config_dict ? config_dict.num_rows : 4,\n\t use_textarea = \"use_textarea\" in config_dict ? config_dict.use_textarea : false,\n\t on_finish = \"on_finish\" in config_dict ? config_dict.on_finish : null,\n\t help_text = \"help_text\" in config_dict ? config_dict.help_text : null;\n\t\n\t // Add element behavior.\n\t var container = $(this);\n\t container.addClass(\"editable-text\").click(function (e) {\n\t // If there's already an input element, editing is active, so do nothing.\n\t if ($(this).children(\":input\").length > 0) {\n\t return;\n\t }\n\t\n\t container.removeClass(\"editable-text\");\n\t\n\t // Handler for setting element text.\n\t var set_text = function (new_text) {\n\t container.find(\":input\").remove();\n\t\n\t if (new_text !== \"\") {\n\t container.text(new_text);\n\t } else {\n\t // No text; need a line so that there is a click target.\n\t container.html(\"
\");\n\t }\n\t container.addClass(\"editable-text\");\n\t\n\t if (on_finish) {\n\t on_finish(new_text);\n\t }\n\t };\n\t\n\t // Create input element(s) for editing.\n\t var cur_text = \"cur_text\" in config_dict ? config_dict.cur_text : container.text(),\n\t input_elt,\n\t button_elt;\n\t\n\t if (use_textarea) {\n\t input_elt = $(\"
\").attr({ rows: num_rows, cols: num_cols }).text($.trim(cur_text)).keyup(function (e) {\n\t if (e.keyCode === 27) {\n\t // Escape key.\n\t set_text(cur_text);\n\t }\n\t });\n\t button_elt = $(\"
\").text(\"Done\").click(function () {\n\t set_text(input_elt.val());\n\t // Return false so that click does not propogate to container.\n\t return false;\n\t });\n\t } else {\n\t input_elt = $(\"
\").attr({ value: $.trim(cur_text), size: num_cols }).blur(function () {\n\t set_text(cur_text);\n\t }).keyup(function (e) {\n\t if (e.keyCode === 27) {\n\t // Escape key.\n\t $(this).trigger(\"blur\");\n\t } else if (e.keyCode === 13) {\n\t // Enter key.\n\t set_text($(this).val());\n\t }\n\t\n\t // Do not propogate event to avoid unwanted side effects.\n\t e.stopPropagation();\n\t });\n\t }\n\t\n\t // Replace text with input object(s) and focus & select.\n\t container.text(\"\");\n\t container.append(input_elt);\n\t if (button_elt) {\n\t container.append(button_elt);\n\t }\n\t input_elt.focus();\n\t input_elt.select();\n\t\n\t // Do not propogate to elements below b/c that blurs input and prevents it from being used.\n\t e.stopPropagation();\n\t });\n\t\n\t // Add help text if there some.\n\t if (help_text) {\n\t container.attr(\"title\", help_text).tooltip();\n\t }\n\t\n\t return container;\n\t };\n\t\n\t // ============================================================================\n\t});\n\n/***/ },\n/* 18 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_FACTORY__, __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function($, _) {(function (root, factory) {\n\t if (true) {\n\t !(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_FACTORY__ = (factory), __WEBPACK_AMD_DEFINE_RESULT__ = (typeof __WEBPACK_AMD_DEFINE_FACTORY__ === 'function' ? (__WEBPACK_AMD_DEFINE_FACTORY__.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__)) : __WEBPACK_AMD_DEFINE_FACTORY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t } else {\n\t root.faIconButton = factory();\n\t }\n\t})(this, function () {\n\t //============================================================================\n\t /** Returns a jQuery object containing a clickable font-awesome button.\n\t * options:\n\t * tooltipConfig : option map for bootstrap tool tip\n\t * classes : array of class names (will always be classed as icon-btn)\n\t * disabled : T/F - add the 'disabled' class?\n\t * title : tooltip/title string\n\t * target : optional href target\n\t * href : optional href\n\t * faIcon : which font awesome icon to use\n\t * onclick : function to call when the button is clicked\n\t */\n\t var faIconButton = function (options) {\n\t options = options || {};\n\t options.tooltipConfig = options.tooltipConfig || { placement: 'bottom' };\n\t\n\t options.classes = ['icon-btn'].concat(options.classes || []);\n\t if (options.disabled) {\n\t options.classes.push('disabled');\n\t }\n\t\n\t var html = ['
',\n\t // could go with something less specific here - like 'html'\n\t ' '].join('');\n\t var $button = $(html).tooltip(options.tooltipConfig);\n\t if (_.isFunction(options.onclick)) {\n\t $button.click(options.onclick);\n\t }\n\t return $button;\n\t };\n\t\n\t //============================================================================\n\t return faIconButton;\n\t});\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(2)))\n\n/***/ },\n/* 19 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {!(__WEBPACK_AMD_DEFINE_RESULT__ = function () {\n\t\n\t /**\n\t * Stringifies a number adding commas for digit grouping as per North America.\n\t */\n\t function commatize(number) {\n\t number += ''; // Convert to string\n\t var rgx = /(\\d+)(\\d{3})/;\n\t while (rgx.test(number)) {\n\t number = number.replace(rgx, '$1' + ',' + '$2');\n\t }\n\t return number;\n\t }\n\t\n\t /**\n\t * Helper to determine if object is jQuery deferred.\n\t */\n\t var is_deferred = function (d) {\n\t return 'promise' in d;\n\t };\n\t\n\t /**\n\t * Implementation of a server-state based deferred. Server is repeatedly polled, and when\n\t * condition is met, deferred is resolved.\n\t */\n\t var ServerStateDeferred = Backbone.Model.extend({\n\t defaults: {\n\t ajax_settings: {},\n\t interval: 1000,\n\t success_fn: function (result) {\n\t return true;\n\t }\n\t },\n\t\n\t /**\n\t * Returns a deferred that resolves when success function returns true.\n\t */\n\t go: function () {\n\t var deferred = $.Deferred(),\n\t self = this,\n\t ajax_settings = self.get('ajax_settings'),\n\t success_fn = self.get('success_fn'),\n\t interval = self.get('interval'),\n\t _go = function () {\n\t $.ajax(ajax_settings).success(function (result) {\n\t if (success_fn(result)) {\n\t // Result is good, so resolve.\n\t deferred.resolve(result);\n\t } else {\n\t // Result not good, try again.\n\t setTimeout(_go, interval);\n\t }\n\t });\n\t };\n\t _go();\n\t return deferred;\n\t }\n\t });\n\t\n\t /**\n\t * Returns a random color in hexadecimal format that is sufficiently different from a single color\n\t * or set of colors.\n\t * @param colors a color or list of colors in the format '#RRGGBB'\n\t */\n\t var get_random_color = function (colors) {\n\t // Default for colors is white.\n\t if (!colors) {\n\t colors = \"#ffffff\";\n\t }\n\t\n\t // If needed, create list of colors.\n\t if (typeof colors === \"string\") {\n\t colors = [colors];\n\t }\n\t\n\t // Convert colors to numbers.\n\t for (var i = 0; i < colors.length; i++) {\n\t colors[i] = parseInt(colors[i].slice(1), 16);\n\t }\n\t\n\t // -- Perceived brightness and difference formulas are from\n\t // -- http://www.w3.org/WAI/ER/WD-AERT/#color-contrast\n\t\n\t // Compute perceived color brightness (based on RGB-YIQ transformation):\n\t var brightness = function (r, g, b) {\n\t return (r * 299 + g * 587 + b * 114) / 1000;\n\t };\n\t\n\t // Compute color difference:\n\t var difference = function (r1, g1, b1, r2, g2, b2) {\n\t return Math.max(r1, r2) - Math.min(r1, r2) + (Math.max(g1, g2) - Math.min(g1, g2)) + (Math.max(b1, b2) - Math.min(b1, b2));\n\t };\n\t\n\t // Create new random color.\n\t var new_color,\n\t nr,\n\t ng,\n\t nb,\n\t other_color,\n\t or,\n\t og,\n\t ob,\n\t n_brightness,\n\t o_brightness,\n\t diff,\n\t ok = false,\n\t num_tries = 0;\n\t do {\n\t // New color is never white b/c random in [0,1)\n\t new_color = Math.round(Math.random() * 0xffffff);\n\t nr = (new_color & 0xff0000) >> 16;\n\t ng = (new_color & 0x00ff00) >> 8;\n\t nb = new_color & 0x0000ff;\n\t n_brightness = brightness(nr, ng, nb);\n\t ok = true;\n\t for (i = 0; i < colors.length; i++) {\n\t other_color = colors[i];\n\t or = (other_color & 0xff0000) >> 16;\n\t og = (other_color & 0x00ff00) >> 8;\n\t ob = other_color & 0x0000ff;\n\t o_brightness = brightness(or, og, ob);\n\t diff = difference(nr, ng, nb, or, og, ob);\n\t // These thresholds may need to be adjusted. Brightness difference range is 125;\n\t // color difference range is 500.\n\t if (Math.abs(n_brightness - o_brightness) < 40 || diff < 200) {\n\t ok = false;\n\t break;\n\t }\n\t }\n\t\n\t num_tries++;\n\t } while (!ok && num_tries <= 10);\n\t\n\t // Add 0x1000000 to left pad number with 0s.\n\t return '#' + (0x1000000 + new_color).toString(16).substr(1, 6);\n\t };\n\t\n\t return {\n\t commatize: commatize,\n\t is_deferred: is_deferred,\n\t ServerStateDeferred: ServerStateDeferred,\n\t get_random_color: get_random_color\n\t };\n\t}.call(exports, __webpack_require__, exports, module), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1)))\n\n/***/ },\n/* 20 */\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__(38), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (parseBibtex, baseMVC, _l) {\n\t /* global Backbone */\n\t // we use amd here to require, but bibtex uses a global or commonjs pattern.\n\t // webpack will load via commonjs and plain requirejs will load as global. Check both\n\t parseBibtex = parseBibtex || window.BibtexParser;\n\t\n\t var logNamespace = 'citation';\n\t //==============================================================================\n\t /** @class model for tool citations.\n\t * @name Citation\n\t * @augments Backbone.Model\n\t */\n\t var Citation = Backbone.Model.extend(baseMVC.LoggableMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t defaults: {\n\t content: ''\n\t },\n\t\n\t initialize: function () {\n\t var parsed;\n\t try {\n\t // TODO: to model.parse/.validate\n\t parsed = parseBibtex(this.attributes.content);\n\t } catch (err) {\n\t return;\n\t }\n\t // bibtex returns successfully parsed in .entries and any parsing errors in .errors\n\t if (parsed.errors.length) {\n\t // the gen. form of these errors seems to be [ line, col, char, error message ]\n\t var errors = parsed.errors.reduce(function (all, current) {\n\t return all + '; ' + current;\n\t });\n\t // throw new Error( 'Error parsing bibtex: ' + errors );\n\t this.log('Error parsing bibtex: ' + errors);\n\t }\n\t\n\t this._fields = {};\n\t this.entry = _.first(parsed.entries);\n\t if (this.entry) {\n\t var rawFields = this.entry.Fields;\n\t for (var key in rawFields) {\n\t var value = rawFields[key];\n\t var lowerKey = key.toLowerCase();\n\t this._fields[lowerKey] = value;\n\t }\n\t }\n\t },\n\t entryType: function () {\n\t return this.entry ? this.entry.EntryType : undefined;\n\t },\n\t fields: function () {\n\t return this._fields;\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone collection of citations.\n\t */\n\t var BaseCitationCollection = Backbone.Collection.extend(baseMVC.LoggableMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t /** root api url */\n\t urlRoot: Galaxy.root + 'api',\n\t partial: true, // Assume some tools in history/workflow may not be properly annotated yet.\n\t model: Citation\n\t });\n\t\n\t var HistoryCitationCollection = BaseCitationCollection.extend({\n\t /** complete api url */\n\t url: function () {\n\t return this.urlRoot + '/histories/' + this.history_id + '/citations';\n\t }\n\t });\n\t\n\t var ToolCitationCollection = BaseCitationCollection.extend({\n\t /** complete api url */\n\t url: function () {\n\t return this.urlRoot + '/tools/' + this.tool_id + '/citations';\n\t },\n\t partial: false });\n\t\n\t //==============================================================================\n\t\n\t return {\n\t Citation: Citation,\n\t HistoryCitationCollection: HistoryCitationCollection,\n\t ToolCitationCollection: ToolCitationCollection\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__(3), __webpack_require__(2)))\n\n/***/ },\n/* 21 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(jQuery, Backbone, $, _) {// This is necessary so that, when nested arrays are used in ajax/post/get methods, square brackets ('[]') are\n\t// not appended to the identifier of a nested array.\n\tjQuery.ajaxSettings.traditional = true;\n\t\n\t// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(48), __webpack_require__(49), __webpack_require__(22)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, GridModel, Templates, PopupMenu) {\n\t\n\t // grid view\n\t return Backbone.View.extend({\n\t\n\t // model\n\t grid: null,\n\t\n\t // Initialize\n\t initialize: function (grid_config) {\n\t this.dict_format = grid_config.dict_format;\n\t var self = this;\n\t window.add_tag_to_grid_filter = function (tag_name, tag_value) {\n\t // Put tag name and value together.\n\t var tag = tag_name + (tag_value !== undefined && tag_value !== \"\" ? \":\" + tag_value : \"\");\n\t var advanced_search = $('#advanced-search').is(\":visible\");\n\t if (!advanced_search) {\n\t $('#standard-search').slideToggle('fast');\n\t $('#advanced-search').slideToggle('fast');\n\t }\n\t self.add_filter_condition(\"tags\", tag);\n\t };\n\t\n\t // set element\n\t if (this.dict_format) {\n\t this.setElement('
');\n\t if (grid_config.url_base && !grid_config.items) {\n\t Utils.get({\n\t url: grid_config.url_base,\n\t success: function (response) {\n\t response.embedded = grid_config.embedded;\n\t self.init_grid(response);\n\t }\n\t });\n\t } else {\n\t this.init_grid(grid_config);\n\t }\n\t } else {\n\t this.setElement('#grid-container');\n\t this.init_grid(grid_config);\n\t }\n\t\n\t // fix padding\n\t if (grid_config.use_panels) {\n\t $('#center').css({\n\t padding: '10px',\n\t overflow: 'auto'\n\t });\n\t }\n\t },\n\t\n\t // refresh frames\n\t handle_refresh: function (refresh_frames) {\n\t if (refresh_frames) {\n\t if ($.inArray('history', refresh_frames) > -1) {\n\t if (top.Galaxy && top.Galaxy.currHistoryPanel) {\n\t top.Galaxy.currHistoryPanel.loadCurrentHistory();\n\t }\n\t }\n\t }\n\t },\n\t\n\t // Initialize\n\t init_grid: function (grid_config) {\n\t // link grid model\n\t this.grid = new GridModel(grid_config);\n\t\n\t // get options\n\t var options = this.grid.attributes;\n\t\n\t // handle refresh requests\n\t this.handle_refresh(options.refresh_frames);\n\t\n\t // strip protocol and domain\n\t var url = this.grid.get('url_base');\n\t url = url.replace(/^.*\\/\\/[^\\/]+/, '');\n\t this.grid.set('url_base', url);\n\t\n\t // append main template\n\t this.$el.html(Templates.grid(options));\n\t\n\t // update div contents\n\t this.$el.find('#grid-table-header').html(Templates.header(options));\n\t this.$el.find('#grid-table-body').html(Templates.body(options));\n\t this.$el.find('#grid-table-footer').html(Templates.footer(options));\n\t\n\t // update message\n\t if (options.message) {\n\t this.$el.find('#grid-message').html(Templates.message(options));\n\t var self = this;\n\t if (options.use_hide_message) {\n\t setTimeout(function () {\n\t self.$el.find('#grid-message').html('');\n\t }, 5000);\n\t }\n\t }\n\t\n\t // configure elements\n\t this.init_grid_elements();\n\t this.init_grid_controls();\n\t\n\t // attach global event handler\n\t // TODO: redundant (the onload/standard page handlers do this) - but needed because these are constructed after page ready\n\t init_refresh_on_change();\n\t },\n\t\n\t // Initialize grid controls\n\t init_grid_controls: function () {\n\t\n\t // link\n\t var self = this;\n\t\n\t // Initialize grid operation button.\n\t this.$el.find('.operation-button').each(function () {\n\t $(this).off();\n\t $(this).click(function () {\n\t self.submit_operation(this);\n\t return false;\n\t });\n\t });\n\t\n\t // Initialize text filters to select text on click and use normal font when user is typing.\n\t this.$el.find('input[type=text]').each(function () {\n\t $(this).off();\n\t $(this).click(function () {\n\t $(this).select();\n\t }).keyup(function () {\n\t $(this).css('font-style', 'normal');\n\t });\n\t });\n\t\n\t // Initialize sort links.\n\t this.$el.find('.sort-link').each(function () {\n\t $(this).off();\n\t $(this).click(function () {\n\t self.set_sort_condition($(this).attr('sort_key'));\n\t return false;\n\t });\n\t });\n\t\n\t // Initialize text filters.\n\t this.$el.find('.text-filter-form').each(function () {\n\t $(this).off();\n\t $(this).submit(function () {\n\t var column_key = $(this).attr('column_key');\n\t var text_input_obj = $('#input-' + column_key + '-filter');\n\t var text_input = text_input_obj.val();\n\t text_input_obj.val('');\n\t self.add_filter_condition(column_key, text_input);\n\t return false;\n\t });\n\t });\n\t\n\t // Initialize categorical filters.\n\t this.$el.find('.text-filter-val > a').each(function () {\n\t $(this).off();\n\t $(this).click(function () {\n\t // Remove visible element.\n\t $(this).parent().remove();\n\t\n\t // Remove filter condition.\n\t self.remove_filter_condition($(this).attr('filter_key'), $(this).attr('filter_val'));\n\t\n\t // Return\n\t return false;\n\t });\n\t });\n\t\n\t // Initialize categorical filters.\n\t this.$el.find('.categorical-filter > a').each(function () {\n\t $(this).off();\n\t $(this).click(function () {\n\t self.set_categorical_filter($(this).attr('filter_key'), $(this).attr('filter_val'));\n\t return false;\n\t });\n\t });\n\t\n\t // Initialize standard, advanced search toggles.\n\t this.$el.find('.advanced-search-toggle').each(function () {\n\t $(this).off();\n\t $(this).click(function () {\n\t self.$el.find('#standard-search').slideToggle('fast');\n\t self.$el.find('#advanced-search').slideToggle('fast');\n\t return false;\n\t });\n\t });\n\t\n\t // Add event to check all box\n\t this.$el.find('#check_all').off();\n\t this.$el.find('#check_all').on('click', function () {\n\t self.check_all_items();\n\t });\n\t },\n\t\n\t // Initialize grid elements.\n\t init_grid_elements: function () {\n\t // Initialize grid selection checkboxes.\n\t this.$el.find('.grid').each(function () {\n\t var checkboxes = $(this).find(\"input.grid-row-select-checkbox\");\n\t var check_count = $(this).find(\"span.grid-selected-count\");\n\t var update_checked = function () {\n\t check_count.text($(checkboxes).filter(\":checked\").length);\n\t };\n\t\n\t $(checkboxes).each(function () {\n\t $(this).change(update_checked);\n\t });\n\t update_checked();\n\t });\n\t\n\t // Initialize ratings.\n\t if (this.$el.find('.community_rating_star').length !== 0) this.$el.find('.community_rating_star').rating({});\n\t\n\t // get options\n\t var options = this.grid.attributes;\n\t var self = this;\n\t\n\t //\n\t // add page click events\n\t //\n\t this.$el.find('.page-link > a').each(function () {\n\t $(this).click(function () {\n\t self.set_page($(this).attr('page_num'));\n\t return false;\n\t });\n\t });\n\t\n\t //\n\t // add inbound/outbound events\n\t //\n\t this.$el.find('.use-target').each(function () {\n\t $(this).click(function (e) {\n\t self.execute({\n\t href: $(this).attr('href'),\n\t target: $(this).attr('target')\n\t });\n\t return false;\n\t });\n\t });\n\t\n\t // empty grid?\n\t var items_length = options.items.length;\n\t if (items_length == 0) {\n\t return;\n\t }\n\t\n\t // add operation popup menus\n\t _.each(options.items, function (item, index) {\n\t var button = self.$('#grid-' + index + '-popup').off();\n\t var popup = new PopupMenu(button);\n\t _.each(options['operations'], function (operation) {\n\t self._add_operation(popup, operation, item);\n\t });\n\t });\n\t },\n\t\n\t /** Add an operation to the items menu */\n\t _add_operation: function (popup, operation, item) {\n\t var self = this;\n\t var settings = item.operation_config[operation.label];\n\t if (settings.allowed && operation.allow_popup) {\n\t popup.addItem({\n\t html: operation.label,\n\t href: settings.url_args,\n\t target: settings.target,\n\t confirmation_text: operation.confirm,\n\t func: function (e) {\n\t e.preventDefault();\n\t var label = $(e.target).html();\n\t if (operation.onclick) {\n\t operation.onclick(item.encode_id);\n\t } else {\n\t self.execute(this.findItemByHtml(label));\n\t }\n\t }\n\t });\n\t }\n\t },\n\t\n\t // Add a condition to the grid filter; this adds the condition and refreshes the grid.\n\t add_filter_condition: function (name, value) {\n\t // Do nothing is value is empty.\n\t if (value === \"\") {\n\t return false;\n\t }\n\t\n\t // Add condition to grid.\n\t this.grid.add_filter(name, value, true);\n\t\n\t // Add button that displays filter and provides a button to delete it.\n\t var t = $(Templates.filter_element(name, value));\n\t var self = this;\n\t t.click(function () {\n\t // Remove visible element.\n\t $(this).remove();\n\t\n\t // Remove filter condition.\n\t self.remove_filter_condition(name, value);\n\t });\n\t\n\t // append to container\n\t var container = this.$el.find('#' + name + '-filtering-criteria');\n\t container.append(t);\n\t\n\t // execute\n\t this.go_page_one();\n\t this.execute();\n\t },\n\t\n\t // Remove a condition to the grid filter; this adds the condition and refreshes the grid.\n\t remove_filter_condition: function (name, value) {\n\t // Remove filter condition.\n\t this.grid.remove_filter(name, value);\n\t\n\t // Execute\n\t this.go_page_one();\n\t this.execute();\n\t },\n\t\n\t // Set sort condition for grid.\n\t set_sort_condition: function (col_key) {\n\t // Set new sort condition. New sort is col_key if sorting new column; if reversing sort on\n\t // currently sorted column, sort is reversed.\n\t var cur_sort = this.grid.get('sort_key');\n\t var new_sort = col_key;\n\t if (cur_sort.indexOf(col_key) !== -1) {\n\t // Reverse sort.\n\t if (cur_sort.substring(0, 1) !== '-') {\n\t new_sort = '-' + col_key;\n\t }\n\t }\n\t\n\t // Remove sort arrows elements.\n\t this.$el.find('.sort-arrow').remove();\n\t\n\t // Add sort arrow element to new sort column.\n\t var sort_arrow = new_sort.substring(0, 1) == '-' ? '↑' : '↓';\n\t var t = $('
' + sort_arrow + ' ').addClass('sort-arrow');\n\t\n\t // Add to header\n\t this.$el.find('#' + col_key + '-header').append(t);\n\t\n\t // Update grid.\n\t this.grid.set('sort_key', new_sort);\n\t this.go_page_one();\n\t this.execute();\n\t },\n\t\n\t // Set new value for categorical filter.\n\t set_categorical_filter: function (name, new_value) {\n\t // Update filter hyperlinks to reflect new filter value.\n\t var category_filter = this.grid.get('categorical_filters')[name],\n\t cur_value = this.grid.get('filters')[name];\n\t var self = this;\n\t this.$el.find('.' + name + '-filter').each(function () {\n\t var text = $.trim($(this).text());\n\t var filter = category_filter[text];\n\t var filter_value = filter[name];\n\t if (filter_value == new_value) {\n\t // Remove filter link since grid will be using this filter. It is assumed that\n\t // this element has a single child, a hyperlink/anchor with text.\n\t $(this).empty();\n\t $(this).addClass('current-filter');\n\t $(this).append(text);\n\t } else if (filter_value == cur_value) {\n\t // Add hyperlink for this filter since grid will no longer be using this filter. It is assumed that\n\t // this element has a single child, a hyperlink/anchor.\n\t $(this).empty();\n\t var t = $('
' + text + ' ');\n\t t.click(function () {\n\t self.set_categorical_filter(name, filter_value);\n\t });\n\t $(this).removeClass('current-filter');\n\t $(this).append(t);\n\t }\n\t });\n\t\n\t // Update grid.\n\t this.grid.add_filter(name, new_value);\n\t this.go_page_one();\n\t this.execute();\n\t },\n\t\n\t // Set page to view.\n\t set_page: function (new_page) {\n\t // Update page hyperlink to reflect new page.\n\t var self = this;\n\t this.$el.find('.page-link').each(function () {\n\t var id = $(this).attr('id'),\n\t page_num = parseInt(id.split('-')[2], 10),\n\t // Id has form 'page-link-
\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 this.execute({\n\t operation: operation_name,\n\t id: item_ids,\n\t confirmation_text: confirmation_text\n\t });\n\t\n\t // return\n\t return true;\n\t },\n\t\n\t check_all_items: function () {\n\t var chk_all = document.getElementById('check_all'),\n\t checks = document.getElementsByTagName('input'),\n\t total = 0,\n\t i;\n\t if (chk_all.checked === true) {\n\t for (i = 0; i < checks.length; i++) {\n\t if (checks[i].name.indexOf('id') !== -1) {\n\t checks[i].checked = true;\n\t total++;\n\t }\n\t }\n\t } else {\n\t for (i = 0; i < checks.length; i++) {\n\t if (checks[i].name.indexOf('id') !== -1) {\n\t checks[i].checked = false;\n\t }\n\t }\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 (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 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\n\t // request new configuration\n\t var json = self.dict_format ? response_text : $.parseJSON(response_text);\n\t\n\t // update\n\t json.embedded = embedded;\n\t json.insert = insert;\n\t\n\t // Initialize new grid config\n\t self.init_grid(json);\n\t\n\t // Hide loading overlay.\n\t self.$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__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ },\n/* 22 */\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 '(no options) ';\n\t }\n\t return _.map(options, function (option) {\n\t if (option.divider) {\n\t return '', option.html, ' ' + '
' + '' + '' + '
' + '
' + '
' + '
';\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__(3), __webpack_require__(1)))\n\n/***/ },\n/* 24 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/** Base class for options based ui elements **/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(12)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Buttons) {\n\t var Base = Backbone.View.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.model = options && options.model || new Backbone.Model({\n\t visible: true,\n\t data: [],\n\t id: Utils.uid(),\n\t error_text: 'No options available.',\n\t wait_text: 'Please wait...',\n\t multiple: false,\n\t optional: false,\n\t onchange: function () {}\n\t }).set(options);\n\t this.listenTo(this.model, 'change:value', this._changeValue, this);\n\t this.listenTo(this.model, 'change:wait', this._changeWait, this);\n\t this.listenTo(this.model, 'change:data', this._changeData, this);\n\t this.listenTo(this.model, 'change:visible', this._changeVisible, this);\n\t this.on('change', function () {\n\t self.model.get('onchange')(self.value());\n\t });\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t this.$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__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ },\n/* 25 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/**\n\t * This class creates/wraps a default html select field as backbone class.\n\t */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(12)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Buttons) {\n\t var View = Backbone.View.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.data = [];\n\t this.data2 = [];\n\t this.model = options && options.model || new Backbone.Model({\n\t id: Utils.uid(),\n\t cls: 'ui-select',\n\t error_text: 'No options available',\n\t empty_text: 'Nothing selected',\n\t visible: true,\n\t wait: false,\n\t multiple: false,\n\t searchable: true,\n\t optional: false,\n\t disabled: false,\n\t onchange: function () {},\n\t value: null,\n\t selectall: true,\n\t pagesize: 20\n\t }).set(options);\n\t this.on('change', function () {\n\t self.model.get('onchange') && self.model.get('onchange')(self.value());\n\t });\n\t this.listenTo(this.model, 'change:data', this._changeData, this);\n\t this.listenTo(this.model, 'change:disabled', this._changeDisabled, this);\n\t this.listenTo(this.model, 'change:wait', this._changeWait, this);\n\t this.listenTo(this.model, 'change:visible', this._changeVisible, this);\n\t this.listenTo(this.model, 'change:value', this._changeValue, this);\n\t this.listenTo(this.model, 'change:multiple change:searchable change:cls change:id', this.render, this);\n\t this.render();\n\t },\n\t\n\t render: function () {\n\t var self = this;\n\t this.model.get('searchable') ? this._renderSearchable() : this._renderClassic();\n\t this.$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.$select.select2('open');\n\t });\n\t }\n\t this.all_button = null;\n\t if (this.model.get('multiple') && this.model.get('selectall')) {\n\t this.all_button = new Buttons.ButtonCheck({\n\t onclick: function () {\n\t var new_value = [];\n\t self.all_button.value() !== 0 && _.each(self.model.get('data'), function (option) {\n\t new_value.push(option.value);\n\t });\n\t self.value(new_value);\n\t self.trigger('change');\n\t }\n\t });\n\t this.$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 ($.isArray(new_value)) {\n\t val = [];\n\t _.each(new_value, function (v) {\n\t var d = _.findWhere(self.data2, { id: v });\n\t d && val.push(d);\n\t });\n\t new_value = val;\n\t } else {\n\t var d = _.findWhere(this.data2, { id: new_value });\n\t new_value = d;\n\t }\n\t this.$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__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ },\n/* 26 */\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_AMD_DEFINE_RESULT__ = function () {\n\t var Model = Backbone.Model.extend({\n\t defaults: {\n\t extension: 'auto',\n\t genome: '?',\n\t url_paste: '',\n\t status: 'init',\n\t info: null,\n\t file_name: '',\n\t file_mode: '',\n\t file_size: 0,\n\t file_type: null,\n\t file_path: '',\n\t file_data: null,\n\t percentage: 0,\n\t space_to_tab: false,\n\t to_posix_lines: true,\n\t enabled: true\n\t },\n\t reset: function (attr) {\n\t this.clear().set(this.defaults).set(attr);\n\t }\n\t });\n\t var Collection = Backbone.Collection.extend({ model: Model });\n\t return { Model: Model, Collection: Collection };\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__(3)))\n\n/***/ },\n/* 27 */,\n/* 28 */\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 = $.extend(true, {}, context);\n\t _.each(inputs, function (input) {\n\t if (input && input.type && input.name) {\n\t context[input.name] = input;\n\t }\n\t });\n\t for (var key in inputs) {\n\t var node = inputs[key];\n\t node.name = node.name || key;\n\t var name = prefix ? prefix + '|' + node.name : node.name;\n\t switch (node.type) {\n\t case 'repeat':\n\t _.each(node.cache, function (cache, j) {\n\t visitInputs(cache, callback, name + '_' + j, context);\n\t });\n\t break;\n\t case 'conditional':\n\t if (node.test_param) {\n\t callback(node.test_param, name + '|' + node.test_param.name, context);\n\t var selectedCase = matchCase(node, node.test_param.value);\n\t if (selectedCase != -1) {\n\t visitInputs(node.cases[selectedCase].inputs, callback, name, context);\n\t } else {\n\t Galaxy.emit.debug('form-data::visitInputs() - Invalid case for ' + name + '.');\n\t }\n\t } else {\n\t Galaxy.emit.debug('form-data::visitInputs() - Conditional test parameter missing for ' + name + '.');\n\t }\n\t break;\n\t case 'section':\n\t visitInputs(node.inputs, callback, name, context);\n\t break;\n\t default:\n\t callback(node, name, context);\n\t }\n\t }\n\t };\n\t\n\t return {\n\t Manager: Manager,\n\t visitInputs: visitInputs\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ },\n/* 29 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function($, _) {/**\n\t This is the base class of the tool form plugin. This class is e.g. inherited by the regular and the workflow tool form.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(33), __webpack_require__(7), __webpack_require__(13), __webpack_require__(20), __webpack_require__(39)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Deferred, Ui, FormBase, CitationModel, CitationView) {\n\t return FormBase.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.deferred = new Deferred();\n\t FormBase.prototype.initialize.call(this, options);\n\t if (this.model.get('inputs')) {\n\t this._buildForm(this.model.attributes);\n\t } else {\n\t this.deferred.execute(function (process) {\n\t self._buildModel(process, self.model.attributes, true);\n\t });\n\t }\n\t // listen to history panel\n\t if (this.model.get('listen_to_history') && parent.Galaxy && parent.Galaxy.currHistoryPanel) {\n\t this.listenTo(parent.Galaxy.currHistoryPanel.collection, 'change', function () {\n\t self.model.get('onchange')();\n\t });\n\t }\n\t // destroy dom elements\n\t this.$el.on('remove', function () {\n\t self._destroy();\n\t });\n\t },\n\t\n\t /** Wait for deferred build processes before removal */\n\t _destroy: function () {\n\t var self = this;\n\t this.$el.off().hide();\n\t this.deferred.execute(function () {\n\t FormBase.prototype.remove.call(self);\n\t Galaxy.emit.debug('tool-form-base::_destroy()', 'Destroy view.');\n\t });\n\t },\n\t\n\t /** Build form */\n\t _buildForm: function (options) {\n\t var self = this;\n\t this.model.set(options);\n\t this.model.set({\n\t title: options.title || '
' + options.name + ' ' + options.description + ' (Galaxy Version ' + options.version + ')',\n\t operations: !this.model.get('hide_operations') && this._operations(),\n\t onchange: function () {\n\t self.deferred.reset();\n\t self.deferred.execute(function (process) {\n\t self.model.get('postchange')(process, self);\n\t });\n\t }\n\t });\n\t this.model.get('customize') && this.model.get('customize')(this);\n\t this.render();\n\t if (!this.model.get('collapsible')) {\n\t this.$el.append($('
').addClass('ui-margin-top-large').append(this._footer()));\n\t }\n\t },\n\t\n\t /** Builds a new model through api call and recreates the entire form */\n\t _buildModel: function (process, new_options, hide_message) {\n\t var self = this;\n\t var options = this.model.attributes;\n\t options.version = new_options.version;\n\t options.id = new_options.id;\n\t\n\t // build request url\n\t var build_url = '';\n\t var build_data = {};\n\t var job_id = '';\n\t // When re-running a job the job_id is found in the new_options object.\n\t // When re-running a job and requesting a new tool_version,\n\t // the job_id is in the options object.\n\t if (new_options.job_id) {\n\t job_id = new_options.job_id;\n\t } else if (options.job_id) {\n\t job_id = options.job_id;\n\t }\n\t if (job_id) {\n\t build_url = Galaxy.root + 'api/jobs/' + job_id + '/build_for_rerun';\n\t } else {\n\t build_url = Galaxy.root + 'api/tools/' + options.id + '/build';\n\t build_data = $.extend({}, Galaxy.params);\n\t build_data['tool_id'] && delete build_data['tool_id'];\n\t }\n\t options.version && (build_data['tool_version'] = options.version);\n\t\n\t // get initial model\n\t Utils.get({\n\t url: build_url,\n\t data: build_data,\n\t success: function (data) {\n\t if (!data.display) {\n\t window.location = Galaxy.root;\n\t return;\n\t }\n\t self._buildForm(data);\n\t !hide_message && self.message.update({\n\t status: 'success',\n\t message: 'Now you are using \\'' + options.name + '\\' version ' + options.version + ', id \\'' + options.id + '\\'.',\n\t persistent: false\n\t });\n\t Galaxy.emit.debug('tool-form-base::_buildModel()', 'Initial tool model ready.', data);\n\t process.resolve();\n\t },\n\t error: function (response, status) {\n\t var error_message = response && response.err_msg || 'Uncaught error.';\n\t if (status == 401) {\n\t window.location = Galaxy.root + 'user/login?' + $.param({ redirect: Galaxy.root + '?tool_id=' + options.id });\n\t } else if (self.$el.is(':empty')) {\n\t self.$el.prepend(new Ui.Message({\n\t message: error_message,\n\t status: 'danger',\n\t persistent: true,\n\t large: true\n\t }).$el);\n\t } else {\n\t Galaxy.modal && Galaxy.modal.show({\n\t title: 'Tool request failed',\n\t body: error_message,\n\t buttons: {\n\t 'Close': function () {\n\t Galaxy.modal.hide();\n\t }\n\t }\n\t });\n\t }\n\t Galaxy.emit.debug('tool-form-base::_buildModel()', 'Initial tool model request failed.', response);\n\t process.reject();\n\t }\n\t });\n\t },\n\t\n\t /** Create tool operation menu */\n\t _operations: function () {\n\t var self = this;\n\t var options = this.model.attributes;\n\t\n\t // button for version selection\n\t var versions_button = new Ui.ButtonMenu({\n\t icon: 'fa-cubes',\n\t title: !options.narrow && 'Versions' || null,\n\t tooltip: 'Select another tool version'\n\t });\n\t if (!options.sustain_version && options.versions && options.versions.length > 1) {\n\t for (var i in options.versions) {\n\t var version = options.versions[i];\n\t if (version != options.version) {\n\t versions_button.addMenu({\n\t title: 'Switch to ' + version,\n\t version: version,\n\t icon: 'fa-cube',\n\t onclick: function () {\n\t // here we update the tool version (some tools encode the version also in the id)\n\t var id = options.id.replace(options.version, this.version);\n\t var version = this.version;\n\t // queue model request\n\t self.deferred.reset();\n\t self.deferred.execute(function (process) {\n\t self._buildModel(process, { id: id, version: version });\n\t });\n\t }\n\t });\n\t }\n\t }\n\t } else {\n\t versions_button.$el.hide();\n\t }\n\t\n\t // button for options e.g. search, help\n\t var menu_button = new Ui.ButtonMenu({\n\t icon: 'fa-caret-down',\n\t title: !options.narrow && 'Options' || null,\n\t tooltip: 'View available options'\n\t });\n\t if (options.biostar_url) {\n\t menu_button.addMenu({\n\t icon: 'fa-question-circle',\n\t title: 'Question?',\n\t onclick: function () {\n\t window.open(options.biostar_url + '/p/new/post/');\n\t }\n\t });\n\t menu_button.addMenu({\n\t icon: 'fa-search',\n\t title: 'Search',\n\t onclick: function () {\n\t window.open(options.biostar_url + '/local/search/page/?q=' + options.name);\n\t }\n\t });\n\t };\n\t menu_button.addMenu({\n\t icon: 'fa-share',\n\t title: 'Share',\n\t onclick: function () {\n\t prompt('Copy to clipboard: Ctrl+C, Enter', window.location.origin + Galaxy.root + 'root?tool_id=' + options.id);\n\t }\n\t });\n\t\n\t // add admin operations\n\t if (Galaxy.user && Galaxy.user.get('is_admin')) {\n\t menu_button.addMenu({\n\t icon: 'fa-download',\n\t title: 'Download',\n\t onclick: function () {\n\t window.location.href = Galaxy.root + 'api/tools/' + options.id + '/download';\n\t }\n\t });\n\t menu_button.addMenu({\n\t icon: 'fa-refresh',\n\t title: 'Reload XML',\n\t onclick: function () {\n\t Utils.get({\n\t url: Galaxy.root + 'api/tools/' + options.id + '/reload',\n\t success: function (response) {\n\t self.message.update({ persistent: false, message: 'Tool XML has been reloaded.', status: 'success' });\n\t },\n\t error: function (response) {\n\t self.message.update({ persistent: false, message: response.err_msg, status: 'danger' });\n\t }\n\t });\n\t }\n\t });\n\t }\n\t\n\t // button for version selection\n\t if (options.requirements && options.requirements.length > 0) {\n\t menu_button.addMenu({\n\t icon: 'fa-info-circle',\n\t title: 'Requirements',\n\t onclick: function () {\n\t if (!this.requirements_visible || self.portlet.collapsed) {\n\t this.requirements_visible = true;\n\t self.portlet.expand();\n\t self.message.update({ persistent: true, message: self._templateRequirements(options), status: 'info' });\n\t } else {\n\t this.requirements_visible = false;\n\t self.message.update({ message: '' });\n\t }\n\t }\n\t });\n\t }\n\t\n\t // add toolshed url\n\t if (options.sharable_url) {\n\t menu_button.addMenu({\n\t icon: 'fa-external-link',\n\t title: 'See in Tool Shed',\n\t onclick: function () {\n\t window.open(options.sharable_url);\n\t }\n\t });\n\t }\n\t\n\t // add tool menu webhooks\n\t $.getJSON('/api/webhooks/tool-menu/all', function (webhooks) {\n\t _.each(webhooks, function (webhook) {\n\t if (webhook.activate && webhook.config.function) {\n\t menu_button.addMenu({\n\t icon: webhook.config.icon,\n\t title: webhook.config.title,\n\t onclick: function () {\n\t var func = new Function('options', webhook.config.function);\n\t func(options);\n\t }\n\t });\n\t }\n\t });\n\t });\n\t\n\t return {\n\t menu: menu_button,\n\t versions: versions_button\n\t };\n\t },\n\t\n\t /** Create footer */\n\t _footer: function () {\n\t var options = this.model.attributes;\n\t var $el = $('
').append(this._templateHelp(options));\n\t if (options.citations) {\n\t var $citations = $('
');\n\t var citations = new CitationModel.ToolCitationCollection();\n\t citations.tool_id = options.id;\n\t var citation_list_view = new CitationView.CitationListView({ el: $citations, collection: citations });\n\t citation_list_view.render();\n\t citations.fetch();\n\t $el.append($citations);\n\t }\n\t return $el;\n\t },\n\t\n\t /** Templates */\n\t _templateHelp: function (options) {\n\t var $tmpl = $('
').addClass('ui-form-help').append(options.help);\n\t $tmpl.find('a').attr('target', '_blank');\n\t return $tmpl;\n\t },\n\t\n\t _templateRequirements: function (options) {\n\t var nreq = options.requirements.length;\n\t if (nreq > 0) {\n\t var requirements_message = 'This tool requires ';\n\t _.each(options.requirements, function (req, i) {\n\t requirements_message += req.name + (req.version ? ' (Version ' + req.version + ')' : '') + (i < nreq - 2 ? ', ' : i == nreq - 2 ? ' and ' : '');\n\t });\n\t var requirements_link = $('
').attr('target', '_blank').attr('href', 'https://galaxyproject.org/tools/requirements/').text('here');\n\t return $('
').append(requirements_message + '. Click ').append(requirements_link).append(' for more information.');\n\t }\n\t return 'No requirements found.';\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)))\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, $, _) {/* This is the regular tool form */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(7), __webpack_require__(8), __webpack_require__(29), __webpack_require__(27)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui, Modal, ToolFormBase, Webhooks) {\n\t var View = Backbone.View.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.modal = parent.Galaxy.modal || new Modal.View();\n\t this.form = new ToolFormBase(Utils.merge({\n\t listen_to_history: true,\n\t always_refresh: false,\n\t customize: function (form) {\n\t var options = form.model.attributes;\n\t // build execute button\n\t options.buttons = {\n\t execute: execute_btn = new Ui.Button({\n\t icon: 'fa-check',\n\t tooltip: 'Execute: ' + options.name + ' (' + options.version + ')',\n\t title: 'Execute',\n\t cls: 'ui-button btn btn-primary',\n\t floating: 'clear',\n\t onclick: function () {\n\t execute_btn.wait();\n\t form.portlet.disable();\n\t self.submit(options, function () {\n\t execute_btn.unwait();\n\t form.portlet.enable();\n\t });\n\t }\n\t })\n\t };\n\t // remap feature\n\t if (options.job_id && options.job_remap) {\n\t options.inputs.push({\n\t label: 'Resume dependencies from this job',\n\t name: 'rerun_remap_job_id',\n\t type: 'select',\n\t display: 'radio',\n\t ignore: '__ignore__',\n\t value: '__ignore__',\n\t options: [['Yes', options.job_id], ['No', '__ignore__']],\n\t help: 'The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run.'\n\t });\n\t }\n\t },\n\t postchange: function (process, form) {\n\t var self = this;\n\t var current_state = {\n\t tool_id: form.model.get('id'),\n\t tool_version: form.model.get('version'),\n\t inputs: $.extend(true, {}, form.data.create())\n\t };\n\t form.wait(true);\n\t Galaxy.emit.debug('tool-form::postchange()', 'Sending current state.', current_state);\n\t Utils.request({\n\t type: 'POST',\n\t url: Galaxy.root + 'api/tools/' + form.model.get('id') + '/build',\n\t data: current_state,\n\t success: function (data) {\n\t form.update(data);\n\t form.wait(false);\n\t Galaxy.emit.debug('tool-form::postchange()', 'Received new model.', data);\n\t process.resolve();\n\t },\n\t error: function (response) {\n\t Galaxy.emit.debug('tool-form::postchange()', 'Refresh request failed.', response);\n\t process.reject();\n\t }\n\t });\n\t }\n\t }, options));\n\t this.deferred = this.form.deferred;\n\t this.setElement('
');\n\t this.$el.append(this.form.$el);\n\t },\n\t\n\t /** Submit a regular job.\n\t * @param{dict} options - Specifies tool id and version\n\t * @param{function} callback - Called when request has completed\n\t */\n\t submit: function (options, callback) {\n\t var self = this;\n\t var job_def = {\n\t tool_id: options.id,\n\t tool_version: options.version,\n\t inputs: this.form.data.create()\n\t };\n\t this.form.trigger('reset');\n\t if (!self.validate(job_def)) {\n\t Galaxy.emit.debug('tool-form::submit()', 'Submission canceled. Validation failed.');\n\t callback && callback();\n\t return;\n\t }\n\t if (options.action !== Galaxy.root + 'tool_runner/index') {\n\t var $f = $('
').attr({ action: options.action, method: options.method, enctype: options.enctype });\n\t _.each(job_def.inputs, function (value, key) {\n\t $f.append($('
').attr({ 'name': key, 'value': value }));\n\t });\n\t $f.hide().appendTo('body').submit().remove();\n\t callback && callback();\n\t return;\n\t }\n\t Galaxy.emit.debug('tool-form::submit()', 'Validation complete.', job_def);\n\t Utils.request({\n\t type: 'POST',\n\t url: Galaxy.root + 'api/tools',\n\t data: job_def,\n\t success: function (response) {\n\t callback && callback();\n\t self.$el.children().hide();\n\t self.$el.append(self._templateSuccess(response));\n\t // Show Webhook if job is running\n\t if (response.jobs && response.jobs.length > 0) {\n\t self.$el.append($('
', { id: 'webhook-view' }));\n\t var WebhookApp = new Webhooks.WebhookView({\n\t urlRoot: Galaxy.root + 'api/webhooks/tool',\n\t toolId: job_def.tool_id\n\t });\n\t }\n\t parent.Galaxy && parent.Galaxy.currHistoryPanel && parent.Galaxy.currHistoryPanel.refreshContents();\n\t },\n\t error: function (response) {\n\t callback && callback();\n\t Galaxy.emit.debug('tool-form::submit', 'Submission failed.', response);\n\t var input_found = false;\n\t if (response && response.err_data) {\n\t var error_messages = self.form.data.matchResponse(response.err_data);\n\t for (var input_id in error_messages) {\n\t self.form.highlight(input_id, error_messages[input_id]);\n\t input_found = true;\n\t break;\n\t }\n\t }\n\t if (!input_found) {\n\t self.modal.show({\n\t title: 'Job submission failed',\n\t body: self._templateError(job_def, response && response.err_msg),\n\t buttons: { 'Close': function () {\n\t self.modal.hide();\n\t } }\n\t });\n\t }\n\t }\n\t });\n\t },\n\t\n\t /** Validate job dictionary.\n\t * @param{dict} job_def - Job execution dictionary\n\t */\n\t validate: function (job_def) {\n\t var job_inputs = job_def.inputs;\n\t var batch_n = -1;\n\t var batch_src = null;\n\t for (var job_input_id in job_inputs) {\n\t var input_value = job_inputs[job_input_id];\n\t var input_id = this.form.data.match(job_input_id);\n\t var input_field = this.form.field_list[input_id];\n\t var input_def = this.form.input_list[input_id];\n\t if (!input_id || !input_def || !input_field) {\n\t Galaxy.emit.debug('tool-form::validate()', 'Retrieving input objects failed.');\n\t continue;\n\t }\n\t if (!input_def.optional && input_value == null) {\n\t this.form.highlight(input_id);\n\t return false;\n\t }\n\t if (input_value && input_value.batch) {\n\t var n = input_value.values.length;\n\t var src = n > 0 && input_value.values[0] && input_value.values[0].src;\n\t if (src) {\n\t if (batch_src === null) {\n\t batch_src = src;\n\t } else if (batch_src !== src) {\n\t this.form.highlight(input_id, 'Please select either dataset or dataset list fields for all batch mode fields.');\n\t return false;\n\t }\n\t }\n\t if (batch_n === -1) {\n\t batch_n = n;\n\t } else if (batch_n !== n) {\n\t this.form.highlight(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains
' + n + ' selection(s) while a previous field contains
' + batch_n + ' .');\n\t return false;\n\t }\n\t }\n\t }\n\t return true;\n\t },\n\t\n\t _templateSuccess: function (response) {\n\t if (response.jobs && response.jobs.length > 0) {\n\t var njobs = response.jobs.length;\n\t var njobs_text = njobs == 1 ? '1 job has' : njobs + ' jobs have';\n\t var $message = $('
').addClass('donemessagelarge').append($('
').text(njobs_text + ' been successfully added to the queue - resulting in the following datasets:'));\n\t _.each(response.outputs, function (output) {\n\t $message.append($('
').addClass('messagerow').append($('
').text(output.hid + ': ' + output.name)));\n\t });\n\t $message.append($('
').append('
').text('You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from \\'running\\' to \\'finished\\' if completed successfully or \\'error\\' if problems were encountered.'));\n\t return $message;\n\t } else {\n\t return this._templateError(response, 'Invalid success response. No jobs found.');\n\t }\n\t },\n\t\n\t _templateError: function (response, err_msg) {\n\t return $('
').addClass('errormessagelarge').append($('
').text('The server could not complete the request. Please contact the Galaxy Team if this error persists. ' + (err_msg || ''))).append($('
').text(JSON.stringify(response, null, 4)));\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__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ },\n/* 31 */,\n/* 32 */\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($('
').append($el));\n\t },\n\t\n\t /** Append header row to table */\n\t appendHeader: function () {\n\t this.$thead.append(this.row);\n\t this.row = $('
');\n\t },\n\t\n\t /** Add cell to row */\n\t add: function ($el, width, align) {\n\t var wrapper = $('
');\n\t if (width) {\n\t wrapper.css('width', width);\n\t }\n\t if (align) {\n\t wrapper.css('text-align', align);\n\t }\n\t this.row.append(wrapper.append($el));\n\t },\n\t\n\t /** Append row to table */\n\t append: function (id, fade) {\n\t this._commit(id, fade, false);\n\t },\n\t\n\t /** Prepend row to table */\n\t prepend: function (id, fade) {\n\t this._commit(id, fade, true);\n\t },\n\t\n\t /** Helper to get row element */\n\t get: function (id) {\n\t return this.$('#' + id);\n\t },\n\t\n\t /** Delete row by id */\n\t del: function (id) {\n\t var item = this.$tbody.find('#' + id);\n\t if (item.length > 0) {\n\t item.remove();\n\t this.row_count--;\n\t this._refresh();\n\t }\n\t },\n\t\n\t /** Delete all rows */\n\t delAll: function () {\n\t this.$tbody.empty();\n\t this.row_count = 0;\n\t this._refresh();\n\t },\n\t\n\t /** Set a value i.e. selects/highlights a particular row by id */\n\t value: function (new_value) {\n\t if (this.options.selectable) {\n\t this.before = this.$tbody.find('.current').attr('id');\n\t if (new_value !== undefined) {\n\t this.$tbody.find('tr').removeClass('current');\n\t if (new_value) {\n\t this.$tbody.find('#' + new_value).addClass('current');\n\t }\n\t }\n\t var after = this.$tbody.find('.current').attr('id');\n\t if (after === undefined) {\n\t return null;\n\t } else {\n\t if (after != this.before && this.options.onchange) {\n\t this.options.onchange(new_value);\n\t }\n\t return after;\n\t }\n\t }\n\t },\n\t\n\t /** Return the number of rows */\n\t size: function () {\n\t return this.$tbody.find('tr').length;\n\t },\n\t\n\t /** Helper to append rows */\n\t _commit: function (id, fade, prepend) {\n\t this.del(id);\n\t this.row.attr('id', id);\n\t if (prepend) {\n\t this.$tbody.prepend(this.row);\n\t } else {\n\t this.$tbody.append(this.row);\n\t }\n\t if (fade) {\n\t this.row.hide();\n\t this.row.fadeIn();\n\t }\n\t this.row = this._row();\n\t this.row_count++;\n\t this._refresh();\n\t },\n\t\n\t /** Helper to create new row */\n\t _row: function () {\n\t return $('
');\n\t },\n\t\n\t /** Handles onclick events */\n\t _onclick: function (e) {\n\t var old_value = this.value();\n\t var new_value = $(e.target).closest('tr').attr('id');\n\t if (new_value != '') {\n\t if (new_value && old_value != new_value) {\n\t if (this.options.onconfirm) {\n\t this.options.onconfirm(new_value);\n\t } else {\n\t this.value(new_value);\n\t }\n\t }\n\t }\n\t },\n\t\n\t /** Handles ondblclick events */\n\t _ondblclick: function (e) {\n\t var value = this.value();\n\t if (value && this.options.ondblclick) {\n\t this.options.ondblclick(value);\n\t }\n\t },\n\t\n\t /** Refresh helper */\n\t _refresh: function () {\n\t if (this.row_count == 0) {\n\t this.$tmessage.show();\n\t } else {\n\t this.$tmessage.hide();\n\t }\n\t },\n\t\n\t /** Template */\n\t _template: function () {\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__(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, $) {/**\n\t * This class defines a queue to ensure that multiple deferred callbacks are executed sequentially.\n\t */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils) {\n\t return Backbone.Model.extend({\n\t initialize: function () {\n\t this.active = {};\n\t this.last = null;\n\t },\n\t\n\t /** Adds a callback to the queue. Upon execution a deferred object is parsed to the callback i.e. callback( deferred ).\n\t * If the callback does not take any arguments, the deferred is resolved instantly.\n\t */\n\t execute: function (callback) {\n\t var self = this;\n\t var id = Utils.uid();\n\t var has_deferred = callback.length > 0;\n\t\n\t // register process\n\t this.active[id] = true;\n\t\n\t // deferred process\n\t var process = $.Deferred();\n\t process.promise().always(function () {\n\t delete self.active[id];\n\t has_deferred && Galaxy.emit.debug('deferred::execute()', this.state().charAt(0).toUpperCase() + this.state().slice(1) + ' ' + id);\n\t });\n\t\n\t // deferred queue\n\t $.when(this.last).always(function () {\n\t if (self.active[id]) {\n\t has_deferred && Galaxy.emit.debug('deferred::execute()', 'Running ' + id);\n\t callback(process);\n\t !has_deferred && process.resolve();\n\t } else {\n\t process.reject();\n\t }\n\t });\n\t this.last = process.promise();\n\t },\n\t\n\t /** Resets the promise queue. All currently queued but unexecuted callbacks/promises will be rejected.\n\t */\n\t reset: function () {\n\t Galaxy.emit.debug('deferred::execute()', 'Reset');\n\t for (var i in this.active) {\n\t this.active[i] = false;\n\t }\n\t },\n\t\n\t /** Returns true if all processes are done.\n\t */\n\t ready: function () {\n\t return $.isEmptyObject(this.active);\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__(3), __webpack_require__(1)))\n\n/***/ },\n/* 34 */,\n/* 35 */,\n/* 36 */,\n/* 37 */,\n/* 38 */\n/***/ function(module, exports) {\n\n\t/**\n\t * Parser.js\n\t * Copyright 2012-13 Mayank Lahiri\n\t * mlahiri@gmail.com\n\t * Released under the BSD License.\n\t *\n\t * A forgiving Bibtex parser that can:\n\t * \n\t * (1) operate in streaming or block mode, extracting entries as dictionaries. \n\t * (2) convert Latex special characters to UTF-8.\n\t * (3) best-effort parse malformed entries.\n\t * (4) run in a CommonJS environment or a browser, without any dependencies.\n\t * (5) be advanced-compiled by Google Closure Compiler.\n\t * \n\t * Handwritten as a labor of love, not auto-generated from a grammar. \n\t *\n\t * Modes of usage:\n\t *\n\t * (1) Synchronous, string\n\t *\n\t * var entries = BibtexParser(text);\n\t * console.log(entries);\n\t *\n\t * (2) Asynchronous, stream\n\t *\n\t * var entryCallback = function(entry) { console.log(entry); }\n\t * var parser = new BibtexParser(entryCallback);\n\t * parser.parse(chunk1);\n\t * parser.parse(chunk2);\n\t * ...\n\t * \n\t * @param {text|function(Object)} arg Either a Bibtex string or callback \n\t * function for processing parsed entries.\n\t * @constructor\n\t */\n\tfunction BibtexParser(arg0) {\n\t // Determine how this function is to be used\n\t if (typeof arg0 == 'string') {\n\t // Passed a string, synchronous call without 'new'\n\t var tempStorage = {};\n\t var entries = [];\n\t function accumulator(entry) {\n\t entries.push(entry);\n\t }\n\t var parser = BibtexParser.call(tempStorage, accumulator);\n\t parser.parse(arg0);\n\t return {\n\t 'entries': entries,\n\t 'errors': parser.getErrors()\n\t };\n\t }\n\t if (typeof arg0 != 'function') {\n\t throw 'Invalid parser construction.';\n\t }\n\t\n\t /** @enum {number} */\n\t this.STATES_ = {\n\t ENTRY_OR_JUNK: 0,\n\t OBJECT_TYPE: 1,\n\t ENTRY_KEY: 2,\n\t KV_KEY: 3,\n\t EQUALS: 4,\n\t KV_VALUE: 5\n\t };\n\t /** @private */this.DATA_ = {};\n\t /** @private */this.CALLBACK_ = arg0;\n\t /** @private */this.CHAR_ = 0;\n\t /** @private */this.LINE_ = 1;\n\t /** @private */this.CHAR_IN_LINE_ = 0;\n\t /** @private */this.SKIPWS_ = true;\n\t /** @private */this.SKIPCOMMENT_ = true;\n\t /** @private */this.PARSETMP_ = {};\n\t /** @private */this.SKIPTILLEOL_ = false;\n\t /** @private */this.VALBRACES_ = null;\n\t /** @private */this.BRACETYPE_ = null;\n\t /** @private */this.BRACECOUNT_ = 0;\n\t /** @private */this.STATE_ = this.STATES_.ENTRY_OR_JUNK;\n\t /** @private */this.ERRORS_ = [];\n\t /** @private */this.ENTRY_TYPES_ = {\n\t 'inproceedings': 1,\n\t 'proceedings': 2,\n\t 'article': 3,\n\t 'techreport': 4,\n\t 'misc': 5,\n\t 'mastersthesis': 6,\n\t 'book': 7,\n\t 'phdthesis': 8,\n\t 'incollection': 9,\n\t 'unpublished': 10,\n\t 'inbook': 11,\n\t 'manual': 12,\n\t 'periodical': 13,\n\t 'booklet': 14,\n\t 'masterthesis': 15,\n\t 'conference': 16,\n\t 'online': 998 // Galaxy MOD: Handle @online entries for preprints.\n\t , 'data': 999 // Galaxy MOD: Handle @data citations coming from figshare.\n\t };\n\t /** @private */this.MACROS_ = {\n\t 'jan': 'January',\n\t 'feb': 'February',\n\t 'mar': 'March',\n\t 'apr': 'April',\n\t 'may': 'May',\n\t 'jun': 'June',\n\t 'jul': 'July',\n\t 'aug': 'August',\n\t 'sep': 'September',\n\t 'oct': 'October',\n\t 'nov': 'November',\n\t 'dec': 'December',\n\t 'Jan': 'January',\n\t 'Feb': 'February',\n\t 'Mar': 'March',\n\t 'Apr': 'April',\n\t 'May': 'May',\n\t 'Jun': 'June',\n\t 'Jul': 'July',\n\t 'Aug': 'August',\n\t 'Sep': 'September',\n\t 'Oct': 'October',\n\t 'Nov': 'November',\n\t 'Dec': 'December'\n\t };\n\t\n\t /**\n\t * Gets an array of all errors encountered during parsing.\n\t * Array entries are of the format:\n\t * [ line number, character in line, character in stream, error text ]\n\t *\n\t * @returns Array
\n\t * @public\n\t */\n\t this.getErrors = function () {\n\t return this.ERRORS_;\n\t };\n\t\n\t /**\n\t * Processes a chunk of data\n\t * @public\n\t */\n\t this.parse = function (chunk) {\n\t for (var i = 0; i < chunk.length; i++) this.processCharacter_(chunk[i]);\n\t };\n\t\n\t /**\n\t * Logs error at current stream position.\n\t *\n\t * @private\n\t */\n\t this.error_ = function (text) {\n\t this.ERRORS_.push([this.LINE_, this.CHAR_IN_LINE_, this.CHAR_, text]);\n\t };\n\t\n\t /**\n\t * Called after an entire entry has been parsed from the stream.\n\t * Performs post-processing and invokes the entry callback pointed to by\n\t * this.CALLBACK_. Parsed (but unprocessed) entry data is in this.DATA_.\n\t */\n\t this.processEntry_ = function () {\n\t var data = this.DATA_;\n\t if (data.Fields) for (var f in data.Fields) {\n\t var raw = data.Fields[f];\n\t\n\t // Convert Latex/Bibtex special characters to UTF-8 equivalents\n\t for (var i = 0; i < this.CHARCONV_.length; i++) {\n\t var re = this.CHARCONV_[i][0];\n\t var rep = this.CHARCONV_[i][1];\n\t raw = raw.replace(re, rep);\n\t }\n\t\n\t // Basic substitutions\n\t raw = raw.replace(/[\\n\\r\\t]/g, ' ').replace(/\\s\\s+/g, ' ').replace(/^\\s+|\\s+$/g, '');\n\t\n\t // Remove braces and backslashes\n\t var len = raw.length;\n\t var processed = '';\n\t for (var i = 0; i < len; i++) {\n\t var c = raw[i];\n\t var skip = false;\n\t if (c == '\\\\' && i < len - 1) c = raw[++i];else {\n\t if (c == '{' || c == '}') skip = true;\n\t }\n\t if (!skip) processed += c;\n\t }\n\t data.Fields[f] = processed;\n\t }\n\t\n\t if (data.ObjectType == 'string') {\n\t for (var f in data.Fields) {\n\t this.MACROS_[f] = data.Fields[f];\n\t }\n\t } else {\n\t // Parsed a new Bibtex entry\n\t this.CALLBACK_(data);\n\t }\n\t };\n\t\n\t /**\n\t * Processes next character in the stream, invoking the callback after \n\t * each entry has been found and processed.\n\t * \n\t * @private\n\t * @param {string} c Next character in input stream\n\t */\n\t this.processCharacter_ = function (c) {\n\t // Housekeeping\n\t this.CHAR_++;\n\t this.CHAR_IN_LINE_++;\n\t if (c == '\\n') {\n\t this.LINE_++;\n\t this.CHAR_IN_LINE_ = 1;\n\t }\n\t\n\t // Convenience states for skipping whitespace when needed\n\t if (this.SKIPTILLEOL_) {\n\t if (c == '\\n') this.SKIPTILLEOL_ = false;\n\t return;\n\t }\n\t if (this.SKIPCOMMENT_ && c == '%') {\n\t this.SKIPTILLEOL_ = true;\n\t return;\n\t }\n\t if (this.SKIPWS_ && /\\s/.test(c)) return;\n\t this.SKIPWS_ = false;\n\t this.SKIPCOMMENT_ = false;\n\t this.SKIPTILLEOL_ = false;\n\t\n\t // Main state machine\n\t var AnotherIteration = true;\n\t while (AnotherIteration) {\n\t //console.log(this.LINE_, this.CHAR_IN_LINE_, this.STATE_, c)\n\t AnotherIteration = false;\n\t switch (this.STATE_) {\n\t // -- Scan for an object marker ('@')\n\t // -- Reset temporary data structure in case previous entry was garbled\n\t case this.STATES_.ENTRY_OR_JUNK:\n\t if (c == '@') {\n\t // SUCCESS: Parsed a valid start-of-object marker.\n\t // NEXT_STATE: OBJECT_TYPE\n\t this.STATE_ = this.STATES_.OBJECT_TYPE;\n\t this.DATA_ = {\n\t ObjectType: ''\n\t };\n\t }\n\t this.BRACETYPE_ = null;\n\t this.SKIPWS_ = true;\n\t this.SKIPCOMMENT_ = true;\n\t break;\n\t\n\t // Start at first non-whitespace character after start-of-object '@'\n\t // -- Accept [A-Za-z], break on non-matching character\n\t // -- Populate this.DATA_.EntryType and this.DATA_.ObjectType\n\t case this.STATES_.OBJECT_TYPE:\n\t if (/[A-Za-z]/.test(c)) {\n\t this.DATA_.ObjectType += c.toLowerCase();\n\t this.SKIPWS_ = true;\n\t this.SKIPCOMMENT_ = true;\n\t } else {\n\t // Break from state and validate object type\n\t var ot = this.DATA_.ObjectType;\n\t if (ot == 'comment') {\n\t this.STATE_ = this.STATES_.ENTRY_OR_JUNK;\n\t } else {\n\t if (ot == 'string') {\n\t this.DATA_.ObjectType = ot;\n\t this.DATA_.Fields = {};\n\t this.BRACETYPE_ = c;\n\t this.BRACECOUNT_ = 1;\n\t this.STATE_ = this.STATES_.KV_KEY;\n\t this.SKIPWS_ = true;\n\t this.SKIPCOMMENT_ = true;\n\t this.PARSETMP_ = {\n\t Key: ''\n\t };\n\t } else {\n\t if (ot == 'preamble') {\n\t this.STATE_ = this.STATES_.ENTRY_OR_JUNK;\n\t } else {\n\t if (ot in this.ENTRY_TYPES_) {\n\t // SUCCESS: Parsed a valid object type.\n\t // NEXT_STATE: ENTRY_KEY\n\t this.DATA_.ObjectType = 'entry';\n\t this.DATA_.EntryType = ot;\n\t this.DATA_.EntryKey = '';\n\t this.STATE_ = this.STATES_.ENTRY_KEY;\n\t AnotherIteration = true;\n\t } else {\n\t // ERROR: Unrecognized object type.\n\t // NEXT_STATE: ENTRY_OR_JUNK\n\t this.error_('Unrecognized object type: \"' + this.DATA_.ObjectType + '\"');\n\t this.STATE_ = this.STATES_.ENTRY_OR_JUNK;\n\t }\n\t }\n\t }\n\t }\n\t }\n\t break;\n\t\n\t // Start at first non-alphabetic character after an entry type\n\t // -- Populate this.DATA_.EntryKey\n\t case this.STATES_.ENTRY_KEY:\n\t if ((c === '{' || c === '(') && this.BRACETYPE_ == null) {\n\t this.BRACETYPE_ = c;\n\t this.BRACECOUNT_ = 1;\n\t this.SKIPWS_ = true;\n\t this.SKIPCOMMENT_ = true;\n\t break;\n\t }\n\t if (/[,%\\s]/.test(c)) {\n\t if (this.DATA_.EntryKey.length < 1) {\n\t // Skip comments and whitespace before entry key\n\t this.SKIPWS_ = true;\n\t this.SKIPCOMMENT_ = true;\n\t } else {\n\t if (this.BRACETYPE_ == null) {\n\t // ERROR: No opening brace for object\n\t // NEXT_STATE: ENTRY_OR_JUNK\n\t this.error_('No opening brace for object.');\n\t this.STATE_ = this.STATES_.ENTRY_OR_JUNK;\n\t } else {\n\t // SUCCESS: Parsed an entry key\n\t // NEXT_STATE: KV_KEY\n\t this.SKIPWS_ = true;\n\t this.SKIPCOMMENT_ = true;\n\t AnotherIteration = true;\n\t this.STATE_ = this.STATES_.KV_KEY;\n\t this.PARSETMP_.Key = '';\n\t this.DATA_.Fields = {};\n\t }\n\t }\n\t } else {\n\t this.DATA_.EntryKey += c;\n\t this.SKIPWS_ = false;\n\t this.SKIPCOMMENT_ = false;\n\t }\n\t break;\n\t\n\t // Start at first non-whitespace/comment character after entry key.\n\t // -- Populate this.PARSETMP_.Key\n\t case this.STATES_.KV_KEY:\n\t // Test for end of entry\n\t if (c == '}' && this.BRACETYPE_ == '{' || c == ')' && this.BRACETYPE_ == '(') {\n\t // SUCCESS: Parsed an entry, possible incomplete\n\t // NEXT_STATE: ENTRY_OR_JUNK\n\t this.processEntry_();\n\t this.SKIPWS_ = true;\n\t this.SKIPCOMMENT_ = true;\n\t this.STATE_ = this.STATES_.ENTRY_OR_JUNK;\n\t break;\n\t }\n\t if (/[\\-A-Za-z:]/.test(c)) {\n\t // Add to key\n\t this.PARSETMP_.Key += c;\n\t this.SKIPWS_ = false;\n\t this.SKIPCOMMENT_ = false;\n\t } else {\n\t // Either end of key or we haven't encountered start of key\n\t if (this.PARSETMP_.Key.length < 1) {\n\t // Keep going till we see a key\n\t this.SKIPWS_ = true;\n\t this.SKIPCOMMENT_ = true;\n\t } else {\n\t // SUCCESS: Found full key in K/V pair\n\t // NEXT_STATE: EQUALS\n\t this.SKIPWS_ = true;\n\t this.SKIPCOMMENT_ = true;\n\t this.STATE_ = this.STATES_.EQUALS;\n\t AnotherIteration = true;\n\t }\n\t }\n\t break;\n\t\n\t // Start at first non-alphabetic character after K/V pair key.\n\t case this.STATES_.EQUALS:\n\t if (c == '}' && this.BRACETYPE_ == '{' || c == ')' && this.BRACETYPE_ == '(') {\n\t // ERROR: K/V pair with key but no value\n\t // NEXT_STATE: ENTRY_OR_JUNK\n\t this.error_('Key-value pair has key \"' + this.PARSETMP_.Key + '\", but no value.');\n\t this.processEntry_();\n\t this.SKIPWS_ = true;\n\t this.SKIPCOMMENT_ = true;\n\t this.STATE_ = this.STATES_.ENTRY_OR_JUNK;\n\t break;\n\t }\n\t if (c == '=') {\n\t // SUCCESS: found an equal signs separating key and value\n\t // NEXT_STATE: KV_VALUE\n\t this.SKIPWS_ = true;\n\t this.SKIPCOMMENT_ = true;\n\t this.STATE_ = this.STATES_.KV_VALUE;\n\t this.PARSETMP_.Value = '';\n\t this.VALBRACES_ = { '\"': [], '{': [] };\n\t }\n\t break;\n\t\n\t // Start at first non-whitespace/comment character after '=' \n\t // -- Populate this.PARSETMP_.Value\n\t case this.STATES_.KV_VALUE:\n\t var delim = this.VALBRACES_;\n\t var val = this.PARSETMP_.Value;\n\t var doneParsingValue = false;\n\t\n\t // Test for special characters\n\t if (c == '\"' || c == '{' || c == '}' || c == ',') {\n\t if (c == ',') {\n\t // This comma can mean:\n\t // (1) just another comma literal\n\t // (2) end of a macro reference\n\t if (0 === delim['\"'].length + delim['{'].length) {\n\t // end of a macro reference\n\t var macro = this.PARSETMP_.Value.trim();\n\t if (macro in this.MACROS_) {\n\t // Successful macro reference\n\t this.PARSETMP_.Value = this.MACROS_[macro];\n\t } else {\n\t // Reference to an undefined macro\n\t this.error_('Reference to an undefined macro: ' + macro);\n\t }\n\t doneParsingValue = true;\n\t }\n\t }\n\t if (c == '\"') {\n\t // This quote can mean:\n\t // (1) opening delimiter\n\t // (2) closing delimiter\n\t // (3) literal, if we have a '{' on the stack\n\t if (0 === delim['\"'].length + delim['{'].length) {\n\t // opening delimiter\n\t delim['\"'].push(this.CHAR_);\n\t this.SKIPWS_ = false;\n\t this.SKIPCOMMENT_ = false;\n\t break;\n\t }\n\t if (delim['\"'].length == 1 && delim['{'].length == 0 && (val.length == 0 || val[val.length - 1] != '\\\\')) {\n\t // closing delimiter\n\t doneParsingValue = true;\n\t } else {\n\t // literal, add to value\n\t }\n\t }\n\t if (c == '{') {\n\t // This brace can mean:\n\t // (1) opening delimiter\n\t // (2) stacked verbatim delimiter\n\t if (val.length == 0 || val[val.length - 1] != '\\\\') {\n\t delim['{'].push(this.CHAR_);\n\t this.SKIPWS_ = false;\n\t this.SKIPCOMMENT_ = false;\n\t } else {\n\t // literal, add to value\n\t }\n\t }\n\t if (c == '}') {\n\t // This brace can mean:\n\t // (1) closing delimiter\n\t // (2) closing stacked verbatim delimiter\n\t // (3) end of object definition if value was a macro\n\t if (0 === delim['\"'].length + delim['{'].length) {\n\t // end of object definition, after macro\n\t var macro = this.PARSETMP_.Value.trim();\n\t if (macro in this.MACROS_) {\n\t // Successful macro reference\n\t this.PARSETMP_.Value = this.MACROS_[macro];\n\t } else {\n\t // Reference to an undefined macro\n\t this.error_('Reference to an undefined macro: ' + macro);\n\t }\n\t AnotherIteration = true;\n\t doneParsingValue = true;\n\t } else {\n\t if (val.length == 0 || val[val.length - 1] != '\\\\') {\n\t if (delim['{'].length > 0) {\n\t // pop stack for stacked verbatim delimiter\n\t delim['{'].splice(delim['{'].length - 1, 1);\n\t if (0 == delim['{'].length + delim['\"'].length) {\n\t // closing delimiter\n\t doneParsingValue = true;\n\t } else {\n\t // end verbatim block\n\t }\n\t }\n\t } else {\n\t // literal, add to value\n\t }\n\t }\n\t }\n\t }\n\t\n\t // If here, then we are either done parsing the value or \n\t // have a literal that should be added to the value.\n\t if (doneParsingValue) {\n\t // SUCCESS: value parsed\n\t // NEXT_STATE: KV_KEY\n\t this.SKIPWS_ = true;\n\t this.SKIPCOMMENT_ = true;\n\t this.STATE_ = this.STATES_.KV_KEY;\n\t this.DATA_.Fields[this.PARSETMP_.Key] = this.PARSETMP_.Value;\n\t this.PARSETMP_ = { Key: '' };\n\t this.VALBRACES_ = null;\n\t } else {\n\t this.PARSETMP_.Value += c;\n\t }\n\t break;\n\t } // end switch (this.STATE_)\n\t } // end while(AnotherIteration)\n\t }; // end function processCharacter \n\t\n\t /** @private */this.CHARCONV_ = [[/\\\\space /g, '\\u0020'], [/\\\\textdollar /g, '\\u0024'], [/\\\\textquotesingle /g, '\\u0027'], [/\\\\ast /g, '\\u002A'], [/\\\\textbackslash /g, '\\u005C'], [/\\\\\\^\\{\\}/g, '\\u005E'], [/\\\\textasciigrave /g, '\\u0060'], [/\\\\lbrace /g, '\\u007B'], [/\\\\vert /g, '\\u007C'], [/\\\\rbrace /g, '\\u007D'], [/\\\\textasciitilde /g, '\\u007E'], [/\\\\textexclamdown /g, '\\u00A1'], [/\\\\textcent /g, '\\u00A2'], [/\\\\textsterling /g, '\\u00A3'], [/\\\\textcurrency /g, '\\u00A4'], [/\\\\textyen /g, '\\u00A5'], [/\\\\textbrokenbar /g, '\\u00A6'], [/\\\\textsection /g, '\\u00A7'], [/\\\\textasciidieresis /g, '\\u00A8'], [/\\\\textcopyright /g, '\\u00A9'], [/\\\\textordfeminine /g, '\\u00AA'], [/\\\\guillemotleft /g, '\\u00AB'], [/\\\\lnot /g, '\\u00AC'], [/\\\\textregistered /g, '\\u00AE'], [/\\\\textasciimacron /g, '\\u00AF'], [/\\\\textdegree /g, '\\u00B0'], [/\\\\pm /g, '\\u00B1'], [/\\\\textasciiacute /g, '\\u00B4'], [/\\\\mathrm\\{\\\\mu\\}/g, '\\u00B5'], [/\\\\textparagraph /g, '\\u00B6'], [/\\\\cdot /g, '\\u00B7'], [/\\\\c\\{\\}/g, '\\u00B8'], [/\\\\textordmasculine /g, '\\u00BA'], [/\\\\guillemotright /g, '\\u00BB'], [/\\\\textonequarter /g, '\\u00BC'], [/\\\\textonehalf /g, '\\u00BD'], [/\\\\textthreequarters /g, '\\u00BE'], [/\\\\textquestiondown /g, '\\u00BF'], [/\\\\`\\{A\\}/g, '\\u00C0'], [/\\\\'\\{A\\}/g, '\\u00C1'], [/\\\\\\^\\{A\\}/g, '\\u00C2'], [/\\\\~\\{A\\}/g, '\\u00C3'], [/\\\\\"\\{A\\}/g, '\\u00C4'], [/\\\\AA /g, '\\u00C5'], [/\\\\AE /g, '\\u00C6'], [/\\\\c\\{C\\}/g, '\\u00C7'], [/\\\\`\\{E\\}/g, '\\u00C8'], [/\\\\'\\{E\\}/g, '\\u00C9'], [/\\\\\\^\\{E\\}/g, '\\u00CA'], [/\\\\\"\\{E\\}/g, '\\u00CB'], [/\\\\`\\{I\\}/g, '\\u00CC'], [/\\\\'\\{I\\}/g, '\\u00CD'], [/\\\\\\^\\{I\\}/g, '\\u00CE'], [/\\\\\"\\{I\\}/g, '\\u00CF'], [/\\\\DH /g, '\\u00D0'], [/\\\\~\\{N\\}/g, '\\u00D1'], [/\\\\`\\{O\\}/g, '\\u00D2'], [/\\\\'\\{O\\}/g, '\\u00D3'], [/\\\\\\^\\{O\\}/g, '\\u00D4'], [/\\\\~\\{O\\}/g, '\\u00D5'], [/\\\\\"\\{O\\}/g, '\\u00D6'], [/\\\\texttimes /g, '\\u00D7'], [/\\\\O /g, '\\u00D8'], [/\\\\`\\{U\\}/g, '\\u00D9'], [/\\\\'\\{U\\}/g, '\\u00DA'], [/\\\\\\^\\{U\\}/g, '\\u00DB'], [/\\\\\"\\{U\\}/g, '\\u00DC'], [/\\\\'\\{Y\\}/g, '\\u00DD'], [/\\\\TH /g, '\\u00DE'], [/\\\\ss /g, '\\u00DF'], [/\\\\`\\{a\\}/g, '\\u00E0'], [/\\\\'\\{a\\}/g, '\\u00E1'], [/\\\\\\^\\{a\\}/g, '\\u00E2'], [/\\\\~\\{a\\}/g, '\\u00E3'], [/\\\\\"\\{a\\}/g, '\\u00E4'], [/\\\\aa /g, '\\u00E5'], [/\\\\ae /g, '\\u00E6'], [/\\\\c\\{c\\}/g, '\\u00E7'], [/\\\\`\\{e\\}/g, '\\u00E8'], [/\\\\'\\{e\\}/g, '\\u00E9'], [/\\\\\\^\\{e\\}/g, '\\u00EA'], [/\\\\\"\\{e\\}/g, '\\u00EB'], [/\\\\`\\{\\\\i\\}/g, '\\u00EC'], [/\\\\'\\{\\\\i\\}/g, '\\u00ED'], [/\\\\\\^\\{\\\\i\\}/g, '\\u00EE'], [/\\\\\"\\{\\\\i\\}/g, '\\u00EF'], [/\\\\dh /g, '\\u00F0'], [/\\\\~\\{n\\}/g, '\\u00F1'], [/\\\\`\\{o\\}/g, '\\u00F2'], [/\\\\'\\{o\\}/g, '\\u00F3'], [/\\\\\\^\\{o\\}/g, '\\u00F4'], [/\\\\~\\{o\\}/g, '\\u00F5'], [/\\\\\"\\{o\\}/g, '\\u00F6'], [/\\\\div /g, '\\u00F7'], [/\\\\o /g, '\\u00F8'], [/\\\\`\\{u\\}/g, '\\u00F9'], [/\\\\'\\{u\\}/g, '\\u00FA'], [/\\\\\\^\\{u\\}/g, '\\u00FB'], [/\\\\\"\\{u\\}/g, '\\u00FC'], [/\\\\'\\{y\\}/g, '\\u00FD'], [/\\\\th /g, '\\u00FE'], [/\\\\\"\\{y\\}/g, '\\u00FF'], [/\\\\=\\{A\\}/g, '\\u0100'], [/\\\\=\\{a\\}/g, '\\u0101'], [/\\\\u\\{A\\}/g, '\\u0102'], [/\\\\u\\{a\\}/g, '\\u0103'], [/\\\\k\\{A\\}/g, '\\u0104'], [/\\\\k\\{a\\}/g, '\\u0105'], [/\\\\'\\{C\\}/g, '\\u0106'], [/\\\\'\\{c\\}/g, '\\u0107'], [/\\\\\\^\\{C\\}/g, '\\u0108'], [/\\\\\\^\\{c\\}/g, '\\u0109'], [/\\\\.\\{C\\}/g, '\\u010A'], [/\\\\.\\{c\\}/g, '\\u010B'], [/\\\\v\\{C\\}/g, '\\u010C'], [/\\\\v\\{c\\}/g, '\\u010D'], [/\\\\v\\{D\\}/g, '\\u010E'], [/\\\\v\\{d\\}/g, '\\u010F'], [/\\\\DJ /g, '\\u0110'], [/\\\\dj /g, '\\u0111'], [/\\\\=\\{E\\}/g, '\\u0112'], [/\\\\=\\{e\\}/g, '\\u0113'], [/\\\\u\\{E\\}/g, '\\u0114'], [/\\\\u\\{e\\}/g, '\\u0115'], [/\\\\.\\{E\\}/g, '\\u0116'], [/\\\\.\\{e\\}/g, '\\u0117'], [/\\\\k\\{E\\}/g, '\\u0118'], [/\\\\k\\{e\\}/g, '\\u0119'], [/\\\\v\\{E\\}/g, '\\u011A'], [/\\\\v\\{e\\}/g, '\\u011B'], [/\\\\\\^\\{G\\}/g, '\\u011C'], [/\\\\\\^\\{g\\}/g, '\\u011D'], [/\\\\u\\{G\\}/g, '\\u011E'], [/\\\\u\\{g\\}/g, '\\u011F'], [/\\\\.\\{G\\}/g, '\\u0120'], [/\\\\.\\{g\\}/g, '\\u0121'], [/\\\\c\\{G\\}/g, '\\u0122'], [/\\\\c\\{g\\}/g, '\\u0123'], [/\\\\\\^\\{H\\}/g, '\\u0124'], [/\\\\\\^\\{h\\}/g, '\\u0125'], [/\\\\Elzxh /g, '\\u0127'], [/\\\\~\\{I\\}/g, '\\u0128'], [/\\\\~\\{\\\\i\\}/g, '\\u0129'], [/\\\\=\\{I\\}/g, '\\u012A'], [/\\\\=\\{\\\\i\\}/g, '\\u012B'], [/\\\\u\\{I\\}/g, '\\u012C'], [/\\\\u\\{\\\\i\\}/g, '\\u012D'], [/\\\\k\\{I\\}/g, '\\u012E'], [/\\\\k\\{i\\}/g, '\\u012F'], [/\\\\.\\{I\\}/g, '\\u0130'], [/\\\\i /g, '\\u0131'], [/\\\\\\^\\{J\\}/g, '\\u0134'], [/\\\\\\^\\{\\\\j\\}/g, '\\u0135'], [/\\\\c\\{K\\}/g, '\\u0136'], [/\\\\c\\{k\\}/g, '\\u0137'], [/\\\\'\\{L\\}/g, '\\u0139'], [/\\\\'\\{l\\}/g, '\\u013A'], [/\\\\c\\{L\\}/g, '\\u013B'], [/\\\\c\\{l\\}/g, '\\u013C'], [/\\\\v\\{L\\}/g, '\\u013D'], [/\\\\v\\{l\\}/g, '\\u013E'], [/\\\\L /g, '\\u0141'], [/\\\\l /g, '\\u0142'], [/\\\\'\\{N\\}/g, '\\u0143'], [/\\\\'\\{n\\}/g, '\\u0144'], [/\\\\c\\{N\\}/g, '\\u0145'], [/\\\\c\\{n\\}/g, '\\u0146'], [/\\\\v\\{N\\}/g, '\\u0147'], [/\\\\v\\{n\\}/g, '\\u0148'], [/\\\\NG /g, '\\u014A'], [/\\\\ng /g, '\\u014B'], [/\\\\=\\{O\\}/g, '\\u014C'], [/\\\\=\\{o\\}/g, '\\u014D'], [/\\\\u\\{O\\}/g, '\\u014E'], [/\\\\u\\{o\\}/g, '\\u014F'], [/\\\\H\\{O\\}/g, '\\u0150'], [/\\\\H\\{o\\}/g, '\\u0151'], [/\\\\OE /g, '\\u0152'], [/\\\\oe /g, '\\u0153'], [/\\\\'\\{R\\}/g, '\\u0154'], [/\\\\'\\{r\\}/g, '\\u0155'], [/\\\\c\\{R\\}/g, '\\u0156'], [/\\\\c\\{r\\}/g, '\\u0157'], [/\\\\v\\{R\\}/g, '\\u0158'], [/\\\\v\\{r\\}/g, '\\u0159'], [/\\\\'\\{S\\}/g, '\\u015A'], [/\\\\'\\{s\\}/g, '\\u015B'], [/\\\\\\^\\{S\\}/g, '\\u015C'], [/\\\\\\^\\{s\\}/g, '\\u015D'], [/\\\\c\\{S\\}/g, '\\u015E'], [/\\\\c\\{s\\}/g, '\\u015F'], [/\\\\v\\{S\\}/g, '\\u0160'], [/\\\\v\\{s\\}/g, '\\u0161'], [/\\\\c\\{T\\}/g, '\\u0162'], [/\\\\c\\{t\\}/g, '\\u0163'], [/\\\\v\\{T\\}/g, '\\u0164'], [/\\\\v\\{t\\}/g, '\\u0165'], [/\\\\~\\{U\\}/g, '\\u0168'], [/\\\\~\\{u\\}/g, '\\u0169'], [/\\\\=\\{U\\}/g, '\\u016A'], [/\\\\=\\{u\\}/g, '\\u016B'], [/\\\\u\\{U\\}/g, '\\u016C'], [/\\\\u\\{u\\}/g, '\\u016D'], [/\\\\r\\{U\\}/g, '\\u016E'], [/\\\\r\\{u\\}/g, '\\u016F'], [/\\\\H\\{U\\}/g, '\\u0170'], [/\\\\H\\{u\\}/g, '\\u0171'], [/\\\\k\\{U\\}/g, '\\u0172'], [/\\\\k\\{u\\}/g, '\\u0173'], [/\\\\\\^\\{W\\}/g, '\\u0174'], [/\\\\\\^\\{w\\}/g, '\\u0175'], [/\\\\\\^\\{Y\\}/g, '\\u0176'], [/\\\\\\^\\{y\\}/g, '\\u0177'], [/\\\\\"\\{Y\\}/g, '\\u0178'], [/\\\\'\\{Z\\}/g, '\\u0179'], [/\\\\'\\{z\\}/g, '\\u017A'], [/\\\\.\\{Z\\}/g, '\\u017B'], [/\\\\.\\{z\\}/g, '\\u017C'], [/\\\\v\\{Z\\}/g, '\\u017D'], [/\\\\v\\{z\\}/g, '\\u017E'], [/\\\\texthvlig /g, '\\u0195'], [/\\\\textnrleg /g, '\\u019E'], [/\\\\eth /g, '\\u01AA'], [/\\\\textdoublepipe /g, '\\u01C2'], [/\\\\'\\{g\\}/g, '\\u01F5'], [/\\\\Elztrna /g, '\\u0250'], [/\\\\Elztrnsa /g, '\\u0252'], [/\\\\Elzopeno /g, '\\u0254'], [/\\\\Elzrtld /g, '\\u0256'], [/\\\\Elzschwa /g, '\\u0259'], [/\\\\varepsilon /g, '\\u025B'], [/\\\\Elzpgamma /g, '\\u0263'], [/\\\\Elzpbgam /g, '\\u0264'], [/\\\\Elztrnh /g, '\\u0265'], [/\\\\Elzbtdl /g, '\\u026C'], [/\\\\Elzrtll /g, '\\u026D'], [/\\\\Elztrnm /g, '\\u026F'], [/\\\\Elztrnmlr /g, '\\u0270'], [/\\\\Elzltlmr /g, '\\u0271'], [/\\\\Elzltln /g, '\\u0272'], [/\\\\Elzrtln /g, '\\u0273'], [/\\\\Elzclomeg /g, '\\u0277'], [/\\\\textphi /g, '\\u0278'], [/\\\\Elztrnr /g, '\\u0279'], [/\\\\Elztrnrl /g, '\\u027A'], [/\\\\Elzrttrnr /g, '\\u027B'], [/\\\\Elzrl /g, '\\u027C'], [/\\\\Elzrtlr /g, '\\u027D'], [/\\\\Elzfhr /g, '\\u027E'], [/\\\\Elzrtls /g, '\\u0282'], [/\\\\Elzesh /g, '\\u0283'], [/\\\\Elztrnt /g, '\\u0287'], [/\\\\Elzrtlt /g, '\\u0288'], [/\\\\Elzpupsil /g, '\\u028A'], [/\\\\Elzpscrv /g, '\\u028B'], [/\\\\Elzinvv /g, '\\u028C'], [/\\\\Elzinvw /g, '\\u028D'], [/\\\\Elztrny /g, '\\u028E'], [/\\\\Elzrtlz /g, '\\u0290'], [/\\\\Elzyogh /g, '\\u0292'], [/\\\\Elzglst /g, '\\u0294'], [/\\\\Elzreglst /g, '\\u0295'], [/\\\\Elzinglst /g, '\\u0296'], [/\\\\textturnk /g, '\\u029E'], [/\\\\Elzdyogh /g, '\\u02A4'], [/\\\\Elztesh /g, '\\u02A7'], [/\\\\textasciicaron /g, '\\u02C7'], [/\\\\Elzverts /g, '\\u02C8'], [/\\\\Elzverti /g, '\\u02CC'], [/\\\\Elzlmrk /g, '\\u02D0'], [/\\\\Elzhlmrk /g, '\\u02D1'], [/\\\\Elzsbrhr /g, '\\u02D2'], [/\\\\Elzsblhr /g, '\\u02D3'], [/\\\\Elzrais /g, '\\u02D4'], [/\\\\Elzlow /g, '\\u02D5'], [/\\\\textasciibreve /g, '\\u02D8'], [/\\\\textperiodcentered /g, '\\u02D9'], [/\\\\r\\{\\}/g, '\\u02DA'], [/\\\\k\\{\\}/g, '\\u02DB'], [/\\\\texttildelow /g, '\\u02DC'], [/\\\\H\\{\\}/g, '\\u02DD'], [/\\\\tone\\{55\\}/g, '\\u02E5'], [/\\\\tone\\{44\\}/g, '\\u02E6'], [/\\\\tone\\{33\\}/g, '\\u02E7'], [/\\\\tone\\{22\\}/g, '\\u02E8'], [/\\\\tone\\{11\\}/g, '\\u02E9'], [/\\\\cyrchar\\\\C/g, '\\u030F'], [/\\\\Elzpalh /g, '\\u0321'], [/\\\\Elzrh /g, '\\u0322'], [/\\\\Elzsbbrg /g, '\\u032A'], [/\\\\Elzxl /g, '\\u0335'], [/\\\\Elzbar /g, '\\u0336'], [/\\\\'\\{A\\}/g, '\\u0386'], [/\\\\'\\{E\\}/g, '\\u0388'], [/\\\\'\\{H\\}/g, '\\u0389'], [/\\\\'\\{\\}\\{I\\}/g, '\\u038A'], [/\\\\'\\{\\}O/g, '\\u038C'], [/\\\\mathrm\\{'Y\\}/g, '\\u038E'], [/\\\\mathrm\\{'\\\\Omega\\}/g, '\\u038F'], [/\\\\acute\\{\\\\ddot\\{\\\\iota\\}\\}/g, '\\u0390'], [/\\\\Alpha /g, '\\u0391'], [/\\\\Beta /g, '\\u0392'], [/\\\\Gamma /g, '\\u0393'], [/\\\\Delta /g, '\\u0394'], [/\\\\Epsilon /g, '\\u0395'], [/\\\\Zeta /g, '\\u0396'], [/\\\\Eta /g, '\\u0397'], [/\\\\Theta /g, '\\u0398'], [/\\\\Iota /g, '\\u0399'], [/\\\\Kappa /g, '\\u039A'], [/\\\\Lambda /g, '\\u039B'], [/\\\\Xi /g, '\\u039E'], [/\\\\Pi /g, '\\u03A0'], [/\\\\Rho /g, '\\u03A1'], [/\\\\Sigma /g, '\\u03A3'], [/\\\\Tau /g, '\\u03A4'], [/\\\\Upsilon /g, '\\u03A5'], [/\\\\Phi /g, '\\u03A6'], [/\\\\Chi /g, '\\u03A7'], [/\\\\Psi /g, '\\u03A8'], [/\\\\Omega /g, '\\u03A9'], [/\\\\mathrm\\{\\\\ddot\\{I\\}\\}/g, '\\u03AA'], [/\\\\mathrm\\{\\\\ddot\\{Y\\}\\}/g, '\\u03AB'], [/\\\\'\\{\\$\\\\alpha\\$\\}/g, '\\u03AC'], [/\\\\acute\\{\\\\epsilon\\}/g, '\\u03AD'], [/\\\\acute\\{\\\\eta\\}/g, '\\u03AE'], [/\\\\acute\\{\\\\iota\\}/g, '\\u03AF'], [/\\\\acute\\{\\\\ddot\\{\\\\upsilon\\}\\}/g, '\\u03B0'], [/\\\\alpha /g, '\\u03B1'], [/\\\\beta /g, '\\u03B2'], [/\\\\gamma /g, '\\u03B3'], [/\\\\delta /g, '\\u03B4'], [/\\\\epsilon /g, '\\u03B5'], [/\\\\zeta /g, '\\u03B6'], [/\\\\eta /g, '\\u03B7'], [/\\\\texttheta /g, '\\u03B8'], [/\\\\iota /g, '\\u03B9'], [/\\\\kappa /g, '\\u03BA'], [/\\\\lambda /g, '\\u03BB'], [/\\\\mu /g, '\\u03BC'], [/\\\\nu /g, '\\u03BD'], [/\\\\xi /g, '\\u03BE'], [/\\\\pi /g, '\\u03C0'], [/\\\\rho /g, '\\u03C1'], [/\\\\varsigma /g, '\\u03C2'], [/\\\\sigma /g, '\\u03C3'], [/\\\\tau /g, '\\u03C4'], [/\\\\upsilon /g, '\\u03C5'], [/\\\\varphi /g, '\\u03C6'], [/\\\\chi /g, '\\u03C7'], [/\\\\psi /g, '\\u03C8'], [/\\\\omega /g, '\\u03C9'], [/\\\\ddot\\{\\\\iota\\}/g, '\\u03CA'], [/\\\\ddot\\{\\\\upsilon\\}/g, '\\u03CB'], [/\\\\'\\{o\\}/g, '\\u03CC'], [/\\\\acute\\{\\\\upsilon\\}/g, '\\u03CD'], [/\\\\acute\\{\\\\omega\\}/g, '\\u03CE'], [/\\\\Pisymbol\\{ppi022\\}\\{87\\}/g, '\\u03D0'], [/\\\\textvartheta /g, '\\u03D1'], [/\\\\Upsilon /g, '\\u03D2'], [/\\\\phi /g, '\\u03D5'], [/\\\\varpi /g, '\\u03D6'], [/\\\\Stigma /g, '\\u03DA'], [/\\\\Digamma /g, '\\u03DC'], [/\\\\digamma /g, '\\u03DD'], [/\\\\Koppa /g, '\\u03DE'], [/\\\\Sampi /g, '\\u03E0'], [/\\\\varkappa /g, '\\u03F0'], [/\\\\varrho /g, '\\u03F1'], [/\\\\textTheta /g, '\\u03F4'], [/\\\\backepsilon /g, '\\u03F6'], [/\\\\cyrchar\\\\CYRYO /g, '\\u0401'], [/\\\\cyrchar\\\\CYRDJE /g, '\\u0402'], [/\\\\cyrchar\\{\\\\'\\\\CYRG\\}/g, '\\u0403'], [/\\\\cyrchar\\\\CYRIE /g, '\\u0404'], [/\\\\cyrchar\\\\CYRDZE /g, '\\u0405'], [/\\\\cyrchar\\\\CYRII /g, '\\u0406'], [/\\\\cyrchar\\\\CYRYI /g, '\\u0407'], [/\\\\cyrchar\\\\CYRJE /g, '\\u0408'], [/\\\\cyrchar\\\\CYRLJE /g, '\\u0409'], [/\\\\cyrchar\\\\CYRNJE /g, '\\u040A'], [/\\\\cyrchar\\\\CYRTSHE /g, '\\u040B'], [/\\\\cyrchar\\{\\\\'\\\\CYRK\\}/g, '\\u040C'], [/\\\\cyrchar\\\\CYRUSHRT /g, '\\u040E'], [/\\\\cyrchar\\\\CYRDZHE /g, '\\u040F'], [/\\\\cyrchar\\\\CYRA /g, '\\u0410'], [/\\\\cyrchar\\\\CYRB /g, '\\u0411'], [/\\\\cyrchar\\\\CYRV /g, '\\u0412'], [/\\\\cyrchar\\\\CYRG /g, '\\u0413'], [/\\\\cyrchar\\\\CYRD /g, '\\u0414'], [/\\\\cyrchar\\\\CYRE /g, '\\u0415'], [/\\\\cyrchar\\\\CYRZH /g, '\\u0416'], [/\\\\cyrchar\\\\CYRZ /g, '\\u0417'], [/\\\\cyrchar\\\\CYRI /g, '\\u0418'], [/\\\\cyrchar\\\\CYRISHRT /g, '\\u0419'], [/\\\\cyrchar\\\\CYRK /g, '\\u041A'], [/\\\\cyrchar\\\\CYRL /g, '\\u041B'], [/\\\\cyrchar\\\\CYRM /g, '\\u041C'], [/\\\\cyrchar\\\\CYRN /g, '\\u041D'], [/\\\\cyrchar\\\\CYRO /g, '\\u041E'], [/\\\\cyrchar\\\\CYRP /g, '\\u041F'], [/\\\\cyrchar\\\\CYRR /g, '\\u0420'], [/\\\\cyrchar\\\\CYRS /g, '\\u0421'], [/\\\\cyrchar\\\\CYRT /g, '\\u0422'], [/\\\\cyrchar\\\\CYRU /g, '\\u0423'], [/\\\\cyrchar\\\\CYRF /g, '\\u0424'], [/\\\\cyrchar\\\\CYRH /g, '\\u0425'], [/\\\\cyrchar\\\\CYRC /g, '\\u0426'], [/\\\\cyrchar\\\\CYRCH /g, '\\u0427'], [/\\\\cyrchar\\\\CYRSH /g, '\\u0428'], [/\\\\cyrchar\\\\CYRSHCH /g, '\\u0429'], [/\\\\cyrchar\\\\CYRHRDSN /g, '\\u042A'], [/\\\\cyrchar\\\\CYRERY /g, '\\u042B'], [/\\\\cyrchar\\\\CYRSFTSN /g, '\\u042C'], [/\\\\cyrchar\\\\CYREREV /g, '\\u042D'], [/\\\\cyrchar\\\\CYRYU /g, '\\u042E'], [/\\\\cyrchar\\\\CYRYA /g, '\\u042F'], [/\\\\cyrchar\\\\cyra /g, '\\u0430'], [/\\\\cyrchar\\\\cyrb /g, '\\u0431'], [/\\\\cyrchar\\\\cyrv /g, '\\u0432'], [/\\\\cyrchar\\\\cyrg /g, '\\u0433'], [/\\\\cyrchar\\\\cyrd /g, '\\u0434'], [/\\\\cyrchar\\\\cyre /g, '\\u0435'], [/\\\\cyrchar\\\\cyrzh /g, '\\u0436'], [/\\\\cyrchar\\\\cyrz /g, '\\u0437'], [/\\\\cyrchar\\\\cyri /g, '\\u0438'], [/\\\\cyrchar\\\\cyrishrt /g, '\\u0439'], [/\\\\cyrchar\\\\cyrk /g, '\\u043A'], [/\\\\cyrchar\\\\cyrl /g, '\\u043B'], [/\\\\cyrchar\\\\cyrm /g, '\\u043C'], [/\\\\cyrchar\\\\cyrn /g, '\\u043D'], [/\\\\cyrchar\\\\cyro /g, '\\u043E'], [/\\\\cyrchar\\\\cyrp /g, '\\u043F'], [/\\\\cyrchar\\\\cyrr /g, '\\u0440'], [/\\\\cyrchar\\\\cyrs /g, '\\u0441'], [/\\\\cyrchar\\\\cyrt /g, '\\u0442'], [/\\\\cyrchar\\\\cyru /g, '\\u0443'], [/\\\\cyrchar\\\\cyrf /g, '\\u0444'], [/\\\\cyrchar\\\\cyrh /g, '\\u0445'], [/\\\\cyrchar\\\\cyrc /g, '\\u0446'], [/\\\\cyrchar\\\\cyrch /g, '\\u0447'], [/\\\\cyrchar\\\\cyrsh /g, '\\u0448'], [/\\\\cyrchar\\\\cyrshch /g, '\\u0449'], [/\\\\cyrchar\\\\cyrhrdsn /g, '\\u044A'], [/\\\\cyrchar\\\\cyrery /g, '\\u044B'], [/\\\\cyrchar\\\\cyrsftsn /g, '\\u044C'], [/\\\\cyrchar\\\\cyrerev /g, '\\u044D'], [/\\\\cyrchar\\\\cyryu /g, '\\u044E'], [/\\\\cyrchar\\\\cyrya /g, '\\u044F'], [/\\\\cyrchar\\\\cyryo /g, '\\u0451'], [/\\\\cyrchar\\\\cyrdje /g, '\\u0452'], [/\\\\cyrchar\\{\\\\'\\\\cyrg\\}/g, '\\u0453'], [/\\\\cyrchar\\\\cyrie /g, '\\u0454'], [/\\\\cyrchar\\\\cyrdze /g, '\\u0455'], [/\\\\cyrchar\\\\cyrii /g, '\\u0456'], [/\\\\cyrchar\\\\cyryi /g, '\\u0457'], [/\\\\cyrchar\\\\cyrje /g, '\\u0458'], [/\\\\cyrchar\\\\cyrlje /g, '\\u0459'], [/\\\\cyrchar\\\\cyrnje /g, '\\u045A'], [/\\\\cyrchar\\\\cyrtshe /g, '\\u045B'], [/\\\\cyrchar\\{\\\\'\\\\cyrk\\}/g, '\\u045C'], [/\\\\cyrchar\\\\cyrushrt /g, '\\u045E'], [/\\\\cyrchar\\\\cyrdzhe /g, '\\u045F'], [/\\\\cyrchar\\\\CYROMEGA /g, '\\u0460'], [/\\\\cyrchar\\\\cyromega /g, '\\u0461'], [/\\\\cyrchar\\\\CYRYAT /g, '\\u0462'], [/\\\\cyrchar\\\\CYRIOTE /g, '\\u0464'], [/\\\\cyrchar\\\\cyriote /g, '\\u0465'], [/\\\\cyrchar\\\\CYRLYUS /g, '\\u0466'], [/\\\\cyrchar\\\\cyrlyus /g, '\\u0467'], [/\\\\cyrchar\\\\CYRIOTLYUS /g, '\\u0468'], [/\\\\cyrchar\\\\cyriotlyus /g, '\\u0469'], [/\\\\cyrchar\\\\CYRBYUS /g, '\\u046A'], [/\\\\cyrchar\\\\CYRIOTBYUS /g, '\\u046C'], [/\\\\cyrchar\\\\cyriotbyus /g, '\\u046D'], [/\\\\cyrchar\\\\CYRKSI /g, '\\u046E'], [/\\\\cyrchar\\\\cyrksi /g, '\\u046F'], [/\\\\cyrchar\\\\CYRPSI /g, '\\u0470'], [/\\\\cyrchar\\\\cyrpsi /g, '\\u0471'], [/\\\\cyrchar\\\\CYRFITA /g, '\\u0472'], [/\\\\cyrchar\\\\CYRIZH /g, '\\u0474'], [/\\\\cyrchar\\\\CYRUK /g, '\\u0478'], [/\\\\cyrchar\\\\cyruk /g, '\\u0479'], [/\\\\cyrchar\\\\CYROMEGARND /g, '\\u047A'], [/\\\\cyrchar\\\\cyromegarnd /g, '\\u047B'], [/\\\\cyrchar\\\\CYROMEGATITLO /g, '\\u047C'], [/\\\\cyrchar\\\\cyromegatitlo /g, '\\u047D'], [/\\\\cyrchar\\\\CYROT /g, '\\u047E'], [/\\\\cyrchar\\\\cyrot /g, '\\u047F'], [/\\\\cyrchar\\\\CYRKOPPA /g, '\\u0480'], [/\\\\cyrchar\\\\cyrkoppa /g, '\\u0481'], [/\\\\cyrchar\\\\cyrthousands /g, '\\u0482'], [/\\\\cyrchar\\\\cyrhundredthousands /g, '\\u0488'], [/\\\\cyrchar\\\\cyrmillions /g, '\\u0489'], [/\\\\cyrchar\\\\CYRSEMISFTSN /g, '\\u048C'], [/\\\\cyrchar\\\\cyrsemisftsn /g, '\\u048D'], [/\\\\cyrchar\\\\CYRRTICK /g, '\\u048E'], [/\\\\cyrchar\\\\cyrrtick /g, '\\u048F'], [/\\\\cyrchar\\\\CYRGUP /g, '\\u0490'], [/\\\\cyrchar\\\\cyrgup /g, '\\u0491'], [/\\\\cyrchar\\\\CYRGHCRS /g, '\\u0492'], [/\\\\cyrchar\\\\cyrghcrs /g, '\\u0493'], [/\\\\cyrchar\\\\CYRGHK /g, '\\u0494'], [/\\\\cyrchar\\\\cyrghk /g, '\\u0495'], [/\\\\cyrchar\\\\CYRZHDSC /g, '\\u0496'], [/\\\\cyrchar\\\\cyrzhdsc /g, '\\u0497'], [/\\\\cyrchar\\\\CYRZDSC /g, '\\u0498'], [/\\\\cyrchar\\\\cyrzdsc /g, '\\u0499'], [/\\\\cyrchar\\\\CYRKDSC /g, '\\u049A'], [/\\\\cyrchar\\\\cyrkdsc /g, '\\u049B'], [/\\\\cyrchar\\\\CYRKVCRS /g, '\\u049C'], [/\\\\cyrchar\\\\cyrkvcrs /g, '\\u049D'], [/\\\\cyrchar\\\\CYRKHCRS /g, '\\u049E'], [/\\\\cyrchar\\\\cyrkhcrs /g, '\\u049F'], [/\\\\cyrchar\\\\CYRKBEAK /g, '\\u04A0'], [/\\\\cyrchar\\\\cyrkbeak /g, '\\u04A1'], [/\\\\cyrchar\\\\CYRNDSC /g, '\\u04A2'], [/\\\\cyrchar\\\\cyrndsc /g, '\\u04A3'], [/\\\\cyrchar\\\\CYRNG /g, '\\u04A4'], [/\\\\cyrchar\\\\cyrng /g, '\\u04A5'], [/\\\\cyrchar\\\\CYRPHK /g, '\\u04A6'], [/\\\\cyrchar\\\\cyrphk /g, '\\u04A7'], [/\\\\cyrchar\\\\CYRABHHA /g, '\\u04A8'], [/\\\\cyrchar\\\\cyrabhha /g, '\\u04A9'], [/\\\\cyrchar\\\\CYRSDSC /g, '\\u04AA'], [/\\\\cyrchar\\\\cyrsdsc /g, '\\u04AB'], [/\\\\cyrchar\\\\CYRTDSC /g, '\\u04AC'], [/\\\\cyrchar\\\\cyrtdsc /g, '\\u04AD'], [/\\\\cyrchar\\\\CYRY /g, '\\u04AE'], [/\\\\cyrchar\\\\cyry /g, '\\u04AF'], [/\\\\cyrchar\\\\CYRYHCRS /g, '\\u04B0'], [/\\\\cyrchar\\\\cyryhcrs /g, '\\u04B1'], [/\\\\cyrchar\\\\CYRHDSC /g, '\\u04B2'], [/\\\\cyrchar\\\\cyrhdsc /g, '\\u04B3'], [/\\\\cyrchar\\\\CYRTETSE /g, '\\u04B4'], [/\\\\cyrchar\\\\cyrtetse /g, '\\u04B5'], [/\\\\cyrchar\\\\CYRCHRDSC /g, '\\u04B6'], [/\\\\cyrchar\\\\cyrchrdsc /g, '\\u04B7'], [/\\\\cyrchar\\\\CYRCHVCRS /g, '\\u04B8'], [/\\\\cyrchar\\\\cyrchvcrs /g, '\\u04B9'], [/\\\\cyrchar\\\\CYRSHHA /g, '\\u04BA'], [/\\\\cyrchar\\\\cyrshha /g, '\\u04BB'], [/\\\\cyrchar\\\\CYRABHCH /g, '\\u04BC'], [/\\\\cyrchar\\\\cyrabhch /g, '\\u04BD'], [/\\\\cyrchar\\\\CYRABHCHDSC /g, '\\u04BE'], [/\\\\cyrchar\\\\cyrabhchdsc /g, '\\u04BF'], [/\\\\cyrchar\\\\CYRpalochka /g, '\\u04C0'], [/\\\\cyrchar\\\\CYRKHK /g, '\\u04C3'], [/\\\\cyrchar\\\\cyrkhk /g, '\\u04C4'], [/\\\\cyrchar\\\\CYRNHK /g, '\\u04C7'], [/\\\\cyrchar\\\\cyrnhk /g, '\\u04C8'], [/\\\\cyrchar\\\\CYRCHLDSC /g, '\\u04CB'], [/\\\\cyrchar\\\\cyrchldsc /g, '\\u04CC'], [/\\\\cyrchar\\\\CYRAE /g, '\\u04D4'], [/\\\\cyrchar\\\\cyrae /g, '\\u04D5'], [/\\\\cyrchar\\\\CYRSCHWA /g, '\\u04D8'], [/\\\\cyrchar\\\\cyrschwa /g, '\\u04D9'], [/\\\\cyrchar\\\\CYRABHDZE /g, '\\u04E0'], [/\\\\cyrchar\\\\cyrabhdze /g, '\\u04E1'], [/\\\\cyrchar\\\\CYROTLD /g, '\\u04E8'], [/\\\\cyrchar\\\\cyrotld /g, '\\u04E9'], [/\\\\hspace\\{0.6em\\}/g, '\\u2002'], [/\\\\hspace\\{1em\\}/g, '\\u2003'], [/\\\\hspace\\{0.33em\\}/g, '\\u2004'], [/\\\\hspace\\{0.25em\\}/g, '\\u2005'], [/\\\\hspace\\{0.166em\\}/g, '\\u2006'], [/\\\\hphantom\\{0\\}/g, '\\u2007'], [/\\\\hphantom\\{,\\}/g, '\\u2008'], [/\\\\hspace\\{0.167em\\}/g, '\\u2009'], [/\\\\mkern1mu /g, '\\u200A'], [/\\\\textendash /g, '\\u2013'], [/\\\\textemdash /g, '\\u2014'], [/\\\\rule\\{1em\\}\\{1pt\\}/g, '\\u2015'], [/\\\\Vert /g, '\\u2016'], [/\\\\Elzreapos /g, '\\u201B'], [/\\\\textquotedblleft /g, '\\u201C'], [/\\\\textquotedblright /g, '\\u201D'], [/\\\\textdagger /g, '\\u2020'], [/\\\\textdaggerdbl /g, '\\u2021'], [/\\\\textbullet /g, '\\u2022'], [/\\\\ldots /g, '\\u2026'], [/\\\\textperthousand /g, '\\u2030'], [/\\\\textpertenthousand /g, '\\u2031'], [/\\\\backprime /g, '\\u2035'], [/\\\\guilsinglleft /g, '\\u2039'], [/\\\\guilsinglright /g, '\\u203A'], [/\\\\mkern4mu /g, '\\u205F'], [/\\\\nolinebreak /g, '\\u2060'], [/\\\\ensuremath\\{\\\\Elzpes\\}/g, '\\u20A7'], [/\\\\mbox\\{\\\\texteuro\\} /g, '\\u20AC'], [/\\\\dddot /g, '\\u20DB'], [/\\\\ddddot /g, '\\u20DC'], [/\\\\mathbb\\{C\\}/g, '\\u2102'], [/\\\\mathscr\\{g\\}/g, '\\u210A'], [/\\\\mathscr\\{H\\}/g, '\\u210B'], [/\\\\mathfrak\\{H\\}/g, '\\u210C'], [/\\\\mathbb\\{H\\}/g, '\\u210D'], [/\\\\hslash /g, '\\u210F'], [/\\\\mathscr\\{I\\}/g, '\\u2110'], [/\\\\mathfrak\\{I\\}/g, '\\u2111'], [/\\\\mathscr\\{L\\}/g, '\\u2112'], [/\\\\mathscr\\{l\\}/g, '\\u2113'], [/\\\\mathbb\\{N\\}/g, '\\u2115'], [/\\\\cyrchar\\\\textnumero /g, '\\u2116'], [/\\\\wp /g, '\\u2118'], [/\\\\mathbb\\{P\\}/g, '\\u2119'], [/\\\\mathbb\\{Q\\}/g, '\\u211A'], [/\\\\mathscr\\{R\\}/g, '\\u211B'], [/\\\\mathfrak\\{R\\}/g, '\\u211C'], [/\\\\mathbb\\{R\\}/g, '\\u211D'], [/\\\\Elzxrat /g, '\\u211E'], [/\\\\texttrademark /g, '\\u2122'], [/\\\\mathbb\\{Z\\}/g, '\\u2124'], [/\\\\Omega /g, '\\u2126'], [/\\\\mho /g, '\\u2127'], [/\\\\mathfrak\\{Z\\}/g, '\\u2128'], [/\\\\ElsevierGlyph\\{2129\\}/g, '\\u2129'], [/\\\\AA /g, '\\u212B'], [/\\\\mathscr\\{B\\}/g, '\\u212C'], [/\\\\mathfrak\\{C\\}/g, '\\u212D'], [/\\\\mathscr\\{e\\}/g, '\\u212F'], [/\\\\mathscr\\{E\\}/g, '\\u2130'], [/\\\\mathscr\\{F\\}/g, '\\u2131'], [/\\\\mathscr\\{M\\}/g, '\\u2133'], [/\\\\mathscr\\{o\\}/g, '\\u2134'], [/\\\\aleph /g, '\\u2135'], [/\\\\beth /g, '\\u2136'], [/\\\\gimel /g, '\\u2137'], [/\\\\daleth /g, '\\u2138'], [/\\\\textfrac\\{1\\}\\{3\\}/g, '\\u2153'], [/\\\\textfrac\\{2\\}\\{3\\}/g, '\\u2154'], [/\\\\textfrac\\{1\\}\\{5\\}/g, '\\u2155'], [/\\\\textfrac\\{2\\}\\{5\\}/g, '\\u2156'], [/\\\\textfrac\\{3\\}\\{5\\}/g, '\\u2157'], [/\\\\textfrac\\{4\\}\\{5\\}/g, '\\u2158'], [/\\\\textfrac\\{1\\}\\{6\\}/g, '\\u2159'], [/\\\\textfrac\\{5\\}\\{6\\}/g, '\\u215A'], [/\\\\textfrac\\{1\\}\\{8\\}/g, '\\u215B'], [/\\\\textfrac\\{3\\}\\{8\\}/g, '\\u215C'], [/\\\\textfrac\\{5\\}\\{8\\}/g, '\\u215D'], [/\\\\textfrac\\{7\\}\\{8\\}/g, '\\u215E'], [/\\\\leftarrow /g, '\\u2190'], [/\\\\uparrow /g, '\\u2191'], [/\\\\rightarrow /g, '\\u2192'], [/\\\\downarrow /g, '\\u2193'], [/\\\\leftrightarrow /g, '\\u2194'], [/\\\\updownarrow /g, '\\u2195'], [/\\\\nwarrow /g, '\\u2196'], [/\\\\nearrow /g, '\\u2197'], [/\\\\searrow /g, '\\u2198'], [/\\\\swarrow /g, '\\u2199'], [/\\\\nleftarrow /g, '\\u219A'], [/\\\\nrightarrow /g, '\\u219B'], [/\\\\arrowwaveright /g, '\\u219C'], [/\\\\arrowwaveright /g, '\\u219D'], [/\\\\twoheadleftarrow /g, '\\u219E'], [/\\\\twoheadrightarrow /g, '\\u21A0'], [/\\\\leftarrowtail /g, '\\u21A2'], [/\\\\rightarrowtail /g, '\\u21A3'], [/\\\\mapsto /g, '\\u21A6'], [/\\\\hookleftarrow /g, '\\u21A9'], [/\\\\hookrightarrow /g, '\\u21AA'], [/\\\\looparrowleft /g, '\\u21AB'], [/\\\\looparrowright /g, '\\u21AC'], [/\\\\leftrightsquigarrow /g, '\\u21AD'], [/\\\\nleftrightarrow /g, '\\u21AE'], [/\\\\Lsh /g, '\\u21B0'], [/\\\\Rsh /g, '\\u21B1'], [/\\\\ElsevierGlyph\\{21B3\\}/g, '\\u21B3'], [/\\\\curvearrowleft /g, '\\u21B6'], [/\\\\curvearrowright /g, '\\u21B7'], [/\\\\circlearrowleft /g, '\\u21BA'], [/\\\\circlearrowright /g, '\\u21BB'], [/\\\\leftharpoonup /g, '\\u21BC'], [/\\\\leftharpoondown /g, '\\u21BD'], [/\\\\upharpoonright /g, '\\u21BE'], [/\\\\upharpoonleft /g, '\\u21BF'], [/\\\\rightharpoonup /g, '\\u21C0'], [/\\\\rightharpoondown /g, '\\u21C1'], [/\\\\downharpoonright /g, '\\u21C2'], [/\\\\downharpoonleft /g, '\\u21C3'], [/\\\\rightleftarrows /g, '\\u21C4'], [/\\\\dblarrowupdown /g, '\\u21C5'], [/\\\\leftrightarrows /g, '\\u21C6'], [/\\\\leftleftarrows /g, '\\u21C7'], [/\\\\upuparrows /g, '\\u21C8'], [/\\\\rightrightarrows /g, '\\u21C9'], [/\\\\downdownarrows /g, '\\u21CA'], [/\\\\leftrightharpoons /g, '\\u21CB'], [/\\\\rightleftharpoons /g, '\\u21CC'], [/\\\\nLeftarrow /g, '\\u21CD'], [/\\\\nLeftrightarrow /g, '\\u21CE'], [/\\\\nRightarrow /g, '\\u21CF'], [/\\\\Leftarrow /g, '\\u21D0'], [/\\\\Uparrow /g, '\\u21D1'], [/\\\\Rightarrow /g, '\\u21D2'], [/\\\\Downarrow /g, '\\u21D3'], [/\\\\Leftrightarrow /g, '\\u21D4'], [/\\\\Updownarrow /g, '\\u21D5'], [/\\\\Lleftarrow /g, '\\u21DA'], [/\\\\Rrightarrow /g, '\\u21DB'], [/\\\\rightsquigarrow /g, '\\u21DD'], [/\\\\DownArrowUpArrow /g, '\\u21F5'], [/\\\\forall /g, '\\u2200'], [/\\\\complement /g, '\\u2201'], [/\\\\partial /g, '\\u2202'], [/\\\\exists /g, '\\u2203'], [/\\\\nexists /g, '\\u2204'], [/\\\\varnothing /g, '\\u2205'], [/\\\\nabla /g, '\\u2207'], [/\\\\in /g, '\\u2208'], [/\\\\not\\\\in /g, '\\u2209'], [/\\\\ni /g, '\\u220B'], [/\\\\not\\\\ni /g, '\\u220C'], [/\\\\prod /g, '\\u220F'], [/\\\\coprod /g, '\\u2210'], [/\\\\sum /g, '\\u2211'], [/\\\\mp /g, '\\u2213'], [/\\\\dotplus /g, '\\u2214'], [/\\\\setminus /g, '\\u2216'], [/\\\\circ /g, '\\u2218'], [/\\\\bullet /g, '\\u2219'], [/\\\\surd /g, '\\u221A'], [/\\\\propto /g, '\\u221D'], [/\\\\infty /g, '\\u221E'], [/\\\\rightangle /g, '\\u221F'], [/\\\\angle /g, '\\u2220'], [/\\\\measuredangle /g, '\\u2221'], [/\\\\sphericalangle /g, '\\u2222'], [/\\\\mid /g, '\\u2223'], [/\\\\nmid /g, '\\u2224'], [/\\\\parallel /g, '\\u2225'], [/\\\\nparallel /g, '\\u2226'], [/\\\\wedge /g, '\\u2227'], [/\\\\vee /g, '\\u2228'], [/\\\\cap /g, '\\u2229'], [/\\\\cup /g, '\\u222A'], [/\\\\int /g, '\\u222B'], [/\\\\int\\\\!\\\\int /g, '\\u222C'], [/\\\\int\\\\!\\\\int\\\\!\\\\int /g, '\\u222D'], [/\\\\oint /g, '\\u222E'], [/\\\\surfintegral /g, '\\u222F'], [/\\\\volintegral /g, '\\u2230'], [/\\\\clwintegral /g, '\\u2231'], [/\\\\ElsevierGlyph\\{2232\\}/g, '\\u2232'], [/\\\\ElsevierGlyph\\{2233\\}/g, '\\u2233'], [/\\\\therefore /g, '\\u2234'], [/\\\\because /g, '\\u2235'], [/\\\\Colon /g, '\\u2237'], [/\\\\ElsevierGlyph\\{2238\\}/g, '\\u2238'], [/\\\\mathbin\\{\\{:\\}\\\\!\\\\!\\{\\-\\}\\\\!\\\\!\\{:\\}\\}/g, '\\u223A'], [/\\\\homothetic /g, '\\u223B'], [/\\\\sim /g, '\\u223C'], [/\\\\backsim /g, '\\u223D'], [/\\\\lazysinv /g, '\\u223E'], [/\\\\wr /g, '\\u2240'], [/\\\\not\\\\sim /g, '\\u2241'], [/\\\\ElsevierGlyph\\{2242\\}/g, '\\u2242'], [/\\\\NotEqualTilde /g, '\\u2242-00338'], [/\\\\simeq /g, '\\u2243'], [/\\\\not\\\\simeq /g, '\\u2244'], [/\\\\cong /g, '\\u2245'], [/\\\\approxnotequal /g, '\\u2246'], [/\\\\not\\\\cong /g, '\\u2247'], [/\\\\approx /g, '\\u2248'], [/\\\\not\\\\approx /g, '\\u2249'], [/\\\\approxeq /g, 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[/\\\\ElsevierGlyph\\{E372\\}/g, '\\u29DC'], [/\\\\blacklozenge /g, '\\u29EB'], [/\\\\RuleDelayed /g, '\\u29F4'], [/\\\\Elxuplus /g, '\\u2A04'], [/\\\\ElzThr /g, '\\u2A05'], [/\\\\Elxsqcup /g, '\\u2A06'], [/\\\\ElzInf /g, '\\u2A07'], [/\\\\ElzSup /g, '\\u2A08'], [/\\\\ElzCint /g, '\\u2A0D'], [/\\\\clockoint /g, '\\u2A0F'], [/\\\\ElsevierGlyph\\{E395\\}/g, '\\u2A10'], [/\\\\sqrint /g, '\\u2A16'], [/\\\\ElsevierGlyph\\{E25A\\}/g, '\\u2A25'], [/\\\\ElsevierGlyph\\{E25B\\}/g, '\\u2A2A'], [/\\\\ElsevierGlyph\\{E25C\\}/g, '\\u2A2D'], [/\\\\ElsevierGlyph\\{E25D\\}/g, '\\u2A2E'], [/\\\\ElzTimes /g, '\\u2A2F'], [/\\\\ElsevierGlyph\\{E25E\\}/g, '\\u2A34'], [/\\\\ElsevierGlyph\\{E25E\\}/g, '\\u2A35'], [/\\\\ElsevierGlyph\\{E259\\}/g, '\\u2A3C'], [/\\\\amalg /g, '\\u2A3F'], [/\\\\ElzAnd /g, '\\u2A53'], [/\\\\ElzOr /g, '\\u2A54'], [/\\\\ElsevierGlyph\\{E36E\\}/g, '\\u2A55'], [/\\\\ElOr /g, '\\u2A56'], [/\\\\perspcorrespond /g, '\\u2A5E'], [/\\\\Elzminhat /g, '\\u2A5F'], [/\\\\ElsevierGlyph\\{225A\\}/g, '\\u2A63'], [/\\\\stackrel\\{*\\}\\{=\\}/g, '\\u2A6E'], [/\\\\Equal /g, '\\u2A75'], [/\\\\leqslant /g, '\\u2A7D'], [/\\\\nleqslant /g, '\\u2A7D-00338'], [/\\\\geqslant /g, '\\u2A7E'], [/\\\\ngeqslant /g, '\\u2A7E-00338'], [/\\\\lessapprox /g, '\\u2A85'], [/\\\\gtrapprox /g, '\\u2A86'], [/\\\\lneq /g, '\\u2A87'], [/\\\\gneq /g, '\\u2A88'], [/\\\\lnapprox /g, '\\u2A89'], [/\\\\gnapprox /g, '\\u2A8A'], [/\\\\lesseqqgtr /g, '\\u2A8B'], [/\\\\gtreqqless /g, '\\u2A8C'], [/\\\\eqslantless /g, '\\u2A95'], [/\\\\eqslantgtr /g, '\\u2A96'], [/\\\\Pisymbol\\{ppi020\\}\\{117\\}/g, '\\u2A9D'], [/\\\\Pisymbol\\{ppi020\\}\\{105\\}/g, '\\u2A9E'], [/\\\\NestedLessLess /g, '\\u2AA1'], [/\\\\NotNestedLessLess /g, '\\u2AA1-00338'], [/\\\\NestedGreaterGreater /g, '\\u2AA2'], [/\\\\NotNestedGreaterGreater /g, '\\u2AA2-00338'], [/\\\\preceq /g, '\\u2AAF'], [/\\\\not\\\\preceq /g, '\\u2AAF-00338'], [/\\\\succeq /g, '\\u2AB0'], [/\\\\not\\\\succeq /g, '\\u2AB0-00338'], [/\\\\precneqq /g, '\\u2AB5'], [/\\\\succneqq /g, '\\u2AB6'], [/\\\\precapprox /g, '\\u2AB7'], [/\\\\succapprox /g, '\\u2AB8'], [/\\\\precnapprox /g, '\\u2AB9'], [/\\\\succnapprox /g, '\\u2ABA'], [/\\\\subseteqq /g, '\\u2AC5'], [/\\\\nsubseteqq /g, '\\u2AC5-00338'], [/\\\\supseteqq /g, '\\u2AC6'], [/\\\\nsupseteqq/g, '\\u2AC6-00338'], [/\\\\subsetneqq /g, '\\u2ACB'], [/\\\\supsetneqq /g, '\\u2ACC'], [/\\\\ElsevierGlyph\\{E30D\\}/g, '\\u2AEB'], [/\\\\Elztdcol /g, '\\u2AF6'], [/\\\\ElsevierGlyph\\{300A\\}/g, '\\u300A'], [/\\\\ElsevierGlyph\\{300B\\}/g, '\\u300B'], [/\\\\ElsevierGlyph\\{3018\\}/g, '\\u3018'], [/\\\\ElsevierGlyph\\{3019\\}/g, '\\u3019'], [/\\\\openbracketleft /g, '\\u301A'], [/\\\\openbracketright /g, '\\u301B']];\n\t\n\t return this;\n\t} // end function BibtexParser\n\t\n\tif (typeof module !== 'undefined' && module.exports) {\n\t module.exports = BibtexParser;\n\t}\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) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(6), __webpack_require__(20), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (baseMVC, citationModel, _l) {\n\t\n\t var CitationView = Backbone.View.extend({\n\t tagName: 'div',\n\t className: 'citations',\n\t render: function () {\n\t this.$el.append(\"\" + this.formattedReference() + \"
\");\n\t return this;\n\t },\n\t formattedReference: function () {\n\t var model = this.model;\n\t var entryType = model.entryType();\n\t var fields = model.fields();\n\t\n\t var ref = \"\";\n\t // Code inspired by...\n\t // https://github.com/vkaravir/bib-publication-list/blob/master/src/bib-publication-list.js\n\t var authorsAndYear = this._asSentence((fields.author ? fields.author : \"\") + (fields.year ? \" (\" + fields.year + \")\" : \"\")) + \" \";\n\t var title = fields.title || \"\";\n\t var pages = fields.pages ? \"pp. \" + fields.pages : \"\";\n\t var address = fields.address;\n\t if (entryType == \"article\") {\n\t var volume = (fields.volume ? fields.volume : \"\") + (fields.number ? \" (\" + fields.number + \")\" : \"\") + (pages ? \", \" + pages : \"\");\n\t ref = authorsAndYear + this._asSentence(title) + (fields.journal ? \"In \" + fields.journal + \", \" : \"\") + this._asSentence(volume) + this._asSentence(fields.address) + \"<\\/em>\";\n\t } else if (entryType == \"inproceedings\" || entryType == \"proceedings\") {\n\t ref = authorsAndYear + this._asSentence(title) + (fields.booktitle ? \"In \" + fields.booktitle + \", \" : \"\") + (pages ? pages : \"\") + (address ? \", \" + address : \"\") + \".<\\/em>\";\n\t } else if (entryType == \"mastersthesis\" || entryType == \"phdthesis\") {\n\t ref = authorsAndYear + this._asSentence(title) + (fields.howpublished ? fields.howpublished + \". \" : \"\") + (fields.note ? fields.note + \".\" : \"\");\n\t } else if (entryType == \"techreport\") {\n\t ref = authorsAndYear + this._asSentence(title) + this._asSentence(fields.institution) + this._asSentence(fields.number) + this._asSentence(fields.type);\n\t } else if (entryType == \"book\" || entryType == \"inbook\" || entryType == \"incollection\") {\n\t ref = authorsAndYear + \" \" + this._formatBookInfo(fields);\n\t } else {\n\t ref = authorsAndYear + \" \" + this._asSentence(title) + this._asSentence(fields.howpublished) + this._asSentence(fields.note);\n\t }\n\t var doiUrl = \"\";\n\t if (fields.doi) {\n\t doiUrl = 'http://dx.doi.org/' + fields.doi;\n\t ref += '[doi:' + fields.doi + \" ]\";\n\t }\n\t var url = fields.url || doiUrl;\n\t if (url) {\n\t ref += '[Link ]';\n\t }\n\t return ref;\n\t },\n\t _formatBookInfo: function (fields) {\n\t var info = \"\";\n\t if (fields.chapter) {\n\t info += fields.chapter + \" in \";\n\t }\n\t if (fields.title) {\n\t info += \"\" + fields.title + \"<\\/em>\";\n\t }\n\t if (fields.editor) {\n\t info += \", Edited by \" + fields.editor + \", \";\n\t }\n\t if (fields.publisher) {\n\t info += \", \" + fields.publisher;\n\t }\n\t if (fields.pages) {\n\t info += \", pp. \" + fields.pages + \"\";\n\t }\n\t if (fields.series) {\n\t info += \", \" + fields.series + \"<\\/em>\";\n\t }\n\t if (fields.volume) {\n\t info += \", Vol.\" + fields.volume;\n\t }\n\t if (fields.issn) {\n\t info += \", ISBN: \" + fields.issn;\n\t }\n\t return info + \".\";\n\t },\n\t _asSentence: function (str) {\n\t return str && str.trim() ? str + \". \" : \"\";\n\t }\n\t });\n\t\n\t var CitationListView = Backbone.View.extend({\n\t el: '#citations',\n\t /**\n\t * Set up view.\n\t */\n\t initialize: function () {\n\t this.listenTo(this.collection, 'add', this.renderCitation);\n\t },\n\t\n\t events: {\n\t 'click .citations-to-bibtex': 'showBibtex',\n\t 'click .citations-to-formatted': 'showFormatted'\n\t },\n\t\n\t renderCitation: function (citation) {\n\t var citationView = new CitationView({ model: citation });\n\t this.$(\".citations-formatted\").append(citationView.render().el);\n\t var rawTextarea = this.$(\".citations-bibtex-text\");\n\t rawTextarea.val(rawTextarea.val() + \"\\n\\r\" + citation.attributes.content);\n\t },\n\t\n\t render: function () {\n\t this.$el.html(this.citationsElement());\n\t this.collection.each(function (item) {\n\t this.renderCitation(item);\n\t }, this);\n\t this.showFormatted();\n\t },\n\t\n\t showBibtex: function () {\n\t this.$(\".citations-to-formatted\").show();\n\t this.$(\".citations-to-bibtex\").hide();\n\t this.$(\".citations-bibtex\").show();\n\t this.$(\".citations-formatted\").hide();\n\t this.$(\".citations-bibtex-text\").select();\n\t },\n\t\n\t showFormatted: function () {\n\t this.$(\".citations-to-formatted\").hide();\n\t this.$(\".citations-to-bibtex\").show();\n\t this.$(\".citations-bibtex\").hide();\n\t this.$(\".citations-formatted\").show();\n\t },\n\t\n\t partialWarningElement: function () {\n\t if (this.collection.partial) {\n\t return ['', '
Warning: This is a experimental feature. Most Galaxy tools will not annotate', ' citations explicitly at this time. When writing up your analysis, please manually', ' review your histories and find all references', ' that should be cited in order to completely describe your work. Also, please remember to', '
cite Galaxy .', '
', _l('There was an error getting the data for this collection'), ': <%- model.error %>', '
', '<% } %>']),\n\t purged: BASE_MVC.wrapTemplate(['<% if( model.purged ){ %>', '', _l('This collection has been deleted and removed from disk'), '
', '<% } %>']),\n\t deleted: BASE_MVC.wrapTemplate([\n\t // deleted not purged\n\t '<% if( model.deleted && !model.purged ){ %>', '', _l('This collection has been deleted'), '
', '<% } %>'])\n\t });\n\t\n\t // use element identifier\n\t var titleBarTemplate = BASE_MVC.wrapTemplate(['', '
', '<%- collection.element_identifier || collection.name %> ', '
', '
', '
', '<% var countText = collection.element_count? ( collection.element_count + \" \" ) : \"\"; %>', '<% if( collection.collection_type === \"list\" ){ %>', _l('a list of <%- countText %>datasets'), '<% } else if( collection.collection_type === \"paired\" ){ %>', _l('a pair of datasets'), '<% } else if( collection.collection_type === \"list:paired\" ){ %>', _l('a list of <%- countText %>dataset pairs'), '<% } else if( collection.collection_type === \"list:list\" ){ %>', _l('a list of <%- countText %>dataset lists'), '<% } %>', '
'], 'collection');\n\t\n\t return _.extend({}, FoldoutListItemView.prototype.templates, {\n\t warnings: warnings,\n\t titleBar: titleBarTemplate,\n\t subtitle: subtitleTemplate\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t /** @class Read only view for DatasetCollectionElement.\n\t */\n\t var DCEListItemView = ListItemView.extend(\n\t /** @lends DCEListItemView.prototype */{\n\t\n\t /** add the DCE class to the list item */\n\t className: ListItemView.prototype.className + \" dataset-collection-element\",\n\t\n\t /** set up */\n\t initialize: function (attributes) {\n\t if (attributes.logger) {\n\t this.logger = this.model.logger = attributes.logger;\n\t }\n\t this.log('DCEListItemView.initialize:', attributes);\n\t ListItemView.prototype.initialize.call(this, attributes);\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'DCEListItemView(' + modelString + ')';\n\t }\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t DCEListItemView.prototype.templates = function () {\n\t\n\t // use the element identifier here - since that will persist and the user will need it\n\t var titleBarTemplate = BASE_MVC.wrapTemplate(['', '
', '<%- element.element_identifier %> ', '
', '
', '
', '
', '
', '<%- element.element_identifier %> ', '
', '
', '<%- element.name %>', ' ', '', _l('Discard'), ' '].join('')),\n\t\n\t /** select this element and pub */\n\t select: function (toggle) {\n\t this.$el.toggleClass('selected', toggle);\n\t this.trigger('select', {\n\t source: this,\n\t selected: this.$el.hasClass('selected')\n\t });\n\t },\n\t\n\t /** animate the removal of this element and pub */\n\t discard: function () {\n\t var view = this,\n\t parentWidth = this.$el.parent().width();\n\t this.$el.animate({ 'margin-right': parentWidth }, 'fast', function () {\n\t view.trigger('discard', {\n\t source: view\n\t });\n\t view.destroy();\n\t });\n\t },\n\t\n\t /** remove the DOM and any listeners */\n\t destroy: function () {\n\t this.off();\n\t this.$el.remove();\n\t },\n\t\n\t events: {\n\t 'click': '_click',\n\t 'click .name': '_clickName',\n\t 'click .discard': '_clickDiscard',\n\t\n\t 'dragstart': '_dragstart',\n\t 'dragend': '_dragend',\n\t 'dragover': '_sendToParent',\n\t 'drop': '_sendToParent'\n\t },\n\t\n\t /** select when the li is clicked */\n\t _click: function (ev) {\n\t ev.stopPropagation();\n\t this.select(ev);\n\t },\n\t\n\t /** rename a pair when the name is clicked */\n\t _clickName: function (ev) {\n\t ev.stopPropagation();\n\t ev.preventDefault();\n\t var promptString = [_l('Enter a new name for the element'), ':\\n(', _l('Note that changing the name here will not rename the dataset'), ')'].join(''),\n\t response = prompt(_l('Enter a new name for the element') + ':', this.element.name);\n\t if (response) {\n\t this.element.name = response;\n\t this.render();\n\t }\n\t //TODO: cancelling with ESC leads to closure of the creator...\n\t },\n\t\n\t /** discard when the discard button is clicked */\n\t _clickDiscard: function (ev) {\n\t ev.stopPropagation();\n\t this.discard();\n\t },\n\t\n\t /** dragging pairs for re-ordering */\n\t _dragstart: function (ev) {\n\t if (ev.originalEvent) {\n\t ev = ev.originalEvent;\n\t }\n\t ev.dataTransfer.effectAllowed = 'move';\n\t ev.dataTransfer.setData('text/plain', JSON.stringify(this.element));\n\t\n\t this.$el.addClass('dragging');\n\t this.$el.parent().trigger('collection-element.dragstart', [this]);\n\t },\n\t\n\t /** dragging for re-ordering */\n\t _dragend: function (ev) {\n\t this.$el.removeClass('dragging');\n\t this.$el.parent().trigger('collection-element.dragend', [this]);\n\t },\n\t\n\t /** manually bubble up an event to the parent/container */\n\t _sendToParent: function (ev) {\n\t this.$el.parent().trigger(ev);\n\t },\n\t\n\t /** string rep */\n\t toString: function () {\n\t return 'DatasetCollectionElementView()';\n\t }\n\t });\n\t\n\t // ============================================================================\n\t /** An interface for building collections.\n\t */\n\t var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin).extend(baseCreator.CollectionCreatorMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t /** the class used to display individual elements */\n\t elementViewClass: DatasetCollectionElementView,\n\t /** the class this creator will create and save */\n\t collectionClass: HDCA.HistoryListDatasetCollection,\n\t className: 'list-collection-creator collection-creator flex-row-container',\n\t\n\t /** minimum number of valid elements to start with in order to build a collection of this type */\n\t minElements: 1,\n\t\n\t defaultAttributes: {\n\t //TODO: remove - use new collectionClass().save()\n\t /** takes elements and creates the proper collection - returns a promise */\n\t creationFn: function () {\n\t throw new TypeError('no creation fn for creator');\n\t },\n\t /** fn to call when the collection is created (scoped to this) */\n\t oncreate: function () {},\n\t /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */\n\t oncancel: function () {},\n\t /** distance from list edge to begin autoscrolling list */\n\t autoscrollDist: 24,\n\t /** Color passed to hoverhighlight */\n\t highlightClr: 'rgba( 64, 255, 255, 1.0 )'\n\t },\n\t\n\t footerSettings: {\n\t '.hide-originals': 'hideOriginals'\n\t },\n\t\n\t /** set up initial options, instance vars, behaviors */\n\t initialize: function (attributes) {\n\t this.metric('ListCollectionCreator.initialize', attributes);\n\t var creator = this;\n\t _.each(this.defaultAttributes, function (value, key) {\n\t value = attributes[key] || value;\n\t creator[key] = value;\n\t });\n\t\n\t /** unordered, original list - cache to allow reversal */\n\t creator.initialElements = attributes.elements || [];\n\t\n\t this._setUpCommonSettings(attributes);\n\t this._instanceSetUp();\n\t this._elementsSetUp();\n\t this._setUpBehaviors();\n\t },\n\t\n\t /** set up instance vars */\n\t _instanceSetUp: function () {\n\t /** Ids of elements that have been selected by the user - to preserve over renders */\n\t this.selectedIds = {};\n\t /** DOM elements currently being dragged */\n\t this.$dragging = null;\n\t /** Used for blocking UI events during ajax/operations (don't post twice) */\n\t this.blocking = false;\n\t },\n\t\n\t // ------------------------------------------------------------------------ process raw list\n\t /** set up main data */\n\t _elementsSetUp: function () {\n\t //this.debug( '-- _dataSetUp' );\n\t /** a list of invalid elements and the reasons they aren't valid */\n\t this.invalidElements = [];\n\t //TODO: handle fundamental problem of syncing DOM, views, and list here\n\t /** data for list in progress */\n\t this.workingElements = [];\n\t /** views for workingElements */\n\t this.elementViews = [];\n\t\n\t // copy initial list, sort, add ids if needed\n\t this.workingElements = this.initialElements.slice(0);\n\t this._ensureElementIds();\n\t this._validateElements();\n\t this._mangleDuplicateNames();\n\t this._sortElements();\n\t },\n\t\n\t /** add ids to dataset objs in initial list if none */\n\t _ensureElementIds: function () {\n\t this.workingElements.forEach(function (element) {\n\t if (!element.hasOwnProperty('id')) {\n\t element.id = _.uniqueId();\n\t }\n\t });\n\t return this.workingElements;\n\t },\n\t\n\t /** separate working list into valid and invalid elements for this collection */\n\t _validateElements: function () {\n\t var creator = this,\n\t existingNames = {};\n\t creator.invalidElements = [];\n\t\n\t this.workingElements = this.workingElements.filter(function (element) {\n\t var problem = creator._isElementInvalid(element);\n\t if (problem) {\n\t creator.invalidElements.push({\n\t element: element,\n\t text: problem\n\t });\n\t }\n\t return !problem;\n\t });\n\t return this.workingElements;\n\t },\n\t\n\t /** describe what is wrong with a particular element if anything */\n\t _isElementInvalid: function (element) {\n\t if (element.history_content_type !== 'dataset') {\n\t return _l(\"is not a dataset\");\n\t }\n\t var validState = element.state === STATES.OK || _.contains(STATES.NOT_READY_STATES, element.state);\n\t if (!validState) {\n\t return _l(\"has errored, is paused, or is not accessible\");\n\t }\n\t if (element.deleted || element.purged) {\n\t return _l(\"has been deleted or purged\");\n\t }\n\t return null;\n\t },\n\t\n\t /** mangle duplicate names using a mac-like '(counter)' addition to any duplicates */\n\t _mangleDuplicateNames: function () {\n\t var SAFETY = 900,\n\t counter = 1,\n\t existingNames = {};\n\t this.workingElements.forEach(function (element) {\n\t var currName = element.name;\n\t while (existingNames.hasOwnProperty(currName)) {\n\t currName = element.name + ' (' + counter + ')';\n\t counter += 1;\n\t if (counter >= SAFETY) {\n\t throw new Error('Safety hit in while loop - thats impressive');\n\t }\n\t }\n\t element.name = currName;\n\t existingNames[element.name] = true;\n\t });\n\t },\n\t\n\t /** sort a list of elements */\n\t _sortElements: function (list) {\n\t // // currently only natural sort by name\n\t // this.workingElements.sort( function( a, b ){ return naturalSort( a.name, b.name ); });\n\t // return this.workingElements;\n\t },\n\t\n\t // ------------------------------------------------------------------------ rendering\n\t // templates : ListCollectionCreator.templates,\n\t /** render the entire interface */\n\t render: function (speed, callback) {\n\t //this.debug( '-- _render' );\n\t if (this.workingElements.length < this.minElements) {\n\t return this._renderInvalid(speed, callback);\n\t }\n\t\n\t this.$el.empty().html(this.templates.main());\n\t this._renderHeader(speed);\n\t this._renderMiddle(speed);\n\t this._renderFooter(speed);\n\t this._addPluginComponents();\n\t this.$('.collection-name').focus();\n\t this.trigger('rendered', this);\n\t return this;\n\t },\n\t\n\t /** render a simplified interface aimed at telling the user why they can't move forward */\n\t _renderInvalid: function (speed, callback) {\n\t //this.debug( '-- _render' );\n\t this.$el.empty().html(this.templates.invalidInitial({\n\t problems: this.invalidElements,\n\t elements: this.workingElements\n\t }));\n\t if (typeof this.oncancel === 'function') {\n\t this.$('.cancel-create.btn').show();\n\t }\n\t this.trigger('rendered', this);\n\t return this;\n\t },\n\t\n\t /** render the header section */\n\t _renderHeader: function (speed, callback) {\n\t var $header = this.$('.header').empty().html(this.templates.header()).find('.help-content').prepend($(this.templates.helpContent()));\n\t //TODO: should only show once despite calling _renderHeader again\n\t if (this.invalidElements.length) {\n\t this._invalidElementsAlert();\n\t }\n\t return $header;\n\t },\n\t\n\t /** render the middle including the elements */\n\t _renderMiddle: function (speed, callback) {\n\t var $middle = this.$('.middle').empty().html(this.templates.middle());\n\t this._renderList(speed);\n\t return $middle;\n\t },\n\t\n\t /** add any jQuery/bootstrap/custom plugins to elements rendered */\n\t _addPluginComponents: function () {\n\t this.$('.help-content i').hoverhighlight('.collection-creator', this.highlightClr);\n\t },\n\t\n\t /** build and show an alert describing any elements that could not be included due to problems */\n\t _invalidElementsAlert: function () {\n\t this._showAlert(this.templates.invalidElements({ problems: this.invalidElements }), 'alert-warning');\n\t },\n\t\n\t _disableNameAndCreate: function (disable) {\n\t disable = !_.isUndefined(disable) ? disable : true;\n\t if (disable) {\n\t this.$('.collection-name').prop('disabled', true);\n\t this.$('.create-collection').toggleClass('disabled', true);\n\t // } else {\n\t // this.$( '.collection-name' ).prop( 'disabled', false );\n\t // this.$( '.create-collection' ).removeClass( 'disable' );\n\t }\n\t },\n\t\n\t // ------------------------------------------------------------------------ rendering elements\n\t /** conv. to the main list display DOM */\n\t $list: function () {\n\t return this.$('.collection-elements');\n\t },\n\t\n\t /** show or hide the clear selected control based on the num of selected elements */\n\t _renderClearSelected: function () {\n\t if (_.size(this.selectedIds)) {\n\t this.$('.collection-elements-controls > .clear-selected').show();\n\t } else {\n\t this.$('.collection-elements-controls > .clear-selected').hide();\n\t }\n\t },\n\t\n\t /** render the elements in order (or a warning if no elements found) */\n\t _renderList: function (speed, callback) {\n\t //this.debug( '-- _renderList' );\n\t var creator = this,\n\t $tmp = jQuery('
'),\n\t $list = creator.$list();\n\t\n\t _.each(this.elementViews, function (view) {\n\t view.destroy();\n\t creator.removeElementView(view);\n\t });\n\t\n\t // if( !this.workingElements.length ){\n\t // this._renderNoValidElements();\n\t // return;\n\t // }\n\t\n\t creator.workingElements.forEach(function (element) {\n\t var elementView = creator._createElementView(element);\n\t $tmp.append(elementView.$el);\n\t });\n\t\n\t creator._renderClearSelected();\n\t $list.empty().append($tmp.children());\n\t _.invoke(creator.elementViews, 'render');\n\t\n\t if ($list.height() > $list.css('max-height')) {\n\t $list.css('border-width', '1px 0px 1px 0px');\n\t } else {\n\t $list.css('border-width', '0px');\n\t }\n\t },\n\t\n\t /** create an element view, cache in elementViews, set up listeners, and return */\n\t _createElementView: function (element) {\n\t var elementView = new this.elementViewClass({\n\t //TODO: use non-generic class or not all\n\t // model : COLLECTION.DatasetDCE( element )\n\t element: element,\n\t selected: _.has(this.selectedIds, element.id)\n\t });\n\t this.elementViews.push(elementView);\n\t this._listenToElementView(elementView);\n\t return elementView;\n\t },\n\t\n\t /** listen to any element events */\n\t _listenToElementView: function (view) {\n\t var creator = this;\n\t creator.listenTo(view, {\n\t select: function (data) {\n\t var element = data.source.element;\n\t if (data.selected) {\n\t creator.selectedIds[element.id] = true;\n\t } else {\n\t delete creator.selectedIds[element.id];\n\t }\n\t creator.trigger('elements:select', data);\n\t },\n\t discard: function (data) {\n\t creator.trigger('elements:discard', data);\n\t }\n\t });\n\t },\n\t\n\t /** add a new element view based on the json in element */\n\t addElementView: function (element) {\n\t //TODO: workingElements is sorted, add element in appropo index\n\t // add element, sort elements, find element index\n\t // var view = this._createElementView( element );\n\t // return view;\n\t },\n\t\n\t /** stop listening to view and remove from caches */\n\t removeElementView: function (view) {\n\t delete this.selectedIds[view.element.id];\n\t this._renderClearSelected();\n\t\n\t this.elementViews = _.without(this.elementViews, view);\n\t this.stopListening(view);\n\t },\n\t\n\t /** render a message in the list that no elements remain to create a collection */\n\t _renderNoElementsLeft: function () {\n\t this._disableNameAndCreate(true);\n\t this.$('.collection-elements').append(this.templates.noElementsLeft());\n\t },\n\t\n\t // /** render a message in the list that no valid elements were found to create a collection */\n\t // _renderNoValidElements : function(){\n\t // this._disableNameAndCreate( true );\n\t // this.$( '.collection-elements' ).append( this.templates.noValidElements() );\n\t // },\n\t\n\t // ------------------------------------------------------------------------ API\n\t /** convert element into JSON compatible with the collections API */\n\t _elementToJSON: function (element) {\n\t // return element.toJSON();\n\t return element;\n\t },\n\t\n\t /** create the collection via the API\n\t * @returns {jQuery.xhr Object} the jquery ajax request\n\t */\n\t createList: function (name) {\n\t if (!this.workingElements.length) {\n\t var message = _l('No valid elements for final list') + '. ';\n\t message += '' + _l('Cancel') + ' ';\n\t message += _l('or');\n\t message += ' ' + _l('start over') + ' .';\n\t this._showAlert(message);\n\t return;\n\t }\n\t\n\t var creator = this,\n\t elements = this.workingElements.map(function (element) {\n\t return creator._elementToJSON(element);\n\t });\n\t\n\t creator.blocking = true;\n\t return creator.creationFn(elements, name, creator.hideOriginals).always(function () {\n\t creator.blocking = false;\n\t }).fail(function (xhr, status, message) {\n\t creator.trigger('error', {\n\t xhr: xhr,\n\t status: status,\n\t message: _l('An error occurred while creating this collection')\n\t });\n\t }).done(function (response, message, xhr) {\n\t creator.trigger('collection:created', response, message, xhr);\n\t creator.metric('collection:created', response);\n\t if (typeof creator.oncreate === 'function') {\n\t creator.oncreate.call(this, response, message, xhr);\n\t }\n\t });\n\t },\n\t\n\t // ------------------------------------------------------------------------ events\n\t /** set up event handlers on self */\n\t _setUpBehaviors: function () {\n\t this.on('error', this._errorHandler);\n\t\n\t this.once('rendered', function () {\n\t this.trigger('rendered:initial', this);\n\t });\n\t\n\t this.on('elements:select', function (data) {\n\t this._renderClearSelected();\n\t });\n\t\n\t this.on('elements:discard', function (data) {\n\t var element = data.source.element;\n\t this.removeElementView(data.source);\n\t\n\t this.workingElements = _.without(this.workingElements, element);\n\t if (!this.workingElements.length) {\n\t this._renderNoElementsLeft();\n\t }\n\t });\n\t\n\t //this.on( 'all', function(){\n\t // this.info( arguments );\n\t //});\n\t return this;\n\t },\n\t\n\t /** handle errors with feedback and details to the user (if available) */\n\t _errorHandler: function (data) {\n\t this.error(data);\n\t\n\t var creator = this;\n\t content = data.message || _l('An error occurred');\n\t if (data.xhr) {\n\t var xhr = data.xhr,\n\t message = data.message;\n\t if (xhr.readyState === 0 && xhr.status === 0) {\n\t content += ': ' + _l('Galaxy could not be reached and may be updating.') + _l(' Try again in a few minutes.');\n\t } else if (xhr.responseJSON) {\n\t content += ':' + JSON.stringify(xhr.responseJSON) + ' ';\n\t } else {\n\t content += ': ' + message;\n\t }\n\t }\n\t creator._showAlert(content, 'alert-danger');\n\t },\n\t\n\t events: {\n\t // header\n\t 'click .more-help': '_clickMoreHelp',\n\t 'click .less-help': '_clickLessHelp',\n\t 'click .main-help': '_toggleHelp',\n\t 'click .header .alert button': '_hideAlert',\n\t\n\t 'click .reset': 'reset',\n\t 'click .clear-selected': 'clearSelectedElements',\n\t\n\t // elements - selection\n\t 'click .collection-elements': 'clearSelectedElements',\n\t\n\t // elements - drop target\n\t // 'dragenter .collection-elements': '_dragenterElements',\n\t // 'dragleave .collection-elements': '_dragleaveElements',\n\t 'dragover .collection-elements': '_dragoverElements',\n\t 'drop .collection-elements': '_dropElements',\n\t\n\t // these bubble up from the elements as custom events\n\t 'collection-element.dragstart .collection-elements': '_elementDragstart',\n\t 'collection-element.dragend .collection-elements': '_elementDragend',\n\t\n\t // footer\n\t 'change .collection-name': '_changeName',\n\t 'keydown .collection-name': '_nameCheckForEnter',\n\t 'change .hide-originals': '_changeHideOriginals',\n\t 'click .cancel-create': '_cancelCreate',\n\t 'click .create-collection': '_clickCreate' //,\n\t },\n\t\n\t // ........................................................................ elements\n\t /** reset all data to the initial state */\n\t reset: function () {\n\t this._instanceSetUp();\n\t this._elementsSetUp();\n\t this.render();\n\t },\n\t\n\t /** deselect all elements */\n\t clearSelectedElements: function (ev) {\n\t this.$('.collection-elements .collection-element').removeClass('selected');\n\t this.$('.collection-elements-controls > .clear-selected').hide();\n\t },\n\t\n\t //_dragenterElements : function( ev ){\n\t // //this.debug( '_dragenterElements:', ev );\n\t //},\n\t //TODO: if selected are dragged out of the list area - remove the placeholder - cuz it won't work anyway\n\t // _dragleaveElements : function( ev ){\n\t // //this.debug( '_dragleaveElements:', ev );\n\t // },\n\t\n\t /** track the mouse drag over the list adding a placeholder to show where the drop would occur */\n\t _dragoverElements: function (ev) {\n\t //this.debug( '_dragoverElements:', ev );\n\t ev.preventDefault();\n\t\n\t var $list = this.$list();\n\t this._checkForAutoscroll($list, ev.originalEvent.clientY);\n\t var $nearest = this._getNearestElement(ev.originalEvent.clientY);\n\t\n\t //TODO: no need to re-create - move instead\n\t this.$('.element-drop-placeholder').remove();\n\t var $placeholder = $('
');\n\t if (!$nearest.length) {\n\t $list.append($placeholder);\n\t } else {\n\t $nearest.before($placeholder);\n\t }\n\t },\n\t\n\t /** If the mouse is near enough to the list's top or bottom, scroll the list */\n\t _checkForAutoscroll: function ($element, y) {\n\t var AUTOSCROLL_SPEED = 2,\n\t offset = $element.offset(),\n\t scrollTop = $element.scrollTop(),\n\t upperDist = y - offset.top,\n\t lowerDist = offset.top + $element.outerHeight() - y;\n\t if (upperDist >= 0 && upperDist < this.autoscrollDist) {\n\t $element.scrollTop(scrollTop - AUTOSCROLL_SPEED);\n\t } else if (lowerDist >= 0 && lowerDist < this.autoscrollDist) {\n\t $element.scrollTop(scrollTop + AUTOSCROLL_SPEED);\n\t }\n\t },\n\t\n\t /** get the nearest element based on the mouse's Y coordinate.\n\t * If the y is at the end of the list, return an empty jQuery object.\n\t */\n\t _getNearestElement: function (y) {\n\t var WIGGLE = 4,\n\t lis = this.$('.collection-elements li.collection-element').toArray();\n\t for (var i = 0; i < lis.length; i++) {\n\t var $li = $(lis[i]),\n\t top = $li.offset().top,\n\t halfHeight = Math.floor($li.outerHeight() / 2) + WIGGLE;\n\t if (top + halfHeight > y && top - halfHeight < y) {\n\t return $li;\n\t }\n\t }\n\t return $();\n\t },\n\t\n\t /** drop (dragged/selected elements) onto the list, re-ordering the internal list */\n\t _dropElements: function (ev) {\n\t if (ev.originalEvent) {\n\t ev = ev.originalEvent;\n\t }\n\t // both required for firefox\n\t ev.preventDefault();\n\t ev.dataTransfer.dropEffect = 'move';\n\t\n\t // insert before the nearest element or after the last.\n\t var $nearest = this._getNearestElement(ev.clientY);\n\t if ($nearest.length) {\n\t this.$dragging.insertBefore($nearest);\n\t } else {\n\t // no nearest before - insert after last element\n\t this.$dragging.insertAfter(this.$('.collection-elements .collection-element').last());\n\t }\n\t // resync the creator's list based on the new DOM order\n\t this._syncOrderToDom();\n\t return false;\n\t },\n\t\n\t /** resync the creator's list of elements based on the DOM order */\n\t _syncOrderToDom: function () {\n\t var creator = this,\n\t newElements = [];\n\t //TODO: doesn't seem wise to use the dom to store these - can't we sync another way?\n\t this.$('.collection-elements .collection-element').each(function () {\n\t var id = $(this).attr('data-element-id'),\n\t element = _.findWhere(creator.workingElements, { id: id });\n\t if (element) {\n\t newElements.push(element);\n\t } else {\n\t console.error('missing element: ', id);\n\t }\n\t });\n\t this.workingElements = newElements;\n\t this._renderList();\n\t },\n\t\n\t /** drag communication with element sub-views: dragstart */\n\t _elementDragstart: function (ev, element) {\n\t // auto select the element causing the event and move all selected\n\t element.select(true);\n\t this.$dragging = this.$('.collection-elements .collection-element.selected');\n\t },\n\t\n\t /** drag communication with element sub-views: dragend - remove the placeholder */\n\t _elementDragend: function (ev, element) {\n\t $('.element-drop-placeholder').remove();\n\t this.$dragging = null;\n\t },\n\t\n\t // ------------------------------------------------------------------------ templates\n\t //TODO: move to require text plugin and load these as text\n\t //TODO: underscore currently unnecc. bc no vars are used\n\t //TODO: better way of localizing text-nodes in long strings\n\t /** underscore template fns attached to class */\n\t templates: _.extend({}, baseCreator.CollectionCreatorMixin._creatorTemplates, {\n\t\n\t /** the header (not including help text) */\n\t header: _.template(['', '', '× ', '
'].join('')),\n\t\n\t /** the middle: element list */\n\t middle: _.template(['', '', '
'].join('')),\n\t\n\t /** creation and cancel controls */\n\t footer: _.template(['', '
', '', _l('Hide original elements'), '?', ' ', '
', '
', '
', '
', _l('Name'), ':
', '
', '
', '
', '
', _l('Cancel'), ' ', '
', '', _l('Create a different kind of collection'), ' ', '', '
', '
', '
', '', _l('Create list'), ' ', '
', '
', _l(['Collections of datasets are permanent, ordered lists of datasets that can be passed to tools and ', 'workflows in order to have analyses done on each member of the entire group. This interface allows ', 'you to create a collection and re-order the final collection.'].join('')), '
', '', '', _l(['Rename elements in the list by clicking on ', 'the existing name .'].join('')), ' ', '', _l(['Discard elements from the final created list by clicking on the ', '\"Discard\" button.'].join('')), ' ', '', _l(['Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ', 'them and you can then move those selected by dragging the ', 'entire group. Deselect them by clicking them again or by clicking the ', 'the \"Clear selected\" link.'].join('')), ' ', '', _l(['Click the \"Start over\" link to begin again as if you had just opened ', 'the interface.'].join('')), ' ', '', _l(['Click the \"Cancel\" button to exit the interface.'].join('')), ' ', ' ', _l(['Once your collection is complete, enter a name and ', 'click \"Create list\" .'].join('')), '
'].join('')),\n\t\n\t /** shown in list when all elements are discarded */\n\t invalidElements: _.template([_l('The following selections could not be included due to problems:'), '<% _.each( problems, function( problem ){ %>', '<%- problem.element.name %> : <%- problem.text %> '].join('')),\n\t\n\t /** shown in list when all elements are discarded */\n\t noElementsLeft: _.template(['', _l('No elements left! '), _l('Would you like to '), '', _l('start over'), ' ?', ' '].join('')),\n\t\n\t /** a simplified page communicating what went wrong and why the user needs to reselect something else */\n\t invalidInitial: _.template(['', ''].join(''))\n\t }),\n\t\n\t // ------------------------------------------------------------------------ misc\n\t /** string rep */\n\t toString: function () {\n\t return 'ListCollectionCreator';\n\t }\n\t });\n\t\n\t //=============================================================================\n\t /** Create a modal and load its body with the given CreatorClass creator type\n\t * @returns {Deferred} resolved when creator has built a collection.\n\t */\n\t var collectionCreatorModal = function _collectionCreatorModal(elements, options, CreatorClass) {\n\t\n\t var deferred = jQuery.Deferred(),\n\t modal = Galaxy.modal || new UI_MODAL.View(),\n\t creator;\n\t\n\t options = _.defaults(options || {}, {\n\t elements: elements,\n\t oncancel: function () {\n\t modal.hide();\n\t deferred.reject('cancelled');\n\t },\n\t oncreate: function (creator, response) {\n\t modal.hide();\n\t deferred.resolve(response);\n\t }\n\t });\n\t\n\t creator = new CreatorClass(options);\n\t modal.show({\n\t title: options.title || _l('Create a collection'),\n\t body: creator.$el,\n\t width: '80%',\n\t height: '100%',\n\t closing_events: true\n\t });\n\t creator.render();\n\t window._collectionCreator = creator;\n\t\n\t //TODO: remove modal header\n\t return deferred;\n\t };\n\t\n\t /** List collection flavor of collectionCreatorModal. */\n\t var listCollectionCreatorModal = function _listCollectionCreatorModal(elements, options) {\n\t options = options || {};\n\t options.title = _l('Create a collection from a list of datasets');\n\t return collectionCreatorModal(elements, options, ListCollectionCreator);\n\t };\n\t\n\t //==============================================================================\n\t /** Use a modal to create a list collection, then add it to the given history contents.\n\t * @returns {Deferred} resolved when the collection is added to the history.\n\t */\n\t function createListCollection(contents, defaultHideSourceItems) {\n\t var elements = contents.toJSON(),\n\t promise = listCollectionCreatorModal(elements, {\n\t defaultHideSourceItems: defaultHideSourceItems,\n\t creationFn: function (elements, name, hideSourceItems) {\n\t elements = elements.map(function (element) {\n\t return {\n\t id: element.id,\n\t name: element.name,\n\t //TODO: this allows for list:list even if the filter above does not - reconcile\n\t src: element.history_content_type === 'dataset' ? 'hda' : 'hdca'\n\t };\n\t });\n\t return contents.createHDCA(elements, 'list', name, hideSourceItems);\n\t }\n\t });\n\t return promise;\n\t }\n\t\n\t //==============================================================================\n\t return {\n\t DatasetCollectionElementView: DatasetCollectionElementView,\n\t ListCollectionCreator: ListCollectionCreator,\n\t\n\t collectionCreatorModal: collectionCreatorModal,\n\t listCollectionCreatorModal: listCollectionCreatorModal,\n\t createListCollection: createListCollection\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__(3), __webpack_require__(2), __webpack_require__(1), __webpack_require__(1)))\n\n/***/ },\n/* 43 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_, jQuery, Backbone, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(54), __webpack_require__(11), __webpack_require__(18), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (LIST_ITEM, STATES, faIconButton, BASE_MVC, _l) {\n\t 'use strict';\n\t\n\t var logNamespace = 'dataset';\n\t /*==============================================================================\n\t TODO:\n\t straighten out state rendering and templates used\n\t inaccessible/STATES.NOT_VIEWABLE is a special case\n\t simplify button rendering\n\t \n\t ==============================================================================*/\n\t var _super = LIST_ITEM.ListItemView;\n\t /** @class Read only list view for either LDDAs, HDAs, or HDADCEs.\n\t * Roughly, any DatasetInstance (and not a raw Dataset).\n\t */\n\t var DatasetListItemView = _super.extend(\n\t /** @lends DatasetListItemView.prototype */{\n\t _logNamespace: logNamespace,\n\t\n\t className: _super.prototype.className + \" dataset\",\n\t //TODO:?? doesn't exactly match an hda's type_id\n\t id: function () {\n\t return ['dataset', this.model.get('id')].join('-');\n\t },\n\t\n\t /** Set up: instance vars, options, and event handlers */\n\t initialize: function (attributes) {\n\t if (attributes.logger) {\n\t this.logger = this.model.logger = attributes.logger;\n\t }\n\t this.log(this + '.initialize:', attributes);\n\t _super.prototype.initialize.call(this, attributes);\n\t\n\t /** where should pages from links be displayed? (default to new tab/window) */\n\t this.linkTarget = attributes.linkTarget || '_blank';\n\t },\n\t\n\t /** event listeners */\n\t _setUpListeners: function () {\n\t _super.prototype._setUpListeners.call(this);\n\t var self = this;\n\t\n\t // re-rendering on any model changes\n\t return self.listenTo(self.model, {\n\t 'change': function (model) {\n\t // if the model moved into the ready state and is expanded without details, fetch those details now\n\t if (self.model.changedAttributes().state && self.model.inReadyState() && self.expanded && !self.model.hasDetails()) {\n\t // normally, will render automatically (due to fetch -> change),\n\t // but! setting_metadata sometimes doesn't cause any other changes besides state\n\t // so, not rendering causes it to seem frozen in setting_metadata state\n\t self.model.fetch({ silent: true }).done(function () {\n\t self.render();\n\t });\n\t } else {\n\t if (_.has(model.changed, 'tags') && _.keys(model.changed).length === 1) {\n\t // If only the tags have changed, rerender specifically\n\t // the titlebar region. Otherwise default to the full\n\t // render.\n\t self.$('.nametags').html(self._renderNametags());\n\t } else {\n\t self.render();\n\t }\n\t }\n\t }\n\t });\n\t },\n\t\n\t // ......................................................................... expandable\n\t /** In this override, only get details if in the ready state, get rerunnable if in other states.\n\t * Note: fetch with no 'change' event triggering to prevent automatic rendering.\n\t */\n\t _fetchModelDetails: function () {\n\t var view = this;\n\t if (view.model.inReadyState() && !view.model.hasDetails()) {\n\t return view.model.fetch({ silent: true });\n\t }\n\t return jQuery.when();\n\t },\n\t\n\t // ......................................................................... removal\n\t /** Remove this view's html from the DOM and remove all event listeners.\n\t * @param {Number or String} speed jq effect speed\n\t * @param {Function} callback an optional function called when removal is done (scoped to this view)\n\t */\n\t remove: function (speed, callback) {\n\t var view = this;\n\t speed = speed || this.fxSpeed;\n\t this.$el.fadeOut(speed, function () {\n\t Backbone.View.prototype.remove.call(view);\n\t if (callback) {\n\t callback.call(view);\n\t }\n\t });\n\t },\n\t\n\t // ......................................................................... rendering\n\t /* TODO:\n\t dataset states are the issue primarily making dataset rendering complex\n\t each state should have it's own way of displaying/set of details\n\t often with different actions that can be applied\n\t throw in deleted/purged/visible and things get complicated easily\n\t I've considered (a couple of times) - creating a view for each state\n\t - but recreating the view during an update...seems wrong\n\t */\n\t /** In this override, add the dataset state as a class for use with state-based CSS */\n\t _swapNewRender: function ($newRender) {\n\t _super.prototype._swapNewRender.call(this, $newRender);\n\t if (this.model.has('state')) {\n\t this.$el.addClass('state-' + this.model.get('state'));\n\t }\n\t return this.$el;\n\t },\n\t\n\t // ................................................................................ titlebar\n\t /** In this override, add the dataset display button. */\n\t _renderPrimaryActions: function () {\n\t // render just the display for read-only\n\t return [this._renderDisplayButton()];\n\t },\n\t\n\t /** Render icon-button to display dataset data */\n\t _renderDisplayButton: function () {\n\t // don't show display if not viewable or not accessible\n\t var state = this.model.get('state');\n\t if (state === STATES.NOT_VIEWABLE || state === STATES.DISCARDED || !this.model.get('accessible')) {\n\t return null;\n\t }\n\t\n\t var displayBtnData = {\n\t target: this.linkTarget,\n\t classes: 'display-btn'\n\t };\n\t\n\t // show a disabled display if the data's been purged\n\t if (this.model.get('purged')) {\n\t displayBtnData.disabled = true;\n\t displayBtnData.title = _l('Cannot display datasets removed from disk');\n\t\n\t // disable if still uploading\n\t } else if (state === STATES.UPLOAD) {\n\t displayBtnData.disabled = true;\n\t displayBtnData.title = _l('This dataset must finish uploading before it can be viewed');\n\t\n\t // disable if still new\n\t } else if (state === STATES.NEW) {\n\t displayBtnData.disabled = true;\n\t displayBtnData.title = _l('This dataset is not yet viewable');\n\t } else {\n\t displayBtnData.title = _l('View data');\n\t\n\t // default link for dataset\n\t displayBtnData.href = this.model.urls.display;\n\t\n\t // add frame manager option onclick event\n\t var self = this;\n\t displayBtnData.onclick = function (ev) {\n\t if (Galaxy.frame && Galaxy.frame.active) {\n\t // Add dataset to frames.\n\t Galaxy.frame.addDataset(self.model.get('id'));\n\t ev.preventDefault();\n\t }\n\t };\n\t }\n\t displayBtnData.faIcon = 'fa-eye';\n\t return faIconButton(displayBtnData);\n\t },\n\t\n\t // ......................................................................... rendering details\n\t /** Render the enclosing div of the hda body and, if expanded, the html in the body\n\t * @returns {jQuery} rendered DOM\n\t */\n\t _renderDetails: function () {\n\t //TODO: generalize to be allow different details for each state\n\t\n\t // no access - render nothing but a message\n\t if (this.model.get('state') === STATES.NOT_VIEWABLE) {\n\t return $(this.templates.noAccess(this.model.toJSON(), this));\n\t }\n\t\n\t var $details = _super.prototype._renderDetails.call(this);\n\t $details.find('.actions .left').empty().append(this._renderSecondaryActions());\n\t $details.find('.summary').html(this._renderSummary()).prepend(this._renderDetailMessages());\n\t $details.find('.display-applications').html(this._renderDisplayApplications());\n\t\n\t this._setUpBehaviors($details);\n\t return $details;\n\t },\n\t\n\t /** Defer to the appropo summary rendering fn based on state */\n\t _renderSummary: function () {\n\t var json = this.model.toJSON(),\n\t summaryRenderFn = this.templates.summaries[json.state];\n\t summaryRenderFn = summaryRenderFn || this.templates.summaries.unknown;\n\t return summaryRenderFn(json, this);\n\t },\n\t\n\t /** Render messages to be displayed only when the details are shown */\n\t _renderDetailMessages: function () {\n\t var view = this,\n\t $warnings = $('
'),\n\t json = view.model.toJSON();\n\t //TODO:! unordered (map)\n\t _.each(view.templates.detailMessages, function (templateFn) {\n\t $warnings.append($(templateFn(json, view)));\n\t });\n\t return $warnings;\n\t },\n\t\n\t /** Render the external display application links */\n\t _renderDisplayApplications: function () {\n\t if (this.model.isDeletedOrPurged()) {\n\t return '';\n\t }\n\t // render both old and new display apps using the same template\n\t return [this.templates.displayApplications(this.model.get('display_apps'), this), this.templates.displayApplications(this.model.get('display_types'), this)].join('');\n\t },\n\t\n\t // ......................................................................... secondary/details actions\n\t /** A series of links/buttons for less commonly used actions: re-run, info, etc. */\n\t _renderSecondaryActions: function () {\n\t this.debug('_renderSecondaryActions');\n\t switch (this.model.get('state')) {\n\t case STATES.NOT_VIEWABLE:\n\t return [];\n\t case STATES.OK:\n\t case STATES.FAILED_METADATA:\n\t case STATES.ERROR:\n\t return [this._renderDownloadButton(), this._renderShowParamsButton()];\n\t }\n\t return [this._renderShowParamsButton()];\n\t },\n\t\n\t /** Render icon-button to show the input and output (stdout/err) for the job that created this.\n\t * @returns {jQuery} rendered DOM\n\t */\n\t _renderShowParamsButton: function () {\n\t // gen. safe to show in all cases\n\t return faIconButton({\n\t title: _l('View details'),\n\t classes: 'params-btn',\n\t href: this.model.urls.show_params,\n\t target: this.linkTarget,\n\t faIcon: 'fa-info-circle',\n\t onclick: function (ev) {\n\t if (Galaxy.frame && Galaxy.frame.active) {\n\t Galaxy.frame.add({ title: 'Dataset details', url: this.href });\n\t ev.preventDefault();\n\t ev.stopPropagation();\n\t }\n\t }\n\t });\n\t },\n\t\n\t /** Render icon-button/popupmenu to download the data (and/or the associated meta files (bai, etc.)) for this.\n\t * @returns {jQuery} rendered DOM\n\t */\n\t _renderDownloadButton: function () {\n\t // don't show anything if the data's been purged\n\t if (this.model.get('purged') || !this.model.hasData()) {\n\t return null;\n\t }\n\t\n\t // return either: a popupmenu with links to download assoc. meta files (if there are meta files)\n\t // or a single download icon-button (if there are no meta files)\n\t if (!_.isEmpty(this.model.get('meta_files'))) {\n\t return this._renderMetaFileDownloadButton();\n\t }\n\t\n\t return $(['', ' '].join(''));\n\t },\n\t\n\t /** Render the download button which opens a dropdown with links to download assoc. meta files (indeces, etc.) */\n\t _renderMetaFileDownloadButton: function () {\n\t var urls = this.model.urls;\n\t return $([''].join('\\n'));\n\t },\n\t\n\t _renderNametags: function () {\n\t var tpl = _.template(['<% _.each(_.sortBy(_.uniq(tags), function(x) { return x }), function(tag){ %>', '<% if (tag.indexOf(\"name:\") == 0){ %>', '<%- tag.slice(5) %> ', '<% } %>', '<% }); %>'].join(''));\n\t return tpl({ tags: this.model.get('tags') });\n\t },\n\t\n\t // ......................................................................... misc\n\t events: _.extend(_.clone(_super.prototype.events), {\n\t 'click .display-btn': function (ev) {\n\t this.trigger('display', this, ev);\n\t },\n\t 'click .params-btn': function (ev) {\n\t this.trigger('params', this, ev);\n\t },\n\t 'click .download-btn': function (ev) {\n\t this.trigger('download', this, ev);\n\t }\n\t }),\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'DatasetListItemView(' + modelString + ')';\n\t }\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t DatasetListItemView.prototype.templates = function () {\n\t //TODO: move to require text! plugin\n\t\n\t var warnings = _.extend({}, _super.prototype.templates.warnings, {\n\t failed_metadata: BASE_MVC.wrapTemplate([\n\t // failed metadata is rendered as a warning on an otherwise ok dataset view\n\t '<% if( model.state === \"failed_metadata\" ){ %>', '', _l('An error occurred setting the metadata for this dataset'), '
', '<% } %>']),\n\t error: BASE_MVC.wrapTemplate([\n\t // error during index fetch - show error on dataset\n\t '<% if( model.error ){ %>', '', _l('There was an error getting the data for this dataset'), ': <%- model.error %>', '
', '<% } %>']),\n\t purged: BASE_MVC.wrapTemplate(['<% if( model.purged ){ %>', '', _l('This dataset has been deleted and removed from disk'), '
', '<% } %>']),\n\t deleted: BASE_MVC.wrapTemplate([\n\t // deleted not purged\n\t '<% if( model.deleted && !model.purged ){ %>', '', _l('This dataset has been deleted'), '
', '<% } %>'])\n\t\n\t //NOTE: hidden warning is only needed for HDAs\n\t });\n\t\n\t var detailsTemplate = BASE_MVC.wrapTemplate(['', '
', '
',\n\t\n\t // do not display tags, annotation, display apps, or peek when deleted\n\t '<% if( !dataset.deleted && !dataset.purged ){ %>', '
', '
', '
', '<% if( dataset.peek ){ %>', '
<%= dataset.peek %> ', '<% } %>', '<% } %>', '
', '
', _l('You do not have permission to view this dataset'), '
', '
', '<%- dataset.misc_blurb %> ', '
', '<% } %>', '<% if( dataset.file_ext ){ %>', '', '', _l('format'), ' ', '<%- dataset.file_ext %> ', '
', '<% } %>', '<% if( dataset.metadata_dbkey ){ %>', '', '', _l('database'), ' ', '', '<%- dataset.metadata_dbkey %>', ' ', '
', '<% } %>', '<% if( dataset.misc_info ){ %>', '', '<%- dataset.misc_info %> ', '
', '<% } %>'], 'dataset');\n\t summaryTemplates[STATES.NEW] = BASE_MVC.wrapTemplate(['', _l('This is a new dataset and not all of its data are available yet'), '
'], 'dataset');\n\t summaryTemplates[STATES.NOT_VIEWABLE] = BASE_MVC.wrapTemplate(['', _l('You do not have permission to view this dataset'), '
'], 'dataset');\n\t summaryTemplates[STATES.DISCARDED] = BASE_MVC.wrapTemplate(['', _l('The job creating this dataset was cancelled before completion'), '
'], 'dataset');\n\t summaryTemplates[STATES.QUEUED] = BASE_MVC.wrapTemplate(['', _l('This job is waiting to run'), '
'], 'dataset');\n\t summaryTemplates[STATES.RUNNING] = BASE_MVC.wrapTemplate(['', _l('This job is currently running'), '
'], 'dataset');\n\t summaryTemplates[STATES.UPLOAD] = BASE_MVC.wrapTemplate(['', _l('This dataset is currently uploading'), '
'], 'dataset');\n\t summaryTemplates[STATES.SETTING_METADATA] = BASE_MVC.wrapTemplate(['', _l('Metadata is being auto-detected'), '
'], 'dataset');\n\t summaryTemplates[STATES.PAUSED] = BASE_MVC.wrapTemplate(['', _l('This job is paused. Use the \"Resume Paused Jobs\" in the history menu to resume'), '
'], 'dataset');\n\t summaryTemplates[STATES.ERROR] = BASE_MVC.wrapTemplate(['<% if( !dataset.purged ){ %>', '<%- dataset.misc_blurb %>
', '<% } %>', '', _l('An error occurred with this dataset'), ': ', '<%- dataset.misc_info %>
'], 'dataset');\n\t summaryTemplates[STATES.EMPTY] = BASE_MVC.wrapTemplate(['', _l('No data'), ': <%- dataset.misc_blurb %>
'], 'dataset');\n\t summaryTemplates.unknown = BASE_MVC.wrapTemplate(['Error: unknown dataset state: \"<%- dataset.state %>\"
'], 'dataset');\n\t\n\t // messages to be displayed only within the details section ('below the fold')\n\t var detailMessageTemplates = {\n\t resubmitted: BASE_MVC.wrapTemplate([\n\t // deleted not purged\n\t '<% if( model.resubmitted ){ %>', '', _l('The job creating this dataset has been resubmitted'), '
', '<% } %>'])\n\t };\n\t\n\t // this is applied to both old and new style display apps\n\t var displayApplicationsTemplate = BASE_MVC.wrapTemplate(['<% _.each( apps, function( app ){ %>', '', '
<%- app.label %> ', '
', '<% _.each( app.links, function( link ){ %>', '\" href=\"<%- link.href %>\">', '<% print( _l( link.text ) ); %>', ' ', '<% }); %>', ' ', '
').addClass('ui-form-element').append($('
').addClass('ui-form-error ui-error').append($('
').addClass('ui-form-title').append($('
').addClass('ui-form-collapsible').append($('
').addClass('ui-form-field').append($('
').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__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ },\n/* 45 */\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__(7), __webpack_require__(59), __webpack_require__(61), __webpack_require__(60), __webpack_require__(57)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui, SelectContent, SelectLibrary, SelectFtp, 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 },\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 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 /** 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__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 46 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/** This class creates a ui component which enables the dynamic creation of portlets */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(9), __webpack_require__(7)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Portlet, Ui) {\n\t var View = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.list = {};\n\t this.options = Utils.merge(options, {\n\t title: 'Repeat',\n\t empty_text: 'Not available.',\n\t max: null,\n\t min: null\n\t });\n\t this.button_new = new Ui.ButtonIcon({\n\t icon: 'fa-plus',\n\t title: 'Insert ' + this.options.title,\n\t tooltip: 'Add new ' + this.options.title + ' block',\n\t floating: 'clear',\n\t cls: 'ui-button-icon form-repeat-add',\n\t onclick: function () {\n\t options.onnew && options.onnew();\n\t }\n\t });\n\t this.setElement($('
').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__(3), __webpack_require__(1), __webpack_require__(2)))\n\n/***/ },\n/* 47 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _, jQuery) {/**\n\t This class creates a form section and populates it with input elements. It also handles repeat blocks and conditionals by recursively creating new sub sections.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(7), __webpack_require__(9), __webpack_require__(46), __webpack_require__(44), __webpack_require__(45)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Ui, Portlet, Repeat, InputElement, Parameters) {\n\t var View = Backbone.View.extend({\n\t initialize: function (app, options) {\n\t this.app = app;\n\t this.inputs = options.inputs;\n\t this.parameters = new Parameters();\n\t this.setElement($('
'));\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__(3), __webpack_require__(1), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 48 */\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') {\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 new_val.push(value);\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\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__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 49 */\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_header(options) + ' ' + ' ' + '' + ' ' + '
' + this.grid_table(options);\n\t }\n\t\n\t // add info text\n\t if (options.info_text) {\n\t tmpl += '' + 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\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 = '';\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\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\n\t // Data columns\n\t for (j in options.columns) {\n\t var column = options.columns[j];\n\t if (column.visible) {\n\t // Nowrap\n\t var nowrap = '';\n\t if (column.nowrap) {\n\t nowrap = 'style=\"white-space:nowrap;\"';\n\t }\n\t\n\t // get column settings\n\t var column_settings = item.column_config[column.label];\n\t\n\t // load attributes\n\t var link = column_settings.link;\n\t var value = column_settings.value;\n\t var target = column_settings.target;\n\t\n\t // unescape value\n\t if (jQuery.type(value) === 'string') {\n\t value = value.replace(/\\/\\//g, '/');\n\t }\n\t\n\t // Attach popup menu?\n\t var id = '';\n\t var cls = '';\n\t if (column.attach_popup) {\n\t id = 'grid-' + i + '-popup';\n\t cls = 'menubutton';\n\t if (link != '') {\n\t cls += ' split';\n\t }\n\t cls += ' popup';\n\t }\n\t\n\t // Check for row wrapping\n\t tmpl += '';\n\t\n\t // Link\n\t if (link) {\n\t if (options.operations.length != 0) {\n\t tmpl += '';\n\t }\n\t tmpl += '';\n\t if (options.operations.length != 0) {\n\t tmpl += '
';\n\t }\n\t } else {\n\t tmpl += '' + (value || '') + '
';\n\t }\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 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 ' + page_index + ' ';\n\t } else {\n\t tmpl += '' + page_index + ' ' + num_pages + ' ';\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 ' + ' ';\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 return '' + '
' + 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 // add standard filters\n\t for (var i in options.columns) {\n\t var column = options.columns[i];\n\t if (column.filterable == 'standard') {\n\t tmpl += this.grid_column_filter(options, column);\n\t }\n\t }\n\t\n\t // finalize standard search\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 += ' ' + ' ' + '
' + '
' + '
' + '' + '' + 'Close Advanced Search ' + ' ' + ' ';\n\t\n\t // add advanced filters\n\t for (var i in options.columns) {\n\t var column = options.columns[i];\n\t if (column.filterable == 'advanced') {\n\t tmpl += this.grid_column_filter(options, column);\n\t }\n\t }\n\t\n\t // finalize advanced search template\n\t tmpl += '
' + '
';\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 (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 (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)))\n\n/***/ },\n/* 50 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(41), __webpack_require__(86), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (DC_MODEL, HISTORY_CONTENT, _l) {\n\t\n\t 'use strict';\n\t\n\t /*==============================================================================\n\t \n\t Models for DatasetCollections contained within a history.\n\t \n\t TODO:\n\t these might be compactable to one class if some duplication with\n\t collection-model is used.\n\t \n\t ==============================================================================*/\n\t\n\t var hcontentMixin = HISTORY_CONTENT.HistoryContentMixin,\n\t ListDC = DC_MODEL.ListDatasetCollection,\n\t PairDC = DC_MODEL.PairDatasetCollection,\n\t ListPairedDC = DC_MODEL.ListPairedDatasetCollection,\n\t ListOfListsDC = DC_MODEL.ListOfListsDatasetCollection;\n\t\n\t //==============================================================================\n\t /** Override to post to contents route w/o id. */\n\t function buildHDCASave(_super) {\n\t return function _save(attributes, options) {\n\t if (this.isNew()) {\n\t options = options || {};\n\t options.url = this.urlRoot + this.get('history_id') + '/contents';\n\t attributes = attributes || {};\n\t attributes.type = 'dataset_collection';\n\t }\n\t return _super.call(this, attributes, options);\n\t };\n\t }\n\t\n\t //==============================================================================\n\t /** @class Backbone model for List Dataset Collection within a History.\n\t */\n\t var HistoryListDatasetCollection = ListDC.extend(hcontentMixin).extend(\n\t /** @lends HistoryListDatasetCollection.prototype */{\n\t\n\t defaults: _.extend(_.clone(ListDC.prototype.defaults), {\n\t history_content_type: 'dataset_collection',\n\t collection_type: 'list',\n\t model_class: 'HistoryDatasetCollectionAssociation'\n\t }),\n\t\n\t /** Override to post to contents route w/o id. */\n\t save: buildHDCASave(ListDC.prototype.save),\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return 'History' + ListDC.prototype.toString.call(this);\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone model for Pair Dataset Collection within a History.\n\t * @constructs\n\t */\n\t var HistoryPairDatasetCollection = PairDC.extend(hcontentMixin).extend(\n\t /** @lends HistoryPairDatasetCollection.prototype */{\n\t\n\t defaults: _.extend(_.clone(PairDC.prototype.defaults), {\n\t history_content_type: 'dataset_collection',\n\t collection_type: 'paired',\n\t model_class: 'HistoryDatasetCollectionAssociation'\n\t }),\n\t\n\t /** Override to post to contents route w/o id. */\n\t save: buildHDCASave(PairDC.prototype.save),\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return 'History' + PairDC.prototype.toString.call(this);\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone model for List of Pairs Dataset Collection within a History. */\n\t var HistoryListPairedDatasetCollection = ListPairedDC.extend(hcontentMixin).extend({\n\t\n\t defaults: _.extend(_.clone(ListPairedDC.prototype.defaults), {\n\t history_content_type: 'dataset_collection',\n\t collection_type: 'list:paired',\n\t model_class: 'HistoryDatasetCollectionAssociation'\n\t }),\n\t\n\t /** Override to post to contents route w/o id. */\n\t save: buildHDCASave(ListPairedDC.prototype.save),\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return 'History' + ListPairedDC.prototype.toString.call(this);\n\t }\n\t });\n\t\n\t //==============================================================================\n\t /** @class Backbone model for List of Lists Dataset Collection within a History. */\n\t var HistoryListOfListsDatasetCollection = ListOfListsDC.extend(hcontentMixin).extend({\n\t\n\t defaults: _.extend(_.clone(ListOfListsDC.prototype.defaults), {\n\t history_content_type: 'dataset_collection',\n\t collection_type: 'list:list',\n\t model_class: 'HistoryDatasetCollectionAssociation'\n\t }),\n\t\n\t /** Override to post to contents route w/o id. */\n\t save: buildHDCASave(ListOfListsDC.prototype.save),\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['HistoryListOfListsDatasetCollection(', this.get('name'), ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t HistoryListDatasetCollection: HistoryListDatasetCollection,\n\t HistoryPairDatasetCollection: HistoryPairDatasetCollection,\n\t HistoryListPairedDatasetCollection: HistoryListPairedDatasetCollection,\n\t HistoryListOfListsDatasetCollection: HistoryListOfListsDatasetCollection\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/* 51 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_, jQuery, Backbone) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(77), __webpack_require__(84), __webpack_require__(50), __webpack_require__(53), __webpack_require__(6), __webpack_require__(147)], __WEBPACK_AMD_DEFINE_RESULT__ = function (CONTROLLED_FETCH_COLLECTION, HDA_MODEL, HDCA_MODEL, HISTORY_PREFS, BASE_MVC, AJAX_QUEUE) {\n\t 'use strict';\n\t\n\t //==============================================================================\n\t\n\t var _super = CONTROLLED_FETCH_COLLECTION.PaginatedCollection;\n\t /** @class Backbone collection for history content.\n\t * NOTE: history content seems like a dataset collection, but differs in that it is mixed:\n\t * each element can be either an HDA (dataset) or a DatasetCollection and co-exist on\n\t * the same level.\n\t * Dataset collections on the other hand are not mixed and (so far) can only contain either\n\t * HDAs or child dataset collections on one level.\n\t * This is why this does not inherit from any of the DatasetCollections (currently).\n\t */\n\t var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({\n\t _logNamespace: 'history',\n\t\n\t // ........................................................................ composite collection\n\t /** since history content is a mix, override model fn into a factory, creating based on history_content_type */\n\t model: function (attrs, options) {\n\t if (attrs.history_content_type === \"dataset\") {\n\t return new HDA_MODEL.HistoryDatasetAssociation(attrs, options);\n\t } else if (attrs.history_content_type === \"dataset_collection\") {\n\t switch (attrs.collection_type) {\n\t case 'list':\n\t return new HDCA_MODEL.HistoryListDatasetCollection(attrs, options);\n\t case 'paired':\n\t return new HDCA_MODEL.HistoryPairDatasetCollection(attrs, options);\n\t case 'list:paired':\n\t return new HDCA_MODEL.HistoryListPairedDatasetCollection(attrs, options);\n\t case 'list:list':\n\t return new HDCA_MODEL.HistoryListOfListsDatasetCollection(attrs, options);\n\t }\n\t // This is a hack inside a hack:\n\t // Raise a plain object with validationError to fake a model.validationError\n\t // (since we don't have a model to use validate with)\n\t // (the outer hack being the mixed content/model function in this collection)\n\t var msg = 'Unknown collection_type: ' + attrs.collection_type;\n\t console.warn(msg, attrs);\n\t return { validationError: msg };\n\t }\n\t return { validationError: 'Unknown history_content_type: ' + attrs.history_content_type };\n\t },\n\t\n\t // ........................................................................ set up\n\t limitPerPage: 500,\n\t\n\t /** @type {Integer} how many contents per call to fetch when using progressivelyFetchDetails */\n\t limitPerProgressiveFetch: 500,\n\t\n\t /** @type {String} order used here and when fetching from server */\n\t order: 'hid',\n\t\n\t /** root api url */\n\t urlRoot: Galaxy.root + 'api/histories',\n\t\n\t /** complete api url */\n\t url: function () {\n\t return this.urlRoot + '/' + this.historyId + '/contents';\n\t },\n\t\n\t /** Set up */\n\t initialize: function (models, options) {\n\t options = options || {};\n\t _super.prototype.initialize.call(this, models, options);\n\t\n\t this.history = options.history || null;\n\t this.setHistoryId(options.historyId || null);\n\t /** @type {Boolean} does this collection contain and fetch deleted elements */\n\t this.includeDeleted = options.includeDeleted || this.includeDeleted;\n\t /** @type {Boolean} does this collection contain and fetch non-visible elements */\n\t this.includeHidden = options.includeHidden || this.includeHidden;\n\t\n\t // backbonejs uses collection.model.prototype.idAttribute to determine if a model is *already* in a collection\n\t // and either merged or replaced. In this case, our 'model' is a function so we need to add idAttribute\n\t // manually here - if we don't, contents will not merge but be replaced/swapped.\n\t this.model.prototype.idAttribute = 'type_id';\n\t },\n\t\n\t setHistoryId: function (newId) {\n\t this.historyId = newId;\n\t this._setUpWebStorage();\n\t },\n\t\n\t /** Set up client side storage. Currently PersistanStorage keyed under 'history:' */\n\t _setUpWebStorage: function (initialSettings) {\n\t // TODO: use initialSettings\n\t if (!this.historyId) {\n\t return;\n\t }\n\t this.storage = new HISTORY_PREFS.HistoryPrefs({\n\t id: HISTORY_PREFS.HistoryPrefs.historyStorageKey(this.historyId)\n\t });\n\t this.trigger('new-storage', this.storage, this);\n\t\n\t this.on({\n\t 'include-deleted': function (newVal) {\n\t this.storage.includeDeleted(newVal);\n\t },\n\t 'include-hidden': function (newVal) {\n\t this.storage.includeHidden(newVal);\n\t }\n\t });\n\t\n\t this.includeDeleted = this.storage.includeDeleted() || false;\n\t this.includeHidden = this.storage.includeHidden() || false;\n\t return this;\n\t },\n\t\n\t // ........................................................................ common queries\n\t /** @type {Object} map of collection available sorting orders containing comparator fns */\n\t comparators: _.extend(_.clone(_super.prototype.comparators), {\n\t 'name': BASE_MVC.buildComparator('name', { ascending: true }),\n\t 'name-dsc': BASE_MVC.buildComparator('name', { ascending: false }),\n\t 'hid': BASE_MVC.buildComparator('hid', { ascending: false }),\n\t 'hid-asc': BASE_MVC.buildComparator('hid', { ascending: true })\n\t }),\n\t\n\t /** Get every model in this collection not in a 'ready' state (running). */\n\t running: function () {\n\t return this.filter(function (c) {\n\t return !c.inReadyState();\n\t });\n\t },\n\t\n\t /** return contents that are not ready and not deleted/hidden */\n\t runningAndActive: function () {\n\t return this.filter(function (c) {\n\t return !c.inReadyState() && c.get('visible')\n\t // TODO: deletedOrPurged?\n\t && !c.get('deleted');\n\t });\n\t },\n\t\n\t /** Get the model with the given hid\n\t * @param {Int} hid the hid to search for\n\t * @returns {HistoryDatasetAssociation} the model with the given hid or undefined if not found\n\t */\n\t getByHid: function (hid) {\n\t // note: there *can* be more than one content with a given hid, this finds the first based on order\n\t return this.findWhere({ hid: hid });\n\t },\n\t\n\t /** return true if all contents have details */\n\t haveDetails: function () {\n\t return this.all(function (c) {\n\t return c.hasDetails();\n\t });\n\t },\n\t\n\t // ........................................................................ hidden / deleted\n\t /** return a new contents collection of only hidden items */\n\t hidden: function () {\n\t return this.filter(function (c) {\n\t return c.hidden();\n\t });\n\t },\n\t\n\t /** return a new contents collection of only hidden items */\n\t deleted: function () {\n\t return this.filter(function (c) {\n\t return c.get('deleted');\n\t });\n\t },\n\t\n\t /** return a new contents collection of only hidden items */\n\t visibleAndUndeleted: function () {\n\t return this.filter(function (c) {\n\t return c.get('visible') &&\n\t // TODO: deletedOrPurged?\n\t !c.get('deleted');\n\t });\n\t },\n\t\n\t /** create a setter in order to publish the change */\n\t setIncludeDeleted: function (setting, options) {\n\t if (_.isBoolean(setting) && setting !== this.includeDeleted) {\n\t this.includeDeleted = setting;\n\t if (_.result(options, 'silent')) {\n\t return;\n\t }\n\t this.trigger('include-deleted', setting, this);\n\t }\n\t },\n\t\n\t /** create a setter in order to publish the change */\n\t setIncludeHidden: function (setting, options) {\n\t if (_.isBoolean(setting) && setting !== this.includeHidden) {\n\t this.includeHidden = setting;\n\t options = options || {};\n\t if (_.result(options, 'silent')) {\n\t return;\n\t }\n\t this.trigger('include-hidden', setting, this);\n\t }\n\t },\n\t\n\t // ........................................................................ ajax\n\t // ............ controlled fetch collection\n\t /** override to get expanded ids from sessionStorage and pass to API as details */\n\t fetch: function (options) {\n\t options = options || {};\n\t if (this.historyId && !options.details) {\n\t var prefs = HISTORY_PREFS.HistoryPrefs.get(this.historyId).toJSON();\n\t if (!_.isEmpty(prefs.expandedIds)) {\n\t options.details = _.values(prefs.expandedIds).join(',');\n\t }\n\t }\n\t return _super.prototype.fetch.call(this, options);\n\t },\n\t\n\t // ............. ControlledFetch stuff\n\t /** override to include the API versioning flag */\n\t _buildFetchData: function (options) {\n\t return _.extend(_super.prototype._buildFetchData.call(this, options), {\n\t v: 'dev'\n\t });\n\t },\n\t\n\t /** Extend to include details and version */\n\t _fetchParams: _super.prototype._fetchParams.concat([\n\t // TODO: remove (the need for) both\n\t /** version */\n\t 'v',\n\t /** dataset ids to get full details of */\n\t 'details']),\n\t\n\t /** override to add deleted/hidden filters */\n\t _buildFetchFilters: function (options) {\n\t var superFilters = _super.prototype._buildFetchFilters.call(this, options) || {};\n\t var filters = {};\n\t if (!this.includeDeleted) {\n\t filters.deleted = false;\n\t filters.purged = false;\n\t }\n\t if (!this.includeHidden) {\n\t filters.visible = true;\n\t }\n\t return _.defaults(superFilters, filters);\n\t },\n\t\n\t // ............ paginated collection\n\t getTotalItemCount: function () {\n\t return this.history.contentsShown();\n\t },\n\t\n\t // ............ history contents specific ajax\n\t /** override to filter requested contents to those updated after the Date 'since' */\n\t fetchUpdated: function (since, options) {\n\t if (since) {\n\t options = options || { filters: {} };\n\t options.remove = false;\n\t options.filters = {\n\t 'update_time-ge': since.toISOString(),\n\t // workflows will produce hidden datasets (non-output datasets) that still\n\t // need to be updated in the collection or they'll update forever\n\t // we can remove the default visible filter by using an 'empty' value\n\t visible: ''\n\t };\n\t }\n\t return this.fetch(options);\n\t },\n\t\n\t /** fetch all the deleted==true contents of this collection */\n\t fetchDeleted: function (options) {\n\t options = options || {};\n\t var self = this;\n\t options.filters = _.extend(options.filters, {\n\t // all deleted, purged or not\n\t deleted: true,\n\t purged: undefined\n\t });\n\t options.remove = false;\n\t\n\t self.trigger('fetching-deleted', self);\n\t return self.fetch(options).always(function () {\n\t self.trigger('fetching-deleted-done', self);\n\t });\n\t },\n\t\n\t /** fetch all the visible==false contents of this collection */\n\t fetchHidden: function (options) {\n\t options = options || {};\n\t var self = this;\n\t options.filters = _.extend(options.filters, {\n\t visible: false\n\t });\n\t options.remove = false;\n\t\n\t self.trigger('fetching-hidden', self);\n\t return self.fetch(options).always(function () {\n\t self.trigger('fetching-hidden-done', self);\n\t });\n\t },\n\t\n\t /** fetch detailed model data for all contents in this collection */\n\t fetchAllDetails: function (options) {\n\t options = options || {};\n\t var detailsFlag = { details: 'all' };\n\t options.data = _.extend(options.data || {}, detailsFlag);\n\t return this.fetch(options);\n\t },\n\t\n\t /** specialty fetch method for retrieving the element_counts of all hdcas in the history */\n\t fetchCollectionCounts: function (options) {\n\t options = options || {};\n\t options.keys = ['type_id', 'element_count'].join(',');\n\t options.filters = _.extend(options.filters || {}, {\n\t history_content_type: 'dataset_collection'\n\t });\n\t options.remove = false;\n\t return this.fetch(options);\n\t },\n\t\n\t // ............. quasi-batch ops\n\t // TODO: to batch\n\t /** helper that fetches using filterParams then calls save on each fetched using updateWhat as the save params */\n\t _filterAndUpdate: function (filterParams, updateWhat) {\n\t var self = this;\n\t var idAttribute = self.model.prototype.idAttribute;\n\t var updateArgs = [updateWhat];\n\t\n\t return self.fetch({ filters: filterParams, remove: false }).then(function (fetched) {\n\t // convert filtered json array to model array\n\t fetched = fetched.reduce(function (modelArray, currJson, i) {\n\t var model = self.get(currJson[idAttribute]);\n\t return model ? modelArray.concat(model) : modelArray;\n\t }, []);\n\t return self.ajaxQueue('save', updateArgs, fetched);\n\t });\n\t },\n\t\n\t /** using a queue, perform ajaxFn on each of the models in this collection */\n\t ajaxQueue: function (ajaxFn, args, collection) {\n\t collection = collection || this.models;\n\t return new AJAX_QUEUE.AjaxQueue(collection.slice().reverse().map(function (content, i) {\n\t var fn = _.isString(ajaxFn) ? content[ajaxFn] : ajaxFn;\n\t return function () {\n\t return fn.apply(content, args);\n\t };\n\t })).deferred;\n\t },\n\t\n\t /** fetch contents' details in batches of limitPerCall - note: only get searchable details here */\n\t progressivelyFetchDetails: function (options) {\n\t options = options || {};\n\t var deferred = jQuery.Deferred();\n\t var self = this;\n\t var limit = options.limitPerCall || self.limitPerProgressiveFetch;\n\t // TODO: only fetch tags and annotations if specifically requested\n\t var searchAttributes = HDA_MODEL.HistoryDatasetAssociation.prototype.searchAttributes;\n\t var detailKeys = searchAttributes.join(',');\n\t\n\t function _recursivelyFetch(offset) {\n\t offset = offset || 0;\n\t var _options = _.extend(_.clone(options), {\n\t view: 'summary',\n\t keys: detailKeys,\n\t limit: limit,\n\t offset: offset,\n\t reset: offset === 0,\n\t remove: false\n\t });\n\t\n\t _.defer(function () {\n\t self.fetch.call(self, _options).fail(deferred.reject).done(function (response) {\n\t deferred.notify(response, limit, offset);\n\t if (response.length !== limit) {\n\t self.allFetched = true;\n\t deferred.resolve(response, limit, offset);\n\t } else {\n\t _recursivelyFetch(offset + limit);\n\t }\n\t });\n\t });\n\t }\n\t _recursivelyFetch();\n\t return deferred;\n\t },\n\t\n\t /** does some bit of JSON represent something that can be copied into this contents collection */\n\t isCopyable: function (contentsJSON) {\n\t var copyableModelClasses = ['HistoryDatasetAssociation', 'HistoryDatasetCollectionAssociation'];\n\t return _.isObject(contentsJSON) && contentsJSON.id && _.contains(copyableModelClasses, contentsJSON.model_class);\n\t },\n\t\n\t /** copy an existing, accessible hda into this collection */\n\t copy: function (json) {\n\t // TODO: somehow showhorn all this into 'save'\n\t var id, type, contentType;\n\t if (_.isString(json)) {\n\t id = json;\n\t contentType = 'hda';\n\t type = 'dataset';\n\t } else {\n\t id = json.id;\n\t contentType = {\n\t 'HistoryDatasetAssociation': 'hda',\n\t 'LibraryDatasetDatasetAssociation': 'ldda',\n\t 'HistoryDatasetCollectionAssociation': 'hdca'\n\t }[json.model_class] || 'hda';\n\t type = contentType === 'hdca' ? 'dataset_collection' : 'dataset';\n\t }\n\t var collection = this,\n\t xhr = jQuery.ajax(this.url(), {\n\t method: 'POST',\n\t contentType: 'application/json',\n\t data: JSON.stringify({\n\t content: id,\n\t source: contentType,\n\t type: type\n\t })\n\t }).done(function (response) {\n\t collection.add([response], { parse: true });\n\t }).fail(function (error, status, message) {\n\t collection.trigger('error', collection, xhr, {}, 'Error copying contents', { type: type, id: id, source: contentType });\n\t });\n\t return xhr;\n\t },\n\t\n\t /** create a new HDCA in this collection */\n\t createHDCA: function (elementIdentifiers, collectionType, name, hideSourceItems, options) {\n\t // normally collection.create returns the new model, but we need the promise from the ajax, so we fake create\n\t //precondition: elementIdentifiers is an array of plain js objects\n\t // in the proper form to create the collectionType\n\t var hdca = this.model({\n\t history_content_type: 'dataset_collection',\n\t collection_type: collectionType,\n\t history_id: this.historyId,\n\t name: name,\n\t hide_source_items: hideSourceItems || false,\n\t // should probably be able to just send in a bunch of json here and restruct per class\n\t // note: element_identifiers is now (incorrectly) an attribute\n\t element_identifiers: elementIdentifiers\n\t // do not create the model on the client until the ajax returns\n\t });\n\t return hdca.save(options);\n\t },\n\t\n\t // ........................................................................ searching\n\t /** return true if all contents have the searchable attributes */\n\t haveSearchDetails: function () {\n\t return this.allFetched && this.all(function (content) {\n\t // null (which is a valid returned annotation value)\n\t // will return false when using content.has( 'annotation' )\n\t //TODO: a bit hacky - formalize\n\t return _.has(content.attributes, 'annotation');\n\t });\n\t },\n\t\n\t /** return a new collection of contents whose attributes contain the substring matchesWhat */\n\t matches: function (matchesWhat) {\n\t return this.filter(function (content) {\n\t return content.matches(matchesWhat);\n\t });\n\t },\n\t\n\t // ........................................................................ misc\n\t /** In this override, copy the historyId to the clone */\n\t clone: function () {\n\t var clone = Backbone.Collection.prototype.clone.call(this);\n\t clone.historyId = this.historyId;\n\t return clone;\n\t },\n\t\n\t /** String representation. */\n\t toString: function () {\n\t return ['HistoryContents(', [this.historyId, this.length].join(), ')'].join('');\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t HistoryContents: HistoryContents\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/* 52 */\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!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(51), __webpack_require__(53), __webpack_require__(77), __webpack_require__(4), __webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (HISTORY_CONTENTS, HISTORY_PREFS, CONTROLLED_FETCH_COLLECTION, UTILS, BASE_MVC, _l) {\n\t 'use strict';\n\t\n\t //==============================================================================\n\t /** @class Model for a Galaxy history resource - both a record of user\n\t * tool use and a collection of the datasets those tools produced.\n\t * @name History\n\t * @augments Backbone.Model\n\t */\n\t\n\t var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(BASE_MVC.mixin(BASE_MVC.SearchableModelMixin, /** @lends History.prototype */{\n\t _logNamespace: 'history',\n\t\n\t /** ms between fetches when checking running jobs/datasets for updates */\n\t UPDATE_DELAY: 4000,\n\t\n\t // values from api (may need more)\n\t defaults: {\n\t model_class: 'History',\n\t id: null,\n\t name: 'Unnamed History',\n\t state: 'new',\n\t\n\t deleted: false,\n\t contents_active: {},\n\t contents_states: {}\n\t },\n\t\n\t urlRoot: Galaxy.root + 'api/histories',\n\t\n\t contentsClass: HISTORY_CONTENTS.HistoryContents,\n\t\n\t /** What model fields to search with */\n\t searchAttributes: ['name', 'annotation', 'tags'],\n\t\n\t /** Adding title and singular tag */\n\t searchAliases: {\n\t title: 'name',\n\t tag: 'tags'\n\t },\n\t\n\t // ........................................................................ set up/tear down\n\t /** Set up the model\n\t * @param {Object} historyJSON model data for this History\n\t * @param {Object} options any extra settings including logger\n\t */\n\t initialize: function (historyJSON, options) {\n\t options = options || {};\n\t this.logger = options.logger || null;\n\t this.log(this + \".initialize:\", historyJSON, options);\n\t\n\t /** HistoryContents collection of the HDAs contained in this history. */\n\t this.contents = new this.contentsClass([], {\n\t history: this,\n\t historyId: this.get('id'),\n\t order: options.order\n\t });\n\t\n\t this._setUpListeners();\n\t this._setUpCollectionListeners();\n\t\n\t /** cached timeout id for the dataset updater */\n\t this.updateTimeoutId = null;\n\t },\n\t\n\t /** set up any event listeners for this history including those to the contained HDAs\n\t * events: error:contents if an error occurred with the contents collection\n\t */\n\t _setUpListeners: function () {\n\t // if the model's id changes ('current' or null -> an actual id), update the contents history_id\n\t return this.on({\n\t 'error': function (model, xhr, options, msg, details) {\n\t this.clearUpdateTimeout();\n\t },\n\t 'change:id': function (model, newId) {\n\t if (this.contents) {\n\t this.contents.historyId = newId;\n\t }\n\t }\n\t });\n\t },\n\t\n\t /** event handlers for the contents submodels */\n\t _setUpCollectionListeners: function () {\n\t if (!this.contents) {\n\t return this;\n\t }\n\t // bubble up errors\n\t return this.listenTo(this.contents, {\n\t 'error': function () {\n\t this.trigger.apply(this, jQuery.makeArray(arguments));\n\t }\n\t });\n\t },\n\t\n\t // ........................................................................ derived attributes\n\t /** */\n\t contentsShown: function () {\n\t var contentsActive = this.get('contents_active');\n\t var shown = contentsActive.active || 0;\n\t shown += this.contents.includeDeleted ? contentsActive.deleted : 0;\n\t shown += this.contents.includeHidden ? contentsActive.hidden : 0;\n\t return shown;\n\t },\n\t\n\t /** convert size in bytes to a more human readable version */\n\t nice_size: function () {\n\t var size = this.get('size');\n\t return size ? UTILS.bytesToString(size, true, 2) : _l('(empty)');\n\t },\n\t\n\t /** override to add nice_size */\n\t toJSON: function () {\n\t return _.extend(Backbone.Model.prototype.toJSON.call(this), {\n\t nice_size: this.nice_size()\n\t });\n\t },\n\t\n\t /** override to allow getting nice_size */\n\t get: function (key) {\n\t if (key === 'nice_size') {\n\t return this.nice_size();\n\t }\n\t return Backbone.Model.prototype.get.apply(this, arguments);\n\t },\n\t\n\t // ........................................................................ common queries\n\t /** T/F is this history owned by the current user (Galaxy.user)\n\t * Note: that this will return false for an anon user even if the history is theirs.\n\t */\n\t ownedByCurrUser: function () {\n\t // no currUser\n\t if (!Galaxy || !Galaxy.user) {\n\t return false;\n\t }\n\t // user is anon or history isn't owned\n\t if (Galaxy.user.isAnonymous() || Galaxy.user.id !== this.get('user_id')) {\n\t return false;\n\t }\n\t return true;\n\t },\n\t\n\t /** Return the number of running jobs assoc with this history (note: unknown === 0) */\n\t numOfUnfinishedJobs: function () {\n\t var unfinishedJobIds = this.get('non_ready_jobs');\n\t return unfinishedJobIds ? unfinishedJobIds.length : 0;\n\t },\n\t\n\t /** Return the number of running hda/hdcas in this history (note: unknown === 0) */\n\t numOfUnfinishedShownContents: function () {\n\t return this.contents.runningAndActive().length || 0;\n\t },\n\t\n\t // ........................................................................ updates\n\t _fetchContentRelatedAttributes: function () {\n\t var contentRelatedAttrs = ['size', 'non_ready_jobs', 'contents_active', 'hid_counter'];\n\t return this.fetch({ data: $.param({ keys: contentRelatedAttrs.join(',') }) });\n\t },\n\t\n\t /** check for any changes since the last time we updated (or fetch all if ) */\n\t refresh: function (options) {\n\t // console.log( this + '.refresh' );\n\t options = options || {};\n\t var self = this;\n\t\n\t // note if there was no previous update time, all summary contents will be fetched\n\t var lastUpdateTime = self.lastUpdateTime;\n\t // if we don't flip this, then a fully-fetched list will not be re-checked via fetch\n\t this.contents.allFetched = false;\n\t var fetchFn = self.contents.currentPage !== 0 ? function () {\n\t return self.contents.fetchPage(self.contents.currentPage);\n\t } : function () {\n\t return self.contents.fetchUpdated(lastUpdateTime);\n\t };\n\t // note: if there was no previous update time, all summary contents will be fetched\n\t return fetchFn().done(function (response, status, xhr) {\n\t var serverResponseDatetime;\n\t try {\n\t serverResponseDatetime = new Date(xhr.getResponseHeader('Date'));\n\t } catch (err) {}\n\t self.lastUpdateTime = serverResponseDatetime || new Date();\n\t self.checkForUpdates(options);\n\t });\n\t },\n\t\n\t /** continuously fetch updated contents every UPDATE_DELAY ms if this history's datasets or jobs are unfinished */\n\t checkForUpdates: function (options) {\n\t // console.log( this + '.checkForUpdates' );\n\t options = options || {};\n\t var delay = this.UPDATE_DELAY;\n\t var self = this;\n\t if (!self.id) {\n\t return;\n\t }\n\t\n\t function _delayThenUpdate() {\n\t // prevent buildup of updater timeouts by clearing previous if any, then set new and cache id\n\t self.clearUpdateTimeout();\n\t self.updateTimeoutId = setTimeout(function () {\n\t self.refresh(options);\n\t }, delay);\n\t }\n\t\n\t // if there are still datasets in the non-ready state, recurse into this function with the new time\n\t var nonReadyContentCount = this.numOfUnfinishedShownContents();\n\t // console.log( 'nonReadyContentCount:', nonReadyContentCount );\n\t if (nonReadyContentCount > 0) {\n\t _delayThenUpdate();\n\t } else {\n\t // no datasets are running, but currently runnning jobs may still produce new datasets\n\t // see if the history has any running jobs and continue to update if so\n\t // (also update the size for the user in either case)\n\t self._fetchContentRelatedAttributes().done(function (historyData) {\n\t // console.log( 'non_ready_jobs:', historyData.non_ready_jobs );\n\t if (self.numOfUnfinishedJobs() > 0) {\n\t _delayThenUpdate();\n\t } else {\n\t // otherwise, let listeners know that all updates have stopped\n\t self.trigger('ready');\n\t }\n\t });\n\t }\n\t },\n\t\n\t /** clear the timeout and the cached timeout id */\n\t clearUpdateTimeout: function () {\n\t if (this.updateTimeoutId) {\n\t clearTimeout(this.updateTimeoutId);\n\t this.updateTimeoutId = null;\n\t }\n\t },\n\t\n\t // ........................................................................ ajax\n\t /** override to use actual Dates objects for create/update times */\n\t parse: function (response, options) {\n\t var parsed = Backbone.Model.prototype.parse.call(this, response, options);\n\t if (parsed.create_time) {\n\t parsed.create_time = new Date(parsed.create_time);\n\t }\n\t if (parsed.update_time) {\n\t parsed.update_time = new Date(parsed.update_time);\n\t }\n\t return parsed;\n\t },\n\t\n\t /** fetch this histories data (using options) then it's contents (using contentsOptions) */\n\t fetchWithContents: function (options, contentsOptions) {\n\t options = options || {};\n\t var self = this;\n\t\n\t // console.log( this + '.fetchWithContents' );\n\t // TODO: push down to a base class\n\t options.view = 'dev-detailed';\n\t\n\t // fetch history then use history data to fetch (paginated) contents\n\t return this.fetch(options).then(function getContents(history) {\n\t self.contents.history = self;\n\t self.contents.setHistoryId(history.id);\n\t return self.fetchContents(contentsOptions);\n\t });\n\t },\n\t\n\t /** fetch this histories contents, adjusting options based on the stored history preferences */\n\t fetchContents: function (options) {\n\t options = options || {};\n\t var self = this;\n\t\n\t // we're updating, reset the update time\n\t self.lastUpdateTime = new Date();\n\t return self.contents.fetchCurrentPage(options);\n\t },\n\t\n\t /** save this history, _Mark_ing it as deleted (just a flag) */\n\t _delete: function (options) {\n\t if (this.get('deleted')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ deleted: true }, options);\n\t },\n\t /** purge this history, _Mark_ing it as purged and removing all dataset data from the server */\n\t purge: function (options) {\n\t if (this.get('purged')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ deleted: true, purged: true }, options);\n\t },\n\t /** save this history, _Mark_ing it as undeleted */\n\t undelete: function (options) {\n\t if (!this.get('deleted')) {\n\t return jQuery.when();\n\t }\n\t return this.save({ deleted: false }, options);\n\t },\n\t\n\t /** Make a copy of this history on the server\n\t * @param {Boolean} current if true, set the copy as the new current history (default: true)\n\t * @param {String} name name of new history (default: none - server sets to: Copy of )\n\t * @fires copied passed this history and the response JSON from the copy\n\t * @returns {xhr}\n\t */\n\t copy: function (current, name, allDatasets) {\n\t current = current !== undefined ? current : true;\n\t if (!this.id) {\n\t throw new Error('You must set the history ID before copying it.');\n\t }\n\t\n\t var postData = { history_id: this.id };\n\t if (current) {\n\t postData.current = true;\n\t }\n\t if (name) {\n\t postData.name = name;\n\t }\n\t if (!allDatasets) {\n\t postData.all_datasets = false;\n\t }\n\t postData.view = 'dev-detailed';\n\t\n\t var history = this;\n\t var copy = jQuery.post(this.urlRoot, postData);\n\t // if current - queue to setAsCurrent before firing 'copied'\n\t if (current) {\n\t return copy.then(function (response) {\n\t var newHistory = new History(response);\n\t return newHistory.setAsCurrent().done(function () {\n\t history.trigger('copied', history, response);\n\t });\n\t });\n\t }\n\t return copy.done(function (response) {\n\t history.trigger('copied', history, response);\n\t });\n\t },\n\t\n\t setAsCurrent: function () {\n\t var history = this,\n\t xhr = jQuery.getJSON(Galaxy.root + 'history/set_as_current?id=' + this.id);\n\t\n\t xhr.done(function () {\n\t history.trigger('set-as-current', history);\n\t });\n\t return xhr;\n\t },\n\t\n\t // ........................................................................ misc\n\t toString: function () {\n\t return 'History(' + this.get('id') + ',' + this.get('name') + ')';\n\t }\n\t }));\n\t\n\t //==============================================================================\n\t var _collectionSuper = CONTROLLED_FETCH_COLLECTION.InfinitelyScrollingCollection;\n\t /** @class A collection of histories (per user)\n\t * that maintains the current history as the first in the collection.\n\t * New or copied histories become the current history.\n\t */\n\t var HistoryCollection = _collectionSuper.extend(BASE_MVC.LoggableMixin).extend({\n\t _logNamespace: 'history',\n\t\n\t model: History,\n\t /** @type {String} initial order used by collection */\n\t order: 'update_time',\n\t /** @type {Number} limit used for the first fetch (or a reset) */\n\t limitOnFirstFetch: 10,\n\t /** @type {Number} limit used for each subsequent fetch */\n\t limitPerFetch: 10,\n\t\n\t initialize: function (models, options) {\n\t options = options || {};\n\t this.log('HistoryCollection.initialize', models, options);\n\t _collectionSuper.prototype.initialize.call(this, models, options);\n\t\n\t /** @type {boolean} should deleted histories be included */\n\t this.includeDeleted = options.includeDeleted || false;\n\t\n\t /** @type {String} encoded id of the history that's current */\n\t this.currentHistoryId = options.currentHistoryId;\n\t\n\t this.setUpListeners();\n\t // note: models are sent to reset *after* this fn ends; up to this point\n\t // the collection *is empty*\n\t },\n\t\n\t urlRoot: Galaxy.root + 'api/histories',\n\t url: function () {\n\t return this.urlRoot;\n\t },\n\t\n\t /** set up reflexive event handlers */\n\t setUpListeners: function setUpListeners() {\n\t return this.on({\n\t // when a history is deleted, remove it from the collection (if optionally set to do so)\n\t 'change:deleted': function (history) {\n\t // TODO: this becomes complicated when more filters are used\n\t this.debug('change:deleted', this.includeDeleted, history.get('deleted'));\n\t if (!this.includeDeleted && history.get('deleted')) {\n\t this.remove(history);\n\t }\n\t },\n\t // listen for a history copy, setting it to current\n\t 'copied': function (original, newData) {\n\t this.setCurrent(new History(newData, []));\n\t },\n\t // when a history is made current, track the id in the collection\n\t 'set-as-current': function (history) {\n\t var oldCurrentId = this.currentHistoryId;\n\t this.trigger('no-longer-current', oldCurrentId);\n\t this.currentHistoryId = history.id;\n\t }\n\t });\n\t },\n\t\n\t /** override to change view */\n\t _buildFetchData: function (options) {\n\t return _.extend(_collectionSuper.prototype._buildFetchData.call(this, options), {\n\t view: 'dev-detailed'\n\t });\n\t },\n\t\n\t /** override to filter out deleted and purged */\n\t _buildFetchFilters: function (options) {\n\t var superFilters = _collectionSuper.prototype._buildFetchFilters.call(this, options) || {};\n\t var filters = {};\n\t if (!this.includeDeleted) {\n\t filters.deleted = false;\n\t filters.purged = false;\n\t } else {\n\t // force API to return both deleted and non\n\t //TODO: when the API is updated, remove this\n\t filters.deleted = null;\n\t }\n\t return _.defaults(superFilters, filters);\n\t },\n\t\n\t /** override to fetch current as well (as it may be outside the first 10, etc.) */\n\t fetchFirst: function (options) {\n\t var self = this;\n\t // TODO: batch?\n\t var xhr = $.when();\n\t if (this.currentHistoryId) {\n\t xhr = _collectionSuper.prototype.fetchFirst.call(self, {\n\t silent: true,\n\t limit: 1,\n\t filters: {\n\t // without these a deleted current history will return [] here and block the other xhr\n\t 'purged': '',\n\t 'deleted': '',\n\t 'encoded_id-in': this.currentHistoryId\n\t }\n\t });\n\t }\n\t return xhr.then(function () {\n\t options = options || {};\n\t options.offset = 0;\n\t return self.fetchMore(options);\n\t });\n\t },\n\t\n\t /** @type {Object} map of collection available sorting orders containing comparator fns */\n\t comparators: _.extend(_.clone(_collectionSuper.prototype.comparators), {\n\t 'name': BASE_MVC.buildComparator('name', { ascending: true }),\n\t 'name-dsc': BASE_MVC.buildComparator('name', { ascending: false }),\n\t 'size': BASE_MVC.buildComparator('size', { ascending: false }),\n\t 'size-asc': BASE_MVC.buildComparator('size', { ascending: true })\n\t }),\n\t\n\t /** override to always have the current history first */\n\t sort: function (options) {\n\t options = options || {};\n\t var silent = options.silent;\n\t var currentHistory = this.remove(this.get(this.currentHistoryId));\n\t _collectionSuper.prototype.sort.call(this, _.defaults({ silent: true }, options));\n\t this.unshift(currentHistory, { silent: true });\n\t if (!silent) {\n\t this.trigger('sort', this, options);\n\t }\n\t return this;\n\t },\n\t\n\t /** create a new history and by default set it to be the current history */\n\t create: function create(data, hdas, historyOptions, xhrOptions) {\n\t //TODO: .create is actually a collection function that's overridden here\n\t var collection = this,\n\t xhr = jQuery.getJSON(Galaxy.root + 'history/create_new_current');\n\t return xhr.done(function (newData) {\n\t collection.setCurrent(new History(newData, [], historyOptions || {}));\n\t });\n\t },\n\t\n\t /** set the current history to the given history, placing it first in the collection.\n\t * Pass standard bbone options for use in unshift.\n\t * @triggers new-current passed history and this collection\n\t */\n\t setCurrent: function (history, options) {\n\t options = options || {};\n\t // new histories go in the front\n\t this.unshift(history, options);\n\t this.currentHistoryId = history.get('id');\n\t if (!options.silent) {\n\t this.trigger('new-current', history, this);\n\t }\n\t return this;\n\t },\n\t\n\t toString: function toString() {\n\t return 'HistoryCollection(' + this.length + ',current:' + this.currentHistoryId + ')';\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t History: History,\n\t HistoryCollection: HistoryCollection\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__(3), __webpack_require__(1), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 53 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(6)], __WEBPACK_AMD_DEFINE_RESULT__ = function (BASE_MVC) {\n\t\n\t 'use strict';\n\t\n\t var logNamespace = 'history';\n\t\n\t // ============================================================================\n\t /** session storage for individual history preferences */\n\t var HistoryPrefs = BASE_MVC.SessionStorageModel.extend(\n\t /** @lends HistoryPrefs.prototype */{\n\t //TODO:?? move to user prefs?\n\t defaults: {\n\t //TODO:?? expandedIds to array?\n\t expandedIds: {},\n\t show_deleted: false,\n\t show_hidden: false\n\t },\n\t\n\t /** add an hda id to the hash of expanded hdas */\n\t addExpanded: function (model) {\n\t //TODO: use type_id and not model\n\t var current = this.get('expandedIds');\n\t current[model.id] = model.get('id');\n\t this.save('expandedIds', current);\n\t },\n\t\n\t /** remove an hda id from the hash of expanded hdas */\n\t removeExpanded: function (model) {\n\t var current = this.get('expandedIds');\n\t delete current[model.id];\n\t this.save('expandedIds', current);\n\t },\n\t\n\t isExpanded: function (contentId) {\n\t return _.result(this.get('expandedIds'), contentId, false);\n\t },\n\t\n\t allExpanded: function () {\n\t return _.values(this.get('expandedIds'));\n\t },\n\t\n\t clearExpanded: function () {\n\t this.set('expandedIds', {});\n\t },\n\t\n\t includeDeleted: function (val) {\n\t // moving the invocation here so other components don't need to know the key\n\t // TODO: change this key later\n\t if (!_.isUndefined(val)) {\n\t this.set('show_deleted', val);\n\t }\n\t return this.get('show_deleted');\n\t },\n\t\n\t includeHidden: function (val) {\n\t // TODO: change this key later\n\t if (!_.isUndefined(val)) {\n\t this.set('show_hidden', val);\n\t }\n\t return this.get('show_hidden');\n\t },\n\t\n\t toString: function () {\n\t return 'HistoryPrefs(' + this.id + ')';\n\t }\n\t\n\t }, {\n\t // ........................................................................ class vars\n\t // class lvl for access w/o instantiation\n\t storageKeyPrefix: 'history:',\n\t\n\t /** key string to store each histories settings under */\n\t historyStorageKey: function historyStorageKey(historyId) {\n\t if (!historyId) {\n\t throw new Error('HistoryPrefs.historyStorageKey needs valid id: ' + historyId);\n\t }\n\t // single point of change\n\t return HistoryPrefs.storageKeyPrefix + historyId;\n\t },\n\t\n\t /** return the existing storage for the history with the given id (or create one if it doesn't exist) */\n\t get: function get(historyId) {\n\t return new HistoryPrefs({ id: HistoryPrefs.historyStorageKey(historyId) });\n\t },\n\t\n\t /** clear all history related items in sessionStorage */\n\t clearAll: function clearAll(historyId) {\n\t for (var key in sessionStorage) {\n\t if (key.indexOf(HistoryPrefs.storageKeyPrefix) === 0) {\n\t sessionStorage.removeItem(key);\n\t }\n\t }\n\t }\n\t });\n\t\n\t //==============================================================================\n\t return {\n\t HistoryPrefs: HistoryPrefs\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/* 54 */\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__ = [__webpack_require__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (BASE_MVC, _l) {\n\t\n\t 'use strict';\n\t\n\t var logNamespace = 'list';\n\t //==============================================================================\n\t /** A view which, when first rendered, shows only summary data/attributes, but\n\t * can be expanded to show further details (and optionally fetch those\n\t * details from the server).\n\t */\n\t var ExpandableView = Backbone.View.extend(BASE_MVC.LoggableMixin).extend({\n\t _logNamespace: logNamespace,\n\t\n\t //TODO: Although the reasoning behind them is different, this shares a lot with HiddenUntilActivated above: combine them\n\t //PRECONDITION: model must have method hasDetails\n\t //PRECONDITION: subclasses must have templates.el and templates.details\n\t\n\t initialize: function (attributes) {\n\t /** are the details of this view expanded/shown or not? */\n\t this.expanded = attributes.expanded || false;\n\t this.log('\\t expanded:', this.expanded);\n\t this.fxSpeed = attributes.fxSpeed !== undefined ? attributes.fxSpeed : this.fxSpeed;\n\t },\n\t\n\t // ........................................................................ render main\n\t /** jq fx speed */\n\t fxSpeed: 'fast',\n\t\n\t /** Render this content, set up ui.\n\t * @param {Number or String} speed the speed of the render\n\t */\n\t render: function (speed) {\n\t var $newRender = this._buildNewRender();\n\t this._setUpBehaviors($newRender);\n\t this._queueNewRender($newRender, speed);\n\t return this;\n\t },\n\t\n\t /** Build a temp div containing the new children for the view's $el.\n\t * If the view is already expanded, build the details as well.\n\t */\n\t _buildNewRender: function () {\n\t // create a new render using a skeleton template, render title buttons, render body, and set up events, etc.\n\t var $newRender = $(this.templates.el(this.model.toJSON(), this));\n\t if (this.expanded) {\n\t this.$details($newRender).replaceWith(this._renderDetails().show());\n\t }\n\t return $newRender;\n\t },\n\t\n\t /** Fade out the old el, swap in the new contents, then fade in.\n\t * @param {Number or String} speed jq speed to use for rendering effects\n\t * @fires rendered when rendered\n\t */\n\t _queueNewRender: function ($newRender, speed) {\n\t speed = speed === undefined ? this.fxSpeed : speed;\n\t var view = this;\n\t\n\t if (speed === 0) {\n\t view._swapNewRender($newRender);\n\t view.trigger('rendered', view);\n\t } else {\n\t $(view).queue('fx', [function (next) {\n\t view.$el.fadeOut(speed, next);\n\t }, function (next) {\n\t view._swapNewRender($newRender);\n\t next();\n\t }, function (next) {\n\t view.$el.fadeIn(speed, next);\n\t }, function (next) {\n\t view.trigger('rendered', view);\n\t next();\n\t }]);\n\t }\n\t },\n\t\n\t /** empty out the current el, move the $newRender's children in */\n\t _swapNewRender: function ($newRender) {\n\t return this.$el.empty().attr('class', _.isFunction(this.className) ? this.className() : this.className).append($newRender.children());\n\t },\n\t\n\t /** set up js behaviors, event handlers for elements within the given container\n\t * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el)\n\t */\n\t _setUpBehaviors: function ($where) {\n\t $where = $where || this.$el;\n\t // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.)\n\t //make_popup_menus( $where );\n\t $where.find('[title]').tooltip({ placement: 'bottom' });\n\t },\n\t\n\t // ......................................................................... details\n\t /** shortcut to details DOM (as jQ) */\n\t $details: function ($where) {\n\t $where = $where || this.$el;\n\t return $where.find('> .details');\n\t },\n\t\n\t /** build the DOM for the details and set up behaviors on it */\n\t _renderDetails: function () {\n\t var $newDetails = $(this.templates.details(this.model.toJSON(), this));\n\t this._setUpBehaviors($newDetails);\n\t return $newDetails;\n\t },\n\t\n\t // ......................................................................... expansion/details\n\t /** Show or hide the details\n\t * @param {Boolean} expand if true, expand; if false, collapse\n\t */\n\t toggleExpanded: function (expand) {\n\t expand = expand === undefined ? !this.expanded : expand;\n\t if (expand) {\n\t this.expand();\n\t } else {\n\t this.collapse();\n\t }\n\t return this;\n\t },\n\t\n\t /** Render and show the full, detailed body of this view including extra data and controls.\n\t * note: if the model does not have detailed data, fetch that data before showing the body\n\t * @fires expanded when a body has been expanded\n\t */\n\t expand: function () {\n\t var view = this;\n\t return view._fetchModelDetails().always(function () {\n\t view._expand();\n\t });\n\t },\n\t\n\t /** Check for model details and, if none, fetch them.\n\t * @returns {jQuery.promise} the model.fetch.xhr if details are being fetched, an empty promise if not\n\t */\n\t _fetchModelDetails: function () {\n\t if (!this.model.hasDetails()) {\n\t return this.model.fetch();\n\t }\n\t return jQuery.when();\n\t },\n\t\n\t /** Inner fn called when expand (public) has fetched the details */\n\t _expand: function () {\n\t var view = this,\n\t $newDetails = view._renderDetails();\n\t view.$details().replaceWith($newDetails);\n\t // needs to be set after the above or the slide will not show\n\t view.expanded = true;\n\t view.$details().slideDown(view.fxSpeed, function () {\n\t view.trigger('expanded', view);\n\t });\n\t },\n\t\n\t /** Hide the body/details of an HDA.\n\t * @fires collapsed when a body has been collapsed\n\t */\n\t collapse: function () {\n\t this.debug(this + '(ExpandableView).collapse');\n\t var view = this;\n\t view.expanded = false;\n\t this.$details().slideUp(view.fxSpeed, function () {\n\t view.trigger('collapsed', view);\n\t });\n\t }\n\t\n\t });\n\t\n\t //==============================================================================\n\t /** A view that is displayed in some larger list/grid/collection.\n\t * Inherits from Expandable, Selectable, Draggable.\n\t * The DOM contains warnings, a title bar, and a series of primary action controls.\n\t * Primary actions are meant to be easily accessible item functions (such as delete)\n\t * that are rendered in the title bar.\n\t *\n\t * Details are rendered when the user clicks the title bar or presses enter/space when\n\t * the title bar is in focus.\n\t *\n\t * Designed as a base class for history panel contents - but usable elsewhere (I hope).\n\t */\n\t var ListItemView = ExpandableView.extend(BASE_MVC.mixin(BASE_MVC.SelectableViewMixin, BASE_MVC.DraggableViewMixin, {\n\t\n\t tagName: 'div',\n\t className: 'list-item',\n\t\n\t /** Set up the base class and all mixins */\n\t initialize: function (attributes) {\n\t ExpandableView.prototype.initialize.call(this, attributes);\n\t BASE_MVC.SelectableViewMixin.initialize.call(this, attributes);\n\t BASE_MVC.DraggableViewMixin.initialize.call(this, attributes);\n\t this._setUpListeners();\n\t },\n\t\n\t /** event listeners */\n\t _setUpListeners: function () {\n\t // hide the primary actions in the title bar when selectable and narrow\n\t this.on('selectable', function (isSelectable) {\n\t if (isSelectable) {\n\t this.$('.primary-actions').hide();\n\t } else {\n\t this.$('.primary-actions').show();\n\t }\n\t }, this);\n\t return this;\n\t },\n\t\n\t // ........................................................................ rendering\n\t /** In this override, call methods to build warnings, titlebar and primary actions */\n\t _buildNewRender: function () {\n\t var $newRender = ExpandableView.prototype._buildNewRender.call(this);\n\t $newRender.children('.warnings').replaceWith(this._renderWarnings());\n\t $newRender.children('.title-bar').replaceWith(this._renderTitleBar());\n\t $newRender.children('.primary-actions').append(this._renderPrimaryActions());\n\t $newRender.find('> .title-bar .subtitle').replaceWith(this._renderSubtitle());\n\t return $newRender;\n\t },\n\t\n\t /** In this override, render the selector controls and set up dragging before the swap */\n\t _swapNewRender: function ($newRender) {\n\t ExpandableView.prototype._swapNewRender.call(this, $newRender);\n\t if (this.selectable) {\n\t this.showSelector(0);\n\t }\n\t if (this.draggable) {\n\t this.draggableOn();\n\t }\n\t return this.$el;\n\t },\n\t\n\t /** Render any warnings the item may need to show (e.g. \"I'm deleted\") */\n\t _renderWarnings: function () {\n\t var view = this,\n\t $warnings = $('
'),\n\t json = view.model.toJSON();\n\t //TODO:! unordered (map)\n\t _.each(view.templates.warnings, function (templateFn) {\n\t $warnings.append($(templateFn(json, view)));\n\t });\n\t return $warnings;\n\t },\n\t\n\t /** Render the title bar (the main/exposed SUMMARY dom element) */\n\t _renderTitleBar: function () {\n\t return $(this.templates.titleBar(this.model.toJSON(), this));\n\t },\n\t\n\t /** Return an array of jQ objects containing common/easily-accessible item controls */\n\t _renderPrimaryActions: function () {\n\t // override this\n\t return [];\n\t },\n\t\n\t /** Render the title bar (the main/exposed SUMMARY dom element) */\n\t _renderSubtitle: function () {\n\t return $(this.templates.subtitle(this.model.toJSON(), this));\n\t },\n\t\n\t // ......................................................................... events\n\t /** event map */\n\t events: {\n\t // expand the body when the title is clicked or when in focus and space or enter is pressed\n\t 'click .title-bar': '_clickTitleBar',\n\t 'keydown .title-bar': '_keyDownTitleBar',\n\t 'click .selector': 'toggleSelect'\n\t },\n\t\n\t /** expand when the title bar is clicked */\n\t _clickTitleBar: function (event) {\n\t event.stopPropagation();\n\t if (event.altKey) {\n\t this.toggleSelect(event);\n\t if (!this.selectable) {\n\t this.showSelector();\n\t }\n\t } else {\n\t this.toggleExpanded();\n\t }\n\t },\n\t\n\t /** expand when the title bar is in focus and enter or space is pressed */\n\t _keyDownTitleBar: function (event) {\n\t // bail (with propagation) if keydown and not space or enter\n\t var KEYCODE_SPACE = 32,\n\t KEYCODE_RETURN = 13;\n\t if (event && event.type === 'keydown' && (event.keyCode === KEYCODE_SPACE || event.keyCode === KEYCODE_RETURN)) {\n\t this.toggleExpanded();\n\t event.stopPropagation();\n\t return false;\n\t }\n\t return true;\n\t },\n\t\n\t // ......................................................................... misc\n\t /** String representation */\n\t toString: function () {\n\t var modelString = this.model ? this.model + '' : '(no model)';\n\t return 'ListItemView(' + modelString + ')';\n\t }\n\t }));\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t ListItemView.prototype.templates = function () {\n\t\n\t var elTemplato = BASE_MVC.wrapTemplate(['',\n\t // errors, messages, etc.\n\t '
',\n\t\n\t // multi-select checkbox\n\t '
', '
',\n\t // space for title bar buttons - gen. floated to the right\n\t '
', '
',\n\t\n\t // expandable area for more details\n\t '
', '
',\n\t //TODO: prob. belongs in dataset-list-item\n\t '
', '
', '<%- element.name %> ', '
', '
', '
']);\n\t\n\t var detailsTemplate = BASE_MVC.wrapTemplate([\n\t // override this\n\t '
']);\n\t\n\t return {\n\t el: elTemplato,\n\t warnings: warnings,\n\t titleBar: titleBarTemplate,\n\t subtitle: subtitleTemplate,\n\t details: detailsTemplate\n\t };\n\t }();\n\t\n\t //==============================================================================\n\t /** A view that is displayed in some larger list/grid/collection.\n\t * *AND* can display some sub-list of it's own when expanded (e.g. dataset collections).\n\t * This list will 'foldout' when the item is expanded depending on this.foldoutStyle:\n\t * If 'foldout': will expand vertically to show the nested list\n\t * If 'drilldown': will overlay the parent list\n\t *\n\t * Inherits from ListItemView.\n\t *\n\t * _renderDetails does the work of creating this.details: a sub-view that shows the nested list\n\t */\n\t var FoldoutListItemView = ListItemView.extend({\n\t\n\t /** If 'foldout': show the sub-panel inside the expanded item\n\t * If 'drilldown': only fire events and handle by pub-sub\n\t * (allow the panel containing this item to attach it, hide itself, etc.)\n\t */\n\t foldoutStyle: 'foldout',\n\t /** Panel view class to instantiate for the sub-panel */\n\t foldoutPanelClass: null,\n\t\n\t /** override to:\n\t * add attributes foldoutStyle and foldoutPanelClass for config poly\n\t * disrespect attributes.expanded if drilldown\n\t */\n\t initialize: function (attributes) {\n\t if (this.foldoutStyle === 'drilldown') {\n\t this.expanded = false;\n\t }\n\t this.foldoutStyle = attributes.foldoutStyle || this.foldoutStyle;\n\t this.foldoutPanelClass = attributes.foldoutPanelClass || this.foldoutPanelClass;\n\t\n\t ListItemView.prototype.initialize.call(this, attributes);\n\t this.foldout = this._createFoldoutPanel();\n\t },\n\t\n\t /** in this override, attach the foldout panel when rendering details */\n\t _renderDetails: function () {\n\t if (this.foldoutStyle === 'drilldown') {\n\t return $();\n\t }\n\t var $newDetails = ListItemView.prototype._renderDetails.call(this);\n\t return this._attachFoldout(this.foldout, $newDetails);\n\t },\n\t\n\t /** In this override, handle collection expansion. */\n\t _createFoldoutPanel: function () {\n\t var model = this.model;\n\t var FoldoutClass = this._getFoldoutPanelClass(model),\n\t options = this._getFoldoutPanelOptions(model),\n\t foldout = new FoldoutClass(_.extend(options, {\n\t model: model\n\t }));\n\t return foldout;\n\t },\n\t\n\t /** Stub to return proper foldout panel class */\n\t _getFoldoutPanelClass: function () {\n\t // override\n\t return this.foldoutPanelClass;\n\t },\n\t\n\t /** Stub to return proper foldout panel options */\n\t _getFoldoutPanelOptions: function () {\n\t return {\n\t // propagate foldout style down\n\t foldoutStyle: this.foldoutStyle,\n\t fxSpeed: this.fxSpeed\n\t };\n\t },\n\t\n\t /** Render the foldout panel inside the view, hiding controls */\n\t _attachFoldout: function (foldout, $whereTo) {\n\t $whereTo = $whereTo || this.$('> .details');\n\t this.foldout = foldout.render(0);\n\t foldout.$('> .controls').hide();\n\t return $whereTo.append(foldout.$el);\n\t },\n\t\n\t /** In this override, branch on foldoutStyle to show expanded */\n\t expand: function () {\n\t var view = this;\n\t return view._fetchModelDetails().always(function () {\n\t if (view.foldoutStyle === 'foldout') {\n\t view._expand();\n\t } else if (view.foldoutStyle === 'drilldown') {\n\t view._expandByDrilldown();\n\t }\n\t });\n\t },\n\t\n\t /** For drilldown, set up close handler and fire expanded:drilldown\n\t * containing views can listen to this and handle other things\n\t * (like hiding themselves) by listening for expanded/collapsed:drilldown\n\t */\n\t _expandByDrilldown: function () {\n\t var view = this;\n\t // attachment and rendering done by listener\n\t view.listenTo(view.foldout, 'close', function () {\n\t view.trigger('collapsed:drilldown', view, view.foldout);\n\t });\n\t view.trigger('expanded:drilldown', view, view.foldout);\n\t }\n\t\n\t });\n\t\n\t // ............................................................................ TEMPLATES\n\t /** underscore templates */\n\t FoldoutListItemView.prototype.templates = function () {\n\t\n\t var detailsTemplate = BASE_MVC.wrapTemplate(['',\n\t // override with more info (that goes above the panel)\n\t '
'], 'collection');\n\t\n\t return _.extend({}, ListItemView.prototype.templates, {\n\t details: detailsTemplate\n\t });\n\t }();\n\t\n\t //==============================================================================\n\t return {\n\t ExpandableView: ExpandableView,\n\t ListItemView: ListItemView,\n\t FoldoutListItemView: FoldoutListItemView\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__(3), __webpack_require__(1), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 55 */\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__(6), __webpack_require__(5)], __WEBPACK_AMD_DEFINE_RESULT__ = function (baseMVC, _l) {\n\t // =============================================================================\n\t /** A view on any model that has a 'tags' attribute (a list of tag strings)\n\t * Incorporates the select2 jQuery plugin for tags display/editing:\n\t * http://ivaynberg.github.io/select2/\n\t */\n\t var TagsEditor = Backbone.View.extend(baseMVC.LoggableMixin).extend(baseMVC.HiddenUntilActivatedViewMixin).extend({\n\t\n\t tagName: 'div',\n\t className: 'tags-display',\n\t\n\t /** Set up listeners, parse options */\n\t initialize: function (options) {\n\t //console.debug( this, options );\n\t // only listen to the model only for changes to tags - re-render\n\t if (options.usePrompt === false) {\n\t this.label = '';\n\t } else {\n\t this.label = '' + _l('Tags') + ' ';\n\t }\n\t this.hiddenUntilActivated(options.$activator, options);\n\t },\n\t\n\t /** Build the DOM elements, call select to on the created input, and set up behaviors */\n\t render: function () {\n\t var self = this;\n\t this.$el.html(this._template());\n\t\n\t this.$input().select2({\n\t placeholder: 'Add tags',\n\t width: '100%',\n\t tags: function () {\n\t // initialize possible tags in the dropdown based on all the tags the user has used so far\n\t return self._getTagsUsed();\n\t }\n\t });\n\t\n\t this._setUpBehaviors();\n\t return this;\n\t },\n\t\n\t _hashToName: function (tag) {\n\t if (tag.startsWith('#')) {\n\t return 'name:' + tag.slice(1);\n\t }\n\t return tag;\n\t },\n\t\n\t _nameToHash: function (tag) {\n\t if (tag.startsWith('name:')) {\n\t tag = '#' + tag.slice(5);\n\t }\n\t return tag;\n\t },\n\t\n\t /** @returns {String} the html text used to build the view's DOM */\n\t _template: function () {\n\t return [this.label,\n\t // set up initial tags by adding as CSV to input vals (necc. to init select2)\n\t '
');\n\t $link.append(templates.tool_link(this.model.toJSON()));\n\t\n\t var formStyle = this.model.get('form_style', null);\n\t // open upload dialog for upload tool\n\t if (this.model.id === 'upload1') {\n\t $link.find('a').on('click', function (e) {\n\t e.preventDefault();\n\t Galaxy.upload.show();\n\t });\n\t } else if (formStyle === 'regular') {\n\t // regular tools\n\t var self = this;\n\t $link.find('a').on('click', function (e) {\n\t e.preventDefault();\n\t Galaxy.router.push('/', { tool_id: self.model.id, version: self.model.get('version') });\n\t });\n\t }\n\t\n\t // add element\n\t this.$el.append($link);\n\t return this;\n\t }\n\t });\n\t\n\t /**\n\t * Panel label/section header.\n\t */\n\t var ToolSectionLabelView = BaseView.extend({\n\t tagName: 'div',\n\t className: 'toolPanelLabel',\n\t\n\t render: function () {\n\t this.$el.append($(\" ',\n\t //TODO: replace with icon\n\t '\" class=\"toolSectionBody\" style=\"display: none;\">', '
', '
'].join('')),\n\t\n\t // a single tool's link in the tool panel; will load the tool form in the center panel\n\t tool_link: _.template(['
', '<% _.each( labels, function( label ){ %>', '\">', '<%- label %>', ' ', '<% }); %>', ' ', '
tool-link\" href=\"<%= link %>\" target=\"<%- target %>\" minsizehint=\"<%- min_width %>\">', '<%- name %>', ' ', ' <%- description %>'].join('')),\n\t\n\t // the tool form for entering tool parameters, viewing help and executing the tool\n\t // loaded when a tool link is clicked in the tool panel\n\t tool_form: _.template(['
<%- tool.name %> (version <%- tool.version %>)
', '
', '<% _.each( tool.inputs, function( input ){ %>', '
', '<% }); %>', '
', '
', '
', '
'].join(''), { variable: 'tool' })\n\t };\n\t\n\t // Exports\n\t return {\n\t ToolParameter: ToolParameter,\n\t IntegerToolParameter: IntegerToolParameter,\n\t SelectToolParameter: SelectToolParameter,\n\t Tool: Tool,\n\t ToolCollection: ToolCollection,\n\t ToolSearch: ToolSearch,\n\t ToolPanel: ToolPanel,\n\t ToolPanelView: ToolPanelView,\n\t ToolFormView: ToolFormView\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__(3), __webpack_require__(1)))\n\n/***/ },\n/* 57 */\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 '
' + '
' + '
';\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 '
' + '