Client build: symlink static/scripts/packed back to static/scripts for backward compatibility, remove cruft

2026-09-24 16:30:27 +08:00 · 2015-03-18 11:01:56 -04:00
parent fdee5896da
commit e351fefdbd
12 changed files with 1 additions and 11 deletions
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+./
@@ -1 +0,0 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/form/form-select-content","mvc/ui/ui-select-library","mvc/ui/ui-color-picker"],function(d,e,a,c,b){return Backbone.Model.extend({types:{text:"_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"},initialize:function(g,f){this.app=g},create:function(f){if(f.value===undefined){f.value=null}if(f.default_value===undefined){f.default_value=f.value}var h=null;var g=this.types[f.type];if(g&&typeof(this[g])==="function"){h=this[g].call(this,f)}if(!h){this.app.incompatible=true;if(f.options){h=this._fieldSelect(f)}else{h=this._fieldText(f)}console.debug("tools-form::_addRow() : Auto matched field type ("+f.type+").")}if(f.value!==undefined){h.value(f.value)}return h},_fieldData:function(f){if(!this.app.options.is_dynamic){f.info="Data input '"+f.name+"' ("+d.textify(f.extensions.toString())+")";f.value=null;return this._fieldHidden(f)}var g=this;return new a.View(this.app,{id:"field-"+f.id,extensions:f.extensions,optional:f.optional,multiple:f.multiple,type:f.type,data:f.options,onchange:function(){g.app.trigger("change")}})},_fieldSelect:function(f){if(!this.app.options.is_dynamic&&f.is_dynamic){return this._fieldText(f)}if(f.type=="data_column"){f.error_text="Missing columns in referenced dataset."}var h=[];for(var j in f.options){var k=f.options[j];h.push({label:k[0],value:k[1]})}var l=e.Select;switch(f.display){case"checkboxes":l=e.Checkbox;break;case"radio":l=e.Radio;break}var g=this;return new l.View({id:"field-"+f.id,data:h,error_text:f.error_text||"No options available",optional:f.optional&&f.default_value===null,multiple:f.multiple,searchable:f.searchable,onchange:function(){g.app.trigger("change")}})},_fieldDrilldown:function(f){if(!this.app.options.is_dynamic&&f.is_dynamic){return this._fieldText(f)}var g=this;return new e.Drilldown.View({id:"field-"+f.id,data:f.options,display:f.display,onchange:function(){g.app.trigger("change")}})},_fieldText:function(f){if(f.options){f.area=f.multiple;if(!d.validate(f.value)){f.value=""}else{if(f.value instanceof Array){f.value=value.toString()}else{f.value=String(f.value).replace(/[\[\]'"\s]/g,"");if(f.multiple){f.value=f.value.replace(/,/g,"\n")}}}}var g=this;return new e.Input({id:"field-"+f.id,area:f.area,onchange:function(){g.app.trigger("change")}})},_fieldSlider:function(f){var g=this;return new e.Slider.View({id:"field-"+f.id,precise:f.type=="float",min:f.min,max:f.max,onchange:function(){g.app.trigger("change")}})},_fieldHidden:function(f){return new e.Hidden({id:"field-"+f.id,info:f.info})},_fieldBoolean:function(f){var g=this;return new e.RadioButton.View({id:"field-"+f.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){g.app.trigger("change")}})},_fieldColor:function(f){var g=this;return new b({id:"field-"+f.id,onchange:function(){g.app.trigger("change")}})},_fieldLibrary:function(f){var g=this;return new c.View({id:"field-"+f.id,optional:f.optional,multiple:f.multiple,onchange:function(){g.app.trigger("change")}})}});return{View:View}});
@@ -1 +0,0 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){history={};var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(this.template_batch());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(h){var f=this;function g(m,j){if(m){var n=[];for(var k in j){var l=j[k];n.push({label:l.hid+": "+l.name,value:l.id});history[l.id+"_"+l.src]=l}m.update(n)}}g(this.select_single,h.hda);g(this.select_multiple,h.hda);g(this.select_collection,h.hdca)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hdca"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=history[k[h]+"_"+this.list[this.current].type];if(g){f.values.push(g)}else{return null}}f.values.sort(function(n,i){return n.hid-i.hid});return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=history[this._select().value()+"_hdca"];if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false},template_batch:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.</div>'}});return{View:d}});
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-define(["mvc/history/history-content-model","mvc/history/hda-model","mvc/history/hdca-model","mvc/base-mvc","utils/localization"],function(g,e,b,a,c){var f=Backbone.Collection.extend(a.LoggableMixin).extend({model:function(i,h){if(i.history_content_type==="dataset"){return new e.HistoryDatasetAssociation(i,h)}else{if(i.history_content_type==="dataset_collection"){switch(i.collection_type){case"list":return new b.HistoryListDatasetCollection(i,h);case"paired":return new b.HistoryPairDatasetCollection(i,h);case"list:paired":return new b.HistoryListPairedDatasetCollection(i,h)}throw new TypeError("Unknown collection_type: "+i.collection_type)}}throw new TypeError("Unknown history_content_type: "+i.history_content_type)},initialize:function(i,h){h=h||{};this.historyId=h.historyId;this.model.prototype.idAttribute="type_id";this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(j){var i=!j.inReadyState();if(i){h.push(j.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];this.debug("checking isVisible");var i=new f(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new f(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(m,j){var i=jQuery.Deferred(),h=this.length,l=[];if(!h){i.resolve([]);return i}var k=this.chain().reverse().map(function(o,n){return function(){var p=m.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){l.push(q);if(k.length){k.shift()()}else{i.resolve(l)}})}}).value();k.shift()();return i},isCopyable:function(i){var h=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return((_.isObject(i)&&i.id)&&(_.contains(h,i.model_class)))},copy:function(h){var m,i,l;if(_.isString(h)){m=h;l="hda";i="dataset"}else{m=h.id;l=({HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"})[h.model_class]||"hda";i=(l==="hdca"?"dataset_collection":"dataset")}var k=this,j=jQuery.post(this.url(),{content:m,source:l,type:i}).done(function(n){k.add([n])}).fail(function(o,n,p){k.trigger("error",k,j,{},"Error copying contents",{type:i,id:m,source:l})});return j},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(i,h){_.each(i,function(j){if(!j.type_id||!j.get("type_id")){j.type_id=g.typeIdStr(j.history_content_type,j.id)}});Backbone.Collection.prototype.set.call(this,i,h)},promoteToHistoryDatasetCollection:function d(m,k,i){i=i||{};i.url=this.url();i.type="POST";var o=k;var l=[],h=null;if(k==="list"){this.chain().each(function(r){var p=r.attributes.name;var s=r.get("id");var q=r.attributes.history_content_type;if(q==="dataset"){if(o!=="list"){this.log("Invalid collection type")}l.push({name:p,src:"hda",id:s})}else{if(o==="list"){o="list:"+r.attributes.collection_type}else{if(o!=="list:"+r.attributes.collection_type){this.log("Invalid collection type")}}l.push({name:p,src:"hdca",id:s})}});h="New Dataset List"}else{if(k==="paired"){var j=this.ids();if(j.length!==2){}l.push({name:"forward",src:"hda",id:j[0]});l.push({name:"reverse",src:"hda",id:j[1]});h="New Dataset Pair"}}i.data={type:"dataset_collection",name:h,collection_type:o,element_identifiers:JSON.stringify(l)};var n=jQuery.ajax(i);n.done(function(r,p,q){m.refresh()});n.fail(function(r,p,q){if(r.responseJSON&&r.responseJSON.error){error=r.responseJSON.error}else{error=r.responseJSON}r.responseText=error});return n},clone:function(){var h=Backbone.Collection.prototype.clone.call(this);h.historyId=this.historyId;return h},print:function(){var h=this;h.each(function(i){h.debug(i);if(i.elements){h.debug("\t elements:",i.elements)}})},toString:function(){return(["HistoryContents(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryContents:f}});
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-define(["mvc/history/history-contents","mvc/base-mvc","utils/localization"],function(h,i,d){var e=Backbone.Model.extend(i.LoggableMixin).extend(i.mixin(i.SearchableModelMixin,{defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(k,l,j){j=j||{};this.logger=j.logger||null;this.log(this+".initialize:",k,l,j);this.log("creating history contents:",l);this.contents=new h.HistoryContents(l||[],{historyId:this.get("id")});this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});if(this.contents){this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(k,j){if(this.contents){this.contents.historyId=j}},this)},errorHandler:function(k,n,j,m,l){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},contentsCount:function(){return _.reduce(_.values(this.get("state_details")),function(j,k){return j+k},0)},searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},checkForUpdates:function(j){if(this.contents.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(j)){j.call(this)}}return this},setUpdateTimeout:function(j){j=j||e.UPDATE_DELAY;var k=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){k.refresh()},j);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(k,j){k=k||[];j=j||{};var l=this;j.data=j.data||{};if(k.length){j.data.details=k.join(",")}var m=this.contents.fetch(j);m.done(function(n){l.checkForUpdates(function(){this.fetch()})});return m},_delete:function(j){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},j)},purge:function(j){if(this.get("purged")){return jQuery.when()}return this.save({deleted:true,purged:true},j)},undelete:function(j){if(!this.get("deleted")){return jQuery.when()}return this.save({deleted:false},j)},copy:function(m,k){m=(m!==undefined)?(m):(true);if(!this.id){throw new Error("You must set the history ID before copying it.")}var j={history_id:this.id};if(m){j.current=true}if(k){j.name=k}var l=this,n=jQuery.post(this.urlRoot,j);if(m){return n.then(function(o){var p=new e(o);return p.setAsCurrent().done(function(){l.trigger("copied",l,o)})})}return n.done(function(o){l.trigger("copied",l,o)})},setAsCurrent:function(){var j=this,k=jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+this.id);k.done(function(){j.trigger("set-as-current",j)});return k},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}}));e.UPDATE_DELAY=4000;e.getHistoryData=function c(j,v){v=v||{};var r=v.detailIdsFn||[];var m=v.hdcaDetailIds||[];var s=jQuery.Deferred(),p=null;function k(w){if(j==="current"){return jQuery.getJSON(galaxy_config.root+"history/current_history_json")}return jQuery.ajax(galaxy_config.root+"api/histories/"+j)}function o(w){return w&&w.empty}function q(x){if(o(x)){return[]}if(_.isFunction(r)){r=r(x)}if(_.isFunction(m)){m=m(x)}var w={};if(r.length){w.dataset_details=r.join(",")}if(m.length){w.dataset_collection_details=m.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+x.id+"/contents",{data:w})}var t=v.historyFn||k,u=v.contentsFn||q;var n=t(j);n.done(function(w){p=w;s.notify({status:"history data retrieved",historyJSON:p})});n.fail(function(y,w,x){s.reject(y,"loading the history")});var l=n.then(u);l.then(function(w){s.notify({status:"contents data retrieved",historyJSON:p,contentsJSON:w});s.resolve(p,w)});l.fail(function(y,w,x){s.reject(y,"loading the contents",{history:p})});return s};var f=Backbone.Collection.extend(i.LoggableMixin).extend({model:e,urlRoot:(window.galaxy_config?galaxy_config.root:"/")+"api/histories",initialize:function(k,j){j=j||{};this.log("HistoryCollection.initialize",arguments);this.includeDeleted=j.includeDeleted||false;this.setUpListeners()},setUpListeners:function a(){var j=this;this.on("change:deleted",function(k){this.debug("change:deleted",j.includeDeleted,k.get("deleted"));if(!j.includeDeleted&&k.get("deleted")){j.remove(k)}});this.on("copied",function(k,l){this.unshift(new e(l,[]))})},create:function g(m,k,j,l){var o=this,n=jQuery.getJSON(galaxy_config.root+"history/create_new_current");return n.done(function(p){var q=new e(p,[],j||{});o.unshift(q);o.trigger("new-current")})},toString:function b(){return"HistoryCollection("+this.length+")"}});return{History:e,HistoryCollection:f}});
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-define(["utils/utils"],function(a){return Backbone.View.extend({optionsDefault:{icons:["fa fa-square-o","fa fa-minus-square-o","fa fa-check-square-o"],value:0,title:"Select/Unselect all"},initialize:function(c){this.options=a.merge(c,this.optionsDefault);this.setElement(this._template());this.$title=this.$(".title");this.$icon=this.$(".icon");this.value(this.options.value);this.$title.html(this.options.title);var b=this;this.$el.on("click",function(){b.current=(b.current===0&&2)||0;b.value(b.current);b.options.onclick&&b.options.onclick()})},value:function(b,c){if(b!==undefined){if(c){if(b!==0){if(b!==c){b=1}else{b=2}}}this.current=b;this.$icon.removeClass().addClass("icon").addClass(this.options.icons[b]);this.options.onchange&&this.options.onchange(b)}return this.current},_template:function(){return'<div class="ui-button-check" ><span class="icon"/><span class="title"/></div>'}})});
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-define(["utils/utils","mvc/ui/ui-button-check"],function(c,e){var b=Backbone.View.extend({initialize:function(i){var h=this;this.optionsDefault={visible:true,data:[],id:c.uid(),error_text:"No data available.",wait_text:"Please wait...",multiple:false};this.options=c.merge(i,this.optionsDefault);this.setElement('<div class="ui-options"/>');this.$message=$("<div/>");this.$options=$(this._template(i));this.$menu=$('<div class="ui-options-menu"/>');this.$el.append(this.$message);this.$el.append(this.$menu);this.$el.append(this.$options);if(this.options.multiple){this.all_button=new e({onclick:function(){h.$("input").prop("checked",h.all_button.value()!==0);h.trigger("change")}});this.$menu.append(this.all_button.$el)}if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}this.on("change",function(){this.options.onchange&&this.options.onchange(this.value())})},update:function(i){var l=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(i))}else{for(var j in i){var k=$(this._templateOption(i[j]));k.addClass("ui-option");k.tooltip({title:i[j].tooltip,placement:"bottom"});this.$options.append(k)}}var h=this;this.$("input").on("change",function(){h.value(h._getValue());h.trigger("change")});this.value(l);this.unwait()},value:function(j){if(j!==undefined){this.$("input").prop("checked",false);if(j!==null){if(!(j instanceof Array)){j=[j]}for(var h in j){this.$('input[value="'+j[h]+'"]').first().prop("checked",true)}}}var l=this._getValue();if(this.all_button){var k=l;if(!(k instanceof Array)){k=0}else{k=k.length}this.all_button.value(k,this._size())}return l},exists:function(j){if(j!==undefined){if(!(j instanceof Array)){j=[j]}for(var h in j){if(this.$('input[value="'+j[h]+'"]').length>0){return true}}}return false},first:function(){var h=this.$("input").first();if(h.length>0){return h.val()}else{return null}},wait:function(){if(this._size()==0){this._messageShow(this.options.wait_text,"info");this.$options.hide();this.$menu.hide()}},unwait:function(){var h=this._size();if(h==0){this._messageShow(this.options.error_text,"danger");this.$options.hide();this.$menu.hide()}else{this._messageHide();this.$options.css("display","inline-block");this.$menu.show()}},_getValue:function(){var h=[];this.$(":checked").each(function(){h.push($(this).val())});if(!c.validate(h)){return null}if(this.options.multiple){return h}else{return h[0]}},_size:function(){return this.$(".ui-option").length},_messageShow:function(i,h){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+h);this.$message.html(i)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}});var a=b.extend({_templateOption:function(h){var i=c.uid();return'<div class="ui-option"><input id="'+i+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+h.value+'"/><label class="ui-options-label" for="'+i+'">'+h.label+"</label></div>"}});var f={};f.View=a.extend({initialize:function(h){h.type="radio";a.prototype.initialize.call(this,h)}});var d={};d.View=a.extend({initialize:function(h){h.multiple=true;h.type="checkbox";a.prototype.initialize.call(this,h)}});var g={};g.View=b.extend({initialize:function(h){b.prototype.initialize.call(this,h)},value:function(h){if(h!==undefined){this.$("input").prop("checked",false);this.$("label").removeClass("active");this.$('[value="'+h+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(j){var h="fa "+j.icon;if(!j.label){h+=" no-padding"}var i='<label class="btn btn-default">';if(j.icon){i+='<i class="'+h+'"/>'}i+='<input type="radio" name="'+this.options.id+'" value="'+j.value+'"/>';if(j.label){i+=j.label}i+="</label>";return i},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:b,BaseIcons:a,Radio:f,RadioButton:g,Checkbox:d}});
@@ -1 +0,0 @@
-define(["utils/utils","mvc/ui/ui-button-check"],function(a,b){var c=Backbone.View.extend({optionsDefault:{id:a.uid(),cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:true,optional:false},initialize:function(e){var d=this;this.options=a.merge(e,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){if(this.options.searchable){this.all_button=new b({onclick:function(){var f=[];if(d.all_button.value()!==0){f=d._availableOptions()}d.value(f);d.trigger("change")}});this.$el.prepend(this.all_button.$el)}this.$el.addClass("ui-select-multiple");this.$select.prop("multiple",true);this.$button.remove()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}this.$select.on("change",function(){d.trigger("change")});this.on("change",function(){d.options.onchange&&d.options.onchange(this.value())})},value:function(d){if(d!==undefined){if(d===null){d="__null__"}if(this.exists(d)||this.options.multiple){this.$select.val(d);if(this.$select.select2){this.$select.select2("val",d)}}}var e=this._getValue();if(this.all_button){this.all_button.value($.isArray(e)&&e.length||0,this._size())}return e},first:function(){var d=this.$select.find("option").first();if(d.length>0){return d.val()}else{return null}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},update:function(d){var f=this._getValue();this.$select.find("option").remove();if(!this.options.multiple&&this.options.optional){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var e in d){this.$select.append(this._templateOption(d[e]))}if(this._size()==0){this.disable();this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))}else{this.enable()}if(this.options.searchable){this.$select.select2("destroy");this.$select.select2()}this.value(f);if(this._getValue()===null&&!(this.options.multiple&&this.options.optional)){this.value(this.first())}},setOnChange:function(d){this.options.onchange=d},exists:function(d){return this.$select.find('option[value="'+d+'"]').length>0},_getValue:function(){var d=this.$select.val();if(!a.validate(d)){return null}return d},_availableOptions:function(){var d=[];this.$select.find("option").each(function(f,g){d.push($(g).attr("value"))});return d},_size:function(){return this.$select.find("option").length},_templateOption:function(d){return'<option value="'+d.value+'">'+d.label+"</option>"},_template:function(d){return'<div id="'+d.id+'" class="'+d.cls+'"><select id="'+d.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:c}});
@@ -1 +0,0 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(e,g,b,a){var d=Backbone.Collection.extend({url:galaxy_config.root+"api/libraries"});var c=Backbone.Collection.extend({initialize:function(){var h=this;this.config=new Backbone.Model({library_id:null});this.config.on("change",function(){h.fetch({reset:true})})},url:function(){return galaxy_config.root+"api/libraries/"+this.config.get("library_id")+"/contents"}});var f=Backbone.View.extend({initialize:function(i){var h=this;this.libraries=new d();this.datasets=new c();this.options=i;this.library_select=new g.Select.View({optional:i.optional,onchange:function(j){h.datasets.config.set("library_id",j)}});this.dataset_select=new g.Select.View({optional:i.optional,multiple:i.multiple,onchange:function(){h.trigger("change")}});this.libraries.on("reset",function(){var j=[];h.libraries.each(function(k){j.push({value:k.id,label:k.get("name")})});h.library_select.update(j);h.trigger("change")});this.datasets.on("reset",function(){var k=[];var j=h.library_select.text();if(j!==null){h.datasets.each(function(l){if(l.get("type")==="file"){k.push({value:l.id,label:j+l.get("name")})}})}h.dataset_select.update(k);h.trigger("change")});this.on("change",function(){i.onchange&&i.onchange(h.value())});this.setElement(this._template());this.$(".library-select").append(this.library_select.$el);this.$(".dataset-select").append(this.dataset_select.$el);this.libraries.fetch({reset:true,success:function(){h.library_select.trigger("change");if(h.options.value!==undefined){h.value(h.options.value)}}})},value:function(h){return this.dataset_select.value()},_template:function(){return'<div class="ui-select-library"><div class="library ui-margin-bottom"><span class="library-title">Select Library</span><span class="library-select"/></div><div class="dataset"><span class="dataset-title">Select Dataset</span><span class="dataset-select"/></div></div>'}});return{View:f}});
				`@@ -1 +0,0 @@`
				define(["utils/utils","mvc/ui/ui-misc","mvc/form/form-select-content","mvc/ui/ui-select-library","mvc/ui/ui-color-picker"],function(d,e,a,c,b){return Backbone.Model.extend({types:{text:"_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"},initialize:function(g,f){this.app=g},create:function(f){if(f.value===undefined){f.value=null}if(f.default_value===undefined){f.default_value=f.value}var h=null;var g=this.types[f.type];if(g&&typeof(this[g])==="function"){h=this[g].call(this,f)}if(!h){this.app.incompatible=true;if(f.options){h=this._fieldSelect(f)}else{h=this._fieldText(f)}console.debug("tools-form::_addRow() : Auto matched field type ("+f.type+").")}if(f.value!==undefined){h.value(f.value)}return h},_fieldData:function(f){if(!this.app.options.is_dynamic){f.info="Data input '"+f.name+"' ("+d.textify(f.extensions.toString())+")";f.value=null;return this._fieldHidden(f)}var g=this;return new a.View(this.app,{id:"field-"+f.id,extensions:f.extensions,optional:f.optional,multiple:f.multiple,type:f.type,data:f.options,onchange:function(){g.app.trigger("change")}})},_fieldSelect:function(f){if(!this.app.options.is_dynamic&&f.is_dynamic){return this._fieldText(f)}if(f.type=="data_column"){f.error_text="Missing columns in referenced dataset."}var h=[];for(var j in f.options){var k=f.options[j];h.push({label:k[0],value:k[1]})}var l=e.Select;switch(f.display){case"checkboxes":l=e.Checkbox;break;case"radio":l=e.Radio;break}var g=this;return new l.View({id:"field-"+f.id,data:h,error_text:f.error_text\|\|"No options available",optional:f.optional&&f.default_value===null,multiple:f.multiple,searchable:f.searchable,onchange:function(){g.app.trigger("change")}})},_fieldDrilldown:function(f){if(!this.app.options.is_dynamic&&f.is_dynamic){return this._fieldText(f)}var g=this;return new e.Drilldown.View({id:"field-"+f.id,data:f.options,display:f.display,onchange:function(){g.app.trigger("change")}})},_fieldText:function(f){if(f.options){f.area=f.multiple;if(!d.validate(f.value)){f.value=""}else{if(f.value instanceof Array){f.value=value.toString()}else{f.value=String(f.value).replace(/[\[\]'"\s]/g,"");if(f.multiple){f.value=f.value.replace(/,/g,"\n")}}}}var g=this;return new e.Input({id:"field-"+f.id,area:f.area,onchange:function(){g.app.trigger("change")}})},_fieldSlider:function(f){var g=this;return new e.Slider.View({id:"field-"+f.id,precise:f.type=="float",min:f.min,max:f.max,onchange:function(){g.app.trigger("change")}})},_fieldHidden:function(f){return new e.Hidden({id:"field-"+f.id,info:f.info})},_fieldBoolean:function(f){var g=this;return new e.RadioButton.View({id:"field-"+f.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){g.app.trigger("change")}})},_fieldColor:function(f){var g=this;return new b({id:"field-"+f.id,onchange:function(){g.app.trigger("change")}})},_fieldLibrary:function(f){var g=this;return new c.View({id:"field-"+f.id,optional:f.optional,multiple:f.multiple,onchange:function(){g.app.trigger("change")}})}});return{View:View}});
				`@@ -1 +0,0 @@`
				define(["mvc/history/history-content-model","mvc/history/hda-model","mvc/history/hdca-model","mvc/base-mvc","utils/localization"],function(g,e,b,a,c){var f=Backbone.Collection.extend(a.LoggableMixin).extend({model:function(i,h){if(i.history_content_type==="dataset"){return new e.HistoryDatasetAssociation(i,h)}else{if(i.history_content_type==="dataset_collection"){switch(i.collection_type){case"list":return new b.HistoryListDatasetCollection(i,h);case"paired":return new b.HistoryPairDatasetCollection(i,h);case"list:paired":return new b.HistoryListPairedDatasetCollection(i,h)}throw new TypeError("Unknown collection_type: "+i.collection_type)}}throw new TypeError("Unknown history_content_type: "+i.history_content_type)},initialize:function(i,h){h=h\|\|{};this.historyId=h.historyId;this.model.prototype.idAttribute="type_id";this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(j){var i=!j.inReadyState();if(i){h.push(j.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j\|\|[];this.debug("checking isVisible");var i=new f(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new f(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i\|\|{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(m,j){var i=jQuery.Deferred(),h=this.length,l=[];if(!h){i.resolve([]);return i}var k=this.chain().reverse().map(function(o,n){return function(){var p=m.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){l.push(q);if(k.length){k.shift()()}else{i.resolve(l)}})}}).value();k.shift()();return i},isCopyable:function(i){var h=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return((_.isObject(i)&&i.id)&&(_.contains(h,i.model_class)))},copy:function(h){var m,i,l;if(_.isString(h)){m=h;l="hda";i="dataset"}else{m=h.id;l=({HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"})[h.model_class]\|\|"hda";i=(l==="hdca"?"dataset_collection":"dataset")}var k=this,j=jQuery.post(this.url(),{content:m,source:l,type:i}).done(function(n){k.add([n])}).fail(function(o,n,p){k.trigger("error",k,j,{},"Error copying contents",{type:i,id:m,source:l})});return j},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(i,h){_.each(i,function(j){if(!j.type_id\|\|!j.get("type_id")){j.type_id=g.typeIdStr(j.history_content_type,j.id)}});Backbone.Collection.prototype.set.call(this,i,h)},promoteToHistoryDatasetCollection:function d(m,k,i){i=i\|\|{};i.url=this.url();i.type="POST";var o=k;var l=[],h=null;if(k==="list"){this.chain().each(function(r){var p=r.attributes.name;var s=r.get("id");var q=r.attributes.history_content_type;if(q==="dataset"){if(o!=="list"){this.log("Invalid collection type")}l.push({name:p,src:"hda",id:s})}else{if(o==="list"){o="list:"+r.attributes.collection_type}else{if(o!=="list:"+r.attributes.collection_type){this.log("Invalid collection type")}}l.push({name:p,src:"hdca",id:s})}});h="New Dataset List"}else{if(k==="paired"){var j=this.ids();if(j.length!==2){}l.push({name:"forward",src:"hda",id:j[0]});l.push({name:"reverse",src:"hda",id:j[1]});h="New Dataset Pair"}}i.data={type:"dataset_collection",name:h,collection_type:o,element_identifiers:JSON.stringify(l)};var n=jQuery.ajax(i);n.done(function(r,p,q){m.refresh()});n.fail(function(r,p,q){if(r.responseJSON&&r.responseJSON.error){error=r.responseJSON.error}else{error=r.responseJSON}r.responseText=error});return n},clone:function(){var h=Backbone.Collection.prototype.clone.call(this);h.historyId=this.historyId;return h},print:function(){var h=this;h.each(function(i){h.debug(i);if(i.elements){h.debug("\t elements:",i.elements)}})},toString:function(){return(["HistoryContents(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryContents:f}});
				`@@ -1 +0,0 @@`
				define(["mvc/history/history-contents","mvc/base-mvc","utils/localization"],function(h,i,d){var e=Backbone.Model.extend(i.LoggableMixin).extend(i.mixin(i.SearchableModelMixin,{defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(k,l,j){j=j\|\|{};this.logger=j.logger\|\|null;this.log(this+".initialize:",k,l,j);this.log("creating history contents:",l);this.contents=new h.HistoryContents(l\|\|[],{historyId:this.get("id")});this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});if(this.contents){this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(k,j){if(this.contents){this.contents.historyId=j}},this)},errorHandler:function(k,n,j,m,l){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy\|\|!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()\|\|Galaxy.currUser.id!==this.get("user_id")){return false}return true},contentsCount:function(){return _.reduce(_.values(this.get("state_details")),function(j,k){return j+k},0)},searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},checkForUpdates:function(j){if(this.contents.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(j)){j.call(this)}}return this},setUpdateTimeout:function(j){j=j\|\|e.UPDATE_DELAY;var k=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){k.refresh()},j);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(k,j){k=k\|\|[];j=j\|\|{};var l=this;j.data=j.data\|\|{};if(k.length){j.data.details=k.join(",")}var m=this.contents.fetch(j);m.done(function(n){l.checkForUpdates(function(){this.fetch()})});return m},_delete:function(j){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},j)},purge:function(j){if(this.get("purged")){return jQuery.when()}return this.save({deleted:true,purged:true},j)},undelete:function(j){if(!this.get("deleted")){return jQuery.when()}return this.save({deleted:false},j)},copy:function(m,k){m=(m!==undefined)?(m):(true);if(!this.id){throw new Error("You must set the history ID before copying it.")}var j={history_id:this.id};if(m){j.current=true}if(k){j.name=k}var l=this,n=jQuery.post(this.urlRoot,j);if(m){return n.then(function(o){var p=new e(o);return p.setAsCurrent().done(function(){l.trigger("copied",l,o)})})}return n.done(function(o){l.trigger("copied",l,o)})},setAsCurrent:function(){var j=this,k=jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+this.id);k.done(function(){j.trigger("set-as-current",j)});return k},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}}));e.UPDATE_DELAY=4000;e.getHistoryData=function c(j,v){v=v\|\|{};var r=v.detailIdsFn\|\|[];var m=v.hdcaDetailIds\|\|[];var s=jQuery.Deferred(),p=null;function k(w){if(j==="current"){return jQuery.getJSON(galaxy_config.root+"history/current_history_json")}return jQuery.ajax(galaxy_config.root+"api/histories/"+j)}function o(w){return w&&w.empty}function q(x){if(o(x)){return[]}if(_.isFunction(r)){r=r(x)}if(_.isFunction(m)){m=m(x)}var w={};if(r.length){w.dataset_details=r.join(",")}if(m.length){w.dataset_collection_details=m.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+x.id+"/contents",{data:w})}var t=v.historyFn\|\|k,u=v.contentsFn\|\|q;var n=t(j);n.done(function(w){p=w;s.notify({status:"history data retrieved",historyJSON:p})});n.fail(function(y,w,x){s.reject(y,"loading the history")});var l=n.then(u);l.then(function(w){s.notify({status:"contents data retrieved",historyJSON:p,contentsJSON:w});s.resolve(p,w)});l.fail(function(y,w,x){s.reject(y,"loading the contents",{history:p})});return s};var f=Backbone.Collection.extend(i.LoggableMixin).extend({model:e,urlRoot:(window.galaxy_config?galaxy_config.root:"/")+"api/histories",initialize:function(k,j){j=j\|\|{};this.log("HistoryCollection.initialize",arguments);this.includeDeleted=j.includeDeleted\|\|false;this.setUpListeners()},setUpListeners:function a(){var j=this;this.on("change:deleted",function(k){this.debug("change:deleted",j.includeDeleted,k.get("deleted"));if(!j.includeDeleted&&k.get("deleted")){j.remove(k)}});this.on("copied",function(k,l){this.unshift(new e(l,[]))})},create:function g(m,k,j,l){var o=this,n=jQuery.getJSON(galaxy_config.root+"history/create_new_current");return n.done(function(p){var q=new e(p,[],j\|\|{});o.unshift(q);o.trigger("new-current")})},toString:function b(){return"HistoryCollection("+this.length+")"}});return{History:e,HistoryCollection:f}});
				`@@ -1 +0,0 @@`
				define(["utils/utils"],function(a){return Backbone.View.extend({optionsDefault:{icons:["fa fa-square-o","fa fa-minus-square-o","fa fa-check-square-o"],value:0,title:"Select/Unselect all"},initialize:function(c){this.options=a.merge(c,this.optionsDefault);this.setElement(this._template());this.$title=this.$(".title");this.$icon=this.$(".icon");this.value(this.options.value);this.$title.html(this.options.title);var b=this;this.$el.on("click",function(){b.current=(b.current===0&&2)\|\|0;b.value(b.current);b.options.onclick&&b.options.onclick()})},value:function(b,c){if(b!==undefined){if(c){if(b!==0){if(b!==c){b=1}else{b=2}}}this.current=b;this.$icon.removeClass().addClass("icon").addClass(this.options.icons[b]);this.options.onchange&&this.options.onchange(b)}return this.current},_template:function(){return'<div class="ui-button-check" ><span class="icon"/><span class="title"/></div>'}})});
				`@@ -1 +0,0 @@`
				define(["utils/utils","mvc/ui/ui-button-check"],function(c,e){var b=Backbone.View.extend({initialize:function(i){var h=this;this.optionsDefault={visible:true,data:[],id:c.uid(),error_text:"No data available.",wait_text:"Please wait...",multiple:false};this.options=c.merge(i,this.optionsDefault);this.setElement('<div class="ui-options"/>');this.$message=$("<div/>");this.$options=$(this._template(i));this.$menu=$('<div class="ui-options-menu"/>');this.$el.append(this.$message);this.$el.append(this.$menu);this.$el.append(this.$options);if(this.options.multiple){this.all_button=new e({onclick:function(){h.$("input").prop("checked",h.all_button.value()!==0);h.trigger("change")}});this.$menu.append(this.all_button.$el)}if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}this.on("change",function(){this.options.onchange&&this.options.onchange(this.value())})},update:function(i){var l=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(i))}else{for(var j in i){var k=$(this._templateOption(i[j]));k.addClass("ui-option");k.tooltip({title:i[j].tooltip,placement:"bottom"});this.$options.append(k)}}var h=this;this.$("input").on("change",function(){h.value(h._getValue());h.trigger("change")});this.value(l);this.unwait()},value:function(j){if(j!==undefined){this.$("input").prop("checked",false);if(j!==null){if(!(j instanceof Array)){j=[j]}for(var h in j){this.$('input[value="'+j[h]+'"]').first().prop("checked",true)}}}var l=this._getValue();if(this.all_button){var k=l;if(!(k instanceof Array)){k=0}else{k=k.length}this.all_button.value(k,this._size())}return l},exists:function(j){if(j!==undefined){if(!(j instanceof Array)){j=[j]}for(var h in j){if(this.$('input[value="'+j[h]+'"]').length>0){return true}}}return false},first:function(){var h=this.$("input").first();if(h.length>0){return h.val()}else{return null}},wait:function(){if(this._size()==0){this._messageShow(this.options.wait_text,"info");this.$options.hide();this.$menu.hide()}},unwait:function(){var h=this._size();if(h==0){this._messageShow(this.options.error_text,"danger");this.$options.hide();this.$menu.hide()}else{this._messageHide();this.$options.css("display","inline-block");this.$menu.show()}},_getValue:function(){var h=[];this.$(":checked").each(function(){h.push($(this).val())});if(!c.validate(h)){return null}if(this.options.multiple){return h}else{return h[0]}},_size:function(){return this.$(".ui-option").length},_messageShow:function(i,h){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+h);this.$message.html(i)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options-list"/>'}});var a=b.extend({_templateOption:function(h){var i=c.uid();return'<div class="ui-option"><input id="'+i+'" type="'+this.options.type+'" name="'+this.options.id+'" value="'+h.value+'"/><label class="ui-options-label" for="'+i+'">'+h.label+"</label></div>"}});var f={};f.View=a.extend({initialize:function(h){h.type="radio";a.prototype.initialize.call(this,h)}});var d={};d.View=a.extend({initialize:function(h){h.multiple=true;h.type="checkbox";a.prototype.initialize.call(this,h)}});var g={};g.View=b.extend({initialize:function(h){b.prototype.initialize.call(this,h)},value:function(h){if(h!==undefined){this.$("input").prop("checked",false);this.$("label").removeClass("active");this.$('[value="'+h+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(j){var h="fa "+j.icon;if(!j.label){h+=" no-padding"}var i='<label class="btn btn-default">';if(j.icon){i+='<i class="'+h+'"/>'}i+='<input type="radio" name="'+this.options.id+'" value="'+j.value+'"/>';if(j.label){i+=j.label}i+="</label>";return i},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:b,BaseIcons:a,Radio:f,RadioButton:g,Checkbox:d}});