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t=a.Model.prototype.toJSON.call(this);return this.elements&&(t.elements=this.elements.toJSON()),t},inReadyState:function(){var t=this.get("populated");return this.isDeletedOrPurged()||t},hasDetails:function(){return this.debug("hasDetails:",this.elements.length),0!==this.elements.length},getVisibleContents:function(t){return this.elements},"delete":function(t){return this.get("deleted")?r.when():this.save({deleted:!0},t)},undelete:function(t){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},t)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name"],toString:function(){var t=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+t.join(",")+")"}}),p=u.extend({collectionClass:h,initialize:function(t,e){this.debug(this+"(ListDatasetCollection).initialize:",t,e),u.prototype.initialize.call(this,t,e)},toString:function(){return["ListDatasetCollection(",this.get("name"),")"].join("")}}),f=p.extend({initialize:function(t,e){this.debug(this+"(PairDatasetCollection).initialize:",t,e),p.prototype.initialize.call(this,t,e)},toString:function(){return["PairDatasetCollection(",this.get("name"),")"].join("")}}),g=u.extend(e.mixin(s,{constructor:function(t,e){this.debug(" NestedDCDCE.constructor:",t,e),s.constructor.call(this,t,e)},toString:function(){var t=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",t,")"].join("")}})),m=c.extend({model:g,initialize:function(t,e){this.debug(this+"(NestedDCDCECollection).initialize:",t,e),c.prototype.initialize.call(this,t,e)},toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),v=f.extend(e.mixin(s,{constructor:function(t,e){this.debug(" NestedPairDCDCE.constructor:",t,e),s.constructor.call(this,t,e)},toString:function(){var t=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",t,")"].join("")}})),_=m.extend({model:v,initialize:function(t,e){this.debug(this+"(NestedPairDCDCECollection).initialize:",t,e),m.prototype.initialize.call(this,t,e)},toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),y=u.extend({collectionClass:_,initialize:function(t,e){this.debug(this+"(ListPairedDatasetCollection).initialize:",t,e),u.prototype.initialize.call(this,t,e)},toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:p,PairDatasetCollection:f,ListPairedDatasetCollection:y}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(45),i(15),i(6),i(10),i(110),i(5),i(107)],s=function(t,e,i,n,s,c){function d(t){var e=t.toJSON(),i=g(e,{creationFn:function(e,i){return 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i=t.data.checksum();i!=e&&(e=i,t.options.onchange&&t.options.onchange())}),this.on("reset",function(){for(var t in this.element_list)this.element_list[t].reset()}),this},_renderForm:function(){this.message=new i.Message,this.section=new n.View(this,{inputs:this.options.inputs}),r(".tooltip").remove(),this.portlet=new e.View({icon:this.options.icon,title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons,collapsible:this.options.collapsible,collapsed:this.options.collapsed}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),Galaxy.emit.debug("form-view::initialize()","Completed")}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(35),i(46),i(5)],s=function(t,e,i){function n(t){return function(e,i){return this.isNew()&&(i=i||{},i.url=this.urlRoot+this.get("history_id")+"/contents",e=e||{},e.type="dataset_collection"),t.call(this,e,i)}}var s=e.HistoryContentMixin,a=t.ListDatasetCollection,r=t.PairDatasetCollection,l=t.ListPairedDatasetCollection,c=a.extend(s).extend({defaults:o.extend(o.clone(a.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){a.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(a.prototype.save),toString:function(){return["HistoryListDatasetCollection(",this.get("name"),")"].join("")}}),d=r.extend(s).extend({defaults:o.extend(o.clone(r.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){r.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(r.prototype.save),toString:function(){return["HistoryPairDatasetCollection(",this.get("name"),")"].join("")}}),h=l.extend(s).extend({defaults:o.extend(o.clone(l.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){l.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(l.prototype.save),toString:function(){return["HistoryListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{HistoryListDatasetCollection:c,HistoryPairDatasetCollection:d,HistoryListPairedDatasetCollection:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a){n=[i(15),i(6),i(5)],s=function(t,e,i){var n="history",s=function(t,e){return[t,e].join("-")},r={defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",constructor:function(t,e){t.type_id=s(t.history_content_type,t.id),this.debug("HistoryContentMixin.constructor:",t.type_id),o.Model.apply(this,arguments)},_typeIdStr:function(){return s(this.get("history_content_type"),this.get("id"))},initialize:function(t,e){this.on("change:id",this._createTypeId)},_createTypeId:function(){this.set("type_id",this._typeIdStr())},isNew:function(){return!this.get("id")},hidden:function(){return!this.get("visible")},isVisible:function(t,e){var i=!0;return t||!this.get("deleted")&&!this.get("purged")||(i=!1),e||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var t=this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id");return t},hide:function(t){return this.get("visible")?this.save({visible:!1},t):a.when()},unhide:function(t){return this.get("visible")?a.when():this.save({visible:!0},t)},toString:function(){var t=this.get("id")||"";return this.get("name")&&(t=this.get("hid")+' :"'+this.get("name")+'",'+t),"HistoryContent("+t+")"}},l=o.Model.extend(e.LoggableMixin).extend(r).extend({_logNamespace:n});return{typeIdStr:s,HistoryContentMixin:r,HistoryContent:l}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(46),i(97),i(45),i(6),i(5)],
-s=function(t,e,i,n,s){var l="history",c=o.Collection.extend(n.LoggableMixin).extend({_logNamespace:l,model:function(t,n){if("dataset"===t.history_content_type)return new e.HistoryDatasetAssociation(t,n);if("dataset_collection"===t.history_content_type){switch(t.collection_type){case"list":return new i.HistoryListDatasetCollection(t,n);case"paired":return new i.HistoryPairDatasetCollection(t,n);case"list:paired":return new i.HistoryListPairedDatasetCollection(t,n)}return{validationError:"Unknown collection_type: "+t.history_content_type}}return{validationError:"Unknown history_content_type: "+t.history_content_type}},initialize:function(t,e){e=e||{},this.historyId=e.historyId,this.model.prototype.idAttribute="type_id",this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(t){return t.get("id")})},notReady:function(){return this.filter(function(t){return!t.inReadyState()})},running:function(){var t=[];return this.each(function(e){var i=!e.inReadyState();i&&t.push(e.get("id"))}),t},getByHid:function(t){return a.first(this.filter(function(e){return e.get("hid")===t}))},getVisible:function(t,e,i){i=i||[],this.debug("checking isVisible");var n=new c(this.filter(function(i){return i.isVisible(t,e)}));return a.each(i,function(t){a.isFunction(t)&&(n=new c(n.filter(t)))}),n},hidden:function(){function t(t){return t.hidden()}return new c(this.filter(t))},deleted:function(){function t(t){return t.get("deleted")}return new c(this.filter(t))},haveDetails:function(){return this.all(function(t){return t.hasDetails()})},fetchAllDetails:function(t){t=t||{};var e={details:"all"};return t.data=t.data?a.extend(t.data,e):e,this.fetch(t)},ajaxQueue:function(t,e){var i=r.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(a,r){return function(){var l=t.call(a,e);l.done(function(t){i.notify({curr:r,total:n,response:t,model:a})}),l.always(function(t){s.push(t),o.length?o.shift()():i.resolve(s)})}}).value();return o.shift()(),i},isCopyable:function(t){var e=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return a.isObject(t)&&t.id&&a.contains(e,t.model_class)},copy:function(t){var e,i,n;a.isString(t)?(e=t,n="hda",i="dataset"):(e=t.id,n={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[t.model_class]||"hda",i="hdca"===n?"dataset_collection":"dataset");var s=this,o=r.post(this.url(),{content:e,source:n,type:i}).done(function(t){s.add([t])}).fail(function(t,a,r){s.trigger("error",s,o,{},"Error copying contents",{type:i,id:e,source:n})});return o},matches:function(t){return this.filter(function(e){return e.matches(t)})},set:function(e,i){e=a.isArray(e)?e:[e],a.each(e,function(e){e.type_id&&e.get&&e.get("type_id")||(e.type_id=t.typeIdStr(e.history_content_type,e.id))}),o.Collection.prototype.set.call(this,e,i)},createHDCA:function(t,e,n,s){var o=this,a={list:i.HistoryListDatasetCollection,paired:i.HistoryPairDatasetCollection},r=new a[e]({history_id:this.historyId,name:n,element_identifiers:t});return r.save().done(function(t){o.add(r)}).fail(function(t,e,i){o.trigger("error",t,e,i)})},clone:function(){var t=o.Collection.prototype.clone.call(this);return t.historyId=this.historyId,t},print:function(){var t=this;t.each(function(e){t.debug(e),e.elements&&t.debug(" elements:",e.elements)})},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});return{HistoryContents:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(6),i(5)],s=function(t,e){var i="list",n=o.View.extend(t.LoggableMixin).extend({_logNamespace:i,initialize:function(t){this.expanded=t.expanded||!1,this.log(" expanded:",this.expanded),this.fxSpeed=void 0!==t.fxSpeed?t.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(t){var e=this._buildNewRender();return this._setUpBehaviors(e),this._queueNewRender(e,t),this},_buildNewRender:function(){var t=a(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(t).replaceWith(this._renderDetails().show()),t},_queueNewRender:function(t,e){e=void 0===e?this.fxSpeed:e;var i=this;a(i).queue("fx",[function(t){this.$el.fadeOut(e,t)},function(e){i._swapNewRender(t),e()},function(t){this.$el.fadeIn(e,t)},function(t){this.trigger("rendered",i),t()}])},_swapNewRender:function(t){return this.$el.empty().attr("class",r.isFunction(this.className)?this.className():this.className).append(t.children())},_setUpBehaviors:function(t){t=t||this.$el,t.find("[title]").tooltip({placement:"bottom"})},$details:function(t){return t=t||this.$el,t.find("> .details")},_renderDetails:function(){var t=a(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(t),t},toggleExpanded:function(t){return t=void 0===t?!this.expanded:t,t?this.expand():this.collapse(),this},expand:function(){var t=this;return t._fetchModelDetails().always(function(){t._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?l.when():this.model.fetch()},_expand:function(){var t=this,e=t._renderDetails();t.$details().replaceWith(e),t.expanded=!0,t.$details().slideDown({duration:t.fxSpeed,step:function(){t.trigger("expanding",t)},complete:function(){t.trigger("expanded",t)}})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var t=this;t.expanded=!1,this.$details().slideUp({duration:t.fxSpeed,step:function(){t.trigger("collapsing",t)},complete:function(){t.trigger("collapsed",t)}})}}),s=n.extend(t.mixin(t.SelectableViewMixin,t.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){n.prototype.initialize.call(this,e),t.SelectableViewMixin.initialize.call(this,e),t.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(t){t?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var t=n.prototype._buildNewRender.call(this);return t.children(".warnings").replaceWith(this._renderWarnings()),t.children(".title-bar").replaceWith(this._renderTitleBar()),t.children(".primary-actions").append(this._renderPrimaryActions()),t.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),t},_swapNewRender:function(t){return n.prototype._swapNewRender.call(this,t),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var t=this,e=a(''),i=t.model.toJSON();return r.each(t.templates.warnings,function(n){e.append(a(n(i,t)))}),e},_renderTitleBar:function(){return a(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return a(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(t){t.stopPropagation(),t.altKey?(this.toggleSelect(t),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(t){var e=32,i=13;return!t||"keydown"!==t.type||t.keyCode!==e&&t.keyCode!==i?!0:(this.toggleExpanded(),t.stopPropagation(),!1)},toString:function(){var t=this.model?this.model+"":"(no model)";return"ListItemView("+t+")"}}));s.prototype.templates=function(){var e=t.wrapTemplate(['','','
"]),i={},n=t.wrapTemplate(['','',"
",'','','',"','','
"],"element"),s=t.wrapTemplate(['']),o=t.wrapTemplate(['']);return{el:e,warnings:i,titleBar:n,subtitle:s,details:o}}();var c=s.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(t){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=t.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=t.foldoutPanelClass||this.foldoutPanelClass,s.prototype.initialize.call(this,t),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return a();var t=s.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,t)},_createFoldoutPanel:function(){var t=this.model,e=this._getFoldoutPanelClass(t),i=this._getFoldoutPanelOptions(t),n=new e(r.extend(i,{model:t}));return n},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(t,e){return e=e||this.$("> .details"),this.foldout=t.render(0),t.$("> .controls").hide(),e.append(t.$el)},expand:function(){var t=this;return t._fetchModelDetails().always(function(){"foldout"===t.foldoutStyle?t._expand():"drilldown"===t.foldoutStyle&&t._expandByDrilldown()})},_expandByDrilldown:function(){var t=this;t.foldout.on("close",function(){t.trigger("collapsed:drilldown",t,t.foldout)}),t.trigger("expanded:drilldown",t,t.foldout)}});return c.prototype.templates=function(){var e=t.wrapTemplate(['','<%- element.name %>',"
",'',"',"
"],"collection");return r.extend({},s.prototype.templates,{details:e})}(),{ExpandableView:n,ListItemView:s,FoldoutListItemView:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(4),i(60),i(7),i(44),i(23),i(21),i(33)],s=function(t,e,i,n,s,a,r){return n.extend({initialize:function(t){var i=this;n.prototype.initialize.call(this,t),this.deferred=new e,t.inputs?(this._buildForm(t),t.needs_update&&this.deferred.execute(function(t){i._updateModel(t)})):this.deferred.execute(function(e){i._buildModel(e,t,!0)})},remove:function(){var t=this;this.$el.hide(),this.deferred.execute(function(){n.prototype.remove.call(t),Galaxy.emit.debug("tool-form-base::remove()","Destroy view.")})},_buildForm:function(e){var i=this;this.options=t.merge(e,this.options),this.options=t.merge({icon:void 0===e.icon&&"fa-wrench"||"",title:""+e.name+" "+e.description+" (Galaxy Version "+e.version+")",operations:this._operations(),onchange:function(){i.deferred.reset(),i.deferred.execute(function(t){i._updateModel(t)})}},this.options),this.options.customize&&this.options.customize(this.options),this.render(),this.options.collapsible||this.$el.append(o("").addClass("ui-margin-top-large").append(this._footer()))},_buildModel:function(e,n,s){var a=this;this.options.id=n.id,this.options.version=n.version;var r="",l={};n.job_id?r=Galaxy.root+"api/jobs/"+n.job_id+"/build_for_rerun":(r=Galaxy.root+"api/tools/"+n.id+"/build",Galaxy.params&&Galaxy.params.tool_id==n.id&&(l=o.extend({},Galaxy.params),n.version&&(l.tool_version=n.version))),t.request({type:"GET",url:r,data:l,success:function(t){a._buildForm(t.tool_model||t),!s&&a.message.update({status:"success",message:"Now you are using '"+a.options.name+"' version "+a.options.version+", id '"+a.options.id+"'.",persistent:!1}),Galaxy.emit.debug("tool-form-base::initialize()","Initial tool model ready.",t),e.resolve()},error:function(t){var n=t&&t.err_msg||"Uncaught error.";a.$el.is(":empty")?a.$el.prepend(new i.Message({message:n,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal.show({title:"Tool request failed",body:n,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form::initialize()","Initial tool model request failed.",t),e.reject()}})},_updateModel:function(e){var i=this,n=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",s={tool_id:this.options.id,tool_version:this.options.version,inputs:o.extend(!0,{},i.data.create())};this.wait(!0),Galaxy.emit.debug("tool-form-base::_updateModel()","Sending current state.",s),t.request({type:"POST",url:n,data:s,success:function(t){i.update(t.tool_model||t),i.options.update&&i.options.update(t),i.wait(!1),Galaxy.emit.debug("tool-form-base::_updateModel()","Received new model.",t),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form-base::_updateModel()","Refresh request failed.",t),e.reject()}})},_operations:function(){var t=this,e=this.options,n=new i.ButtonMenu({icon:"fa-cubes",title:!e.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!e.sustain_version&&e.versions&&e.versions.length>1)for(var o in e.versions){var a=e.versions[o];a!=e.version&&n.addMenu({title:"Switch to "+a,version:a,icon:"fa-cube",onclick:function(){var i=e.id.replace(e.version,this.version),n=this.version;t.deferred.reset(),t.deferred.execute(function(e){t._buildModel(e,{id:i,version:n})})}})}else n.$el.hide();var r=new i.ButtonMenu({icon:"fa-caret-down",title:!e.narrow&&"Options"||null,tooltip:"View available options"});return e.biostar_url&&(r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/p/new/post/")}}),r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/local/search/page/?q="+e.name)}})),r.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+e.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+e.id+"/download"}}),e.requirements&&e.requirements.length>0&&r.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,t.message.update({message:""})):(this.visible=!0,t.message.update({persistent:!0,message:s.requirements(e),status:"info"}))}}),e.sharable_url&&r.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(e.sharable_url)}}),{menu:r,versions:n}},_footer:function(){var t=this.options,e=o("").append(s.help(t));if(t.citations){var i=o(""),n=new a.ToolCitationCollection;n.tool_id=t.id;var l=new r.CitationListView({el:i,collection:n});l.render(),n.fetch(),e.append(i)}return e}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1))},function(t,e,i){var n,s;(function(o,a){n=[i(3),i(20),i(14),i(22),i(64),i(65),i(63),i(66)],s=function(t,e,i,n,s,r,l,c){var d={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}},h=o.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(t){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new h(this.toJSON())},set_value:function(t){this.set("value",t||"")}}),u=o.Collection.extend({model:h}),p=h.extend({}),f=h.extend({set_value:function(t){this.set("value",parseInt(t,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),g=f.extend({set_value:function(t){this.set("value",parseFloat(t))}}),m=h.extend({get_samples:function(){return t.map(this.get("options"),function(t){return t[0]})}});h.subModelTypes={integer:f,"float":g,data:p,select:m};var v=o.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:Galaxy.root+"api/tools",initialize:function(e){this.set("inputs",new u(t.map(e.inputs,function(t){var e=h.subModelTypes[t.type]||h;return new e(t)})))},toJSON:function(){var t=o.Model.prototype.toJSON.call(this);return t.inputs=this.get("inputs").map(function(t){return t.toJSON()}),t},remove_inputs:function(t){var e=this,i=e.get("inputs").filter(function(e){return-1!==t.indexOf(e.get("type"))});e.get("inputs").remove(i)},copy:function(t){var e=new v(this.toJSON());if(t){var i=new o.Collection;e.get("inputs").each(function(t){t.get_samples()&&i.push(t)}),e.set("inputs",i)}return e},apply_search_results:function(e){return-1!==t.indexOf(e,this.attributes.id)?this.show():this.hide(),this.is_visible()},set_input_value:function(t,e){this.get("inputs").find(function(e){return e.get("name")===t}).set("value",e)},set_input_values:function(e){var i=this;t.each(t.keys(e),function(t){i.set_input_value(t,e[t])})},run:function(){return this._run()},rerun:function(t,e){return this._run({action:"rerun",target_dataset_id:t.id,regions:e})},get_inputs_dict:function(){var t={};return this.get("inputs").each(function(e){t[e.get("name")]=e.get("value")}),t},_run:function(n){var s=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},n),o=a.Deferred(),r=new e.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(s),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});return a.when(r.go()).then(function(t){o.resolve(new i.DatasetCollection(t))}),o}});t.extend(v.prototype,d);var _=(o.View.extend({}),o.Collection.extend({model:v})),y=o.Model.extend(d),w=o.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){t.each(this.attributes.elems,function(t){t.show()}),this.show(),this.set("open",!1)},apply_search_results:function(e){var i,n=!0;t.each(this.attributes.elems,function(t){t instanceof y?(i=t,i.hide()):t instanceof v&&t.apply_search_results(e)&&(n=!1,i&&i.show())}),n?this.hide():(this.show(),this.set("open",!0))}});t.extend(w.prototype,d);var b=o.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_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 t=this.attributes.query;if(t.length- ',this._templateOptions(e),"
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r({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldLibrary:function(t){var e=this;return new n.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:function(){e.app.trigger("change")}})},_fieldFtp:function(t){var e=this;return new s.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:function(){e.app.trigger("change")}})}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(17),i(11),i(7)],s=function(t,e,i,n){var s=o.View.extend({initialize:function(i){this.options=t.merge(i,{title:"Section",empty_text:"Not available.",max:null,min:null}),this.setElement("");this.button_new=new n.ButtonIcon({icon:"fa-plus",title:"Insert "+i.title_new,tooltip:"Add new "+i.title_new+" block",floating:"clear",onclick:function(){i.onnew&&i.onnew()}}),this.table=new e.View({cls:"ui-table-plain",content:""}),this.$el.append(this.table.$el),this.$el.append(a("").append(this.button_new.$el)),this.list={},this.n=0},size:function(){return this.n},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate repeat block id.");this.n++;var e=new n.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){t.ondel&&t.ondel()}}),s=new i.View({id:t.id,title:"placeholder",cls:"ui-portlet-repeat",operations:{button_delete:e}});s.append(t.$el),s.$el.addClass("section-row"),this.list[t.id]=s,this.table.add(s.$el),this.table.append("row_"+t.id,!0),this.options.max>0&&this.n>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){if(!this.list[t])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.n--;var e=this.table.get("row_"+t);e.remove(),delete this.list[t],this.button_new.enable(),this._refresh()},hideOptions:function(){this.button_new.$el.hide(),r.each(this.list,function(t){t.hideOperation("button_delete")}),r.isEmpty(this.list)&&this.$el.append(a("").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var i=this.list[e];i.title(++t+": "+this.options.title),this.n>this.options.min?i.showOperation("button_delete"):i.hideOperation("button_delete")}}});return{View:s}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(4),i(17),i(7),i(11),i(41),i(39),i(40)],s=function(t,e,i,n,s,c,d){var h=o.View.extend({initialize:function(t,i){this.app=t,this.inputs=i.inputs,i.cls="ui-table-plain",i.cls_tr="section-row",this.table=new e.View(i),this.parameters=new d(t,i),this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var t in this.inputs)this.add(this.inputs[t])},add:function(e){var i=a.extend(!0,{},e);i.id=e.id=t.uid(),this.app.input_list[i.id]=i;var n=i.type;switch(n){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(t){var e=this;t.test_param.id=t.id,this.app.options.sustain_conditionals&&(t.test_param.disabled=!0);var i=this._addRow(t.test_param);i.options.onchange=function(i){var n=e.app.data.matchCase(t,i);for(var s in t.cases){var o=t.cases[s],a=t.id+"-section-"+s,r=e.table.get(a),l=!1;for(var c in o.inputs)if(!o.inputs[c].hidden){l=!0;break}s==n&&l?r.fadeIn("fast"):r.hide()}e.app.trigger("change")};for(var n in t.cases){var s=t.id+"-section-"+n,o=new h(this.app,{inputs:t.cases[n].inputs});o.$el.addClass("ui-table-section"),this.table.add(o.$el),this.table.append(s)}i.trigger("change")},_addRepeat:function(t){function e(e){var s=t.id+"-section-"+n++,a=new h(i.app,{inputs:e});o.add({id:s,$el:a.$el,ondel:function(){o.del(s),i.app.trigger("change")}})}for(var i=this,n=0,o=new s.View({title:t.title||"Repeat",title_new:t.title||"",min:t.min,max:t.max,onnew:function(){e(t.inputs),i.app.trigger("change")}}),a=t.min,l=r.size(t.cache),d=0;dd?t.cache[d]:t.inputs,e(u)}this.app.options.sustain_repeats&&o.hideOptions();var p=new c(this.app,{label:t.title||t.name,help:t.help,field:o});this.table.add(p.$el),this.table.append(t.id)},_addSection:function(t){var e=this,s=new h(e.app,{inputs:t.inputs}),o=new i.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"}),a=new n.View({title:t.title||t.name,cls:"ui-portlet-section",collapsible:!0,collapsed:!0,operations:{button_visible:o}});a.append(s.$el),a.append(l("").addClass("ui-form-info").html(t.help)),a.setOperation("button_visible",function(){a.collapsed?a.expand():a.collapse()}),a.on("expanded",function(){o.setIcon("fa-eye")}),a.on("collapsed",function(){o.setIcon("fa-eye-slash")}),this.app.on("expand",function(t){a.$("#"+t).length>0&&a.expand()}),t.expanded&&a.expand(),this.table.add(a.$el),this.table.append(t.id)},_addRow:function(t){var e=t.id,i=this.parameters.create(t);this.app.field_list[e]=i;var n=new c(this.app,{name:t.name,label:t.label||t.name,value:t.value,default_value:t.default_value,text_value:t.text_value||t.value,collapsible_value:t.collapsible_value,collapsible_preview:t.collapsible_preview,help:t.help,argument:t.argument,disabled:t.disabled,field:i});return this.app.element_list[e]=n,this.table.add(n.$el),this.table.append(e),t.hidden&&this.table.get(e).hide(),i}});return{View:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(7),i(31)],s=function(t,e,i){var n=o.View.extend({initialize:function(i,n){this.app=i,this.options=n,this.history={};var s=this;this.setElement(''),this.list={};var o=[];"data_collection"==n.type?this.mode="collection":n.multiple?this.mode="multiple":this.mode="single",this.current=this.mode,this.list={};var l=t.textify(n.extensions),c="No dataset available.";l&&(c="No "+l+" dataset available.");var d="No dataset list available.";if(l&&(d="No "+l+" dataset collection available."),"single"==this.mode&&(o.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new e.Select.View({optional:n.optional,error_text:c,onchange:function(){s.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),("single"==this.mode||"multiple"==this.mode)&&(o.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new e.Select.View({multiple:!0,searchable:!1,optional:n.optional,error_text:c,onchange:function(){s.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),"single"==this.mode||"multiple"==this.mode||"collection"==this.mode){o.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});var h="multiple"==this.mode;this.select_collection=new e.Select.View({error_text:d,multiple:h,searchable:!1,optional:n.optional,onchange:function(){s.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:o,onchange:function(t){s.current=t,s.refresh(),s.trigger("change")}}),this.$batch=a(this.template_batch());var u=r.size(this.list),p=0;u>1&&(this.$el.append(this.button_type.$el),p=Math.max(0,35*r.size(this.list))+"px");for(var f in this.list)this.$el.append(this.list[f].field.$el.css({"margin-left":p}));this.$el.append(this.$batch.css({"margin-left":p})),this.update(n.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){n.onchange&&n.onchange(s.value())})},wait:function(){for(var t in this.list)this.list[t].field.wait()},unwait:function(){for(var t in this.list)this.list[t].field.unwait()},update:function(t){function e(t,e){if(t){var n=[];for(var s in e){var o=e[s];n.push({label:o.hid+": "+o.name,value:o.id}),i.history[o.id+"_"+o.src]=o}t.update(n)}}var i=this;e(this.select_single,t.hda),e(this.select_multiple,t.hda),e(this.select_collection,t.hdca)},value:function(t){if(void 0!==t)if(t&&t.values)try{var e=[];for(var i in t.values)e.push(t.values[i].id);t&&t.values.length>0&&"hdca"==t.values[0].src?(this.current="collection",this.select_collection.value(e)):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(e)):(this.current="single",this.select_single.value(e[0]))}catch(n){Galaxy.emit.debug("tools-select-content::value()","Skipped.")}else for(var i in this.list)this.list[i].field.value(null);this.refresh();var s=this._select().value();if(null===s)return null;if(s instanceof Array||(s=[s]),0===s.length)return null;var o={batch:this._batch(),values:[]};for(var i in s){var a=this.history[s[i]+"_"+this.list[this.current].type];if(!a)return null;o.values.push(a)}return o.values.sort(function(t,e){return t.hid-e.hid}),o},refresh:function(){this.button_type.value(this.current);for(var t in this.list){var e=this.list[t].field.$el;this.current==t?e.show():e.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var t=this.history[this._select().value()+"_hdca"];if(t&&t.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode?!0:!1},template_batch:function(){return'");if(t.append(r(this.model.toJSON())),"upload1"===this.model.id)t.find("a").on("click",function(t){t.preventDefault(),Galaxy.upload.show()});else if("Tool"===this.model.get("model_class")){var e=this;t.find("a").on("click",function(t){t.preventDefault();var i=new n.View({id:e.model.id,version:e.model.get("version")});i.deferred.execute(function(){Galaxy.app.display(i)})})}return this.$el.append(t),this}}),$=C.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append(a("").text(this.model.attributes.text)),this}}),S=C.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){C.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(l(this.model.toJSON()));var e=this.$el.find(".toolSectionBody");return t.each(this.model.attributes.elems,function(t){if(t instanceof v){var i=new E({model:t,className:"toolTitle"});i.render(),e.append(i.$el)}else if(t instanceof y){var n=new $({model:t});n.render(),e.append(n.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),k=o.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(c(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(t){return this.model.attributes.clear_key&&this.model.attributes.clear_key===t.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),T=o.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var t=this,e=new k({model:this.model.get("tool_search")});return e.render(),t.$el.append(e.$el),this.model.get("layout").each(function(e){if(e instanceof w){var i=new S({model:e});i.render(),t.$el.append(i.$el)}else if(e instanceof v){var n=new E({model:e,className:"toolTitleNoSection"});n.render(),t.$el.append(n.$el)}else if(e instanceof y){var s=new $({model:e});s.render(),t.$el.append(s.$el)}}),t.$el.find("a.tool-link").click(function(e){var i=a(this).attr("class").split(/\s+/)[0],n=t.model.get("tools").get(i);t.trigger("tool_link_click",e,n)}),this},handle_search_results:function(){var t=this.model.get("tool_search").get("results");t&&0===t.length?a("#search-no-results").show():a("#search-no-results").hide()}}),D=o.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(s(this.model.toJSON()))}});o.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new T({collection:this.collection}),this.tool_form_view=new D},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var t=this;this.tool_panel_view.on("tool_link_click",function(e,i){e.preventDefault(),t.show_tool(i)})},show_tool:function(t){var e=this;t.fetch().done(function(){e.tool_form_view.model=t,e.tool_form_view.render(),e.tool_form_view.$el.show(),a("#left").width("650px")})}});return{ToolParameter:h,IntegerToolParameter:f,SelectToolParameter:m,Tool:v,ToolCollection:_,ToolSearch:b,ToolPanel:x,ToolPanelView:T,ToolFormView:D}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(i,o,a,r){n=[],s=function(){var t=i.View.extend({initialize:function(t,e){this.$button=t,this.$button.size()||(this.$button=o("")),this.options=e||[],this.$button.data("popupmenu",this);var i=this;this.$button.click(function(t){return o(".popmenu-wrapper").remove(),i._renderAndShow(t),!1})},_renderAndShow:function(t){this.render(),this.$el.appendTo("body").css(this._getShownPosition(t)).show(),this._setUpCloseBehavior()},render:function(){if(this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options)),this.options.length){var t=this;this.$el.find("li").each(function(e,i){var n=t.options[e];n.func&&o(this).children("a.popupmenu-option").click(function(e){n.func.call(t,e,n),e.preventDefault()})})}return this},template:function(t,e){return['',t.html," "].join("");var e=t.href||"javascript:void(0);",i=t.target?' target="'+t.target+'"':"",n=t.checked?'':"";return['",n,t.html," "].join("")}).join(""):"(no options) "},_getShownPosition:function(t){var e=this.$el.width(),i=t.pageX-e/2;return i=Math.min(i,o(document).scrollLeft()+o(window).width()-e-5),i=Math.max(i,o(document).scrollLeft()+5),{top:t.pageY,left:i}},_setUpCloseBehavior:function(){function t(t){if(o(document).off("click.close_popup"),window.parent!==window)try{o(window.parent.document).off("click.close_popup")}catch(i){}else try{o("iframe#galaxy_main").contents().off("click.close_popup")}catch(i){}e.remove()}var e=this;if(o("html").one("click.close_popup",t),window.parent!==window)try{o(window.parent.document).find("html").one("click.close_popup",t)}catch(i){}else try{o("iframe#galaxy_main").contents().one("click.close_popup",t)}catch(i){}},addItem:function(t,e){return e=e>=0?e:this.options.length,this.options.splice(e,0,t),this},removeItem:function(t){return t>=0&&this.options.splice(t,1),this},findIndexByHtml:function(t){for(var e=0;e
\n \n
\n'},compiler:[7,">= 4.0.0"],main:function(t,e,i,n,s){var o,a,r=null!=e?e:{},l=i.helperMissing,c="function",d=t.escapeExpression;return'\n '+(null!=(a=null!=(a=i.html||(null!=e?e.html:e))?a:l,o=typeof a===c?a.call(r,{name:"html",hash:{},data:s}):a)?o:"")+'\n
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"},useData:!0})},function(t,e,i){var n=i(12);t.exports=(n["default"]||n).template({1:function(t,e,i,n,s){var o=t.lambda,a=t.escapeExpression;return''+a(o(e,e))+" "},compiler:[7,">= 4.0.0"],main:function(t,e,i,n,s){var o,a,r=null!=e?e:{},l=i.helperMissing,c="function",d=t.escapeExpression;return''+(null!=(o=i.each.call(r,null!=e?e.labels:e,{name:"each",hash:{},fn:t.program(1,s,0),inverse:t.noop,data:s}))?o:"")+'\n'+d((a=null!=(a=i.name||(null!=e?e.name:e))?a:l,typeof a===c?a.call(r,{name:"name",hash:{},data:s}):a))+"\n"+d((a=null!=(a=i.description||(null!=e?e.description:e))?a:l,typeof a===c?a.call(r,{name:"description",hash:{},data:s}):a))+"\n"},useData:!0})},function(t,e,i){var n=i(12);t.exports=(n["default"]||n).template({compiler:[7,">= 4.0.0"],main:function(t,e,i,n,s){var o,a=null!=e?e:{},r=i.helperMissing,l="function",c=t.escapeExpression;return'\n \n'+d((a=null!=(a=i.help||(null!=e?e.help:e))?a:l,typeof a===c?a.call(r,{name:"help",hash:{},data:s}):a))+"
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"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off(),this.stopListening(this.model),o.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}});return{AnnotationEditor:i}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3))},function(t,e,i){var n,s;(function(o){n=[i(100),i(35),i(34),i(6),i(5)],s=function(t,e,i,n,s){var a="collections",r=t.ModelListPanel,l=r.extend({_logNamespace:a,className:r.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:i.DatasetDCEListItemView,NestedDCDCEViewClass:i.NestedDCDCEListItemView,modelCollectionKey:"elements",initialize:function(t){r.prototype.initialize.call(this,t),this.linkTarget=t.linkTarget||"_blank",this.hasUser=t.hasUser,this.panelStack=[],this.parentName=t.parentName,this.foldoutStyle=t.foldoutStyle||"foldout"},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(t){switch(t.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",t.get("element_type"))},_getItemViewOptions:function(t){var e=r.prototype._getItemViewOptions.call(this,t);return o.extend(e,{linkTarget:this.linkTarget,hasUser:this.hasUser,foldoutStyle:this.foldoutStyle})},_setUpItemViewListeners:function(t){var e=this;return r.prototype._setUpItemViewListeners.call(e,t),t.on("expanded:drilldown",function(t,e){this._expandDrilldownPanel(e)},this),t.on("collapsed:drilldown",function(t,e){this._collapseDrilldownPanel(e)},this),this},_expandDrilldownPanel:function(t){this.panelStack.push(t),this.$("> .controls").add(this.$list()).hide(),t.parentName=this.model.get("name"),this.$el.append(t.render().$el)},_collapseDrilldownPanel:function(t){this.panelStack.pop(),this.render()},events:{"click .navigation .back":"close"},close:function(t){this.$el.remove(),this.trigger("close")},toString:function(){return"CollectionView("+(this.model?this.model.get("name"):"")+")"}});l.prototype.templates=function(){var t=n.wrapTemplate(['','",'
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+this.model.on("change",function(t,e){this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()?this.model.fetch():this.render()},this)},_fetchModelDetails:function(){var t=this;return t.model.inReadyState()&&!t.model.hasDetails()?t.model.fetch({silent:!0}):o.when()},remove:function(t,e){var i=this;t=t||this.fxSpeed,this.$el.fadeOut(t,function(){a.View.prototype.remove.call(i),e&&e.call(i)})},render:function(t){return d.prototype.render.call(this,t)},_swapNewRender:function(t){return d.prototype._swapNewRender.call(this,t),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var t=this.model.get("state");if(t===e.NOT_VIEWABLE||t===e.DISCARDED||!this.model.get("accessible"))return null;var n={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))n.disabled=!0,n.title=s("Cannot display datasets removed from disk");else if(t===e.UPLOAD)n.disabled=!0,n.title=s("This dataset must finish uploading before it can be viewed");else if(t===e.NEW)n.disabled=!0,n.title=s("This dataset is not yet viewable");else{n.title=s("View data"),n.href=this.model.urls.display;var o=this;n.onclick=function(t){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.addDataset(o.model.get("id")),t.preventDefault())}}return n.faIcon="fa-eye",i(n)},_renderDetails:function(){if(this.model.get("state")===e.NOT_VIEWABLE)return r(this.templates.noAccess(this.model.toJSON(),this));var t=d.prototype._renderDetails.call(this);return t.find(".actions .left").empty().append(this._renderSecondaryActions()),t.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),t.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(t),t},_renderSummary:function(){var t=this.model.toJSON(),e=this.templates.summaries[t.state];return(e=e||this.templates.summaries.unknown)(t,this)},_renderDetailMessages:function(){var t=this,e=r(''),i=t.model.toJSON();return l.each(t.templates.detailMessages,function(n){e.append(r(n(i,t)))}),e},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case e.NOT_VIEWABLE:return[];case e.OK:case e.FAILED_METADATA:case e.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return i({title:s("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:l.isEmpty(this.model.get("meta_files"))?r(['','',""].join("")):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var t=this.model.urls;return r(['','
","<%- 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"),"<% } %>","
","','','',"",'
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- ',s("Download dataset")," ",l.map(this.model.get("meta_files"),function(e){return['
- ',s("Download")," ",e.file_type," "].join("")}).join("\n"),"
',s("An error occurred setting the metadata for this dataset"),"
","<% } %>"]),error:n.wrapTemplate(["<% if( model.error ){ %>",'',s("There was an error getting the data for this dataset"),": <%- model.error %>","
","<% } %>"]),purged:n.wrapTemplate(["<% if( model.purged ){ %>",'',s("This dataset has been deleted and removed from disk"),"
","<% } %>"]),deleted:n.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'',s("This dataset has been deleted"),"
","<% } %>"])}),i=n.wrapTemplate(['','','
"],"dataset"),o=n.wrapTemplate(['','','',"
","<% if( !dataset.deleted && !dataset.purged ){ %>",'','','',"<% if( dataset.peek ){ %>",'<%= dataset.peek %>',"<% } %>","<% } %>","
','
"],"dataset"),a={};a[e.OK]=a[e.FAILED_METADATA]=n.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'',s("You do not have permission to view this dataset"),"
","','<%- dataset.misc_blurb %>',"
","<% } %>","<% if( dataset.file_ext ){ %>",'','",'<%- dataset.file_ext %>',"
","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'','",'',"<%- dataset.metadata_dbkey %>","","
","<% } %>","<% if( dataset.misc_info ){ %>",'','<%- dataset.misc_info %>',"
","<% } %>"],"dataset"),a[e.NEW]=n.wrapTemplate(["",s("This is a new dataset and not all of its data are available yet"),"
"],"dataset"),a[e.NOT_VIEWABLE]=n.wrapTemplate(["",s("You do not have permission to view this dataset"),"
"],"dataset"),a[e.DISCARDED]=n.wrapTemplate(["",s("The job creating this dataset was cancelled before completion"),"
"],"dataset"),a[e.QUEUED]=n.wrapTemplate(["",s("This job is waiting to run"),"
"],"dataset"),a[e.RUNNING]=n.wrapTemplate(["",s("This job is currently running"),"
"],"dataset"),a[e.UPLOAD]=n.wrapTemplate(["",s("This dataset is currently uploading"),"
"],"dataset"),a[e.SETTING_METADATA]=n.wrapTemplate(["",s("Metadata is being auto-detected"),"
"],"dataset"),a[e.PAUSED]=n.wrapTemplate(["",s('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"
"],"dataset"),a[e.ERROR]=n.wrapTemplate(["<% if( !dataset.purged ){ %>","<%- dataset.misc_blurb %>
","<% } %>",'',s("An error occurred with this dataset"),":",'<%- dataset.misc_info %>
'],"dataset"),a[e.EMPTY]=n.wrapTemplate(["",s("No data"),": <%- dataset.misc_blurb %>
"],"dataset"),a.unknown=n.wrapTemplate(['Error: unknown dataset state: "<%- dataset.state %>"
'],"dataset");var r={resubmitted:n.wrapTemplate(["<% if( model.resubmitted ){ %>",'',s("The job creating this dataset has been resubmitted"),"
","<% } %>"])},c=n.wrapTemplate(["<% _.each( apps, function( app ){ %>",'','<%- app.label %> ','',"<% _.each( app.links, function( link ){ %>",'',"<% print( _l( link.text ) ); %>"," ","<% }); %>","","
","<% }); %>"],"apps");return l.extend({},d.prototype.templates,{warnings:t,details:i,noAccess:o,summaries:a,detailMessages:r,displayApplications:c})}(),{DatasetListItemView:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1),i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4)],s=function(t){var e=o.Model.extend({initialize:function(t){this.app=t},checksum:function(){var t="",e=this;return this.app.section.$el.find(".section-row").each(function(){var i=a(this).attr("id"),n=e.app.field_list[i];n&&(t+=i+":"+JSON.stringify(n.value&&n.value())+":"+n.collapsed+";")}),t},create:function(){function t(t,e,i){n.flat_dict[t]=e,o[t]=i}function e(s,o){for(var a in o){var r=o[a];if(r.input){var l=r.input,c=s;switch(""!=s&&(c+="|"),c+=l.name,l.type){case"repeat":var d="section-",h=[],u=null;for(var p in r){var f=p.indexOf(d);-1!=f&&(f+=d.length,h.push(parseInt(p.substr(f))),u||(u=p.substr(0,f)))}h.sort(function(t,e){return t-e});var a=0;for(var g in h)e(c+"_"+a++,r[u+h[g]]);break;case"conditional":var m=n.app.field_list[l.id].value();t(c+"|"+l.test_param.name,l.id,m);var v=i(l,m);-1!=v&&e(c,o[l.id+"-section-"+v]);break;case"section":e(!l.flat&&c||"",r);break;default:var _=n.app.field_list[l.id];if(_&&_.value){var m=_.value();if((void 0===l.ignore||l.ignore!=m)&&(_.collapsed&&l.collapsible_value&&(m=l.collapsible_value),t(c,l.id,m),l.payload))for(var y in l.payload)t(y,l.id,l.payload[y])}}}}}var n=this,s={};this._iterate(this.app.section.$el,s);var o={};return this.flat_dict={},e("",s),o},match:function(t){return this.flat_dict&&this.flat_dict[t]},matchCase:function(t,e){return i(t,e)},matchModel:function(t,e){return s(t.inputs,this.flat_dict,e)},matchResponse:function(t){function e(t,s){if("string"==typeof s){var o=n.flat_dict[t];o&&(i[o]=s)}else for(var a in s){var r=a;if(""!==t){var l="|";s instanceof Array&&(l="_"),r=t+l+r}e(r,s[a])}}var i={},n=this;return e("",t),i},_iterate:function(t,e){var i=this,n=a(t).children();n.each(function(){var t=this,n=a(t).attr("id");if(a(t).hasClass("section-row")){var s=i.app.input_list[n];e[n]=s&&{input:s}||{},i._iterate(t,e[n])}else i._iterate(t,e)})}}),i=function(t,e){"boolean"==t.test_param.type&&(e="true"==e?t.test_param.truevalue||"true":t.test_param.falsevalue||"false");for(var i in t.cases)if(t.cases[i].value==e)return i;return-1},n=function(t,e,i,s){s=a.extend(!0,{},s),r.each(t,function(t){t&&t.type&&(s[t.name]=t)}),r.each(t,function(t){r.isObject(t)&&(t.type&&s[t[e]]?i(t,s[t[e]]):n(t,e,i,s))})},s=function(t,e,n){function s(t,o){for(var a in o){var r=o[a],l=r.name;switch(""!=t&&(l=t+"|"+l),r.type){case"repeat":for(var c in r.cache)s(l+"_"+c,r.cache[c]);break;case"conditional":var d=i(r,r.test_param&&r.test_param.value);-1!=d&&s(l,r.cases[d].inputs);break;case"section":s(l,r.inputs);break;default:var h=e[l];h&&n(h,r)}}}var o={};return s("",t),o};return{Manager:e,matchIds:s,matchContext:n}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(i){n=[],s=function(){return i.View.extend({initialize:function(t,e){this.app=t,this.field=e.field,this.text_enable=t.options.text_enable||"Enable",this.text_disable=t.options.text_disable||"Disable",this.cls_enable=t.options.cls_enable||"fa fa-caret-square-o-down",this.cls_disable=t.options.cls_disable||"fa fa-caret-square-o-up",this.setElement(this._template(e)),this.$field=this.$(".ui-form-field"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_icon=this.$(".ui-form-collapsible").find(".icon"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el),this.field.collapsed=void 0!==e.collapsible_value&&JSON.stringify(e.value)==JSON.stringify(e.collapsible_value),this._refresh();var i=this;this.$collapsible.on("click",function(){i.field.collapsed=!i.field.collapsed,i._refresh()})},disable:function(t){this.$backdrop.show(),t&&this.$backdrop.css({opacity:0,cursor:"default"})},error:function(t){this.$error_text.html(t),this.$error.show(),this.$el.addClass("ui-error")},reset:function(){this.$error.hide(),this.$el.removeClass("ui-error")},_refresh:function(){this.$collapsible_icon.removeClass().addClass("icon"),this.field.collapsed?(this.$field.hide(),this.$preview.show(),this._tooltip(this.text_enable,this.cls_enable)):(this.$field.fadeIn("fast"),this.$preview.hide(),this._tooltip(this.text_disable,this.cls_disable)),this.app.trigger("change")},_tooltip:function(t,e){this.$collapsible_icon.addClass(e).tooltip({placement:"bottom"}).attr("data-original-title",t).tooltip("fixTitle").tooltip("hide")},_template:function(t){var e='';return e+=t.disabled||void 0===t.collapsible_value?t.label:'
'+t.label+"
",e+='',e+='
',t.collapsible_preview&&(e+='',t.help&&(e+=t.help,t.argument&&-1==t.help.indexOf("("+t.argument+")")&&(e+=" ("+t.argument+")")),e+='
'+t.text_value+"
"),e+="This is a batch mode input field. A separate job will be triggered for each dataset.
'}});return{View:n}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(11),i(7),i(42),i(38)],s=function(t,e,i,n,s){return o.View.extend({initialize:function(e){this.options=t.merge(e,{initial_errors:!1,cls:"ui-portlet-limited",icon:""}),this.modal=parent.Galaxy&&parent.Galaxy.modal||new i.Modal.View,this.setElement(""),this.render()},update:function(t){var e=this;this.data.matchModel(t,function(t,i){var n=e.input_list[t];if(n&&n.options&&!a.isEqual(n.options,i.options)){n.options=i.options;var s=e.field_list[t];if(s.update){var o=[];if(-1!=["data","data_collection","drill_down"].indexOf(n.type))o=n.options;else for(var r in i.options){var l=i.options[r];l.length>2&&o.push({label:l[0],value:l[1]})}s.update(o),s.trigger("change"),Galaxy.emit.debug("form-view::update()","Updating options for "+t)}}})},wait:function(t){for(var e in this.input_list){var i=this.field_list[e],n=this.input_list[e];n.is_dynamic&&i.wait&&i.unwait&&(t?i.wait():i.unwait())}},highlight:function(t,e,i){var n=this.element_list[t];if(n&&(n.error(e||"Please verify this parameter."),this.trigger("expand",t),!i))if(self==top){var s=this.$el.parents().filter(function(){return"auto"==r(this).css("overflow")}).first();s.animate({scrollTop:s.scrollTop()+n.$el.offset().top-50},500)}else r("html, body").animate({scrollTop:n.$el.offset().top-20},500)},errors:function(t){if(this.trigger("reset"),t&&t.errors){var e=this.data.matchResponse(t.errors);for(var i in this.element_list){this.element_list[i];e[i]&&this.highlight(i,e[i],!0)}}},render:function(){var t=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new s.Manager(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var e=this.data.checksum();return this.on("change",function(){var i=t.data.checksum();i!=e&&(e=i,t.options.onchange&&t.options.onchange())}),this.on("reset",function(){for(var t in this.element_list)this.element_list[t].reset()}),this},_renderForm:function(){this.message=new i.Message,this.section=new n.View(this,{inputs:this.options.inputs}),r(".tooltip").remove(),this.portlet=new e.View({icon:this.options.icon,title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons,collapsible:this.options.collapsible,collapsed:this.options.collapsed}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),Galaxy.emit.debug("form-view::initialize()","Completed")}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(35),i(46),i(5)],s=function(t,e,i){function n(t){return function(e,i){return this.isNew()&&(i=i||{},i.url=this.urlRoot+this.get("history_id")+"/contents",e=e||{},e.type="dataset_collection"),t.call(this,e,i)}}var s=e.HistoryContentMixin,a=t.ListDatasetCollection,r=t.PairDatasetCollection,l=t.ListPairedDatasetCollection,c=a.extend(s).extend({defaults:o.extend(o.clone(a.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){a.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(a.prototype.save),toString:function(){return["HistoryListDatasetCollection(",this.get("name"),")"].join("")}}),d=r.extend(s).extend({defaults:o.extend(o.clone(r.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){r.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(r.prototype.save),toString:function(){return["HistoryPairDatasetCollection(",this.get("name"),")"].join("")}}),h=l.extend(s).extend({defaults:o.extend(o.clone(l.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){l.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(l.prototype.save),toString:function(){return["HistoryListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{HistoryListDatasetCollection:c,HistoryPairDatasetCollection:d,HistoryListPairedDatasetCollection:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a){n=[i(15),i(6),i(5)],s=function(t,e,i){var n="history",s=function(t,e){return[t,e].join("-")},r={defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",constructor:function(t,e){t.type_id=s(t.history_content_type,t.id),this.debug("HistoryContentMixin.constructor:",t.type_id),o.Model.apply(this,arguments)},_typeIdStr:function(){return s(this.get("history_content_type"),this.get("id"))},initialize:function(t,e){this.on("change:id",this._createTypeId)},_createTypeId:function(){this.set("type_id",this._typeIdStr())},isNew:function(){return!this.get("id")},hidden:function(){return!this.get("visible")},isVisible:function(t,e){var i=!0;return t||!this.get("deleted")&&!this.get("purged")||(i=!1),e||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var t=this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id");return t},hide:function(t){return this.get("visible")?this.save({visible:!1},t):a.when()},unhide:function(t){return this.get("visible")?a.when():this.save({visible:!0},t)},toString:function(){var t=this.get("id")||"";return this.get("name")&&(t=this.get("hid")+' :"'+this.get("name")+'",'+t),"HistoryContent("+t+")"}},l=o.Model.extend(e.LoggableMixin).extend(r).extend({_logNamespace:n});return{typeIdStr:s,HistoryContentMixin:r,HistoryContent:l}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;
+(function(o,a,r){n=[i(46),i(97),i(45),i(6),i(5)],s=function(t,e,i,n,s){var l="history",c=o.Collection.extend(n.LoggableMixin).extend({_logNamespace:l,model:function(t,n){if("dataset"===t.history_content_type)return new e.HistoryDatasetAssociation(t,n);if("dataset_collection"===t.history_content_type){switch(t.collection_type){case"list":return new i.HistoryListDatasetCollection(t,n);case"paired":return new i.HistoryPairDatasetCollection(t,n);case"list:paired":return new i.HistoryListPairedDatasetCollection(t,n)}return{validationError:"Unknown collection_type: "+t.history_content_type}}return{validationError:"Unknown history_content_type: "+t.history_content_type}},initialize:function(t,e){e=e||{},this.historyId=e.historyId,this.model.prototype.idAttribute="type_id",this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(t){return t.get("id")})},notReady:function(){return this.filter(function(t){return!t.inReadyState()})},running:function(){var t=[];return this.each(function(e){var i=!e.inReadyState();i&&t.push(e.get("id"))}),t},getByHid:function(t){return a.first(this.filter(function(e){return e.get("hid")===t}))},getVisible:function(t,e,i){i=i||[],this.debug("checking isVisible");var n=new c(this.filter(function(i){return i.isVisible(t,e)}));return a.each(i,function(t){a.isFunction(t)&&(n=new c(n.filter(t)))}),n},hidden:function(){function t(t){return t.hidden()}return new c(this.filter(t))},deleted:function(){function t(t){return t.get("deleted")}return new c(this.filter(t))},haveDetails:function(){return this.all(function(t){return t.hasDetails()})},fetchAllDetails:function(t){t=t||{};var e={details:"all"};return t.data=t.data?a.extend(t.data,e):e,this.fetch(t)},ajaxQueue:function(t,e){var i=r.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(a,r){return function(){var l=t.call(a,e);l.done(function(t){i.notify({curr:r,total:n,response:t,model:a})}),l.always(function(t){s.push(t),o.length?o.shift()():i.resolve(s)})}}).value();return o.shift()(),i},isCopyable:function(t){var e=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return a.isObject(t)&&t.id&&a.contains(e,t.model_class)},copy:function(t){var e,i,n;a.isString(t)?(e=t,n="hda",i="dataset"):(e=t.id,n={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[t.model_class]||"hda",i="hdca"===n?"dataset_collection":"dataset");var s=this,o=r.post(this.url(),{content:e,source:n,type:i}).done(function(t){s.add([t])}).fail(function(t,a,r){s.trigger("error",s,o,{},"Error copying contents",{type:i,id:e,source:n})});return o},matches:function(t){return this.filter(function(e){return e.matches(t)})},set:function(e,i){e=a.isArray(e)?e:[e],a.each(e,function(e){e.type_id&&e.get&&e.get("type_id")||(e.type_id=t.typeIdStr(e.history_content_type,e.id))}),o.Collection.prototype.set.call(this,e,i)},createHDCA:function(t,e,n,s){var o=this,a={list:i.HistoryListDatasetCollection,paired:i.HistoryPairDatasetCollection},r=new a[e]({history_id:this.historyId,name:n,element_identifiers:t});return r.save().done(function(t){o.add(r)}).fail(function(t,e,i){o.trigger("error",t,e,i)})},clone:function(){var t=o.Collection.prototype.clone.call(this);return t.historyId=this.historyId,t},print:function(){var t=this;t.each(function(e){t.debug(e),e.elements&&t.debug(" elements:",e.elements)})},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});return{HistoryContents:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(6),i(5)],s=function(t,e){var i="list",n=o.View.extend(t.LoggableMixin).extend({_logNamespace:i,initialize:function(t){this.expanded=t.expanded||!1,this.log(" expanded:",this.expanded),this.fxSpeed=void 0!==t.fxSpeed?t.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(t){var e=this._buildNewRender();return this._setUpBehaviors(e),this._queueNewRender(e,t),this},_buildNewRender:function(){var t=a(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(t).replaceWith(this._renderDetails().show()),t},_queueNewRender:function(t,e){e=void 0===e?this.fxSpeed:e;var i=this;a(i).queue("fx",[function(t){this.$el.fadeOut(e,t)},function(e){i._swapNewRender(t),e()},function(t){this.$el.fadeIn(e,t)},function(t){this.trigger("rendered",i),t()}])},_swapNewRender:function(t){return this.$el.empty().attr("class",r.isFunction(this.className)?this.className():this.className).append(t.children())},_setUpBehaviors:function(t){t=t||this.$el,t.find("[title]").tooltip({placement:"bottom"})},$details:function(t){return t=t||this.$el,t.find("> .details")},_renderDetails:function(){var t=a(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(t),t},toggleExpanded:function(t){return t=void 0===t?!this.expanded:t,t?this.expand():this.collapse(),this},expand:function(){var t=this;return t._fetchModelDetails().always(function(){t._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?l.when():this.model.fetch()},_expand:function(){var t=this,e=t._renderDetails();t.$details().replaceWith(e),t.expanded=!0,t.$details().slideDown({duration:t.fxSpeed,step:function(){t.trigger("expanding",t)},complete:function(){t.trigger("expanded",t)}})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var t=this;t.expanded=!1,this.$details().slideUp({duration:t.fxSpeed,step:function(){t.trigger("collapsing",t)},complete:function(){t.trigger("collapsed",t)}})}}),s=n.extend(t.mixin(t.SelectableViewMixin,t.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){n.prototype.initialize.call(this,e),t.SelectableViewMixin.initialize.call(this,e),t.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(t){t?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var t=n.prototype._buildNewRender.call(this);return t.children(".warnings").replaceWith(this._renderWarnings()),t.children(".title-bar").replaceWith(this._renderTitleBar()),t.children(".primary-actions").append(this._renderPrimaryActions()),t.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),t},_swapNewRender:function(t){return n.prototype._swapNewRender.call(this,t),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var t=this,e=a(''),i=t.model.toJSON();return r.each(t.templates.warnings,function(n){e.append(a(n(i,t)))}),e},_renderTitleBar:function(){return a(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return a(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(t){t.stopPropagation(),t.altKey?(this.toggleSelect(t),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(t){var e=32,i=13;return!t||"keydown"!==t.type||t.keyCode!==e&&t.keyCode!==i?!0:(this.toggleExpanded(),t.stopPropagation(),!1)},toString:function(){var t=this.model?this.model+"":"(no model)";return"ListItemView("+t+")"}}));s.prototype.templates=function(){var e=t.wrapTemplate(['','','
"]),i={},n=t.wrapTemplate(['','',"
",'','','',"','','
"],"element"),s=t.wrapTemplate(['']),o=t.wrapTemplate(['']);return{el:e,warnings:i,titleBar:n,subtitle:s,details:o}}();var c=s.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(t){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=t.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=t.foldoutPanelClass||this.foldoutPanelClass,s.prototype.initialize.call(this,t),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return a();var t=s.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,t)},_createFoldoutPanel:function(){var t=this.model,e=this._getFoldoutPanelClass(t),i=this._getFoldoutPanelOptions(t),n=new e(r.extend(i,{model:t}));return n},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(t,e){return e=e||this.$("> .details"),this.foldout=t.render(0),t.$("> .controls").hide(),e.append(t.$el)},expand:function(){var t=this;return t._fetchModelDetails().always(function(){"foldout"===t.foldoutStyle?t._expand():"drilldown"===t.foldoutStyle&&t._expandByDrilldown()})},_expandByDrilldown:function(){var t=this;t.foldout.on("close",function(){t.trigger("collapsed:drilldown",t,t.foldout)}),t.trigger("expanded:drilldown",t,t.foldout)}});return c.prototype.templates=function(){var e=t.wrapTemplate(['','<%- element.name %>',"
",'',"',"
"],"collection");return r.extend({},s.prototype.templates,{details:e})}(),{ExpandableView:n,ListItemView:s,FoldoutListItemView:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(4),i(60),i(7),i(44),i(23),i(21),i(33)],s=function(t,e,i,n,s,a,r){return n.extend({initialize:function(t){var i=this;n.prototype.initialize.call(this,t),this.deferred=new e,t.inputs?(this._buildForm(t),t.needs_update&&this.deferred.execute(function(t){i._updateModel(t)})):this.deferred.execute(function(e){i._buildModel(e,t,!0)})},remove:function(){var t=this;this.$el.hide(),this.deferred.execute(function(){n.prototype.remove.call(t),Galaxy.emit.debug("tool-form-base::remove()","Destroy view.")})},_buildForm:function(e){var i=this;this.options=t.merge(e,this.options),this.options=t.merge({icon:void 0===e.icon&&"fa-wrench"||"",title:""+e.name+" "+e.description+" (Galaxy Version "+e.version+")",operations:this._operations(),onchange:function(){i.deferred.reset(),i.deferred.execute(function(t){i._updateModel(t)})}},this.options),this.options.customize&&this.options.customize(this.options),this.render(),this.options.collapsible||this.$el.append(o("").addClass("ui-margin-top-large").append(this._footer()))},_buildModel:function(e,n,s){var a=this;this.options.id=n.id,this.options.version=n.version;var r="",l={};n.job_id?r=Galaxy.root+"api/jobs/"+n.job_id+"/build_for_rerun":(r=Galaxy.root+"api/tools/"+n.id+"/build",Galaxy.params&&Galaxy.params.tool_id==n.id&&(l=o.extend({},Galaxy.params),n.version&&(l.tool_version=n.version))),t.request({type:"GET",url:r,data:l,success:function(t){a._buildForm(t.tool_model||t),!s&&a.message.update({status:"success",message:"Now you are using '"+a.options.name+"' version "+a.options.version+", id '"+a.options.id+"'.",persistent:!1}),Galaxy.emit.debug("tool-form-base::initialize()","Initial tool model ready.",t),e.resolve()},error:function(t){var n=t&&t.err_msg||"Uncaught error.";a.$el.is(":empty")?a.$el.prepend(new i.Message({message:n,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal.show({title:"Tool request failed",body:n,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form::initialize()","Initial tool model request failed.",t),e.reject()}})},_updateModel:function(e){var i=this,n=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",s={tool_id:this.options.id,tool_version:this.options.version,inputs:o.extend(!0,{},i.data.create())};this.wait(!0),Galaxy.emit.debug("tool-form-base::_updateModel()","Sending current state.",s),t.request({type:"POST",url:n,data:s,success:function(t){i.update(t.tool_model||t),i.options.update&&i.options.update(t),i.wait(!1),Galaxy.emit.debug("tool-form-base::_updateModel()","Received new model.",t),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form-base::_updateModel()","Refresh request failed.",t),e.reject()}})},_operations:function(){var t=this,e=this.options,n=new i.ButtonMenu({icon:"fa-cubes",title:!e.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!e.sustain_version&&e.versions&&e.versions.length>1)for(var o in e.versions){var a=e.versions[o];a!=e.version&&n.addMenu({title:"Switch to "+a,version:a,icon:"fa-cube",onclick:function(){var i=e.id.replace(e.version,this.version),n=this.version;t.deferred.reset(),t.deferred.execute(function(e){t._buildModel(e,{id:i,version:n})})}})}else n.$el.hide();var r=new i.ButtonMenu({icon:"fa-caret-down",title:!e.narrow&&"Options"||null,tooltip:"View available options"});return e.biostar_url&&(r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/p/new/post/")}}),r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/local/search/page/?q="+e.name)}})),r.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+e.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+e.id+"/download"}}),e.requirements&&e.requirements.length>0&&r.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,t.message.update({message:""})):(this.visible=!0,t.message.update({persistent:!0,message:s.requirements(e),status:"info"}))}}),e.sharable_url&&r.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(e.sharable_url)}}),{menu:r,versions:n}},_footer:function(){var t=this.options,e=o("").append(s.help(t));if(t.citations){var i=o(""),n=new a.ToolCitationCollection;n.tool_id=t.id;var l=new r.CitationListView({el:i,collection:n});l.render(),n.fetch(),e.append(i)}return e}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1))},function(t,e,i){var n,s;(function(o,a){n=[i(3),i(20),i(14),i(22),i(64),i(65),i(63),i(66)],s=function(t,e,i,n,s,r,l,c){var d={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}},h=o.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(t){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new h(this.toJSON())},set_value:function(t){this.set("value",t||"")}}),u=o.Collection.extend({model:h}),p=h.extend({}),f=h.extend({set_value:function(t){this.set("value",parseInt(t,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),g=f.extend({set_value:function(t){this.set("value",parseFloat(t))}}),m=h.extend({get_samples:function(){return t.map(this.get("options"),function(t){return t[0]})}});h.subModelTypes={integer:f,"float":g,data:p,select:m};var v=o.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:Galaxy.root+"api/tools",initialize:function(e){this.set("inputs",new u(t.map(e.inputs,function(t){var e=h.subModelTypes[t.type]||h;return new e(t)})))},toJSON:function(){var t=o.Model.prototype.toJSON.call(this);return t.inputs=this.get("inputs").map(function(t){return t.toJSON()}),t},remove_inputs:function(t){var e=this,i=e.get("inputs").filter(function(e){return-1!==t.indexOf(e.get("type"))});e.get("inputs").remove(i)},copy:function(t){var e=new v(this.toJSON());if(t){var i=new o.Collection;e.get("inputs").each(function(t){t.get_samples()&&i.push(t)}),e.set("inputs",i)}return e},apply_search_results:function(e){return-1!==t.indexOf(e,this.attributes.id)?this.show():this.hide(),this.is_visible()},set_input_value:function(t,e){this.get("inputs").find(function(e){return e.get("name")===t}).set("value",e)},set_input_values:function(e){var i=this;t.each(t.keys(e),function(t){i.set_input_value(t,e[t])})},run:function(){return this._run()},rerun:function(t,e){return this._run({action:"rerun",target_dataset_id:t.id,regions:e})},get_inputs_dict:function(){var t={};return this.get("inputs").each(function(e){t[e.get("name")]=e.get("value")}),t},_run:function(n){var s=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},n),o=a.Deferred(),r=new e.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(s),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});return a.when(r.go()).then(function(t){o.resolve(new i.DatasetCollection(t))}),o}});t.extend(v.prototype,d);var _=(o.View.extend({}),o.Collection.extend({model:v})),y=o.Model.extend(d),w=o.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){t.each(this.attributes.elems,function(t){t.show()}),this.show(),this.set("open",!1)},apply_search_results:function(e){var i,n=!0;t.each(this.attributes.elems,function(t){t instanceof y?(i=t,i.hide()):t instanceof v&&t.apply_search_results(e)&&(n=!1,i&&i.show())}),n?this.hide():(this.show(),this.set("open",!0))}});t.extend(w.prototype,d);var b=o.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_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 t=this.attributes.query;if(t.length- ',this._templateOptions(e),"
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e=0;ei?this.views.slice(i,n+1):this.views.slice(n,i+1)},_renderSearch:function(t){return t.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:a.bind(this._firstSearch,this),onsearch:a.bind(this.searchItems,this),onclear:a.bind(this.clearSearch,this)}),t},_firstSearch:function(t){return this.log("onFirstSearch",t),this.searchItems(t)},searchItems:function(t){return this.searchFor=t,this.trigger("search:searching",t,this),this.renderItems(),this.$("> .controls .search-query").val(t),this},clearSearch:function(t){return this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.renderItems(),this},THROTTLE_SELECTORS_AT:20,showSelectors:function(t){t=void 0!==t?t:this.fxSpeed,this.selecting=!0,this.$(".list-actions").slideDown(t),t=this.views.length>=this.THROTTLE_SELECTORS_AT?0:t,a.each(this.views,function(e){e.showSelector(t)})},hideSelectors:function(t){t=void 0!==t?t:this.fxSpeed,this.selecting=!1,this.$(".list-actions").slideUp(t),t=this.views.length>=this.THROTTLE_SELECTORS_AT?0:t,a.each(this.views,function(e){e.hideSelector(t)}),this.selected=[],this.lastSelected=null},toggleSelectors:function(){this.selecting?this.hideSelectors():this.showSelectors()},selectAll:function(t){a.each(this.views,function(e){e.select(t)})},deselectAll:function(t){this.lastSelected=null,a.each(this.views,function(e){e.deselect(t)})},selectRange:function(t,e){var i=this.viewRange(t,e);return a.each(i,function(t){t.select()}),i},getSelectedViews:function(){return a.filter(this.views,function(t){return t.selected})},getSelectedModels:function(){return new this.collection.constructor(a.map(this.getSelectedViews(),function(t){return t.model}))},_showLoadingIndicator:function(t,i,n){this.debug("_showLoadingIndicator",this.indicator,t,i,n),i=void 0!==i?i:this.fxSpeed,this.indicator||(this.indicator=new e(this.$el,this.$el.parent()),this.debug(" created",this.indicator)),this.$el.is(":visible")?(this.$el.fadeOut(i),this.indicator.show(t,i,n)):this.indicator.show(0,n)},_hideLoadingIndicator:function(t,e){this.debug("_hideLoadingIndicator",this.indicator,t,e),t=void 0!==t?t:this.fxSpeed,this.indicator&&this.indicator.hide(t,e)},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(t,e){return e=e||0,this.$scrollContainer().animate({scrollTop:t},e),this},scrollToTop:function(t){return this.scrollTo(0,t)},scrollToItem:function(t,e){if(!t)return this;var i=t.$el.position().top;return this.scrollTo(i,e)},scrollToId:function(t,e){return this.scrollToItem(this.viewFromModelId(t),e)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});l.prototype.templates=function(){var t=i.wrapTemplate(["'+e.path+' '+t.bytesToString(e.size)+' '+e.ctime+"
'},_templateInfo:function(){return'
\n \n
\n'},compiler:[7,">= 4.0.0"],main:function(t,e,i,n,s){var o,a,r=null!=e?e:{},l=i.helperMissing,c="function",d=t.escapeExpression;return'\n '+(null!=(a=null!=(a=i.html||(null!=e?e.html:e))?a:l,o=typeof a===c?a.call(r,{name:"html",hash:{},data:s}):a)?o:"")+'\n
\n \n '+d((a=null!=(a=i.help||(null!=e?e.help:e))?a:l,typeof a===c?a.call(r,{name:"help",hash:{},data:s}):a))+'\n
\n \n '+d((a=null!=(a=i.name||(null!=e?e.name:e))?a:l,typeof a===c?a.call(r,{name:"name",hash:{},data:s}):a))+" (version "+d((a=null!=(a=i.version||(null!=e?e.version:e))?a:l,typeof a===c?a.call(r,{name:"version",hash:{},data:s}):a))+')
\n \n'+(null!=(o=i.each.call(r,null!=e?e.inputs:e,{name:"each",hash:{},fn:t.program(1,s,0),inverse:t.noop,data:s}))?o:"")+'
\n \n \n
\n\n
"},useData:!0})},function(t,e,i){var n=i(12);t.exports=(n["default"]||n).template({1:function(t,e,i,n,s){var o=t.lambda,a=t.escapeExpression;return''+a(o(e,e))+" "},compiler:[7,">= 4.0.0"],main:function(t,e,i,n,s){var o,a,r=null!=e?e:{},l=i.helperMissing,c="function",d=t.escapeExpression;return''+(null!=(o=i.each.call(r,null!=e?e.labels:e,{name:"each",hash:{},fn:t.program(1,s,0),inverse:t.noop,data:s}))?o:"")+'\n'+d((a=null!=(a=i.name||(null!=e?e.name:e))?a:l,typeof a===c?a.call(r,{name:"name",hash:{},data:s}):a))+"\n"+d((a=null!=(a=i.description||(null!=e?e.description:e))?a:l,typeof a===c?a.call(r,{name:"description",hash:{},data:s}):a))+"\n"},useData:!0})},function(t,e,i){var n=i(12);t.exports=(n["default"]||n).template({compiler:[7,">= 4.0.0"],main:function(t,e,i,n,s){var o,a=null!=e?e:{},r=i.helperMissing,l="function",c=t.escapeExpression;return'\n \n'+d((a=null!=(a=i.help||(null!=e?e.help:e))?a:l,typeof a===c?a.call(r,{name:"help",hash:{},data:s}):a))+"
\n',a.escape(t),"
"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off(),this.stopListening(this.model),o.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}});return{AnnotationEditor:i}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3))},function(t,e,i){var n,s;(function(o){n=[i(100),i(35),i(34),i(6),i(5)],s=function(t,e,i,n,s){var a="collections",r=t.ModelListPanel,l=r.extend({_logNamespace:a,className:r.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:i.DatasetDCEListItemView,NestedDCDCEViewClass:i.NestedDCDCEListItemView,modelCollectionKey:"elements",initialize:function(t){r.prototype.initialize.call(this,t),this.linkTarget=t.linkTarget||"_blank",this.hasUser=t.hasUser,this.panelStack=[],this.parentName=t.parentName,this.foldoutStyle=t.foldoutStyle||"foldout"},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(t){switch(t.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",t.get("element_type"))},_getItemViewOptions:function(t){var e=r.prototype._getItemViewOptions.call(this,t);return o.extend(e,{linkTarget:this.linkTarget,hasUser:this.hasUser,foldoutStyle:this.foldoutStyle})},_setUpItemViewListeners:function(t){var e=this;return r.prototype._setUpItemViewListeners.call(e,t),t.on("expanded:drilldown",function(t,e){this._expandDrilldownPanel(e)},this),t.on("collapsed:drilldown",function(t,e){this._collapseDrilldownPanel(e)},this),this},_expandDrilldownPanel:function(t){this.panelStack.push(t),this.$("> .controls").add(this.$list()).hide(),t.parentName=this.model.get("name"),this.$el.append(t.render().$el)},_collapseDrilldownPanel:function(t){this.panelStack.pop(),this.render()},events:{"click .navigation .back":"close"},close:function(t){this.$el.remove(),this.trigger("close")},toString:function(){return"CollectionView("+(this.model?this.model.get("name"):"")+")"}});l.prototype.templates=function(){var t=n.wrapTemplate(['','",'
"],"collection");return o.extend(o.clone(r.prototype.templates),{controls:t})}();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"):"")+")"}});return{CollectionView:l,ListCollectionView:c,PairCollectionView:d,ListOfPairsCollectionView:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a){n=[i(15),i(37),i(101),i(92),i(26),i(6),i(5)],s=function(t,e,n,s,r,l,c){var d=e.DatasetListItemView,h=d.extend({initialize:function(t){d.prototype.initialize.call(this,t),this.hasUser=t.hasUser,this.purgeAllowed=t.purgeAllowed||!1,this.tagsEditorShown=t.tagsEditorShown||!1,this.annotationEditorShown=t.annotationEditorShown||!1},_renderPrimaryActions:function(){var e=d.prototype._renderPrimaryActions.call(this);return this.model.get("state")===t.NOT_VIEWABLE?e:d.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){if(this.model.get("state")===t.DISCARDED||!this.model.get("accessible"))return null;var e=this.model.get("purged"),i=this.model.get("deleted"),n={title:c("Edit attributes"),href:this.model.urls.edit,target:this.linkTarget,faIcon:"fa-pencil",classes:"edit-btn"};return i||e?(n.disabled=!0,e?n.title=c("Cannot edit attributes of datasets removed from disk"):i&&(n.title=c("Undelete dataset to edit attributes"))):o.contains([t.UPLOAD,t.NEW],this.model.get("state"))&&(n.disabled=!0,n.title=c("This dataset is not yet editable")),r(n)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var t=this,e=this.model.isDeletedOrPurged();return r({title:c(e?"Dataset is already deleted":"Delete"),disabled:e,faIcon:"fa-times",classes:"delete-btn",onclick:function(){t.$el.find(".icon-btn.delete-btn").trigger("mouseout"),t.model["delete"]()}})},_renderDetails:function(){var e=d.prototype._renderDetails.call(this),i=this.model.get("state");return!this.model.isDeletedOrPurged()&&o.contains([t.OK,t.FAILED_METADATA],i)&&(this._renderTags(e),this._renderAnnotation(e),this._makeDbkeyEditLink(e)),this._setUpBehaviors(e),e},_renderSecondaryActions:function(){var e=d.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case t.UPLOAD:case t.NEW:case t.NOT_VIEWABLE:return e;case t.ERROR:return e.unshift(this._renderErrButton()),e.concat([this._renderRerunButton()]);case t.OK:case t.FAILED_METADATA:return e.concat([this._renderRerunButton(),this._renderVisualizationsButton()])}return e.concat([this._renderRerunButton()])},_renderErrButton:function(){return r({title:c("View or report this error"),href:this.model.urls.report_error,classes:"report-error-btn",target:this.linkTarget,faIcon:"fa-bug"})},_renderRerunButton:function(){var t=this.model.get("creating_job");return this.model.get("rerunnable")?r({title:c("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(e){e.preventDefault(),!function(){var e=[i(22)];(function(e){var i=new e.View({job_id:t});i.deferred.execute(function(){Galaxy.app.display(i)})}).apply(null,e)}()}}):void 0},_renderVisualizationsButton:function(){var t=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||o.isEmpty(t))return null;if(!o.isObject(t[0]))return this.warn("Visualizations have been switched off"),null;var e=a(this.templates.visualizations(t,this));return e.find('[target="galaxy_main"]').attr("target",this.linkTarget),
this._addScratchBookFn(e.find(".visualization-link").addBack(".visualization-link")),e},_addScratchBookFn:function(t){t.click(function(t){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Visualization",url:a(this).attr("href")}),t.preventDefault(),t.stopPropagation())})},_renderTags:function(t){if(this.hasUser){var e=this;this.tagsEditor=new n.TagsEditor({model:this.model,el:t.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){e.tagsEditorShown=!0},onhide:function(){e.tagsEditorShown=!1},$activator:r({title:c("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(t.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(t){if(this.hasUser){var e=this;this.annotationEditor=new s.AnnotationEditor({model:this.model,el:t.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){e.annotationEditorShown=!0},onhide:function(){e.annotationEditorShown=!1},$activator:r({title:c("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(t.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(t){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var e=a('?').attr("href",this.model.urls.edit).attr("target",this.linkTarget);t.find(".dbkey .value").replaceWith(e)}},events:o.extend(o.clone(d.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(t){this.trigger("edit",this,t)},"click .delete-btn":function(t){this.trigger("delete",this,t)},"click .rerun-btn":function(t){this.trigger("rerun",this,t)},"click .report-err-btn":function(t){this.trigger("report-err",this,t)},"click .visualization-btn":function(t){this.trigger("visualize",this,t)},"click .dbkey a":function(t){this.trigger("edit",this,t)}}),_clickUndeleteLink:function(t){return this.model.undelete(),!1},_clickPurgeLink:function(t){return this.model.purge(),!1},toString:function(){var t=this.model?this.model+"":"(no model)";return"HDAEditView("+t+")"}});return h.prototype.templates=function(){var t=o.extend({},d.prototype.templates.warnings,{failed_metadata:l.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','','
","<%- 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"),"<% } %>","
","',c("An error occurred setting the metadata for this dataset"),'
',c("Set it manually or retry auto-detection"),"","
","<% } %>"],"dataset"),deleted:l.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'',c("Set it manually or retry auto-detection"),"","
',c("This dataset has been deleted"),'
',c("Undelete it"),"","<% if( view.purgeAllowed ){ %>",'
',c("Permanently remove it from disk"),"","<% } %>","
","<% } %>"],"dataset")}),e=l.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'',c("Undelete it"),"","<% if( view.purgeAllowed ){ %>",'
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','','',"",'
","<% } %>"],"visualizations");return o.extend({},d.prototype.templates,{warnings:t,visualizations:e})}(),{DatasetListItemEdit:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(15),i(6),i(5)],s=function(t,e,i){var n="dataset",s=e.SearchableModelMixin,l=o.Model.extend(e.LoggableMixin).extend(e.mixin(s,{_logNamespace:n,defaults:{state:t.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(e,i){this.debug(this+"(Dataset).initialize",e,i),this.get("accessible")||this.set("state",t.NOT_VIEWABLE),this.urls=this._generateUrls(),this._setUpListeners()},_generateUrls:function(){var t=this.get("id");if(!t)return{};var e={purge:"datasets/"+t+"/purge_async",display:"datasets/"+t+"/display/?preview=True",edit:"datasets/"+t+"/edit",download:"datasets/"+t+"/display?to_ext="+this.get("file_ext"),report_error:"dataset/errors?id="+t,rerun:"tool_runner/rerun?id="+t,show_params:"datasets/"+t+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+t+"&metadata_name="};return a.each(e,function(t,i){e[i]=Galaxy.root+t}),this.urls=e,e},_setUpListeners:function(){this.on("change:state",function(t,e){this.log(this+" has changed state:",t,e),this.inReadyState()&&this.trigger("state:ready",t,e,this.previous("state"))}),this.on("change:id change:file_ext",function(t){this._generateUrls()})},toJSON:function(){var t=o.Model.prototype.toJSON.call(this);return a.extend(t,{urls:this.urls})},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},inReadyState:function(){var e=a.contains(t.READY_STATES,this.get("state"));return this.isDeletedOrPurged()||e},hasDetails:function(){return a.has(this.attributes,"genome_build")},hasData:function(){return this.get("file_size")>0},fetch:function(t){var e=this;return o.Model.prototype.fetch.call(this,t).always(function(){e._generateUrls()})},"delete":function(t){return this.get("deleted")?r.when():this.save({deleted:!0},t)},undelete:function(t){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},t)},purge:function(t){if(this.get("purged"))return r.when();t=t||{},t.url=this.urls.purge;var e=this,n=r.ajax(t);return n.done(function(t,i,n){e.set({deleted:!0,purged:!0})}),n.fail(function(n,s,o){var a=i("Unable to purge dataset"),r="Removal of datasets by users is not allowed in this Galaxy instance";n.responseJSON&&n.responseJSON.error?a=n.responseJSON.error:-1!==n.responseText.indexOf(r)&&(a=r),n.responseText=a,e.trigger("error",e,n,t,i(a),{error:a})}),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 t=this.get("id")||"";return this.get("name")&&(t='"'+this.get("name")+'",'+t),"Dataset("+t+")"}})),c=o.Collection.extend(e.LoggableMixin).extend({_logNamespace:n,model:l,urlRoot:Galaxy.root+"api/datasets",url:function(){return this.urlRoot},ids:function(){return this.map(function(t){return t.get("id")})},notReady:function(){return this.filter(function(t){return!t.inReadyState()})},haveDetails:function(){return this.all(function(t){return t.hasDetails()})},ajaxQueue:function(t,e){var i=r.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(a,r){return function(){var l=t.call(a,e);l.done(function(t){i.notify({curr:r,total:n,response:t,model:a})}),l.always(function(t){s.push(t),o.length?o.shift()():i.resolve(s)})}}).value();return o.shift()(),i},matches:function(t){return this.filter(function(e){return e.matches(t)})},toString:function(){return["DatasetAssociationCollection(",this.length,")"].join("")}});return{DatasetAssociation:l,DatasetAssociationCollection:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(37),i(6),i(5)],s=function(t,e,i){var n=t.DatasetListItemView,s=n.extend({className:n.prototype.className+" history-content",initialize:function(t,e){n.prototype.initialize.call(this,t,e)},toString:function(){var t=this.model?this.model+"":"(no model)";return"HDAListItemView("+t+")"}});return s.prototype.templates=function(){var t=e.wrapTemplate(['- ',"<% _.each( visualizations, function( visualization ){ %>",'
- ',"<%- visualization.html %>"," ","<% }); %>","
','','
"],"dataset"),s=o.extend({},n.prototype.templates.warnings,{hidden:e.wrapTemplate(["<% if( !dataset.visible ){ %>",'','<%- dataset.hid %> ','<%- dataset.name %>',"
","',i("This dataset has been hidden"),"
","<% } %>"],"dataset")});return o.extend({},n.prototype.templates,{titleBar:t,warnings:s})}(),{HDAListItemView:s}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o){n=[i(95),i(46),i(6),i(5)],s=function(t,e,i,n){var s=t.DatasetAssociation,a=e.HistoryContentMixin,r=s.extend(i.mixin(a,{constructor:function(t,e){a.constructor.call(this,t,e)},defaults:o.extend({},s.prototype.defaults,a.defaults,{model_class:"HistoryDatasetAssociation"}),initialize:function(t,e){s.prototype.initialize.call(this,t,e),a.initialize.call(this,t,e)},toString:function(){var t=this.get("id")||"";return this.get("name")&&(t=this.get("hid")+' :"'+this.get("name")+'",'+t),"HDA("+t+")"}}));return{HistoryDatasetAssociation:r}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o){n=[i(15),i(34),i(93),i(6),i(5)],s=function(t,e,i,n,s){var a=e.DCListItemView,r=a.extend({className:a.prototype.className+" history-content",_setUpListeners:function(){a.prototype._setUpListeners.call(this),this.model.on({"change:populated change:visible":function(t,e){this.render()}},this)},_getFoldoutPanelClass:function(){switch(this.model.get("collection_type")){case"list":return i.ListCollectionView;case"paired":return i.PairCollectionView;case"list:paired":return i.ListOfPairsCollectionView}throw new TypeError("Uknown collection_type: "+this.model.get("collection_type"))},_swapNewRender:function(e){a.prototype._swapNewRender.call(this,e);var i=this.model.get("populated")?t.OK:t.RUNNING;return this.$el.addClass("state-"+i),this.$el},toString:function(){var t=this.model?this.model+"":"(no model)";return"HDCAListItemView("+t+")"}});return r.prototype.templates=function(){var t=o.extend({},a.prototype.templates.warnings,{hidden:n.wrapTemplate(["<% if( !collection.visible ){ %>",'',s("This collection has been hidden"),"
","<% } %>"],"collection")}),e=n.wrapTemplate(['','','
"],"collection");return o.extend({},a.prototype.templates,{warnings:t,titleBar:e})}(),{HDCAListItemView:r}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(47),i(4),i(6),i(5)],s=function(t,e,i,n){var s="history",l=o.Model.extend(i.LoggableMixin).extend(i.mixin(i.SearchableModelMixin,{_logNamespace:s,defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",deleted:!1},urlRoot:Galaxy.root+"api/histories",initialize:function(e,i,n){n=n||{},this.logger=n.logger||null,this.log(this+".initialize:",e,i,n),this.log("creating history contents:",i),this.contents=new t.HistoryContents(i||[],{historyId:this.get("id")}),this._setUpListeners(),this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(t,e,i,n,s){this.errorHandler(t,e,i,n,s)}),this.contents&&this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(a.makeArray(arguments)))}),this.on("change:id",function(t,e){this.contents&&(this.contents.historyId=e)},this)},errorHandler:function(t,e,i,n,s){this.clearUpdateTimeout()},nice_size:function(){return e.bytesToString(this.get("size"),!0,2)},toJSON:function(){return r.extend(o.Model.prototype.toJSON.call(this),{nice_size:this.nice_size()})},get:function(t){return"nice_size"===t?this.nice_size():o.Model.prototype.get.apply(this,arguments)},ownedByCurrUser:function(){return Galaxy&&Galaxy.user?Galaxy.user.isAnonymous()||Galaxy.user.id!==this.get("user_id")?!1:!0:!1},contentsCount:function(){return r.reduce(r.values(this.get("state_details")),function(t,e){return t+e},0)},searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},checkForUpdates:function(t){return this.contents.running().length?this.setUpdateTimeout():(this.trigger("ready"),r.isFunction(t)&&t.call(this)),this},setUpdateTimeout:function(t){t=t||l.UPDATE_DELAY;var e=this;return this.clearUpdateTimeout(),this.updateTimeoutId=setTimeout(function(){e.refresh()},t),this.updateTimeoutId},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},refresh:function(t,e){t=t||[],e=e||{};var i=this;e.data=e.data||{},t.length&&(e.data.details=t.join(","));var n=this.contents.fetch(e);return n.done(function(t){i.checkForUpdates(function(){this.fetch()})}),n},_delete:function(t){return this.get("deleted")?a.when():this.save({deleted:!0},t)},purge:function(t){return this.get("purged")?a.when():this.save({deleted:!0,purged:!0},t)},undelete:function(t){return this.get("deleted")?this.save({deleted:!1},t):a.when()},copy:function(t,e,i){if(t=void 0!==t?t:!0,!this.id)throw new Error("You must set the history ID before copying it.");var n={history_id:this.id};t&&(n.current=!0),e&&(n.name=e),i||(n.all_datasets=!1);var s=this,o=a.post(this.urlRoot,n);return t?o.then(function(t){var e=new l(t);return e.setAsCurrent().done(function(){s.trigger("copied",s,t)})}):o.done(function(t){s.trigger("copied",s,t)})},setAsCurrent:function(){var t=this,e=a.getJSON(Galaxy.root+"history/set_as_current?id="+this.id);return e.done(function(){t.trigger("set-as-current",t)}),e},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}}));l.UPDATE_DELAY=4e3,l.getHistoryData=function(t,e){function i(e){return"current"===t?a.getJSON(Galaxy.root+"history/current_history_json"):a.ajax(Galaxy.root+"api/histories/"+t)}function n(t){return t&&t.empty}function s(t){if(n(t))return[];r.isFunction(o)&&(o=o(t)),r.isFunction(l)&&(l=l(t));var e={};return o.length&&(e.dataset_details=o.join(",")),l.length&&(e.dataset_collection_details=l.join(",")),a.ajax(Galaxy.root+"api/histories/"+t.id+"/contents",{data:e})}e=e||{};var o=e.detailIdsFn||[],l=e.hdcaDetailIds||[],c=a.Deferred(),d=null,h=e.historyFn||i,u=e.contentsFn||s,p=h(t);p.done(function(t){d=t,c.notify({status:"history data retrieved",historyJSON:d})}),p.fail(function(t,e,i){c.reject(t,"loading the history")});var f=p.then(u);return f.then(function(t){c.notify({status:"contents data retrieved",historyJSON:d,contentsJSON:t}),c.resolve(d,t)}),f.fail(function(t,e,i){c.reject(t,"loading the contents",{history:d})}),c};var c={fetch:function(t){return t=t||{},t.data=t.data||this._buildFetchData(t),t.traditional=!0,o.Collection.prototype.fetch.call(this,t)},_fetchOptions:["order","limit","offset","view","keys"],_buildFetchData:function(t){var e={},i=this._fetchDefaults();t=r.defaults(t||{},i),e=r.pick(t,this._fetchOptions);var n=r.has(t,"filters")?t.filters:i.filters||{};return r.isEmpty(n)||r.extend(e,this._buildFetchFilters(n)),e},_fetchDefaults:function(){return{}},_buildFetchFilters:function(t){var e={q:[],qv:[]};return r.each(t,function(t,i){t===!0&&(t="True"),t===!1&&(t="False"),e.q.push(i),e.qv.push(t)}),e}},d=o.Collection.extend(i.LoggableMixin).extend(c).extend({_logNamespace:s,model:l,DEFAULT_ORDER:"update_time",sortOrders:{update_time:{getter:function(t){return new Date(t.get("update_time"))},asc:!1},"update_time-asc":{getter:function(t){return new Date(t.get("update_time"))},asc:!0},name:{getter:function(t){return t.get("name")},asc:!0},"name-dsc":{getter:function(t){return t.get("name")},asc:!1},size:{getter:function(t){return t.get("size")},asc:!1},"size-asc":{getter:function(t){return t.get("size")},asc:!0}},initialize:function(t,e){e=e||{},this.log("HistoryCollection.initialize",arguments),this.includeDeleted=e.includeDeleted||!1,this.setOrder(e.order||this.DEFAULT_ORDER),this.currentHistoryId=e.currentHistoryId,this.allFetched=e.allFetched||!1,this.setUpListeners()},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot},_fetchDefaults:function(){var t={order:this.order,view:"detailed"};return this.includeDeleted||(t.filters={deleted:!1,purged:!1}),t},setUpListeners:function(){this.on({"change:deleted":function(t){this.debug("change:deleted",this.includeDeleted,t.get("deleted")),!this.includeDeleted&&t.get("deleted")&&this.remove(t)},copied:function(t,e){this.setCurrent(new l(e,[]))},"set-as-current":function(t){var e=this.currentHistoryId;this.trigger("no-longer-current",e),this.currentHistoryId=t.id}},this)},sort:function(t){return t=t||{},this.setOrder(t.order),o.Collection.prototype.sort.call(this,t)},setOrder:function(t){var e=this,i=this.sortOrders[t];if(!r.isUndefined(i))return e.order=t,e.comparator=function(t,n){var s=e.currentHistoryId;return t.id===s?-1:n.id===s?1:(t=i.getter(t),n=i.getter(n),i.asc?t===n?0:t>n?1:-1:t===n?0:t>n?-1:1)},e.trigger("changed-order",e.order,e),e},fetch:function(t){if(t=t||{},this.allFetched)return a.when({});var e=this,i=r.defaults(t,{remove:!1,offset:e.length>=1?e.length-1:0,order:e.order}),n=t.limit;return r.isUndefined(n)||(i.limit=n),c.fetch.call(this,i).done(function(t){var i=r.isArray(t)?t.length:0;(!n||n>i)&&(e.allFetched=!0,e.trigger("all-fetched",e))})},create:function(t,e,i,n){var s=this,o=a.getJSON(Galaxy.root+"history/create_new_current");return o.done(function(t){s.setCurrent(new l(t,[],i||{}))})},setCurrent:function(t,e){return e=e||{},this.unshift(t,e),this.currentHistoryId=t.get("id"),e.silent||this.trigger("new-current",t,this),this},reset:function(t,e){return this.allFetched=!1,o.Collection.prototype.reset.call(this,t,e)},toString:function(){return"HistoryCollection("+this.length+")"}});return{History:l,HistoryCollection:d}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(48),i(143),i(6),i(5),i(108)],s=function(t,e,i,n){var s="list",l=o.View.extend(i.LoggableMixin).extend({_logNamespace:s,viewClass:t.ListItemView,collectionClass:o.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(t,i){t=t||{},t.logger&&(this.logger=t.logger),this.log(this+".initialize:",t),this.fxSpeed=a.has(t,"fxSpeed")?t.fxSpeed:this.fxSpeed,this.filters=[],this.searchFor=t.searchFor||"",this.indicator=new e(this.$el),this.selecting=void 0!==t.selecting?t.selecting:!0,this.selected=t.selected||[],this.lastSelected=null,this.dragItems=t.dragItems||!1,this.viewClass=t.viewClass||this.viewClass,this.views=[],this.collection=t.collection||new this.collectionClass([]),this.filters=t.filters||[],this.$scrollContainer=t.$scrollContainer||this.$scrollContainer,this.title=t.title||"",this.subtitle=t.subtitle||"",this._setUpListeners()},freeViews:function(){return a.each(this.views,function(t){t.off()}),this.views=[],this},_setUpListeners:function(){return this.off(),this.on("error",function(t,e,i,n,s){console.error(t,e,i,n,s)},this),this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this),this.on("loading-done",function(){this._hideLoadingIndicator(40)},this),this.once("rendered",function(){this.trigger("rendered:initial",this)},this),this.logger&&this.on("all",function(t){this.log(this+"",arguments)},this),this._setUpCollectionListeners(),this._setUpViewListeners(),this},_setUpCollectionListeners:function(){return this.log(this+"._setUpCollectionListeners",this.collection),this.collection.off(),this.collection.on("error",function(t,e,i,n,s){this.trigger("error",t,e,i,n,s)},this),this.collection.on("reset",function(){this.renderItems()},this),this.collection.on("add",this.addItemView,this),this.collection.on("remove",this.removeItemView,this),this.logger&&this.collection.on("all",function(t){this.info(this+"(collection)",arguments)},this),this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners"),this.on("view:selected",function(t,e){if(e&&e.shiftKey&&this.lastSelected){var i=this.viewFromModelId(this.lastSelected);i&&this.selectRange(t,i)}else e&&e.altKey&&!this.selecting&&this.showSelectors();this.selected.push(t.model.id),this.lastSelected=t.model.id},this),this.on("view:de-selected",function(t,e){this.selected=a.without(this.selected,t.model.id)},this)},render:function(t){this.log(this+".render",t);var e=this._buildNewRender();return this._setUpBehaviors(e),this._queueNewRender(e,t),this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var t=r(this.templates.el({},this));return this._renderControls(t),this._renderTitle(t),this._renderSubtitle(t),this._renderSearch(t),this.renderItems(t),t},_renderControls:function(t){this.debug(this+"(ListPanel)._renderControls");var e=r(this.templates.controls({},this));return t.find(".controls").replaceWith(e),e},_renderTitle:function(t){},_renderSubtitle:function(t){},_queueNewRender:function(t,e){e=void 0===e?this.fxSpeed:e;var i=this;i.log("_queueNewRender:",t,e),r(i).queue("fx",[function(t){this.$el.fadeOut(e,t)},function(e){i._swapNewRender(t),e()},function(t){this.$el.fadeIn(e,t)},function(t){i.trigger("rendered",i),t()}])},_swapNewRender:function(t){return this.$el.empty().attr("class",this.className).append(t.children()),this.selecting&&this.showSelectors(0),this},_setUpBehaviors:function(t){return t=t||this.$el,t.find(".controls [title]").tooltip({placement:"bottom"}),this._renderMultiselectActionMenu(t),this},_renderMultiselectActionMenu:function(t){t=t||this.$el;var e=t.find(".list-action-menu"),i=this.multiselectActions();if(!i.length)return e.empty();var s=r(['','<%- collection.hid %> ','<%- collection.name %>',"
",'',"','",'
"].join("")),o=i.map(function(t){var e=['- ',"
",'','','',"
"]),e=i.wrapTemplate(['','
"]);return{el:t,controls:e}}();var c=l.extend({modelCollectionKey:"contents",initialize:function(t){l.prototype.initialize.call(this,t),this.selecting=void 0!==t.selecting?t.selecting:!1,this.setModel(this.model,t)},setModel:function(t,e){if(e=e||{},this.debug(this+".setModel:",t,e),this.freeModel(),this.freeViews(),t){var i=this.model?this.model.get("id"):null;this.model=t,this.logger&&(this.model.logger=this.logger),this._setUpModelListeners(),this.collection.off(),this.collection=this.model[this.modelCollectionKey]?this.model[this.modelCollectionKey]:e.collection||new this.collectionClass([]),this._setUpCollectionListeners(),i&&t.get("id")!==i&&this.trigger("new-model",this)}return this},freeModel:function(){return this.model&&this.stopListening(this.model),this},_setUpModelListeners:function(){return this.log(this+"._setUpModelListeners",this.model),this.model.on("error",function(){var t=Array.prototype.slice.call(arguments,0);t.unshift("error"),this.trigger.apply(this,t)},this),this},_renderControls:function(t){this.debug(this+"(ListPanel)._renderControls");var e=this.model?this.model.toJSON():{},i=r(this.templates.controls(e,this));return t.find(".controls").replaceWith(i),i},toString:function(){return"ModelListPanel("+this.model+")"}});return c.prototype.templates=function(){var t=i.wrapTemplate(['','
",'<%- view.title %>
',"<%- view.subtitle %>
','','','','',"
",'','
","','",'","
",'',"
","','
"]);return a.extend(a.clone(l.prototype.templates),{controls:t})}(),{ListPanel:l,ModelListPanel:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o,a){n=[i(6),i(5)],s=function(t,e){var i=o.View.extend(t.LoggableMixin).extend(t.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",initialize:function(t){this.listenTo(this.model,"change:tags",function(){this.render()}),this.hiddenUntilActivated(t.$activator,t)},render:function(){var t=this;return this.$el.html(this._template()),this.$input().select2({placeholder:"Add tags",width:"100%",tags:function(){return t._getTagsUsed();
}}),this._setUpBehaviors(),this},_template:function(){return['",''].join("")},tagsToCSV:function(){var t=this.model.get("tags");return!a.isArray(t)||a.isEmpty(t)?"":t.map(function(t){return a.escape(t)}).sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){return Galaxy.user.get("tags_used")},_setUpBehaviors:function(){var t=this;this.$input().on("change",function(e){t.model.save({tags:e.val},{silent:!0}),e.added&&t._addNewTagToTagsUsed(e.added.text+"")})},_addNewTagToTagsUsed:function(t){var e=Galaxy.user.get("tags_used");a.contains(e,t)||(e.push(t),e.sort(),Galaxy.user.set("tags_used",e))},remove:function(){this.$input.off(),this.stopListening(this.model),o.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",this.model+"",")"].join("")}});return{TagsEditor:i}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3))},,function(t,e,i){var n,s;(function(o,a){n=[i(4)],s=function(t){return o.View.extend({initialize:function(e){this.options=t.merge(e,{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(){}});var i=this;this.collection=this.options.collection,this.setElement(this._template()),this.rows=[],t.get({url:Galaxy.root+"api/remote_files",success:function(t){i._fill(t)},error:function(){i._fill()}})},_fill:function(e){if(e&&e.length>0){this.$el.find("#upload-ftp-content").html(a(this._templateTable()));var i=0;for(index in e)this.rows.push(this._add(e[index])),i+=e[index].size;if(this.$el.find("#upload-ftp-number").html(e.length+" files"),this.$el.find("#upload-ftp-disk").html(t.bytesToString(i,!0)),this.collection){var n=this;this.$("._has_collection").show(),this.$select_all=a("#upload-selectall"),this.$select_all.addClass(this.options.class_add),this.$select_all.on("click",function(){var t=n.$select_all.hasClass(n.options.class_add);for(index in e){var i=e[index],s=n._find(i);(!s&&t||s&&!t)&&n.rows[index].trigger("click")}}),this._refresh()}}else this.$el.find("#upload-ftp-content").html(a(this._templateInfo()));this.$el.find("#upload-ftp-wait").hide()},_add:function(t){var e=this,i=a(this._templateRow(t)),n=i.find(".icon");if(a(this.el).find("tbody").append(i),this.collection){var s="";s=this._find(t)?this.options.class_remove:this.options.class_add,n.addClass(s),i.on("click",function(){var i=e._find(t);n.removeClass(),i?(e.options.onremove(i),n.addClass(e.options.class_add)):(e.options.onadd(t),n.addClass(e.options.class_remove)),e._refresh()})}else i.on("click",function(){e.options.onchange(t)});return i},_refresh:function(){var t=this.collection.where({file_mode:"ftp",enabled:!0});this.$select_all.removeClass(),0==t.length?this.$select_all.addClass(this.options.class_add):t.length==this.rows.length?this.$select_all.addClass(this.options.class_remove):this.$select_all.addClass(this.options.class_partial)},_find:function(t){var e=this.collection.findWhere({file_path:t.path,file_mode:"ftp",enabled:!0});return e&&e.get("id")},_templateRow:function(e){return'','
",'<%- model.name %>
',"<%- view.subtitle %>
','','','','',"
",'','
","','",'","
",'',"
","| Name | Size | Created |
|---|
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(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o){n=[i(4)],s=function(t){return o.View.extend({options:{class_check:"upload-icon-button fa fa-check-square-o",class_uncheck:"upload-icon-button fa fa-square-o"},initialize:function(t){this.app=t;var e=this;this.setElement(this._template()),this.model=this.app.model,this.$("#upload-space-to-tab").on("click",function(){e._switchState("#upload-space-to-tab","space_to_tab")}),this.$("#upload-to-posix-lines").on("click",function(){e._switchState("#upload-to-posix-lines","to_posix_lines")}),this.render()},render:function(){this._renderState("#upload-space-to-tab",this.model.get("space_to_tab")),this._renderState("#upload-to-posix-lines",this.model.get("to_posix_lines"));var t=this.$("#upload-settings-cover");this.model.get("enabled")?t.hide():t.show()},_switchState:function(t,e){if(this.model.get("enabled")){var i=!this.model.get(e);this.model.set(e,i),this._renderState(t,i)}},_renderState:function(t,e){var i=this.$(t);i.removeClass(),e?i.addClass(this.options.class_check):i.addClass(this.options.class_uncheck)},_template:function(){return'
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this.$el.attr("draggable",!0).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container"),this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(t){t.currentTarget.style.opacity="0.4",t.originalEvent&&(t=t.originalEvent),t.dataTransfer.effectAllowed="move",t.dataTransfer.setData("text/plain",JSON.stringify(this.pair)),this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(t){t.currentTarget.style.opacity="1.0",this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(t){this.$el.parent().trigger(t)},toString:function(){return"PairView("+this.pair.name+")"}}),p=o.View.extend(n.LoggableMixin).extend({_logNamespace:h,className:"list-of-pairs-collection-creator collection-creator 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t.sort(function(t,i){return e(t.name,i.name)}),t},_ensureIds:function(){return this.initialList.forEach(function(t){t.hasOwnProperty("id")||(t.id=a.uniqueId())}),this.initialList},_splitByFilters:function(){function t(t,e){return e.test(t.name)}var e=this.filters.map(function(t){return new RegExp(t)}),i=[[],[]];return this.unpaired.forEach(function(n){e.forEach(function(e,s){t(n,e)&&i[s].push(n)})}),i},_addToUnpaired:function(t){var i=function(n,s){if(n===s)return n;var o=Math.floor((s-n)/2)+n,a=e(t.name,this.unpaired[o].name);if(0>a)return i(n,o);if(a>0)return i(o+1,s);for(;this.unpaired[o]&&this.unpaired[o].name===t.name;)o++;return o}.bind(this);this.unpaired.splice(i(0,this.unpaired.length),0,t)},autoPair:function(t){var e=this._splitByFilters(),i=[];return this.twoPassAutopairing&&(i=this.autopairSimple({listA:e[0],listB:e[1]}),e=this._splitByFilters()),t=t||this.strategy,e=this._splitByFilters(),i=i.concat(this[t].call(this,{listA:e[0],listB:e[1]}))},autopairSimple:c({scoreThreshold:function(){return 1},match:function(t){return t=t||{},t.matchTo===t.possible?{index:t.index,score:1}:t.bestMatch}}),autopairLevenshtein:c({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var i=t(e.matchTo,e.possible),n=1-i/Math.max(e.matchTo.length,e.possible.length);return n>e.bestMatch.score?{index:e.index,score:n}:e.bestMatch}}),autopairLCS:c({scoreThreshold:function(){return this.matchPercentage},match:function(t){t=t||{};var e=this._naiveStartingAndEndingLCS(t.matchTo,t.possible).length,i=e/Math.max(t.matchTo.length,t.possible.length);return i>t.bestMatch.score?{index:t.index,score:i}:t.bestMatch}}),_naiveStartingAndEndingLCS:function(t,e){for(var i="",n="",s=0,o=0;s=0&&o>=0&&t[s]===e[o];)n=[t[s],n].join(""),s-=1,o-=1;return i+n},_pair:function(t,e,i){i=i||{},this.debug("_pair:",t,e);var n=this._createPair(t,e,i.name);return this.paired.push(n),this.unpaired=a.without(this.unpaired,t,e),i.silent||this.trigger("pair:new",n),n},_createPair:function(t,e,i){if(!t||!e||t===e)throw new Error("Bad pairing: "+[JSON.stringify(t),JSON.stringify(e)]);return i=i||this._guessNameForPair(t,e),{forward:t,name:i,reverse:e}},_guessNameForPair:function(t,e,i){i=void 0!==i?i:this.removeExtensions;var n=t.name,s=e.name,o=this._naiveStartingAndEndingLCS(n.replace(new RegExp(this.filters[0]),""),s.replace(new RegExp(this.filters[1]),""));if(i){var a=o.lastIndexOf(".");if(a>0){var r=o.slice(a,o.length);o=o.replace(r,""),n=n.replace(r,""),s=s.replace(r,"")}}return o||n+" & "+s},_unpair:function(t,e){if(e=e||{},!t)throw new Error("Bad pair: "+JSON.stringify(t));return this.paired=a.without(this.paired,t),this._addToUnpaired(t.forward),this._addToUnpaired(t.reverse),e.silent||this.trigger("pair:unpair",[t]),t},unpairAll:function(){for(var t=[];this.paired.length;)t.push(this._unpair(this.paired[0],{silent:!0}));this.trigger("pair:unpair",t)},_pairToJSON:function(t,e){return e=e||"hda",{collection_type:"paired",src:"new_collection",name:t.name,element_identifiers:[{name:"forward",id:t.forward.id,src:e},{name:"reverse",id:t.reverse.id,src:e}]}},createList:function(t){var e=this,i=Galaxy.root+"api/histories/"+this.historyId+"/contents/dataset_collections",n={type:"dataset_collection",collection_type:"list:paired",name:a.escape(t||e.$(".collection-name").val()),element_identifiers:e.paired.map(function(t){return e._pairToJSON(t)})};return e.blocking=!0,r.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(n)}).always(function(){e.blocking=!1}).fail(function(t,i,n){e._ajaxErrHandler(t,i,n)}).done(function(t,i,n){e.trigger("collection:created",t,i,n),e.metric("collection:created",t),"function"==typeof e.oncreate&&e.oncreate.call(this,t,i,n)})},_ajaxErrHandler:function(t,e,i){this.error(t,e,i);var n=s("An error occurred while creating this collection");t&&(n+=0===t.readyState&&0===t.status?": "+s("Galaxy could not be reached and may be updating.")+s(" Try again in a few minutes."):t.responseJSON?"
=0&&at&&t>o-a)return s}return l()},_dropPairedColumns:function(t){t.preventDefault(),t.dataTransfer.dropEffect="move";var e=this._getNearestPairedDatasetLi(t.originalEvent.clientY);return e.size()?this.$dragging.insertBefore(e):this.$dragging.insertAfter(this.$(".paired-columns .unpair-btn").last()),this._syncPairsToDom(),!1},_syncPairsToDom:function(){var t=[];this.$(".paired-columns .dataset.paired").each(function(){t.push(l(this).data("pair"))}),this.paired=t,this._renderPaired()},_pairDragstart:function(t,e){e.$el.addClass("selected");var i=this.$(".paired-columns .dataset.selected");this.$dragging=i},_pairDragend:function(t,e){l(".element-drop-placeholder").remove(),this.$dragging=null},toggleExtensions:function(t){var e=this;e.removeExtensions=void 0!==t?t:!e.removeExtensions,a.each(e.paired,function(t){t.customizedName||(t.name=e._guessNameForPair(t.forward,t.reverse))}),e._renderPaired(),e._renderFooter()},_changeName:function(t){this._validationWarning("name",!!this._getName())},_nameCheckForEnter:function(t){13!==t.keyCode||this.blocking||this._clickCreate()},_getName:function(){return a.escape(this.$(".collection-name").val())},_clickCreate:function(t){var e=this._getName();e?this.blocking||this.createList():this._validationWarning("name")},_printList:function(t){var e=this;a.each(t,function(i){t===e.paired&&e._printPair(i)})},_printPair:function(t){this.debug(t.forward.name,t.reverse.name,": ->",t.name)},toString:function(){return"PairedCollectionCreator"}});p.templates=p.templates||{main:a.template(['','','
| Convert spaces to tabs | |
| Use POSIX standard |
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index ea4fc1e8406..e898f7b61c3 100644
--- a/static/scripts/bundled/analysis.bundled.js.map
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0 */\n/***/ function(module, exports, __webpack_require__) {\n\n\t/* WEBPACK VAR INJECTION */(function(_, Backbone) {\n\tvar jQuery = __webpack_require__( 1 ),\n\t $ = jQuery,\n\t GalaxyApp = __webpack_require__( 82 ).GalaxyApp,\n\t QUERY_STRING = __webpack_require__( 61 ),\n\t PANEL = __webpack_require__( 13 ),\n\t ToolPanel = __webpack_require__( 113 ),\n\t HistoryPanel = __webpack_require__( 112 ),\n\t PAGE = __webpack_require__( 84 ),\n\t ToolForm = __webpack_require__( 22 );\n\t\n\t/** define the 'Analyze Data'/analysis/main/home page for Galaxy\n\t * * has a masthead\n\t * * a left tool menu to allow the user to load tools in the center panel\n\t * * a right history menu that shows the user's current data\n\t * * a center panel\n\t * Both panels (generally) persist while the center panel shows any\n\t * UI needed for the current step of an analysis, like:\n\t * * tool forms to set tool parameters,\n\t * * tables showing the contents of datasets\n\t * * etc.\n\t */\n\twindow.app = function app( options, bootstrapped ){\n\t window.Galaxy = new GalaxyApp( options, bootstrapped );\n\t Galaxy.debug( 'analysis app' );\n\t // TODO: use router as App base (combining with Galaxy)\n\t\n\t // .................................................... panels and page\n\t var config = options.config,\n\t toolPanel = new ToolPanel({\n\t el : '#left',\n\t userIsAnonymous : Galaxy.user.isAnonymous(),\n\t spinner_url : config.spinner_url,\n\t search_url : config.search_url,\n\t toolbox : config.toolbox,\n\t toolbox_in_panel : config.toolbox_in_panel,\n\t stored_workflow_menu_entries : config.stored_workflow_menu_entries,\n\t nginx_upload_path : config.nginx_upload_path,\n\t ftp_upload_site : config.ftp_upload_site,\n\t default_genome : config.default_genome,\n\t default_extension : config.default_extension,\n\t }),\n\t centerPanel = new PANEL.CenterPanel({\n\t el : '#center'\n\t }),\n\t historyPanel = new HistoryPanel({\n\t el : '#right',\n\t galaxyRoot : Galaxy.root,\n\t userIsAnonymous : Galaxy.user.isAnonymous(),\n\t allow_user_dataset_purge: config.allow_user_dataset_purge,\n\t }),\n\t analysisPage = new PAGE.PageLayoutView( _.extend( options, {\n\t el : 'body',\n\t left : toolPanel,\n\t center : centerPanel,\n\t right : historyPanel,\n\t }));\n\t\n\t // .................................................... decorate the galaxy object\n\t // TODO: most of this is becoming unnecessary as we move to apps\n\t Galaxy.page = analysisPage;\n\t Galaxy.params = Galaxy.config.params;\n\t\n\t // add tool panel to Galaxy object\n\t Galaxy.toolPanel = toolPanel.tool_panel;\n\t Galaxy.upload = toolPanel.uploadButton;\n\t\n\t Galaxy.currHistoryPanel = historyPanel.historyView;\n\t Galaxy.currHistoryPanel.listenToGalaxy( Galaxy );\n\t\n\t //HACK: move there\n\t Galaxy.app = {\n\t display : function( view, target ){\n\t // TODO: Remove this line after select2 update\n\t $( '.select2-hidden-accessible' ).remove();\n\t centerPanel.display( view );\n\t },\n\t };\n\t\n\t // .................................................... routes\n\t /** */\n\t var router = new ( Backbone.Router.extend({\n\t // TODO: not many client routes at this point - fill and remove from server.\n\t // since we're at root here, this may be the last to be routed entirely on the client.\n\t initialize : function( options ){\n\t this.options = options;\n\t },\n\t\n\t /** override to parse query string into obj and send to each route */\n\t execute: function( callback, args, name ){\n\t Galaxy.debug( 'router execute:', callback, args, name );\n\t var queryObj = QUERY_STRING.parse( args.pop() );\n\t args.push( queryObj );\n\t if( callback ){\n\t callback.apply( this, args );\n\t }\n\t },\n\t\n\t routes : {\n\t '(/)' : 'home',\n\t // TODO: remove annoying 'root' from root urls\n\t '(/)root*' : 'home',\n\t },\n\t\n\t /** */\n\t home : function( params ){\n\t // TODO: to router, remove Globals\n\t // load a tool by id (tool_id) or rerun a previous tool execution (job_id)\n\t if( ( params.tool_id || params.job_id ) && params.tool_id !== 'upload1' ){\n\t this._loadToolForm( params );\n\t\n\t } else {\n\t // show the workflow run form\n\t if( params.workflow_id ){\n\t this._loadCenterIframe( 'workflow/run?id=' + params.workflow_id );\n\t // load the center iframe with controller.action: galaxy.org/?m_c=history&m_a=list -> history/list\n\t } else if( params.m_c ){\n\t this._loadCenterIframe( params.m_c + '/' + params.m_a );\n\t // show the workflow run form\n\t } else {\n\t this._loadCenterIframe( 'welcome' );\n\t }\n\t }\n\t },\n\t\n\t /** load the center panel with a tool form described by the given params obj */\n\t _loadToolForm : function( params ){\n\t //TODO: load tool form code async\n\t params.id = params.tool_id;\n\t centerPanel.display( new ToolForm.View( params ) );\n\t },\n\t\n\t /** load the center panel iframe using the given url */\n\t _loadCenterIframe : function( url, root ){\n\t root = root || Galaxy.root;\n\t url = root + url;\n\t centerPanel.$( '#galaxy_main' ).prop( 'src', url );\n\t },\n\t\n\t }))( options );\n\t\n\t // .................................................... when the page is ready\n\t // render and start the router\n\t $(function(){\n\t analysisPage\n\t .render()\n\t .right.historyView.loadCurrentHistory();\n\t\n\t // use galaxy to listen to history size changes and then re-fetch the user's total size (to update the quota meter)\n\t // TODO: we have to do this here (and after every page.render()) because the masthead is re-created on each\n\t // page render. It's re-created each time because there is no render function and can't be re-rendered without\n\t // re-creating it.\n\t Galaxy.listenTo( analysisPage.right.historyView, 'history-size-change', function(){\n\t // fetch to update the quota meter adding 'current' for any anon-user's id\n\t Galaxy.user.fetch({ url: Galaxy.user.urlRoot() + '/' + ( Galaxy.user.id || 'current' ) });\n\t });\n\t analysisPage.right.historyView.connectToQuotaMeter( analysisPage.masthead.quotaMeter );\n\t\n\t // start the router - which will call any of the routes above\n\t Backbone.history.start({\n\t root : Galaxy.root,\n\t pushState : true,\n\t });\n\t });\n\t};\n\t\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2)))\n\n/***/ },\n/* 1 */,\n/* 2 */,\n/* 3 */,\n/* 4 */,\n/* 5 */,\n/* 6 */,\n/* 7 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/**\n\t * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc.\n\t */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4),\n\t __webpack_require__(54),\n\t __webpack_require__(57),\n\t __webpack_require__(25),\n\t __webpack_require__(53),\n\t __webpack_require__(16),\n\t __webpack_require__(10)], __WEBPACK_AMD_DEFINE_RESULT__ = function( Utils, Select, Slider, Options, Drilldown, Buttons, Modal ) {\n\t\n\t /** Image wrapper */\n\t var Image = Backbone.View.extend({\n\t initialize : function(options) {\n\t this.options = Utils.merge(options, {\n\t url : '',\n\t cls : ''\n\t });\n\t this.setElement(this._template(this.options));\n\t },\n\t _template: function(options) {\n\t return '',n("Unhide it"),"","
' +\n\t ' ' +\n\t options.title +\n\t '
';\n\t }\n\t });\n\t\n\t /** Renders an anchor element */\n\t var Anchor = Backbone.View.extend({\n\t initialize : function(options) {\n\t this.options = Utils.merge(options, {\n\t title : '',\n\t cls : ''\n\t });\n\t this.setElement(this._template(this.options));\n\t $(this.el).on('click', options.onclick);\n\t },\n\t _template: function(options) {\n\t return '';\n\t }\n\t });\n\t\n\t /** Displays messages used e.g. in the tool form */\n\t var Message = Backbone.View.extend({\n\t initialize : function(options) {\n\t this.options = Utils.merge(options, {\n\t message : null,\n\t status : 'info',\n\t cls : '',\n\t persistent : false\n\t });\n\t this.setElement('');\n\t this.options.message && this.update(this.options);\n\t },\n\t\n\t // update\n\t update: function(options) {\n\t // get options\n\t this.options = Utils.merge(options, this.options);\n\t\n\t // show message\n\t if (options.message != '') {\n\t this.$el.html(this._template(this.options));\n\t this.$el.fadeIn();\n\t\n\t // clear previous timeouts\n\t if (this.timeout) {\n\t window.clearTimeout(this.timeout);\n\t }\n\t\n\t // set timeout if message is not persistent\n\t if (!options.persistent) {\n\t var self = this;\n\t this.timeout = window.setTimeout(function() {\n\t if (self.$el.is(':visible')) {\n\t self.$el.fadeOut();\n\t } else {\n\t self.$el.hide();\n\t }\n\t }, 3000);\n\t }\n\t } else {\n\t this.$el.fadeOut();\n\t }\n\t },\n\t\n\t // template\n\t _template: function(options) {\n\t var cls_status = 'ui-message alert alert-' + options.status;\n\t if (options.large) {\n\t cls_status = ( ( options.status == 'success' && 'done' ) ||\n\t ( options.status == 'danger' && 'error' ) ||\n\t options.status ) + 'messagelarge';\n\t }\n\t return '' +\n\t options.message +\n\t '
';\n\t }\n\t });\n\t\n\t /** Render a search box */\n\t var Searchbox = Backbone.View.extend({\n\t initialize : function(options) {\n\t this.options = Utils.merge(options, {\n\t onclick : null,\n\t searchword : ''\n\t });\n\t this.setElement(this._template(this.options));\n\t var self = this;\n\t if (this.options.onclick) {\n\t this.$el.on('submit', function(e) {\n\t var search_field = self.$el.find('#search');\n\t self.options.onclick(search_field.val());\n\t });\n\t }\n\t },\n\t _template: function(options) {\n\t return '' +\n\t '' +\n\t '
';\n\t }\n\t });\n\t\n\t /** Renders an input element used e.g. in the tool form */\n\t var Input = Backbone.View.extend({\n\t initialize : function(options) {\n\t // configure options\n\t this.options = Utils.merge(options, {\n\t type : 'text',\n\t placeholder : '',\n\t disabled : false,\n\t visible : true,\n\t cls : '',\n\t area : false\n\t });\n\t\n\t // create new element\n\t this.setElement(this._template(this.options));\n\t\n\t // set initial value\n\t if (this.options.value !== undefined) {\n\t this.value(this.options.value);\n\t }\n\t\n\t // disable input field\n\t if (this.options.disabled) {\n\t this.$el.prop('disabled', true);\n\t }\n\t\n\t // hide input field\n\t if (!this.options.visible) {\n\t this.$el.hide();\n\t }\n\t\n\t // onchange event handler. fires on user activity.\n\t var self = this;\n\t this.$el.on('input', function() {\n\t if (self.options.onchange) {\n\t self.options.onchange(self.$el.val());\n\t }\n\t });\n\t },\n\t\n\t // value\n\t value : function (new_val) {\n\t if (new_val !== undefined) {\n\t this.$el.val( ( typeof new_val === 'string' && new_val ) || '' );\n\t }\n\t return this.$el.val();\n\t },\n\t\n\t // template\n\t _template: function(options) {\n\t if (options.area) {\n\t return '';\n\t } else {\n\t return '';\n\t }\n\t }\n\t });\n\t\n\t /** Creates a hidden element input field used e.g. in the tool form */\n\t var Hidden = Backbone.View.extend({\n\t initialize : function(options) {\n\t this.options = options;\n\t this.setElement(this._template(this.options));\n\t if (this.options.value !== undefined) {\n\t this.value(this.options.value);\n\t }\n\t },\n\t value : function (new_val) {\n\t if (new_val !== undefined) {\n\t this.$('hidden').val(new_val);\n\t }\n\t return this.$('hidden').val();\n\t },\n\t _template: function(options) {\n\t var tmpl = '';\n\t if (options.info) {\n\t tmpl += '
';\n\t return tmpl;\n\t }\n\t });\n\t\n\t return {\n\t Anchor : Anchor,\n\t Button : Buttons.ButtonDefault,\n\t ButtonIcon : Buttons.ButtonIcon,\n\t ButtonCheck : Buttons.ButtonCheck,\n\t ButtonMenu : Buttons.ButtonMenu,\n\t ButtonLink : Buttons.ButtonLink,\n\t Icon : Icon,\n\t Image : Image,\n\t Input : Input,\n\t Label : Label,\n\t Message : Message,\n\t Modal : Modal,\n\t RadioButton : Options.RadioButton,\n\t Checkbox : Options.Checkbox,\n\t Radio : Options.Radio,\n\t Searchbox : Searchbox,\n\t Select : Select,\n\t Hidden : Hidden,\n\t Slider : Slider,\n\t Drilldown : Drilldown\n\t }\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 8 */\n/***/ function(module, exports) {\n\n\t'use strict';\n\t\n\texports.__esModule = true;\n\texports.extend = extend;\n\texports.indexOf = indexOf;\n\texports.escapeExpression = escapeExpression;\n\texports.isEmpty = isEmpty;\n\texports.createFrame = createFrame;\n\texports.blockParams = blockParams;\n\texports.appendContextPath = appendContextPath;\n\tvar escape = {\n\t '&': '&',\n\t '<': '<',\n\t '>': '>',\n\t '\"': '"',\n\t \"'\": ''',\n\t '`': '`',\n\t '=': '='\n\t};\n\t\n\tvar badChars = /[&<>\"'`=]/g,\n\t possible = /[&<>\"'`=]/;\n\t\n\tfunction escapeChar(chr) {\n\t return escape[chr];\n\t}\n\t\n\tfunction extend(obj /* , ...source */) {\n\t for (var i = 1; i < arguments.length; i++) {\n\t for (var key in arguments[i]) {\n\t if (Object.prototype.hasOwnProperty.call(arguments[i], key)) {\n\t obj[key] = arguments[i][key];\n\t }\n\t }\n\t }\n\t\n\t return obj;\n\t}\n\t\n\tvar toString = Object.prototype.toString;\n\t\n\texports.toString = toString;\n\t// Sourced from lodash\n\t// https://github.com/bestiejs/lodash/blob/master/LICENSE.txt\n\t/* eslint-disable func-style */\n\tvar isFunction = function isFunction(value) {\n\t return typeof value === 'function';\n\t};\n\t// fallback for older versions of Chrome and Safari\n\t/* istanbul ignore next */\n\tif (isFunction(/x/)) {\n\t exports.isFunction = isFunction = function (value) {\n\t return typeof value === 'function' && toString.call(value) === '[object Function]';\n\t };\n\t}\n\texports.isFunction = isFunction;\n\t\n\t/* eslint-enable func-style */\n\t\n\t/* istanbul ignore next */\n\tvar isArray = Array.isArray || function (value) {\n\t return value && typeof value === 'object' ? toString.call(value) === '[object Array]' : false;\n\t};\n\t\n\texports.isArray = isArray;\n\t// Older IE versions do not directly support indexOf so we must implement our own, sadly.\n\t\n\tfunction indexOf(array, value) {\n\t for (var i = 0, len = array.length; i < len; i++) {\n\t if (array[i] === value) {\n\t return i;\n\t }\n\t }\n\t return -1;\n\t}\n\t\n\tfunction escapeExpression(string) {\n\t if (typeof string !== 'string') {\n\t // don't escape SafeStrings, since they're already safe\n\t if (string && string.toHTML) {\n\t return string.toHTML();\n\t } else if (string == null) {\n\t return '';\n\t } else if (!string) {\n\t return string + '';\n\t }\n\t\n\t // Force a string conversion as this will be done by the append regardless and\n\t // the regex test will do this transparently behind the scenes, causing issues if\n\t // an object's to string has escaped characters in it.\n\t string = '' + string;\n\t }\n\t\n\t if (!possible.test(string)) {\n\t return string;\n\t }\n\t return string.replace(badChars, escapeChar);\n\t}\n\t\n\tfunction isEmpty(value) {\n\t if (!value && value !== 0) {\n\t return true;\n\t } else if (isArray(value) && value.length === 0) {\n\t return true;\n\t } else {\n\t return false;\n\t }\n\t}\n\t\n\tfunction createFrame(object) {\n\t var frame = extend({}, object);\n\t frame._parent = object;\n\t return frame;\n\t}\n\t\n\tfunction blockParams(params, ids) {\n\t params.path = ids;\n\t return params;\n\t}\n\t\n\tfunction appendContextPath(contextPath, id) {\n\t return (contextPath ? contextPath + '.' : '') + id;\n\t}\n\t//# 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},\n/* 9 */\n/***/ function(module, exports) {\n\n\t'use strict';\n\t\n\texports.__esModule = true;\n\t\n\tvar errorProps = ['description', 'fileName', 'lineNumber', 'message', 'name', 'number', 'stack'];\n\t\n\tfunction Exception(message, node) {\n\t var loc = node && node.loc,\n\t line = undefined,\n\t column = undefined;\n\t if (loc) {\n\t line = loc.start.line;\n\t column = loc.start.column;\n\t\n\t message += ' - ' + line + ':' + column;\n\t }\n\t\n\t var tmp = Error.prototype.constructor.call(this, message);\n\t\n\t // Unfortunately errors are not enumerable in Chrome (at least), so `for prop in tmp` doesn't work.\n\t for (var idx = 0; idx < errorProps.length; idx++) {\n\t this[errorProps[idx]] = tmp[errorProps[idx]];\n\t }\n\t\n\t /* istanbul ignore else */\n\t if (Error.captureStackTrace) {\n\t Error.captureStackTrace(this, Exception);\n\t }\n\t\n\t if (loc) {\n\t this.lineNumber = line;\n\t this.column = column;\n\t }\n\t}\n\t\n\tException.prototype = new Error();\n\t\n\texports['default'] = Exception;\n\tmodule.exports = exports['default'];\n\t//# 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},\n/* 10 */,\n/* 11 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function( Utils ) {\n\tvar View = Backbone.View.extend({\n\t visible : false,\n\t initialize : function( options ) {\n\t var self = this;\n\t this.options = Utils.merge( options, {\n\t id : Utils.uid(),\n\t title : '',\n\t icon : '',\n\t buttons : null,\n\t body : null,\n\t scrollable : true,\n\t nopadding : false,\n\t operations : null,\n\t placement : 'bottom',\n\t cls : 'ui-portlet',\n\t operations_flt : 'right',\n\t collapsible : false,\n\t collapsed : false\n\t });\n\t this.setElement( this._template( this.options ) );\n\t\n\t // link content\n\t this.$body = this.$( '.portlet-body' );\n\t this.$title = this.$( '.portlet-title-text' );\n\t this.$header = this.$( '.portlet-header' );\n\t this.$content = this.$( '.portlet-content' );\n\t this.$footer = this.$( '.portlet-footer' );\n\t\n\t // set content padding\n\t if ( this.options.nopadding ) {\n\t this.$content.css( 'padding', '0px' );\n\t this.$body.css( 'padding', '0px' );\n\t }\n\t\n\t // append buttons\n\t this.$buttons = this.$( '.portlet-buttons' );\n\t if ( this.options.buttons ) {\n\t $.each( this.options.buttons, function( name, item ) {\n\t item.$el.prop( 'id', name );\n\t self.$buttons.append( item.$el );\n\t });\n\t } else {\n\t this.$buttons.remove();\n\t }\n\t\n\t // append operations\n\t this.$operations = this.$( '.portlet-operations' );\n\t if ( this.options.operations ) {\n\t $.each( this.options.operations, function( name, item ) {\n\t item.$el.prop( 'id', name );\n\t self.$operations.append( item.$el );\n\t });\n\t }\n\t\n\t // add body\n\t this.options.body && this.append( this.options.body );\n\t\n\t // make portlet collapsible\n\t this.collapsed = false;\n\t if ( this.options.collapsible ) {\n\t this.$title.addClass( 'no-highlight' ).css({\n\t 'cursor' : 'pointer',\n\t 'text-decoration' : 'underline'\n\t });\n\t this.$title.on( 'click', function() {\n\t if ( self.collapsed ) { self.expand(); } else { self.collapse(); }\n\t });\n\t this.options.collapsed && this.collapse();\n\t }\n\t },\n\t\n\t // append\n\t append: function( $el ) {\n\t this.$body.append( $el );\n\t },\n\t\n\t // remove all content\n\t empty: function() {\n\t this.$body.empty();\n\t },\n\t\n\t // header\n\t header: function() {\n\t return this.$header;\n\t },\n\t\n\t // body\n\t body: function() {\n\t return this.$body;\n\t },\n\t\n\t // footer\n\t footer: function() {\n\t return this.$footer;\n\t },\n\t\n\t // show\n\t show: function(){\n\t this.visible = true;\n\t this.$el.fadeIn( 'fast' );\n\t },\n\t\n\t // hide\n\t hide: function(){\n\t this.visible = false;\n\t this.$el.fadeOut( 'fast' );\n\t },\n\t\n\t // enable buttons\n\t enableButton: function( id ) {\n\t this.$buttons.find( '#' + id ).prop( 'disabled', false );\n\t },\n\t\n\t // disable buttons\n\t disableButton: function( id ) {\n\t this.$buttons.find( '#' + id ).prop( 'disabled', true );\n\t },\n\t\n\t // hide operation\n\t hideOperation: function( id ) {\n\t this.$operations.find( '#' + id ).hide();\n\t },\n\t\n\t // show operation\n\t showOperation: function( id ) {\n\t this.$operations.find( '#' + id ).show();\n\t },\n\t\n\t // set operation\n\t setOperation: function( id, callback ) {\n\t var $el = this.$operations.find( '#' + id );\n\t $el.off( 'click' );\n\t $el.on( 'click', callback );\n\t },\n\t\n\t // title\n\t title: function( new_title ) {\n\t var $el = this.$title;\n\t if ( new_title ) {\n\t $el.html( new_title );\n\t }\n\t return $el.html();\n\t },\n\t\n\t // collapse portlet\n\t collapse: function() {\n\t this.collapsed = true;\n\t this.$content.height( '0%' );\n\t this.$body.hide();\n\t this.$footer.hide();\n\t this.trigger( 'collapsed' );\n\t },\n\t\n\t // expand portlet\n\t expand: function() {\n\t this.collapsed = false;\n\t this.$content.height( '100%' );\n\t this.$body.fadeIn( 'fast' );\n\t this.$footer.fadeIn( 'fast' );\n\t this.trigger( 'expanded' );\n\t },\n\t\n\t // disable content access\n\t disable: function() {\n\t this.$( '.portlet-backdrop' ).show();\n\t },\n\t\n\t // enable content access\n\t enable: function() {\n\t this.$( '.portlet-backdrop' ).hide();\n\t },\n\t\n\t // fill regular modal template\n\t _template: function( options ) {\n\t var tmpl = '' + options.info + '
';\n\t }\n\t tmpl += '';\n\t if ( options.title ) {\n\t tmpl += '
' +\n\t '' +\n\t '
';\n\t }\n\t tmpl += '';\n\t if ( options.icon ) {\n\t tmpl += ' ';\n\t }\n\t tmpl += '' + options.title + '' +\n\t '
' +\n\t '';\n\t if ( options.placement == 'top' ) {\n\t tmpl += '
';\n\t }\n\t tmpl += '
';\n\t if ( options.placement == 'bottom' ) {\n\t tmpl += '
';\n\t }\n\t tmpl += '
' +\n\t '' +\n\t '
').attr({\n\t id: 'content_table',\n\t cellpadding: 0\n\t });\n\t this.$el.append(data_table);\n\t var column_names = this.model.get_metadata('column_names'),\n\t header_container = $('').appendTo(data_table),\n\t header_row = $('' + 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 }\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 = $(' '),\n\t num_columns = this.model.get_metadata('columns');\n\t\n\t if (this.row_count % 2 !== 0) {\n\t row.addClass('dark_row');\n\t }\n\t\n\t if (cells.length === num_columns) {\n\t _.each(cells, function(cell_contents, index) {\n\t row.append(this._renderCell(cell_contents, index));\n\t }, this);\n\t }\n\t else if (cells.length > num_columns) {\n\t // SAM file or like format with optional metadata included.\n\t _.each(cells.slice(0, num_columns - 1), function(cell_contents, index) {\n\t row.append(this._renderCell(cell_contents, index));\n\t }, this);\n\t row.append(this._renderCell(cells.slice(num_columns - 1).join('\\t'), num_columns - 1));\n\t }\n\t else if (num_columns > 5 && cells.length === num_columns - 1 ) {\n\t // SAM file or like format with optional metadata missing.\n\t _.each(cells, function(cell_contents, index) {\n\t row.append(this._renderCell(cell_contents, index));\n\t }, this);\n\t row.append($(''));\n\t }\n\t else {\n\t // Comment line, just return the one cell.\n\t row.append(this._renderCell(line, 0, num_columns));\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.$el.find('table');\n\t _.each(chunk.ck_data.split('\\n'), function(line, index) {\n\t if (line !== ''){\n\t data_table.append(this._renderRow(line));\n\t }\n\t }, this);\n\t }\n\t});\n\t\n\t/**\n\t * Tabular view that is placed at the top level of page. Scrolling occurs\n\t * view top-level elements outside of view.\n\t */\n\tvar TopLevelTabularDatasetChunkedView = TabularDatasetChunkedView.extend({\n\t\n\t initialize: function(options) {\n\t TabularDatasetChunkedView.prototype.initialize.call(this, options);\n\t\n\t // Scrolling happens in top-level elements.\n\t scroll_elt = _.find(this.$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) { scroll_elt = window; }\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\tvar 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\tvar 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 {\n\t // verify that metadata exists\n\t if (metadata.get('chromCol') && metadata.get('startCol') && metadata.get('endCol'))\n\t {\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 {\n\t // search array\n\t function search (str, array) {\n\t for (var j = 0; j < array.length; j++)\n\t 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 // backbone events\n\t events:\n\t {\n\t 'mouseover tr' : 'show',\n\t 'mouseleave' : 'hide'\n\t },\n\t\n\t // show button\n\t show: function (e) {\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)\n\t 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(this.create_trackster_action(this.url_viz, btn_viz_pars, this.genome_build));\n\t\n\t // show the button\n\t $('#btn_viz').show();\n\t } else {\n\t // hide the button\n\t $('#btn_viz').hide();\n\t }\n\t },\n\t\n\t // hide button\n\t hide: function () {\n\t this.$el.find('#btn_viz').hide();\n\t },\n\t\n\t // create action\n\t create_trackster_action : function (vis_url, dataset_params, dbkey) {\n\t // link this\n\t var self = this;\n\t\n\t // create function\n\t return function() {\n\t var listTracksParams = {};\n\t if (dbkey) {\n\t listTracksParams[ 'f-dbkey' ] = dbkey;\n\t }\n\t $.ajax({\n\t url: vis_url + '/list_tracks?' + $.param( listTracksParams ),\n\t dataType: 'html',\n\t error: function() {\n\t // show error message\n\t self.modal.show({\n\t title : 'Something went wrong!',\n\t body : 'Unfortunately we could not add this dataset to the track browser. Please try again or contact us.',\n\t buttons : {\n\t 'Cancel': function(){\n\t self.modal.hide();\n\t }\n\t }\n\t });\n\t },\n\t success: function(table_html) {\n\t self.modal.show({\n\t title : 'View Data in a New or Saved Visualization',\n\t buttons :{\n\t 'Cancel': function(){\n\t self.modal.hide();\n\t },\n\t 'View in saved visualization': function(){\n\t // show modal with saved visualizations\n\t self.modal.show(\n\t {\n\t title : 'Add Data to Saved Visualization',\n\t body : table_html,\n\t buttons : {\n\t 'Cancel': function(){\n\t self.modal.hide();\n\t },\n\t 'Add to visualization': function(){\n\t // hide\n\t self.modal.hide();\n\t\n\t // search selected fields\n\t self.modal.$el.find('input[name=id]:checked').each(function(){\n\t // get visualization id\n\t var vis_id = $(this).val();\n\t dataset_params.id = vis_id;\n\t\n\t // add widget\n\t self.frame.add({\n\t title : 'Trackster',\n\t type : 'url',\n\t content : vis_url + '/trackster?' + $.param(dataset_params)\n\t });\n\t });\n\t }\n\t }\n\t });\n\t },\n\t 'View in new visualization': function(){\n\t // hide\n\t self.modal.hide();\n\t\n\t // add widget\n\t self.frame.add({\n\t title : 'Trackster',\n\t type : 'url',\n\t content : vis_url + '/trackster?' + $.param(dataset_params)\n\t });\n\t }\n\t }\n\t });\n\t }\n\t });\n\t return false;\n\t };\n\t }\n\t});\n\t\n\t// -- Utility functions. --\n\t\n\t/**\n\t * Create a model, attach it to a view, render view, and attach it to a parent element.\n\t */\n\tvar createModelAndView = function(model, view, model_config, parent_elt) {\n\t // Create model, view.\n\t var a_view = new view({\n\t model: new model(model_config)\n\t });\n\t\n\t // Render view and add to parent element.\n\t a_view.render();\n\t if (parent_elt) {\n\t parent_elt.append(a_view.$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\tvar 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) :\n\t 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\treturn {\n\t Dataset: Dataset,\n\t TabularDataset: TabularDataset,\n\t DatasetCollection: DatasetCollection,\n\t TabularDatasetChunkedView: TabularDatasetChunkedView,\n\t createTabularDatasetChunkedView: createTabularDatasetChunkedView\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\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ },\n/* 15 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;!(__WEBPACK_AMD_DEFINE_ARRAY__ = [\n\t], __WEBPACK_AMD_DEFINE_RESULT__ = function(){\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\tvar 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\tSTATES.READY_STATES = [\n\t STATES.OK,\n\t STATES.EMPTY,\n\t STATES.PAUSED,\n\t STATES.FAILED_METADATA,\n\t STATES.NOT_VIEWABLE,\n\t STATES.DISCARDED,\n\t STATES.ERROR\n\t];\n\t\n\tSTATES.NOT_READY_STATES = [\n\t STATES.UPLOAD,\n\t STATES.QUEUED,\n\t STATES.RUNNING,\n\t STATES.SETTING_METADATA,\n\t STATES.NEW\n\t];\n\t\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/***/ },\n/* 16 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/** This class contains all button views.\n\t*/\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 */\n\t var ButtonBase = Backbone.View.extend({\n\t initialize: function( options ) {\n\t this.options = Utils.merge( options, {\n\t id : Utils.uid(),\n\t title : '',\n\t floating : 'right',\n\t icon : '',\n\t cls : 'ui-button btn btn-default',\n\t cls_wait : 'btn btn-info'\n\t } );\n\t this.setElement( this._template( this.options ) );\n\t var self = this;\n\t $( this.el ).on( 'click' , function() {\n\t $( '.tooltip' ).hide();\n\t if ( options.onclick && !self.disabled ) {\n\t options.onclick();\n\t }\n\t } );\n\t $( this.el ).tooltip( { title: options.tooltip, placement: 'bottom' } );\n\t },\n\t\n\t // disable\n\t disable: function() {\n\t this.$el.addClass( 'disabled' );\n\t this.disabled = true;\n\t },\n\t\n\t // enable\n\t enable: function() {\n\t this.$el.removeClass( 'disabled' );\n\t this.disabled = false;\n\t },\n\t\n\t // show spinner\n\t wait: function() {\n\t this.$el.removeClass( this.options.cls ).addClass( this.options.cls_wait ).prop( 'disabled', true );\n\t this.$( '.icon' ).removeClass( this.options.icon ).addClass( 'fa-spinner fa-spin' );\n\t this.$( '.title' ).html( 'Sending...' );\n\t },\n\t\n\t // hide spinner\n\t unwait: function() {\n\t this.$el.removeClass( this.options.cls_wait ).addClass( this.options.cls ).prop( 'disabled', false );\n\t this.$( '.icon' ).removeClass( 'fa-spinner fa-spin' ).addClass( this.options.icon );\n\t this.$( '.title' ).html( this.options.title );\n\t },\n\t\n\t // template\n\t _template: function( options ) {\n\t var str = '';\n\t return str;\n\t }\n\t });\n\t\n\t /** This button allows the right-click/open-in-new-tab feature, its used e.g. for panel buttons.\n\t */\n\t var ButtonLink = ButtonBase.extend({\n\t initialize: function( options ) {\n\t ButtonBase.prototype.initialize.call( this, options );\n\t },\n\t _template: function( options ) {\n\t return '' + '' +\n\t '';\n\t }\n\t });\n\t\n\t /** The check button is used in the tool form and allows to distinguish between multiple states e.g. all, partially and nothing selected.\n\t */\n\t var ButtonCheck = Backbone.View.extend({\n\t initialize: function( options ) {\n\t // configure options\n\t this.options = Utils.merge(options, {\n\t title : 'Select/Unselect all',\n\t icons : ['fa fa-square-o', 'fa fa-minus-square-o', 'fa fa-check-square-o'],\n\t value : 0\n\t });\n\t\n\t // create new element\n\t this.setElement( this._template() );\n\t this.$title = this.$( '.title' );\n\t this.$icon = this.$( '.icon' );\n\t\n\t // set initial value\n\t this.value( this.options.value );\n\t\n\t // set title\n\t this.$title.html( this.options.title );\n\t\n\t // add event handler\n\t var self = this;\n\t this.$el.on('click', function() {\n\t self.current = ( self.current === 0 && 2 ) || 0;\n\t self.value( self.current );\n\t self.options.onclick && self.options.onclick();\n\t });\n\t },\n\t\n\t /* Sets a new value and/or returns the current value.\n\t * @param{Integer} new_val - Set a new value 0=unchecked, 1=partial and 2=checked.\n\t * OR:\n\t * @param{Integer} new_val - Number of selected options.\n\t * @param{Integer} total - Total number of available options.\n\t */\n\t value: function ( new_val, total ) {\n\t if ( new_val !== undefined ) {\n\t if ( total ) {\n\t if ( new_val !== 0 ) {\n\t new_val = ( new_val !== total ) && 1 || 2;\n\t }\n\t }\n\t this.current = new_val;\n\t this.$icon.removeClass()\n\t .addClass( 'icon' )\n\t .addClass( this.options.icons[ new_val ] );\n\t this.options.onchange && this.options.onchange( new_val );\n\t }\n\t return this.current;\n\t },\n\t\n\t /** Template containing the check button and the title\n\t */\n\t _template: function() {\n\t return '' +\n\t '';\n\t }\n\t tmpl += ' ' + options.title +\n\t '' +\n\t ' ';\n\t return tmpl;\n\t },\n\t\n\t // fill template header\n\t _templateMenu: function () {\n\t return '
' +\n\t '
';\n\t return tmpl;\n\t }\n\t});\n\treturn {\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\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 12 */\n/***/ function(module, exports, __webpack_require__) {\n\n\t// Create a simple path alias to allow browserify to resolve\n\t// the runtime on a supported path.\n\tmodule.exports = __webpack_require__(67)['default'];\n\n\n/***/ },\n/* 13 */,\n/* 14 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {// Additional dependencies: jQuery, underscore.\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(10), __webpack_require__(28), __webpack_require__(18)], __WEBPACK_AMD_DEFINE_RESULT__ = function(Modal, Frames, mod_icon_btn) {\n\t\n\t/**\n\t * Dataset metedata.\n\t */\n\tvar DatasetMetadata = Backbone.Model.extend({});\n\t\n\t/**\n\t * A dataset. In Galaxy, datasets are associated with a history, so\n\t * this object is also known as a HistoryDatasetAssociation.\n\t */\n\tvar 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\tvar TabularDataset = Dataset.extend({\n\t defaults: _.extend({}, Dataset.prototype.defaults, {\n\t chunk_url: null,\n\t first_data_chunk: null,\n\t chunk_index: -1,\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 this.attributes.chunk_index = (this.attributes.first_data_chunk ? 1 : 0);\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 chunk: self.attributes.chunk_index++\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 }\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\tvar 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\tvar 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 = $('' +\n\t '' +\n\t '' +\n\t '
';\n\t }\n\t });\n\t\n\t /** This renders a differently styled, more compact button version.\n\t TODO: Consolidate with icon-button.js and/or button-default.js.\n\t */\n\t var ButtonIcon = Backbone.View.extend({\n\t initialize : function( options ) {\n\t // get options\n\t this.options = Utils.merge( options, {\n\t id : Utils.uid(),\n\t title : '',\n\t floating : 'right',\n\t cls : 'ui-button-icon',\n\t icon : '',\n\t tooltip : '',\n\t onclick : null\n\t });\n\t\n\t // create new element\n\t this.setElement( this._template( this.options ) );\n\t\n\t // link button element\n\t this.$button = this.$el.find( '.button' );\n\t\n\t // add event\n\t var self = this;\n\t $(this.el).on('click', function() {\n\t // hide all tooltips\n\t $( '.tooltip' ).hide();\n\t\n\t // execute onclick callback\n\t if ( options.onclick && !self.disabled ) {\n\t options.onclick();\n\t }\n\t });\n\t\n\t // add tooltip\n\t this.$button.tooltip( { title: options.tooltip, placement: 'bottom' } );\n\t },\n\t\n\t // disable\n\t disable: function() {\n\t this.$button.addClass( 'disabled' );\n\t this.disabled = true;\n\t },\n\t\n\t // enable\n\t enable: function() {\n\t this.$button.removeClass( 'disabled' );\n\t this.disabled = false;\n\t },\n\t\n\t // change icon\n\t setIcon: function(icon_cls) {\n\t this.$('i').removeClass( this.options.icon ).addClass( icon_cls );\n\t this.options.icon = icon_cls;\n\t },\n\t\n\t // template\n\t _template: function( options ) {\n\t // width\n\t var width = '';\n\t if ( options.title ) {\n\t width = 'width: auto;';\n\t }\n\t\n\t // string\n\t var str = '' +\n\t '
';\n\t return str;\n\t }\n\t });\n\t\n\t /** This class creates a button with dropdown menu. It extends the functionality of the Ui.ButtonIcon class.\n\t TODO: Consolidate class, use common base class\n\t */\n\t var ButtonMenu = Backbone.View.extend({\n\t // optional sub menu\n\t $menu: null,\n\t\n\t // initialize\n\t initialize: function ( options ) {\n\t // get options\n\t this.options = Utils.merge( options, {\n\t // same as Ui.ButtonIcon\n\t id : '',\n\t title : '',\n\t floating : 'right',\n\t pull : 'right',\n\t icon : null,\n\t onclick : null,\n\t cls : 'ui-button-icon ui-button-menu',\n\t tooltip : '',\n\t \n\t // additional options\n\t target : '',\n\t href : '',\n\t onunload : null,\n\t visible : true,\n\t tag : ''\n\t } );\n\t\n\t // add template for tab\n\t this.setElement( $( this._template( this.options ) ) );\n\t\n\t // find root\n\t var $root = $( this.el ).find( '.root' );\n\t\n\t // link head\n\t var self = this;\n\t $root.on( 'click', function( e ) {\n\t // hide all tooltips\n\t $( '.tooltip' ).hide();\n\t\n\t // prevent default\n\t e.preventDefault();\n\t\n\t // add click event\n\t if( self.options.onclick ) {\n\t self.options.onclick();\n\t }\n\t });\n\t\n\t // visiblity\n\t if ( !this.options.visible )\n\t this.hide();\n\t\n\t // add tooltip\n\t $root.tooltip( { title: options.tooltip, placement: 'bottom' } );\n\t },\n\t\n\t // show\n\t show: function() {\n\t $( this.el ).show();\n\t },\n\t\n\t // hide\n\t hide: function() {\n\t $( this.el ).hide();\n\t },\n\t\n\t // add menu item\n\t addMenu: function ( options ) {\n\t // menu option defaults\n\t var menuOptions = {\n\t title : '',\n\t target : '',\n\t href : '',\n\t onclick : null,\n\t divider : false,\n\t icon : null,\n\t cls : 'button-menu btn-group'\n\t }\n\t\n\t // get options\n\t menuOptions = Utils.merge( options, menuOptions );\n\t\n\t // check if submenu element is available\n\t if ( !this.$menu ) {\n\t // insert submenu element into root\n\t $( this.el ).append( this._templateMenu() );\n\t\n\t // update element link\n\t this.$menu = $( this.el ).find( '.menu' );\n\t }\n\t\n\t // create\n\t var $item = $( this._templateMenuItem( menuOptions ) );\n\t\n\t // add events\n\t $item.on( 'click', function( e ) {\n\t if( menuOptions.onclick ) {\n\t e.preventDefault();\n\t menuOptions.onclick();\n\t }\n\t });\n\t\n\t // append menu\n\t this.$menu.append( $item );\n\t\n\t // append divider\n\t if ( menuOptions.divider ) {\n\t this.$menu.append( $( this._templateDivider() ) );\n\t }\n\t },\n\t\n\t // fill template header\n\t _templateMenuItem: function ( options ) {\n\t var tmpl = '';\n\t if (options.title) {\n\t str += ' ' +\n\t '' + options.title + '';\n\t } else {\n\t str += '';\n\t }\n\t str += '
' +\n\t '- ';\n\t },\n\t\n\t _templateDivider: function() {\n\t return '
- ';\n\t },\n\t\n\t // element\n\t _template: function(options) {\n\t // TODO: width/margin should be set in css\n\t var width = '';\n\t var margin = '';\n\t if ( options.title ) {\n\t width = 'width: auto;';\n\t } else {\n\t margin = 'margin: 0px;';\n\t }\n\t var str = '' +\n\t '';\n\t return str;\n\t }\n\t });\n\t\n\t return {\n\t ButtonDefault : ButtonBase,\n\t ButtonLink : ButtonLink,\n\t ButtonIcon : ButtonIcon,\n\t ButtonCheck : ButtonCheck,\n\t ButtonMenu : ButtonMenu\n\t }\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 17 */\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 * This class creates a ui table element.\n\t */\n\tvar View = Backbone.View.extend({\n\t // current row\n\t row: null,\n\t \n\t // count rows\n\t row_count: 0,\n\t \n\t // defaults options\n\t optionsDefault: {\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 cls_tr : ''\n\t },\n\t \n\t // events\n\t events : {\n\t 'click' : '_onclick',\n\t 'dblclick' : '_ondblclick'\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 var $el = $(this._template(this.options));\n\t \n\t // link sub-elements\n\t this.$thead = $el.find('thead');\n\t this.$tbody = $el.find('tbody');\n\t this.$tmessage = $el.find('tmessage');\n\t \n\t // set element\n\t this.setElement($el);\n\t \n\t // initialize row\n\t this.row = this._row();\n\t },\n\t \n\t // add header cell\n\t addHeader: function($el) {\n\t var wrapper = $('' +\n\t '';\n\t if ( options.title ) {\n\t str += ' ' + options.title + '';\n\t }\n\t str += '' +\n\t '
');\n\t wrapper.append($el);\n\t this.row.append(wrapper);\n\t },\n\t \n\t // header\n\t appendHeader: function() {\n\t // append header row\n\t this.$thead.append(this.row);\n\t\n\t // row\n\t this.row = $(' ');\n\t },\n\t \n\t // add row cell\n\t add: function($el, width, align) {\n\t var wrapper = $(' ');\n\t if (width) {\n\t wrapper.css('width', width);\n\t }\n\t if (align) {\n\t wrapper.css('text-align', align);\n\t }\n\t wrapper.append($el);\n\t this.row.append(wrapper);\n\t },\n\t \n\t // append\n\t append: function(id, fade) {\n\t this._commit(id, fade, false);\n\t },\n\t \n\t // prepend\n\t prepend: function(id, fade) {\n\t this._commit(id, fade, true);\n\t },\n\t \n\t // get element\n\t get: function(id) {\n\t return this.$el.find('#' + id);\n\t },\n\t \n\t // delete\n\t del: function(id) {\n\t var item = this.$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\n\t delAll: function() {\n\t this.$tbody.empty();\n\t this.row_count = 0;\n\t this._refresh();\n\t },\n\t \n\t // value\n\t value: function(new_value) {\n\t // get current id/value\n\t this.before = this.$tbody.find('.current').attr('id');\n\t \n\t // check if new_value is defined\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 \n\t // get current id/value\n\t var after = this.$tbody.find('.current').attr('id');\n\t if(after === undefined) {\n\t return null;\n\t } else {\n\t // fire onchange\n\t if (after != this.before && this.options.onchange) {\n\t this.options.onchange(new_value);\n\t }\n\t \n\t // return current value\n\t return after;\n\t }\n\t },\n\t \n\t // size\n\t size: function() {\n\t return this.$tbody.find('tr').length;\n\t },\n\t \n\t // commit\n\t _commit: function(id, fade, prepend) {\n\t // remove previous item with same id\n\t this.del(id);\n\t \n\t // add\n\t this.row.attr('id', id);\n\t \n\t // add row\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 \n\t // fade mode\n\t if (fade) {\n\t this.row.hide();\n\t this.row.fadeIn();\n\t }\n\t \n\t // row\n\t this.row = this._row();\n\t \n\t // row count\n\t this.row_count++;\n\t this._refresh();\n\t },\n\t \n\t // create new row\n\t _row: function() {\n\t return $(' ');\n\t },\n\t \n\t // onclick\n\t _onclick: function(e) {\n\t // get values\n\t var old_value = this.value();\n\t var new_value = $(e.target).closest('tr').attr('id');\n\t if (new_value != ''){\n\t // check equality\n\t if (new_value && old_value != new_value) {\n\t if (this.options.onconfirm) {\n\t this.options.onconfirm(new_value);\n\t } else {\n\t this.value(new_value);\n\t }\n\t }\n\t }\n\t },\n\t\n\t // ondblclick\n\t _ondblclick: function(e) {\n\t var value = this.value();\n\t if (value && this.options.ondblclick) {\n\t this.options.ondblclick(value);\n\t }\n\t },\n\t \n\t // refresh\n\t _refresh: function() {\n\t if (this.row_count == 0) {\n\t this.$tmessage.show();\n\t } else {\n\t this.$tmessage.hide();\n\t }\n\t },\n\t \n\t // load html template\n\t _template: function(options) {\n\t return ' ' +\n\t '' +\n\t '' +\n\t '' +\n\t '
' +\n\t '' + options.content + ' ' +\n\t '';\n\t }\n\t});\n\t\n\treturn {\n\t View: View\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\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 18 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [\n\t //jquery\n\t //backbone\n\t], __WEBPACK_AMD_DEFINE_RESULT__ = function(){\n\t//=============================================================================\n\t/**\n\t * backbone model for icon buttons\n\t */\n\tvar IconButton = Backbone.Model.extend({\n\t defaults: {\n\t title : \"\",\n\t icon_class : \"\",\n\t on_click : null,\n\t menu_options : null,\n\t is_menu_button : true,\n\t id : null,\n\t href : null,\n\t target : null,\n\t enabled : true,\n\t visible : true,\n\t tooltip_config : {}\n\t }\n\t});\n\t\n\t/**\n\t * backbone view for icon buttons\n\t */\n\tvar IconButtonView = Backbone.View.extend({\n\t\n\t initialize : function(){\n\t // better rendering this way\n\t this.model.attributes.tooltip_config = { placement : 'bottom' };\n\t this.model.bind( 'change', this.render, this );\n\t },\n\t\n\t render : function( ){\n\t // hide tooltip\n\t this.$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 } else {\n\t buffer = '';\n\t }\n\t\n\t // return element\n\t return $( buffer );\n\t }\n\t} );\n\t\n\t// define collection\n\tvar IconButtonCollection = Backbone.Collection.extend({\n\t model: IconButton\n\t});\n\t\n\t/**\n\t * menu with multiple icon buttons\n\t * views are not needed nor used for individual buttons\n\t */\n\tvar IconButtonMenuView = Backbone.View.extend({\n\t\n\t tagName: 'div',\n\t\n\t initialize: function(){\n\t this.render();\n\t },\n\t\n\t render: function(){\n\t // initialize icon buttons\n\t var self = this;\n\t this.collection.each(function(button){\n\t // create and add icon button to menu\n\t var elt = $('')\n\t .attr('href', 'javascript:void(0)')\n\t .attr('title', button.attributes.title)\n\t .addClass('icon-button menu-button')\n\t .addClass(button.attributes.icon_class)\n\t .appendTo(self.$el)\n\t .click(button.attributes.on_click);\n\t\n\t // configure tooltip\n\t if (button.attributes.tooltip_config){\n\t elt.tooltip(button.attributes.tooltip_config);\n\t }\n\t\n\t // add popup menu to icon\n\t var menu_options = button.get('options');\n\t if (menu_options){\n\t make_popupmenu(elt, menu_options);\n\t }\n\t });\n\t\n\t // return\n\t return this;\n\t }\n\t});\n\t\n\t/**\n\t * Returns an IconButtonMenuView for the provided configuration.\n\t * Configuration is a list of dictionaries where each dictionary\n\t * defines an icon button. Each dictionary must have the following\n\t * elements: icon_class, title, and on_click.\n\t */\n\tvar create_icon_buttons_menu = function(config, global_config)\n\t{\n\t // initialize global configuration\n\t if (!global_config) global_config = {};\n\t\n\t // create and initialize menu\n\t var buttons = new IconButtonCollection(\n\t _.map(config, function(button_config){\n\t return new IconButton(_.extend(button_config, global_config));\n\t })\n\t );\n\t\n\t // return menu\n\t return new IconButtonMenuView( {collection: buttons} );\n\t};\n\t\n\t\n\t//=============================================================================\n\t return {\n\t IconButton : IconButton,\n\t IconButtonView : IconButtonView,\n\t IconButtonCollection : IconButtonCollection,\n\t IconButtonMenuView : IconButtonMenuView,\n\t create_icon_buttons_menu: create_icon_buttons_menu\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__))\n\t\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ },\n/* 19 */\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\n\t}(function ( jQuery ) {\n\t'use_strict';\n\t\n\tvar $ = 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, button_elt;\n\t\n\t if (use_textarea) {\n\t input_elt = $(\"\")\n\t .attr({ rows: num_rows, cols: num_cols }).text($.trim(cur_text))\n\t .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 }\n\t else {\n\t input_elt = $(\"\").attr({ value: $.trim(cur_text), size: num_cols })\n\t .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/***/ },\n/* 20 */\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\tfunction 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\tvar 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\tvar ServerStateDeferred = Backbone.Model.extend({\n\t defaults: {\n\t ajax_settings: {},\n\t interval: 1000,\n\t success_fn: function(result) { return true; }\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 }\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\tvar get_random_color = function(colors) {\n\t // Default for colors is white.\n\t if (!colors) { colors = \"#ffffff\"; }\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) ) +\n\t ( Math.max(g1, g2) - Math.min(g1, g2) ) +\n\t ( Math.max(b1, b2) - Math.min(b1, b2) );\n\t };\n\t\n\t // Create new random color.\n\t var new_color, nr, ng, nb,\n\t other_color, or, og, ob,\n\t n_brightness, o_brightness,\n\t diff, 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 ) ||\n\t ( 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\treturn {\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\n\t}.call(exports, __webpack_require__, exports, module), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\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(Backbone) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [\n\t __webpack_require__(32),\n\t __webpack_require__(6),\n\t __webpack_require__(5)\n\t], __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\tparseBibtex = parseBibtex || window.BibtexParser;\n\t\n\tvar logNamespace = 'citation';\n\t//==============================================================================\n\t/** @class model for tool citations.\n\t * @name Citation\n\t * @augments Backbone.Model\n\t */\n\tvar Citation = Backbone.Model.extend( baseMVC.LoggableMixin ).extend( {\n\t _logNamespace : logNamespace,\n\t\n\t initialize: function() {\n\t var bibtex = this.get( 'content' );\n\t var entry = parseBibtex(bibtex).entries[0];\n\t this.entry = entry;\n\t this._fields = {};\n\t var rawFields = 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 entryType: function() {\n\t return this.entry.EntryType;\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\tvar 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\tvar 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\tvar 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, // If a tool has citations, assume they are complete.\n\t} );\n\t\n\t\n\t//==============================================================================\n\treturn {\n\t Citation : Citation,\n\t HistoryCitationCollection : HistoryCitationCollection,\n\t ToolCitationCollection: ToolCitationCollection\n\t};\n\t\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ },\n/* 22 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/**\n\t This is the regular tool form.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(7), __webpack_require__(49), __webpack_require__(23)], __WEBPACK_AMD_DEFINE_RESULT__ = function( Utils, Ui, ToolFormBase, ToolTemplate ) {\n\t var View = ToolFormBase.extend({\n\t initialize: function( options ) {\n\t var self = this;\n\t ToolFormBase.prototype.initialize.call( this, Utils.merge({\n\t customize : function( options ) {\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 : 'btn btn-primary',\n\t floating : 'clear',\n\t onclick : function() {\n\t execute_btn.wait();\n\t self.portlet.disable();\n\t self.submit( options, function() {\n\t execute_btn.unwait();\n\t self.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[ 'rerun_remap_job_id' ] = {\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 }, options ) );\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.data.create()\n\t }\n\t this.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 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.empty().append( ToolTemplate.success( response ) );\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 if ( response && response.err_data ) {\n\t var error_messages = self.data.matchResponse( response.err_data );\n\t for (var input_id in error_messages) {\n\t self.highlight( input_id, error_messages[ input_id ]);\n\t break;\n\t }\n\t } else {\n\t self.modal.show({\n\t title : 'Job submission failed',\n\t body : ( response && response.err_msg ) || ToolTemplate.error( job_def ),\n\t buttons : {\n\t 'Close' : function() {\n\t self.modal.hide();\n\t }\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.data.match( job_input_id );\n\t var input_field = this.field_list[ input_id ];\n\t var input_def = this.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.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.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.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\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\n/***/ },\n/* 23 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function($) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function() {\n\t\n\t// tool form templates\n\treturn {\n\t help: 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 success: function(response) {\n\t // check\n\t if (!response.jobs || !response.jobs.length) {\n\t return this.error(response);\n\t }\n\t\n\t // number of jobs\n\t var njobs = response.jobs.length;\n\t\n\t // job count info text\n\t var njobs_text = '';\n\t if (njobs == 1) {\n\t njobs_text = '1 job has';\n\t } else {\n\t njobs_text = njobs + ' jobs have';\n\t }\n\t\n\t // create template string\n\t var tmpl = '' +\n\t '';\n\t\n\t // return success message element\n\t return tmpl;\n\t },\n\t\n\t error: function(response) {\n\t return '' + njobs_text + ' been successfully added to the queue - resulting in the following datasets:
';\n\t for (var i in response.outputs) {\n\t tmpl += '' + response.outputs[i].hid + ': ' + response.outputs[i].name + '
';\n\t }\n\t tmpl += '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 '' +\n\t '';\n\t },\n\t\n\t requirements: function(options) {\n\t var requirements_message = 'This tool requires ';\n\t for (var i in options.requirements) {\n\t var req = options.requirements[i];\n\t requirements_message += req.name;\n\t if (req.version) {\n\t requirements_message += ' (Version ' + req.version + ')';\n\t }\n\t if (i < options.requirements.length - 2) {\n\t requirements_message += ', ';\n\t }\n\t if (i == options.requirements.length - 2) {\n\t requirements_message += ' and ';\n\t }\n\t }\n\t return requirements_message + '. Click here for more information.';\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)))\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, $) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(11), __webpack_require__(7)], __WEBPACK_AMD_DEFINE_RESULT__ = function(Utils, Portlet, Ui) {\n\t\n\t// ui list element\n\tvar View = Backbone.View.extend({\n\t // create portlet to keep track of selected list elements\n\t initialize : function(options) {\n\t // link this\n\t var self = this;\n\t\n\t // initialize options\n\t this.options = options;\n\t this.name = options.name || 'element';\n\t this.multiple = options.multiple || false;\n\t\n\t // create message handler\n\t this.message = new Ui.Message({ cls: 'ui-margin-top' });\n\t\n\t // create portlet\n\t this.portlet = new Portlet.View({ cls: 'ui-portlet-section' });\n\t\n\t // create select field containing the options which can be inserted into the list\n\t this.select = new Ui.Select.View({ optional : options.optional });\n\t\n\t // create insert new list element button\n\t this.button = new Ui.ButtonIcon({\n\t icon : 'fa fa-sign-in',\n\t floating : 'left',\n\t tooltip : 'Insert new ' + this.name,\n\t onclick : function() {\n\t self.add({\n\t id : self.select.value(),\n\t name : self.select.text()\n\t });\n\t }\n\t });\n\t\n\t // build main element\n\t this.setElement(this._template(options));\n\t this.$('.ui-list-message').append(this.message.$el);\n\t this.$('.ui-list-portlet').append(this.portlet.$el);\n\t this.$('.ui-list-button').append(this.button.$el);\n\t this.$('.ui-list-select').append(this.select.$el);\n\t },\n\t\n\t /** Return/Set currently selected list elements */\n\t value: function(val) {\n\t // set new value\n\t if (val !== undefined) {\n\t this.portlet.empty();\n\t if ($.isArray(val)) {\n\t for (var i in val) {\n\t var v = val[i];\n\t var v_id = null;\n\t var v_name = null;\n\t if ($.type(v) != 'string') {\n\t v_id = v.id;\n\t v_name = v.name;\n\t } else {\n\t v_id = v_name = v;\n\t }\n\t if (v_id != null) {\n\t this.add({\n\t id : v_id,\n\t name : v_name\n\t });\n\t }\n\t }\n\t }\n\t this._refresh();\n\t }\n\t // get current value\n\t var lst = [];\n\t this.$('.ui-list-id').each(function() {\n\t lst.push({\n\t id : $(this).prop('id'),\n\t name : $(this).find('.ui-list-name').html()\n\t });\n\t });\n\t if (lst.length == 0) {\n\t return null;\n\t }\n\t return lst;\n\t },\n\t\n\t /** Add row */\n\t add: function(options) {\n\t var self = this;\n\t if (this.$('[id=\"' + options.id + '\"]').length === 0) {\n\t if (Utils.validate(options.id)) {\n\t var $el = $(this._templateRow({\n\t id : options.id,\n\t name : options.name\n\t }));\n\t $el.on('click', function() {\n\t $el.remove();\n\t self._refresh();\n\t });\n\t $el.on('mouseover', function() {\n\t $el.addClass('portlet-highlight');\n\t });\n\t $el.on('mouseout', function() {\n\t $el.removeClass('portlet-highlight');\n\t });\n\t this.portlet.append($el);\n\t this._refresh();\n\t } else {\n\t this.message.update({ message: 'Please select a valid ' + this.name + '.', status: 'danger' });\n\t }\n\t } else {\n\t this.message.update({ message: 'This ' + this.name + ' is already in the list.' });\n\t }\n\t },\n\t\n\t /** Update available options */\n\t update: function(options) {\n\t this.select.update(options);\n\t },\n\t\n\t /** Refresh view */\n\t _refresh: function() {\n\t if (this.$('.ui-list-id').length > 0) {\n\t !this.multiple && this.button.disable();\n\t this.$('.ui-list-portlet').show();\n\t } else {\n\t this.button.enable();\n\t this.$('.ui-list-portlet').hide();\n\t }\n\t this.options.onchange && this.options.onchange();\n\t },\n\t\n\t /** Main Template */\n\t _template: function(options) {\n\t return '' +\n\t 'The server could not complete the request. Please contact the Galaxy Team if this error persists.' +\n\t '
' +\n\t '' +\n\t '' +\n\t '' +\n\t '' +\n\t '' +\n\t '' +\n\t '' +\n\t '' +\n\t '';\n\t },\n\t\n\t /** Row Template */\n\t _templateRow: function(options) {\n\t return '' +\n\t '' +\n\t '' + options.name + '' +\n\t '';\n\t }\n\t});\n\t\n\treturn {\n\t View: View\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\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\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, $) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(16)], __WEBPACK_AMD_DEFINE_RESULT__ = function(Utils, Buttons) {\n\t\n\t/** Base class for options based ui elements **/\n\tvar Base = Backbone.View.extend({\n\t // initialize\n\t initialize: function(options) {\n\t // link this\n\t var self = this;\n\t\n\t // configure options\n\t this.options = Utils.merge(options, {\n\t visible : true,\n\t data : [],\n\t id : Utils.uid(),\n\t error_text : 'No options available.',\n\t wait_text : 'Please wait...',\n\t multiple : false\n\t });\n\t\n\t // create new element\n\t this.setElement('');\n\t\n\t // create elements\n\t this.$message = $('');\n\t this.$options = $(this._template(options));\n\t this.$menu = $('');\n\t\n\t // append\n\t this.$el.append(this.$message);\n\t this.$el.append(this.$menu);\n\t this.$el.append(this.$options);\n\t\n\t // add select/unselect all button\n\t if (this.options.multiple) {\n\t this.all_button = new Buttons.ButtonCheck({\n\t onclick: function() {\n\t self.$('input').prop('checked', self.all_button.value() !== 0);\n\t self.trigger('change');\n\t }\n\t });\n\t this.$menu.append(this.all_button.$el);\n\t }\n\t\n\t // hide input field\n\t if (!this.options.visible) {\n\t this.$el.hide();\n\t }\n\t\n\t // initialize data\n\t this.update(this.options.data);\n\t\n\t // set initial value\n\t if (this.options.value !== undefined) {\n\t this.value(this.options.value);\n\t }\n\t\n\t // add change event. fires on trigger\n\t this.on('change', function() {\n\t this.options.onchange && this.options.onchange(this.value());\n\t });\n\t },\n\t\n\t /** Update options\n\t */\n\t update: function(options) {\n\t // backup current value\n\t var current = this._getValue();\n\t\n\t // remove all options\n\t this.$options.empty();\n\t\n\t // add new options using single option templates or full template\n\t if (this._templateOptions) {\n\t // rebuild options using full template\n\t this.$options.append(this._templateOptions(options));\n\t } else {\n\t // rebuild options using single option templates\n\t for (var key in options) {\n\t var $option = $(this._templateOption(options[key]));\n\t $option.addClass('ui-option');\n\t $option.tooltip({title: options[key].tooltip, placement: 'bottom'});\n\t this.$options.append($option);\n\t }\n\t }\n\t\n\t // add change events\n\t var self = this;\n\t this.$('input').on('change', function() {\n\t self.value(self._getValue());\n\t self.trigger('change');\n\t });\n\t\n\t // set previous value\n\t this.value(current);\n\t\n\t // data initialization has been completed\n\t this.unwait();\n\t },\n\t\n\t /** Return/Set current value\n\t */\n\t value: function (new_value) {\n\t // set new value if available\n\t if (new_value !== undefined) {\n\t // reset selection\n\t this.$('input').prop('checked', false);\n\t // set value\n\t if (new_value !== null) {\n\t // check if its an array\n\t if (!(new_value instanceof Array)) {\n\t new_value = [new_value];\n\t }\n\t // update to new selection\n\t for (var i in new_value) {\n\t this.$('input[value=\"' + new_value[i] + '\"]').first().prop('checked', true);\n\t }\n\t };\n\t }\n\t // get current value\n\t var current = this._getValue();\n\t if (this.all_button) {\n\t var value = current;\n\t if (!(value instanceof Array)) {\n\t value = 0;\n\t } else {\n\t value = value.length;\n\t }\n\t this.all_button.value(value, this._size());\n\t }\n\t return current;\n\t },\n\t\n\t /** Check if selected value exists (or any if multiple)\n\t */\n\t exists: function(value) {\n\t if (value !== undefined) {\n\t if (!(value instanceof Array)) {\n\t value = [value];\n\t }\n\t for (var i in value) {\n\t if (this.$('input[value=\"' + value[i] + '\"]').length > 0) {\n\t return true;\n\t }\n\t }\n\t }\n\t return false;\n\t },\n\t\n\t /** Return first available option\n\t */\n\t first: function() {\n\t var options = this.$('input').first();\n\t if (options.length > 0) {\n\t return options.val();\n\t } else {\n\t return null;\n\t }\n\t },\n\t\n\t /** Wait message during request processing\n\t */\n\t wait: function() {\n\t if (this._size() == 0) {\n\t this._messageShow(this.options.wait_text, 'info');\n\t this.$options.hide();\n\t this.$menu.hide();\n\t }\n\t },\n\t\n\t /** Hide wait message\n\t */\n\t unwait: function() {\n\t var total = this._size();\n\t if (total == 0) {\n\t this._messageShow(this.options.error_text, 'danger');\n\t this.$options.hide();\n\t this.$menu.hide();\n\t } else {\n\t this._messageHide();\n\t this.$options.css('display', 'inline-block');\n\t this.$menu.show();\n\t }\n\t },\n\t\n\t /** Return current selection\n\t */\n\t _getValue: function() {\n\t // track values in array\n\t var selected = [];\n\t this.$(':checked').each(function() {\n\t selected.push($(this).val());\n\t });\n\t\n\t // get selected elements\n\t if (!Utils.validate(selected)) {\n\t return null;\n\t }\n\t\n\t // return multiple or single value\n\t if (this.options.multiple) {\n\t return selected;\n\t } else {\n\t return selected[0];\n\t }\n\t },\n\t\n\t /** Returns the number of options\n\t */\n\t _size: function() {\n\t return this.$('.ui-option').length;\n\t },\n\t\n\t /** Show message instead if options\n\t */\n\t _messageShow: function(text, status) {\n\t this.$message.show();\n\t this.$message.removeClass();\n\t this.$message.addClass('ui-message alert alert-' + status);\n\t this.$message.html(text);\n\t },\n\t\n\t /** Hide message\n\t */\n\t _messageHide: function() {\n\t this.$message.hide();\n\t },\n\t\n\t /** Main template function\n\t */\n\t _template: function() {\n\t return '';\n\t }\n\t});\n\t\n\t/** Iconized **/\n\tvar BaseIcons = Base.extend({\n\t _templateOption: function(pair) {\n\t var id = Utils.uid();\n\t return '' +\n\t '' +\n\t '' +\n\t '';\n\t }\n\t});\n\t\n\t/** Radio button field **/\n\tvar Radio = {};\n\tRadio.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\tvar Checkbox = {};\n\tCheckbox.View = BaseIcons.extend({\n\t initialize: function(options) {\n\t options.multiple = true;\n\t options.type = 'checkbox';\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\tvar RadioButton = {};\n\tRadioButton.View = Base.extend({\n\t // initialize\n\t initialize: function(options) {\n\t Base.prototype.initialize.call(this, options);\n\t },\n\t\n\t /** Return/Set current value\n\t */\n\t value: function (new_value) {\n\t // set new value\n\t if (new_value !== undefined) {\n\t this.$('input').prop('checked', false);\n\t this.$('label').removeClass('active');\n\t this.$('[value=\"' + new_value + '\"]').prop('checked', true).closest('label').addClass('active');\n\t }\n\t\n\t // get and return value\n\t return this._getValue();\n\t },\n\t\n\t /** Template for a single option\n\t */\n\t _templateOption: function(pair) {\n\t var cls = 'fa ' + pair.icon;\n\t if (!pair.label) {\n\t cls += ' no-padding';\n\t }\n\t var tmpl = '';\n\t return tmpl;\n\t },\n\t\n\t /** Main template function\n\t */\n\t _template: function() {\n\t return '';\n\t }\n\t});\n\t\n\treturn {\n\t Base : Base,\n\t BaseIcons : BaseIcons,\n\t Radio : Radio,\n\t RadioButton : RadioButton,\n\t Checkbox : Checkbox\n\t};\n\t\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 26 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_FACTORY__, __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function($, _) {(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\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 '',\n\t // could go with something less specific here - like 'html'\n\t '',\n\t ''\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\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 27 */\n/***/ function(module, exports, __webpack_require__) {\n\n\t'use strict';\n\t\n\texports.__esModule = true;\n\texports.HandlebarsEnvironment = HandlebarsEnvironment;\n\t// istanbul ignore next\n\t\n\tfunction _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { 'default': obj }; }\n\t\n\tvar _utils = __webpack_require__(8);\n\t\n\tvar _exception = __webpack_require__(9);\n\t\n\tvar _exception2 = _interopRequireDefault(_exception);\n\t\n\tvar _helpers = __webpack_require__(70);\n\t\n\tvar _decorators = __webpack_require__(68);\n\t\n\tvar _logger = __webpack_require__(78);\n\t\n\tvar _logger2 = _interopRequireDefault(_logger);\n\t\n\tvar VERSION = '4.0.5';\n\texports.VERSION = VERSION;\n\tvar COMPILER_REVISION = 7;\n\t\n\texports.COMPILER_REVISION = COMPILER_REVISION;\n\tvar REVISION_CHANGES = {\n\t 1: '<= 1.0.rc.2', // 1.0.rc.2 is actually rev2 but doesn't report it\n\t 2: '== 1.0.0-rc.3',\n\t 3: '== 1.0.0-rc.4',\n\t 4: '== 1.x.x',\n\t 5: '== 2.0.0-alpha.x',\n\t 6: '>= 2.0.0-beta.1',\n\t 7: '>= 4.0.0'\n\t};\n\t\n\texports.REVISION_CHANGES = REVISION_CHANGES;\n\tvar objectType = '[object Object]';\n\t\n\tfunction HandlebarsEnvironment(helpers, partials, decorators) {\n\t this.helpers = helpers || {};\n\t this.partials = partials || {};\n\t this.decorators = decorators || {};\n\t\n\t _helpers.registerDefaultHelpers(this);\n\t _decorators.registerDefaultDecorators(this);\n\t}\n\t\n\tHandlebarsEnvironment.prototype = {\n\t constructor: HandlebarsEnvironment,\n\t\n\t logger: _logger2['default'],\n\t log: _logger2['default'].log,\n\t\n\t registerHelper: function registerHelper(name, fn) {\n\t if (_utils.toString.call(name) === objectType) {\n\t if (fn) {\n\t throw new _exception2['default']('Arg not supported with multiple helpers');\n\t }\n\t _utils.extend(this.helpers, name);\n\t } else {\n\t this.helpers[name] = fn;\n\t }\n\t },\n\t unregisterHelper: function unregisterHelper(name) {\n\t delete this.helpers[name];\n\t },\n\t\n\t registerPartial: function registerPartial(name, partial) {\n\t if (_utils.toString.call(name) === objectType) {\n\t _utils.extend(this.partials, name);\n\t } else {\n\t if (typeof partial === 'undefined') {\n\t throw new _exception2['default']('Attempting to register a partial called \"' + name + '\" as undefined');\n\t }\n\t this.partials[name] = partial;\n\t }\n\t },\n\t unregisterPartial: function unregisterPartial(name) {\n\t delete this.partials[name];\n\t },\n\t\n\t registerDecorator: function registerDecorator(name, fn) {\n\t if (_utils.toString.call(name) === objectType) {\n\t if (fn) {\n\t throw new _exception2['default']('Arg not supported with multiple decorators');\n\t }\n\t _utils.extend(this.decorators, name);\n\t } else {\n\t this.decorators[name] = fn;\n\t }\n\t },\n\t unregisterDecorator: function unregisterDecorator(name) {\n\t delete this.decorators[name];\n\t }\n\t};\n\t\n\tvar log = _logger2['default'].log;\n\t\n\texports.log = log;\n\texports.createFrame = _utils.createFrame;\n\texports.logger = _logger2['default'];\n\t//# 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\n\n\n/***/ },\n/* 28 */,\n/* 29 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {/**\n\t * Popover wrapper\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [ __webpack_require__(4) ], __WEBPACK_AMD_DEFINE_RESULT__ = function( Utils ) {\n\tvar View = Backbone.View.extend({\n\t optionsDefault: {\n\t with_close : true,\n\t title : null,\n\t placement : 'top',\n\t container : 'body',\n\t body : null\n\t },\n\t\n\t initialize: function ( options ) {\n\t this.setElement( this._template() );\n\t this.uid = Utils.uid();\n\t this.options = _.defaults( options || {}, this.optionsDefault );\n\t this.options.container.parent().append( this.el );\n\t this.$title = this.$( '.popover-title-label' );\n\t this.$close = this.$( '.popover-close' );\n\t this.$body = this.$( '.popover-content' );\n\t\n\t // add initial content\n\t this.options.body && this.append( this.options.body );\n\t\n\t // add event to hide if click is outside of popup and not on container\n\t var self = this;\n\t $( 'body' ).on( 'mousedown.' + this.uid, function( e ) {\n\t // the 'is' for buttons that trigger popups\n\t // the 'has' for icons within a button that triggers a popup\n\t self.visible && !$( self.options.container ).is( e.target ) && !$( self.el ).is( e.target ) &&\n\t $( self.el ).has( e.target ).length === 0 && self.hide();\n\t });\n\t },\n\t\n\t /**\n\t * Render popover\n\t */\n\t render: function() {\n\t this.$title.html( this.options.title );\n\t this.$el.removeClass().addClass( 'ui-popover popover fade in' ).addClass( this.options.placement );\n\t this.$el.css( this._get_placement( this.options.placement ) );\n\t\n\t // configure close option\n\t var self = this;\n\t if ( this.options.with_close ) {\n\t this.$close.on( 'click', function() { self.hide() } ).show();\n\t } else {\n\t this.$close.off().hide();\n\t }\n\t },\n\t\n\t /**\n\t * Set the popover title\n\t * @params{ String } newTitle - New popover title\n\t */\n\t title: function( newTitle ) {\n\t if ( newTitle !== undefined ) {\n\t this.options.title = newTitle;\n\t this.$title.html( newTitle );\n\t }\n\t },\n\t\n\t /**\n\t * Show popover\n\t */\n\t show: function() {\n\t this.render();\n\t this.$el.show();\n\t this.visible = true;\n\t },\n\t\n\t /**\n\t * Hide popover\n\t */\n\t hide: function() {\n\t this.$el.hide();\n\t this.visible = false;\n\t },\n\t\n\t /**\n\t * Append new content to the popover\n\t * @params{ Object } $el - Dom element\n\t */\n\t append: function( $el ) {\n\t this.$body.append( $el );\n\t },\n\t\n\t /**\n\t * Remove all content\n\t */\n\t empty: function() {\n\t this.$body.empty();\n\t },\n\t\n\t /**\n\t * Remove popover\n\t */\n\t remove: function() {\n\t $( 'body' ).off( 'mousedown.' + this.uid );\n\t this.$el.remove();\n\t },\n\t\n\t /**\n\t * Improve popover location/placement\n\t */\n\t _get_placement: function( placement ) {\n\t // get popover dimensions\n\t var width = this._get_width( this.$el );\n\t var height = this.$el.height();\n\t\n\t // get container details\n\t var $container = this.options.container;\n\t var container_width = this._get_width( $container );\n\t var container_height = this._get_height( $container );\n\t var container_position = $container.position();\n\t\n\t // get position\n\t var top = left = 0;\n\t if ([ 'top', 'bottom' ].indexOf( placement ) != -1) {\n\t left = container_position.left - width + ( container_width + width ) / 2;\n\t switch ( placement ) {\n\t case 'top':\n\t top = container_position.top - height - 5;\n\t break;\n\t case 'bottom':\n\t top = container_position.top + container_height + 5;\n\t break;\n\t }\n\t } else {\n\t top = container_position.top - height + ( container_height + height ) / 2;\n\t switch ( placement ) {\n\t case 'right':\n\t left = container_position.left + container_width;\n\t break;\n\t }\n\t }\n\t return { top: top, left: left };\n\t },\n\t\n\t /**\n\t * Returns padding/margin corrected width\n\t */\n\t _get_width: function( $el ) {\n\t return $el.width() + parseInt( $el.css( 'padding-left' ) ) + parseInt( $el.css( 'margin-left' ) ) +\n\t parseInt( $el.css( 'padding-right' ) ) + parseInt( $el.css( 'margin-right' ) );\n\t },\n\t\n\t /**\n\t * Returns padding corrected height\n\t */\n\t _get_height: function( $el ) {\n\t return $el.height() + parseInt( $el.css( 'padding-top' ) ) + parseInt( $el.css( 'padding-bottom' ) );\n\t },\n\t\n\t /**\n\t * Return the popover template\n\t */\n\t _template: function( options ) {\n\t return '' +\n\t '' +\n\t '' +\n\t '' +\n\t '' +\n\t '' +\n\t '' +\n\t '';\n\t }\n\t});\n\t\n\treturn {\n\t View: View\n\t}\n\t\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ },\n/* 30 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function(Utils) {\n\t\n\t/**\n\t * A plugin for initializing select2 input items.\n\t * Make sure the select2 library itself is loaded beforehand.\n\t * Also the element to which select2 will be appended has to \n\t * be created before select2 initialization (and passed as option).\n\t */\n\tvar View = Backbone.View.extend(\n\t{\n\t // options\n\t optionsDefault: {\n\t css : '',\n\t placeholder : 'No data available',\n\t data : [],\n\t value : null,\n\t multiple : false,\n\t minimumInputLength : 0,\n\t // example format of initial data: \"id:name,55:anotherrole@role.com,27:role@role.com\"\n\t initialData : ''\n\t },\n\t \n\t // initialize\n\t initialize : function(options) {\n\t // configure options\n\t this.options = Utils.merge(options, this.optionsDefault);\n\t \n\t // create new element\n\t this.setElement(this._template(this.options));\n\t \n\t // check if container exists\n\t if (!this.options.container) {\n\t console.log('ui-select::initialize() : container not specified.');\n\t return;\n\t }\n\t \n\t // add to dom\n\t this.options.container.append(this.$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 // search index\n\t for (var key in this.select_data) {\n\t if (this.select_data[key].id == value) {\n\t return key;\n\t }\n\t }\n\t \n\t // not found\n\t return -1;\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\treturn {\n\t View : View\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\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ },\n/* 31 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function(Utils) {\n\t\n\t// return\n\tvar View = Backbone.View.extend({\n\t // defaults options\n\t optionsDefault: {\n\t title_new : '',\n\t operations : null,\n\t onnew : null,\n\t max : null,\n\t onchange : null\n\t },\n\t \n\t // initialize\n\t initialize : function(options) {\n\t // configure\n\t this.visible = false;\n\t this.$nav = null;\n\t this.$content = null;\n\t this.first_tab = null;\n\t this.current_id = null;\n\t \n\t // configure options\n\t this.options = Utils.merge(options, this.optionsDefault);\n\t \n\t // create tabs\n\t var $tabs = $(this._template(this.options));\n\t \n\t // link elements\n\t this.$nav = $tabs.find('.tab-navigation');\n\t this.$content = $tabs.find('.tab-content');\n\t \n\t // create new element\n\t this.setElement($tabs);\n\t \n\t // clear list\n\t this.list = {};\n\t \n\t // link this\n\t var self = this;\n\t \n\t // append operations\n\t if (this.options.operations) {\n\t $.each(this.options.operations, function(name, item) {\n\t item.$el.prop('id', name);\n\t self.$nav.find('.operations').append(item.$el);\n\t });\n\t }\n\t \n\t // add built-in add-new-tab tab\n\t if (this.options.onnew) {\n\t // create tab object\n\t var $tab_new = $(this._template_tab_new(this.options));\n\t \n\t // append to navbar\n\t this.$nav.append($tab_new);\n\t \n\t // add tooltip\n\t $tab_new.tooltip({title: 'Add a new tab', placement: 'bottom', container: self.$el});\n\t \n\t // link click event\n\t $tab_new.on('click', function(e) {\n\t $tab_new.tooltip('hide');\n\t self.options.onnew();\n\t });\n\t }\n\t },\n\t \n\t // size\n\t size: function() {\n\t return _.size(this.list);\n\t },\n\t \n\t // front\n\t current: function() {\n\t return this.$el.find('.tab-pane.active').attr('id');\n\t },\n\t \n\t // append\n\t add: function(options) {\n\t // self\n\t var self = this;\n\t \n\t // get tab id\n\t var id = options.id;\n\t\n\t // create tab object\n\t var $tab_title = $(this._template_tab(options));\n\t var $tab_content = $(this._template_tab_content(options));\n\t \n\t // add to list\n\t this.list[id] = options.ondel ? true : false;\n\t \n\t // add a new tab either before the add-new-tab tab or behind the last tab\n\t if (this.options.onnew) {\n\t this.$nav.find('#new-tab').before($tab_title);\n\t } else {\n\t this.$nav.append($tab_title);\n\t }\n\t \n\t // add content\n\t $tab_content.append(options.$el);\n\t this.$content.append($tab_content);\n\t \n\t // activate this tab if this is the first tab\n\t if (this.size() == 1) {\n\t $tab_title.addClass('active');\n\t $tab_content.addClass('active');\n\t this.first_tab = id;\n\t }\n\t \n\t // hide add tab\n\t if (this.options.max && this.size() >= this.options.max) {\n\t this.$el.find('#new-tab').hide();\n\t }\n\t \n\t // add click event to remove tab\n\t if (options.ondel) {\n\t var $del_icon = $tab_title.find('#delete');\n\t $del_icon.tooltip({title: 'Delete this tab', placement: 'bottom', container: self.$el});\n\t $del_icon.on('click', function() {\n\t $del_icon.tooltip('destroy');\n\t self.$el.find('.tooltip').remove();\n\t options.ondel();\n\t return false;\n\t });\n\t }\n\t \n\t // add custom click event handler\n\t $tab_title.on('click', function(e) {\n\t // prevent default\n\t e.preventDefault();\n\t \n\t // click\n\t if (options.onclick) {\n\t options.onclick();\n\t } else {\n\t self.show(id);\n\t }\n\t });\n\t \n\t // initialize current id\n\t if (!this.current_id) {\n\t this.current_id = id;\n\t }\n\t },\n\t \n\t // delete tab\n\t del: function(id) {\n\t // delete tab from dom\n\t this.$el.find('#tab-' + id).remove();\n\t this.$el.find('#' + id).remove();\n\t \n\t // check if first tab has been deleted\n\t if (this.first_tab == id) {\n\t this.first_tab = null;\n\t }\n\t \n\t // show first tab\n\t if (this.first_tab != null) {\n\t this.show(this.first_tab);\n\t }\n\t \n\t // delete from list\n\t if (this.list[id]) {\n\t delete this.list[id];\n\t }\n\t \n\t // show add tab\n\t if (this.size() < this.options.max) {\n\t this.$el.find('#new-tab').show();\n\t }\n\t },\n\t \n\t // delete tab\n\t delRemovable: function() {\n\t for (var id in this.list) {\n\t this.del(id);\n\t }\n\t },\n\t \n\t // show\n\t show: function(id){\n\t // show tab view\n\t this.$el.fadeIn('fast');\n\t this.visible = true;\n\t \n\t // show selected tab\n\t if (id) {\n\t // reassign active class\n\t this.$el.find('#tab-' + this.current_id).removeClass('active');\n\t this.$el.find('#' + this.current_id).removeClass('active');\n\t this.$el.find('#tab-' + id).addClass('active');\n\t this.$el.find('#' + id).addClass('active');\n\t \n\t // update current id\n\t this.current_id = id;\n\t }\n\t \n\t // change\n\t if (this.options.onchange) {\n\t this.options.onchange(id);\n\t }\n\t },\n\t \n\t // hide\n\t hide: function(){\n\t this.$el.fadeOut('fast');\n\t this.visible = false;\n\t },\n\t\n\t // hide operation\n\t hideOperation: function(id) {\n\t this.$nav.find('#' + id).hide();\n\t },\n\t\n\t // show operation\n\t showOperation: function(id) {\n\t this.$nav.find('#' + id).show();\n\t },\n\t \n\t // set operation\n\t setOperation: function(id, callback) {\n\t var $el = this.$nav.find('#' + id);\n\t $el.off('click');\n\t $el.on('click', callback);\n\t },\n\t \n\t // title\n\t title: function(id, new_title) {\n\t var $el = this.$el.find('#tab-title-text-' + id);\n\t if (new_title) {\n\t $el.html(new_title);\n\t }\n\t return $el.html();\n\t },\n\t \n\t // retitle\n\t retitle: function(new_title) {\n\t var index = 0;\n\t for (var id in this.list) {\n\t this.title(id, ++index + ': ' + new_title);\n\t }\n\t },\n\t \n\t // fill template\n\t _template: function(options) {\n\t return '' +\n\t '- ' +\n\t '' +\n\t '
' +\n\t '';\n\t },\n\t \n\t // fill template tab\n\t _template_tab_new: function(options) {\n\t return '- ' +\n\t '' +\n\t '' +\n\t options.title_new +\n\t '' +\n\t '
';\n\t },\n\t \n\t // fill template tab\n\t _template_tab: function(options) {\n\t var tmpl = '- ' +\n\t '' +\n\t '' + options.title + '';\n\t \n\t if (options.ondel) {\n\t tmpl += '';\n\t }\n\t \n\t tmpl += '' +\n\t '
';\n\t \n\t return tmpl;\n\t },\n\t \n\t // fill template tab content\n\t _template_tab_content: function(options) {\n\t return '';\n\t }\n\t});\n\t\n\treturn {\n\t View : View\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\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 32 */\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++)\n\t 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_, \n\t this.CHAR_IN_LINE_,\n\t this.CHAR_,\n\t 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) \n\t 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, ' ')\n\t .replace(/\\s\\s+/g, ' ')\n\t .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) \n\t c = raw[++i];\n\t else {\n\t if (c == '{' || c == '}')\n\t skip = true;\n\t }\n\t if (!skip)\n\t 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 /**\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')\n\t 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))\n\t 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: \"' +\n\t 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_ == '{') ||\n\t (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_ == '{') ||\n\t (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 \"' +\n\t 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 &&\n\t (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 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'\\u2ABA' ],\n\t [ /\\\\subseteqq /g, '\\u2AC5' ],\n\t [ /\\\\nsubseteqq /g, '\\u2AC5-00338' ],\n\t [ /\\\\supseteqq /g, '\\u2AC6' ],\n\t [ /\\\\nsupseteqq/g, '\\u2AC6-00338' ],\n\t [ /\\\\subsetneqq /g, '\\u2ACB' ],\n\t [ /\\\\supsetneqq /g, '\\u2ACC' ],\n\t [ /\\\\ElsevierGlyph\\{E30D\\}/g, '\\u2AEB' ],\n\t [ /\\\\Elztdcol /g, '\\u2AF6' ],\n\t [ /\\\\ElsevierGlyph\\{300A\\}/g, '\\u300A' ],\n\t [ /\\\\ElsevierGlyph\\{300B\\}/g, '\\u300B' ],\n\t [ /\\\\ElsevierGlyph\\{3018\\}/g, '\\u3018' ],\n\t [ /\\\\ElsevierGlyph\\{3019\\}/g, '\\u3019' ],\n\t [ /\\\\openbracketleft /g, '\\u301A' ],\n\t [ /\\\\openbracketright /g, '\\u301B' ]\n\t ]\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/***/ },\n/* 33 */\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 __webpack_require__(6),\n\t __webpack_require__(21),\n\t __webpack_require__(5)\n\t], __WEBPACK_AMD_DEFINE_RESULT__ = function( baseMVC, citationModel, _l ){\n\t\n\tvar 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 : \"\") +\n\t (fields.number ? ( \" (\" + fields.number + \")\" ) : \"\") +\n\t (pages ? \", \" + pages : \"\");\n\t ref = authorsAndYear + this._asSentence(title) +\n\t (fields.journal ? (\"In \" + fields.journal + \", \") : \"\") +\n\t this._asSentence(volume) + \n\t this._asSentence(fields.address) +\n\t \"<\\/em>\";\n\t } else if( entryType == \"inproceedings\" || entryType == \"proceedings\" ) {\n\t ref = authorsAndYear + \n\t this._asSentence(title) + \n\t (fields.booktitle ? (\"In \" + fields.booktitle + \", \") : \"\") +\n\t (pages ? pages : \"\") +\n\t (address ? \", \" + address : \"\") + \n\t \".<\\/em>\";\n\t } else if( entryType == \"mastersthesis\" || entryType == \"phdthesis\" ) {\n\t ref = authorsAndYear + this._asSentence(title) +\n\t (fields.howpublished ? fields.howpublished + \". \" : \"\") +\n\t (fields.note ? fields.note + \".\" : \"\");\n\t } else if( entryType == \"techreport\" ) {\n\t ref = authorsAndYear + this._asSentence(title) +\n\t this._asSentence(fields.institution) +\n\t this._asSentence(fields.number) +\n\t 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) +\n\t this._asSentence(fields.howpublished) +\n\t 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\tvar 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 [\n\t '',\n\t 'Warning: This is a experimental feature. Most Galaxy tools will not annotate',\n\t ' citations explicitly at this time. When writing up your analysis, please manually',\n\t ' review your histories and find all references',\n\t ' that should be cited in order to completely describe your work. Also, please remember to',\n\t ' cite Galaxy.',\n\t '',\n\t ].join('');\n\t } else {\n\t return '';\n\t }\n\t },\n\t\n\t citationsElement: function() {\n\t return [\n\t '',\n\t ''\n\t ].join( '' );\n\t }\n\t});\n\t\n\t//==============================================================================\n\treturn {\n\t CitationView : CitationView,\n\t CitationListView : CitationListView\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\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ },\n/* 34 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(_, $, jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [\n\t __webpack_require__(48),\n\t __webpack_require__(37),\n\t __webpack_require__(6),\n\t __webpack_require__(5)\n\t], __WEBPACK_AMD_DEFINE_RESULT__ = function( LIST_ITEM, DATASET_LI, BASE_MVC, _l ){\n\t/* global Backbone */\n\t//==============================================================================\n\tvar FoldoutListItemView = LIST_ITEM.FoldoutListItemView,\n\t ListItemView = LIST_ITEM.ListItemView;\n\t/** @class Read only view for DatasetCollection.\n\t */\n\tvar DCListItemView = FoldoutListItemView.extend(\n\t/** @lends DCListItemView.prototype */{\n\t//TODO: may not be needed\n\t\n\t /** logger used to record this.log messages, commonly set to console */\n\t //logger : console,\n\t\n\t className : FoldoutListItemView.prototype.className + \" dataset-collection\",\n\t id : function(){\n\t return [ 'dataset_collection', this.model.get( 'id' ) ].join( '-' );\n\t },\n\t\n\t /** override to add linkTarget */\n\t initialize : function( attributes ){\n\t this.linkTarget = attributes.linkTarget || '_blank';\n\t this.hasUser = attributes.hasUser;\n\t FoldoutListItemView.prototype.initialize.call( this, attributes );\n\t },\n\t\n\t /** event listeners */\n\t _setUpListeners : function(){\n\t FoldoutListItemView.prototype._setUpListeners.call( this );\n\t // re-rendering on deletion\n\t this.model.on( 'change', function( model, options ){\n\t if( _.isEqual( _.keys( model.changed ), [ 'deleted' ] ) ){\n\t this.render();\n\t }\n\t }, this );\n\t },\n\t\n\t // ......................................................................... rendering\n\t //TODO:?? possibly move to listItem\n\t /** render a subtitle to show the user what sort of collection this is */\n\t _renderSubtitle : function(){\n\t var $subtitle = $( '' );\n\t //TODO: would be good to get this in the subtitle\n\t //var len = this.model.elements.length;\n\t switch( this.model.get( 'collection_type' ) ){\n\t case 'list':\n\t return $subtitle.text( _l( 'a list of datasets' ) );\n\t case 'paired':\n\t return $subtitle.text( _l( 'a pair of datasets' ) );\n\t case 'list:paired':\n\t return $subtitle.text( _l( 'a list of paired datasets' ) );\n\t }\n\t return $subtitle;\n\t },\n\t\n\t // ......................................................................... foldout\n\t /** override to add linktarget to sub-panel */\n\t _getFoldoutPanelOptions : function(){\n\t var options = FoldoutListItemView.prototype._getFoldoutPanelOptions.call( this );\n\t return _.extend( options, {\n\t linkTarget : this.linkTarget,\n\t hasUser : this.hasUser\n\t });\n\t },\n\t\n\t /** override to not catch sub-panel selectors */\n\t $selector : function(){\n\t return this.$( '> .selector' );\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 'DCListItemView(' + modelString + ')';\n\t }\n\t});\n\t\n\t// ............................................................................ TEMPLATES\n\t/** underscore templates */\n\tDCListItemView.prototype.templates = (function(){\n\t\n\t var warnings = _.extend( {}, FoldoutListItemView.prototype.templates.warnings, {\n\t error : BASE_MVC.wrapTemplate([\n\t // error during index fetch - show error on dataset\n\t '<% if( model.error ){ %>',\n\t '',\n\t _l(\"Citations\"),\n\t ' ',\n\t ' ',\n\t '',\n\t '',\n\t this.partialWarningElement(),\n\t '',\n\t '',\n\t '',\n\t '',\n\t '',\n\t '',\n\t _l( 'There was an error getting the data for this collection' ), ': <%- model.error %>',\n\t '',\n\t '<% } %>'\n\t ]),\n\t purged : BASE_MVC.wrapTemplate([\n\t '<% if( model.purged ){ %>',\n\t '',\n\t _l( 'This collection has been deleted and removed from disk' ),\n\t '',\n\t '<% } %>'\n\t ]),\n\t deleted : BASE_MVC.wrapTemplate([\n\t // deleted not purged\n\t '<% if( model.deleted && !model.purged ){ %>',\n\t '',\n\t _l( 'This collection has been deleted' ),\n\t '',\n\t '<% } %>'\n\t ])\n\t });\n\t\n\t // use element identifier\n\t var titleBarTemplate = BASE_MVC.wrapTemplate([\n\t '',\n\t ''\n\t ], 'collection' );\n\t\n\t return _.extend( {}, FoldoutListItemView.prototype.templates, {\n\t warnings : warnings,\n\t titleBar : titleBarTemplate\n\t });\n\t}());\n\t\n\t\n\t//==============================================================================\n\t/** @class Read only view for DatasetCollectionElement.\n\t */\n\tvar DCEListItemView = ListItemView.extend(\n\t/** @lends DCEListItemView.prototype */{\n\t//TODO: this might be expendable - compacted with HDAListItemView\n\t\n\t /** logger used to record this.log messages, commonly set to console */\n\t //logger : console,\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 ){ this.logger = this.model.logger = attributes.logger; }\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\tDCEListItemView.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([\n\t '',\n\t '<%- collection.element_identifier || collection.name %>',\n\t '',\n\t '',\n\t '',\n\t ''\n\t ], 'element' );\n\t\n\t return _.extend( {}, ListItemView.prototype.templates, {\n\t titleBar : titleBarTemplate\n\t });\n\t}());\n\t\n\t\n\t//==============================================================================\n\t/** @class Read only view for a DatasetCollectionElement that is also an DatasetAssociation\n\t * (a dataset contained in a dataset collection).\n\t */\n\tvar DatasetDCEListItemView = DATASET_LI.DatasetListItemView.extend(\n\t/** @lends DatasetDCEListItemView.prototype */{\n\t\n\t className : DATASET_LI.DatasetListItemView.prototype.className + \" dataset-collection-element\",\n\t\n\t /** logger used to record this.log messages, commonly set to console */\n\t //logger : console,\n\t\n\t /** set up */\n\t initialize : function( attributes ){\n\t if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; }\n\t this.log( 'DatasetDCEListItemView.initialize:', attributes );\n\t DATASET_LI.DatasetListItemView.prototype.initialize.call( this, attributes );\n\t },\n\t\n\t /** In this override, only get details if in the ready state.\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 // ......................................................................... misc\n\t /** String representation */\n\t toString : function(){\n\t var modelString = ( this.model )?( this.model + '' ):( '(no model)' );\n\t return 'DatasetDCEListItemView(' + modelString + ')';\n\t }\n\t});\n\t\n\t// ............................................................................ TEMPLATES\n\t/** underscore templates */\n\tDatasetDCEListItemView.prototype.templates = (function(){\n\t\n\t // use the element identifier here and not the dataset name\n\t //TODO:?? can we steal the DCE titlebar?\n\t var titleBarTemplate = BASE_MVC.wrapTemplate([\n\t '',\n\t '<%- element.element_identifier %>',\n\t '',\n\t '',\n\t '',\n\t '',\n\t ''\n\t ], 'element' );\n\t\n\t return _.extend( {}, DATASET_LI.DatasetListItemView.prototype.templates, {\n\t titleBar : titleBarTemplate\n\t });\n\t}());\n\t\n\t\n\t//==============================================================================\n\t/** @class Read only view for a DatasetCollectionElement that is also a DatasetCollection\n\t * (a nested DC).\n\t */\n\tvar NestedDCDCEListItemView = DCListItemView.extend(\n\t/** @lends NestedDCDCEListItemView.prototype */{\n\t\n\t className : DCListItemView.prototype.className + \" dataset-collection-element\",\n\t\n\t /** logger used to record this.log messages, commonly set to console */\n\t // comment this out to suppress log output\n\t //logger : console,\n\t\n\t /** In this override, add the state as a class for use with state-based CSS */\n\t _swapNewRender : function( $newRender ){\n\t DCListItemView.prototype._swapNewRender.call( this, $newRender );\n\t//TODO: model currently has no state\n\t var state = this.model.get( 'state' ) || 'ok';\n\t //if( this.model.has( 'state' ) ){\n\t this.$el.addClass( 'state-' + state );\n\t //}\n\t return this.$el;\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 'NestedDCDCEListItemView(' + modelString + ')';\n\t }\n\t});\n\t\n\t\n\t//==============================================================================\n\t return {\n\t DCListItemView : DCListItemView,\n\t DCEListItemView : DCEListItemView,\n\t DatasetDCEListItemView : DatasetDCEListItemView,\n\t NestedDCDCEListItemView : NestedDCDCEListItemView\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(1), __webpack_require__(1)))\n\n/***/ },\n/* 35 */\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 __webpack_require__(95),\n\t __webpack_require__(6),\n\t __webpack_require__(5)\n\t], __WEBPACK_AMD_DEFINE_RESULT__ = function( DATASET_MODEL, BASE_MVC, _l ){\n\t\n\tvar logNamespace = 'collections';\n\t//==============================================================================\n\t/*\n\tNotes:\n\t\n\tTerminology:\n\t DatasetCollection/DC : a container of datasets or nested DatasetCollections\n\t Element/DatasetCollectionElement/DCE : an item contained in a DatasetCollection\n\t HistoryDatasetCollectionAssociation/HDCA: a DatasetCollection contained in a history\n\t\n\t\n\tThis all seems too complex unfortunately:\n\t\n\t- Terminology collision between DatasetCollections (DCs) and Backbone Collections.\n\t- In the DatasetCollections API JSON, DC Elements use a 'Has A' stucture to *contain*\n\t either a dataset or a nested DC. This would make the hierarchy much taller. I've\n\t decided to merge the contained JSON with the DC element json - making the 'has a'\n\t relation into an 'is a' relation. This seems simpler to me and allowed a lot of\n\t DRY in both models and views, but may make tracking or tracing within these models\n\t more difficult (since DatasetCollectionElements are now *also* DatasetAssociations\n\t or DatasetCollections (nested)). This also violates the rule of thumb about\n\t favoring aggregation over inheritance.\n\t- Currently, there are three DatasetCollection subclasses: List, Pair, and ListPaired.\n\t These each should a) be usable on their own, b) be usable in the context of\n\t nesting within a collection model (at least in the case of ListPaired), and\n\t c) be usable within the context of other container models (like History or\n\t LibraryFolder, etc.). I've tried to separate/extract classes in order to\n\t handle those three situations, but it's proven difficult to do in a simple,\n\t readable manner.\n\t- Ideally, histories and libraries would inherit from the same server models as\n\t dataset collections do since they are (in essence) dataset collections themselves -\n\t making the whole nested structure simpler. This would be a large, error-prone\n\t refactoring and migration.\n\t\n\tMany of the classes and heirarchy are meant as extension points so, while the\n\trelations and flow may be difficult to understand initially, they'll allow us to\n\thandle the growth or flux dataset collection in the future (w/o actually implementing\n\tany YAGNI).\n\t\n\t*/\n\t//_________________________________________________________________________________________________ ELEMENTS\n\t/** @class mixin for Dataset collection elements.\n\t * When collection elements are passed from the API, the underlying element is\n\t * in a sub-object 'object' (IOW, a DCE representing an HDA will have HDA json in element.object).\n\t * This mixin uses the constructor and parse methods to merge that JSON with the DCE attribtues\n\t * effectively changing a DCE from a container to a subclass (has a --> is a).\n\t */\n\tvar DatasetCollectionElementMixin = {\n\t\n\t /** default attributes used by elements in a dataset collection */\n\t defaults : {\n\t model_class : 'DatasetCollectionElement',\n\t element_identifier : null,\n\t element_index : null,\n\t element_type : null\n\t },\n\t\n\t /** merge the attributes of the sub-object 'object' into this model */\n\t _mergeObject : function( attributes ){\n\t // if we don't preserve and correct ids here, the element id becomes the object id\n\t // and collision in backbone's _byId will occur and only\n\t _.extend( attributes, attributes.object, { element_id: attributes.id });\n\t delete attributes.object;\n\t return attributes;\n\t },\n\t\n\t /** override to merge this.object into this */\n\t constructor : function( attributes, options ){\n\t // console.debug( '\\t DatasetCollectionElement.constructor:', attributes, options );\n\t attributes = this._mergeObject( attributes );\n\t this.idAttribute = 'element_id';\n\t Backbone.Model.apply( this, arguments );\n\t },\n\t\n\t /** when the model is fetched, merge this.object into this */\n\t parse : function( response, options ){\n\t var attributes = response;\n\t attributes = this._mergeObject( attributes );\n\t return attributes;\n\t }\n\t};\n\t\n\t//TODO: unused?\n\t/** @class Concrete class of Generic DatasetCollectionElement */\n\tvar DatasetCollectionElement = Backbone.Model\n\t .extend( BASE_MVC.LoggableMixin )\n\t .extend( DatasetCollectionElementMixin )\n\t .extend({ _logNamespace : logNamespace });\n\t\n\t\n\t//==============================================================================\n\t/** @class Base/Abstract Backbone collection for Generic DCEs. */\n\tvar DCECollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend(\n\t/** @lends DCECollection.prototype */{\n\t _logNamespace : logNamespace,\n\t\n\t model: DatasetCollectionElement,\n\t\n\t /** logger used to record this.log messages, commonly set to console */\n\t //logger : console,\n\t\n\t//TODO: unused?\n\t /** Set up.\n\t * @see Backbone.Collection#initialize\n\t */\n\t initialize : function( attributes, options ){\n\t this.debug( this + '(DCECollection).initialize:', attributes, options );\n\t options = options || {};\n\t //this._setUpListeners();\n\t },\n\t\n\t /** String representation. */\n\t toString : function(){\n\t return ([ 'DatasetCollectionElementCollection(', this.length, ')' ].join( '' ));\n\t }\n\t});\n\t\n\t\n\t//==============================================================================\n\t/** @class Backbone model for a dataset collection element that is a dataset (HDA).\n\t */\n\tvar DatasetDCE = DATASET_MODEL.DatasetAssociation.extend( BASE_MVC.mixin( DatasetCollectionElementMixin,\n\t/** @lends DatasetDCE.prototype */{\n\t\n\t /** logger used to record this.log messages, commonly set to console */\n\t //logger : console,\n\t\n\t /** url fn */\n\t url : function(){\n\t // won't always be an hda\n\t if( !this.has( 'history_id' ) ){\n\t console.warn( 'no endpoint for non-hdas within a collection yet' );\n\t // (a little silly since this api endpoint *also* points at hdas)\n\t return Galaxy.root + 'api/datasets';\n\t }\n\t return Galaxy.root + 'api/histories/' + this.get( 'history_id' ) + '/contents/' + this.get( 'id' );\n\t },\n\t\n\t defaults : _.extend( {},\n\t DATASET_MODEL.DatasetAssociation.prototype.defaults,\n\t DatasetCollectionElementMixin.defaults\n\t ),\n\t\n\t // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n\t // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n\t // - re-apply manually for now\n\t /** call the mixin constructor */\n\t constructor : function( attributes, options ){\n\t this.debug( '\\t DatasetDCE.constructor:', attributes, options );\n\t //DATASET_MODEL.DatasetAssociation.prototype.constructor.call( this, attributes, options );\n\t DatasetCollectionElementMixin.constructor.call( this, attributes, options );\n\t },\n\t\n\t//TODO: unused?\n\t /** set up */\n\t initialize : function( attributes, options ){\n\t this.debug( this + '(DatasetDCE).initialize:', attributes, options );\n\t DATASET_MODEL.DatasetAssociation.prototype.initialize.call( this, attributes, options );\n\t },\n\t\n\t /** Does this model already contain detailed data (as opposed to just summary level data)? */\n\t hasDetails : function(){\n\t // dataset collection api does return genome_build but doesn't return annotation\n\t return _.has( this.attributes, 'annotation' );\n\t },\n\t\n\t /** String representation. */\n\t toString : function(){\n\t var objStr = this.get( 'element_identifier' );\n\t return ([ 'DatasetDCE(', objStr, ')' ].join( '' ));\n\t }\n\t}));\n\t\n\t\n\t//==============================================================================\n\t/** @class DCECollection of DatasetDCE's (a list of datasets, a pair of datasets).\n\t */\n\tvar DatasetDCECollection = DCECollection.extend(\n\t/** @lends DatasetDCECollection.prototype */{\n\t model: DatasetDCE,\n\t\n\t /** logger used to record this.log messages, commonly set to console */\n\t //logger : console,\n\t\n\t//TODO: unused?\n\t /** set up */\n\t initialize : function( attributes, options ){\n\t this.debug( this + '(DatasetDCECollection).initialize:', attributes, options );\n\t DCECollection.prototype.initialize.call( this, attributes, options );\n\t },\n\t\n\t /** String representation. */\n\t toString : function(){\n\t return ([ 'DatasetDCECollection(', this.length, ')' ].join( '' ));\n\t }\n\t});\n\t\n\t\n\t//_________________________________________________________________________________________________ COLLECTIONS\n\t/** @class Backbone model for Dataset Collections.\n\t * The DC API returns an array of JSON objects under the attribute elements.\n\t * This model:\n\t * - removes that array/attribute ('elements') from the model,\n\t * - creates a bbone collection (of the class defined in the 'collectionClass' attribute),\n\t * - passes that json onto the bbone collection\n\t * - caches the bbone collection in this.elements\n\t */\n\tvar DatasetCollection = Backbone.Model\n\t .extend( BASE_MVC.LoggableMixin )\n\t .extend( BASE_MVC.SearchableModelMixin )\n\t .extend(/** @lends DatasetCollection.prototype */{\n\t _logNamespace : logNamespace,\n\t\n\t /** logger used to record this.log messages, commonly set to console */\n\t //logger : console,\n\t\n\t /** default attributes for a model */\n\t defaults : {\n\t /* 'list', 'paired', or 'list:paired' */\n\t collection_type : null,\n\t //??\n\t deleted : false\n\t },\n\t\n\t /** Which class to use for elements */\n\t collectionClass : DCECollection,\n\t\n\t /** set up: create elements instance var and (on changes to elements) update them */\n\t initialize : function( model, options ){\n\t this.debug( this + '(DatasetCollection).initialize:', model, options, this );\n\t //historyContent.HistoryContent.prototype.initialize.call( this, attrs, options );\n\t this.elements = this._createElementsModel();\n\t this.on( 'change:elements', function(){\n\t this.log( 'change:elements' );\n\t//TODO: prob. better to update the collection instead of re-creating it\n\t this.elements = this._createElementsModel();\n\t });\n\t },\n\t\n\t /** move elements model attribute to full collection */\n\t _createElementsModel : function(){\n\t this.debug( this + '._createElementsModel', this.collectionClass, this.get( 'elements' ), this.elements );\n\t//TODO: same patterns as DatasetCollectionElement _createObjectModel - refactor to BASE_MVC.hasSubModel?\n\t var elements = this.get( 'elements' ) || [];\n\t this.unset( 'elements', { silent: true });\n\t this.elements = new this.collectionClass( elements );\n\t //this.debug( 'collectionClass:', this.collectionClass + '', this.elements );\n\t return this.elements;\n\t },\n\t\n\t // ........................................................................ common queries\n\t /** pass the elements back within the model json when this is serialized */\n\t toJSON : function(){\n\t var json = Backbone.Model.prototype.toJSON.call( this );\n\t if( this.elements ){\n\t json.elements = this.elements.toJSON();\n\t }\n\t return json;\n\t },\n\t\n\t /** Is this collection in a 'ready' state no processing (for the collection) is left\n\t * to do on the server.\n\t */\n\t inReadyState : function(){\n\t var populated = this.get( 'populated' );\n\t return ( this.isDeletedOrPurged() || populated );\n\t },\n\t\n\t //TODO:?? the following are the same interface as DatasetAssociation - can we combine?\n\t /** Does the DC contain any elements yet? Is a fetch() required? */\n\t hasDetails : function(){\n\t//TODO: this is incorrect for (accidentally) empty collections\n\t this.debug( 'hasDetails:', this.elements.length );\n\t return this.elements.length !== 0;\n\t },\n\t\n\t /** Given the filters, what models in this.elements would be returned? */\n\t getVisibleContents : function( filters ){\n\t // filters unused for now\n\t return this.elements;\n\t },\n\t\n\t // ........................................................................ ajax\n\t /** save this dataset, _Mark_ing it as deleted (just a flag) */\n\t 'delete' : function( options ){\n\t if( this.get( 'deleted' ) ){ return jQuery.when(); }\n\t return this.save( { deleted: true }, options );\n\t },\n\t /** save this dataset, _Mark_ing it as undeleted */\n\t undelete : function( options ){\n\t if( !this.get( 'deleted' ) || this.get( 'purged' ) ){ return jQuery.when(); }\n\t return this.save( { deleted: false }, options );\n\t },\n\t\n\t /** Is this collection deleted or purged? */\n\t isDeletedOrPurged : function(){\n\t return ( this.get( 'deleted' ) || this.get( 'purged' ) );\n\t },\n\t\n\t // ........................................................................ searchable\n\t /** searchable attributes for collections */\n\t searchAttributes : [\n\t 'name'\n\t ],\n\t\n\t // ........................................................................ misc\n\t /** String representation */\n\t toString : function(){\n\t var idAndName = [ this.get( 'id' ), this.get( 'name' ) || this.get( 'element_identifier' ) ];\n\t return 'DatasetCollection(' + ( idAndName.join(',') ) + ')';\n\t }\n\t});\n\t\n\t\n\t//==============================================================================\n\t/** Model for a DatasetCollection containing datasets (non-nested).\n\t */\n\tvar ListDatasetCollection = DatasetCollection.extend(\n\t/** @lends ListDatasetCollection.prototype */{\n\t\n\t /** logger used to record this.log messages, commonly set to console */\n\t //logger : console,\n\t\n\t /** override since we know the collection will only contain datasets */\n\t collectionClass : DatasetDCECollection,\n\t\n\t//TODO: unused?\n\t initialize : function( attrs, options ){\n\t this.debug( this + '(ListDatasetCollection).initialize:', attrs, options );\n\t DatasetCollection.prototype.initialize.call( this, attrs, options );\n\t },\n\t\n\t /** String representation. */\n\t toString : function(){\n\t return ([ 'ListDatasetCollection(', this.get( 'name' ), ')' ].join( '' ));\n\t }\n\t});\n\t\n\t\n\t//==============================================================================\n\t/** Model for a DatasetCollection containing fwd/rev datasets (a list of 2).\n\t */\n\tvar PairDatasetCollection = ListDatasetCollection.extend(\n\t/** @lends PairDatasetCollection.prototype */{\n\t\n\t /** logger used to record this.log messages, commonly set to console */\n\t //logger : console,\n\t\n\t//TODO: unused?\n\t /** */\n\t initialize : function( attrs, options ){\n\t this.debug( this + '(PairDatasetCollection).initialize:', attrs, options );\n\t ListDatasetCollection.prototype.initialize.call( this, attrs, options );\n\t },\n\t\n\t /** String representation. */\n\t toString : function(){\n\t return ([ 'PairDatasetCollection(', this.get( 'name' ), ')' ].join( '' ));\n\t }\n\t});\n\t\n\t\n\t//_________________________________________________________________________________________________ NESTED COLLECTIONS\n\t// this is where things get weird, man. Weird.\n\t//TODO: it might be possible to compact all the following...I think.\n\t//==============================================================================\n\t/** @class Backbone model for a Generic DatasetCollectionElement that is also a DatasetCollection\n\t * (a nested collection). Currently only list:paired.\n\t */\n\tvar NestedDCDCE = DatasetCollection.extend( BASE_MVC.mixin( DatasetCollectionElementMixin,\n\t/** @lends NestedDCDCE.prototype */{\n\t\n\t /** logger used to record this.log messages, commonly set to console */\n\t //logger : console,\n\t\n\t // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n\t // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n\t // - re-apply manually it now\n\t /** call the mixin constructor */\n\t constructor : function( attributes, options ){\n\t this.debug( '\\t NestedDCDCE.constructor:', attributes, options );\n\t DatasetCollectionElementMixin.constructor.call( this, attributes, options );\n\t },\n\t\n\t /** String representation. */\n\t toString : function(){\n\t var objStr = ( this.object )?( '' + this.object ):( this.get( 'element_identifier' ) );\n\t return ([ 'NestedDCDCE(', objStr, ')' ].join( '' ));\n\t }\n\t}));\n\t\n\t\n\t//==============================================================================\n\t/** @class Backbone collection containing Generic NestedDCDCE's (nested dataset collections).\n\t */\n\tvar NestedDCDCECollection = DCECollection.extend(\n\t/** @lends NestedDCDCECollection.prototype */{\n\t\n\t /** logger used to record this.log messages, commonly set to console */\n\t //logger : console,\n\t\n\t /** This is a collection of nested collections */\n\t model: NestedDCDCE,\n\t\n\t//TODO: unused?\n\t /** set up */\n\t initialize : function( attrs, options ){\n\t this.debug( this + '(NestedDCDCECollection).initialize:', attrs, options );\n\t DCECollection.prototype.initialize.call( this, attrs, options );\n\t },\n\t\n\t /** String representation. */\n\t toString : function(){\n\t return ([ 'NestedDCDCECollection(', this.length, ')' ].join( '' ));\n\t }\n\t});\n\t\n\t\n\t//==============================================================================\n\t/** @class Backbone model for a paired dataset collection within a list:paired dataset collection.\n\t */\n\tvar NestedPairDCDCE = PairDatasetCollection.extend( BASE_MVC.mixin( DatasetCollectionElementMixin,\n\t/** @lends NestedPairDCDCE.prototype */{\n\t//TODO:?? possibly rename to NestedDatasetCollection?\n\t\n\t /** logger used to record this.log messages, commonly set to console */\n\t //logger : console,\n\t\n\t // because all objects have constructors (as this hashmap would even if this next line wasn't present)\n\t // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model\n\t // - re-apply manually it now\n\t /** This is both a collection and a collection element - call the constructor */\n\t constructor : function( attributes, options ){\n\t this.debug( '\\t NestedPairDCDCE.constructor:', attributes, options );\n\t //DatasetCollection.constructor.call( this, attributes, options );\n\t DatasetCollectionElementMixin.constructor.call( this, attributes, options );\n\t },\n\t\n\t /** String representation. */\n\t toString : function(){\n\t var objStr = ( this.object )?( '' + this.object ):( this.get( 'element_identifier' ) );\n\t return ([ 'NestedPairDCDCE(', objStr, ')' ].join( '' ));\n\t }\n\t}));\n\t\n\t\n\t//==============================================================================\n\t/** @class Backbone collection for a backbone collection containing paired dataset collections.\n\t */\n\tvar NestedPairDCDCECollection = NestedDCDCECollection.extend(\n\t/** @lends PairDCDCECollection.prototype */{\n\t\n\t /** logger used to record this.log messages, commonly set to console */\n\t //logger : console,\n\t\n\t /** We know this collection is composed of only nested pair collections */\n\t model: NestedPairDCDCE,\n\t\n\t//TODO: unused?\n\t /** set up */\n\t initialize : function( attrs, options ){\n\t this.debug( this + '(NestedPairDCDCECollection).initialize:', attrs, options );\n\t NestedDCDCECollection.prototype.initialize.call( this, attrs, options );\n\t },\n\t\n\t /** String representation. */\n\t toString : function(){\n\t return ([ 'NestedPairDCDCECollection(', this.length, ')' ].join( '' ));\n\t }\n\t});\n\t\n\t\n\t//==============================================================================\n\t/** @class Backbone Model for a DatasetCollection (list) that contains DatasetCollections (pairs).\n\t */\n\tvar ListPairedDatasetCollection = DatasetCollection.extend(\n\t/** @lends ListPairedDatasetCollection.prototype */{\n\t\n\t /** logger used to record this.log messages, commonly set to console */\n\t //logger : console,\n\t\n\t /** list:paired is the only collection that itself contains collections */\n\t collectionClass : NestedPairDCDCECollection,\n\t\n\t//TODO: unused?\n\t /** set up */\n\t initialize : function( attributes, options ){\n\t this.debug( this + '(ListPairedDatasetCollection).initialize:', attributes, options );\n\t DatasetCollection.prototype.initialize.call( this, attributes, options );\n\t },\n\t\n\t /** String representation. */\n\t toString : function(){\n\t return ([ 'ListPairedDatasetCollection(', this.get( 'name' ), ')' ].join( '' ));\n\t }\n\t});\n\t\n\t\n\t//==============================================================================\n\t return {\n\t ListDatasetCollection : ListDatasetCollection,\n\t PairDatasetCollection : PairDatasetCollection,\n\t ListPairedDatasetCollection : ListPairedDatasetCollection\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3), __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 36 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $, jQuery) {\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [\n\t __webpack_require__(45),\n\t __webpack_require__(15),\n\t __webpack_require__(6),\n\t __webpack_require__(10),\n\t __webpack_require__(110),\n\t __webpack_require__(5),\n\t __webpack_require__(107)\n\t], __WEBPACK_AMD_DEFINE_RESULT__ = function( HDCA, STATES, BASE_MVC, UI_MODAL, naturalSort, _l ){\n\t\n\tvar logNamespace = 'collections';\n\t/*==============================================================================\n\tTODO:\n\t use proper Element model and not just json\n\t straighten out createFn, collection.createHDCA\n\t possibly stop using modals for this\n\t It would be neat to do a drag and drop\n\t\n\t==============================================================================*/\n\t/** A view for both DatasetDCEs and NestedDCDCEs\n\t * (things that implement collection-model:DatasetCollectionElementMixin)\n\t */\n\tvar DatasetCollectionElementView = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({\n\t _logNamespace : logNamespace,\n\t\n\t//TODO: use proper class (DatasetDCE or NestedDCDCE (or the union of both))\n\t tagName : 'li',\n\t className : 'collection-element',\n\t\n\t initialize : function( attributes ){\n\t this.element = attributes.element || {};\n\t this.selected = attributes.selected || false;\n\t },\n\t\n\t render : function(){\n\t this.$el\n\t .attr( 'data-element-id', this.element.id )\n\t .attr( 'draggable', true )\n\t .html( this.template({ element: this.element }) );\n\t if( this.selected ){\n\t this.$el.addClass( 'selected' );\n\t }\n\t return this;\n\t },\n\t\n\t //TODO: lots of unused space in the element - possibly load details and display them horiz.\n\t template : _.template([\n\t '',\n\t '<%- element.name %>',\n\t '',\n\t '',\n\t ].join('')),\n\t\n\t /** select this element and pub */\n\t select : function( toggle ){\n\t this.$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(',\n\t _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 ){ ev = ev.originalEvent; }\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// ============================================================================\n\t/** An interface for building collections.\n\t */\n\tvar ListCollectionCreator = Backbone.View.extend( BASE_MVC.LoggableMixin ).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(){ throw new TypeError( 'no creation fn for creator' ); },\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 /** 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._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 if( element.state !== STATES.OK ){\n\t if( _.contains( STATES.NOT_READY_STATES, element.state ) ){\n\t return _l( \"hasn't finished running yet\" );\n\t }\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\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() )\n\t .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 /** render the footer, completion controls, and cancel controls */\n\t _renderFooter : function( speed, callback ){\n\t var $footer = this.$( '.footer' ).empty().html( this.templates.footer() );\n\t if( typeof this.oncancel === 'function' ){\n\t this.$( '.cancel-create.btn' ).show();\n\t }\n\t return $footer;\n\t },\n\t\n\t /** add any jQuery/bootstrap/custom plugins to elements rendered */\n\t _addPluginComponents : function(){\n\t this.$( '.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 /** add (or clear if clear is truthy) a validation warning to the DOM element described in what */\n\t _validationWarning : function( what, clear ){\n\t var VALIDATION_CLASS = 'validation-warning';\n\t if( what === 'name' ){\n\t what = this.$( '.collection-name' ).add( this.$( '.collection-name-prompt' ) );\n\t this.$( '.collection-name' ).focus().select();\n\t }\n\t if( clear ){\n\t what = what || this.$( '.' + VALIDATION_CLASS );\n\t what.removeClass( VALIDATION_CLASS );\n\t } else {\n\t what.addClass( VALIDATION_CLASS );\n\t }\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 )\n\t .always( function(){\n\t creator.blocking = false;\n\t })\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 })\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.' ) +\n\t _l( ' Try again in a few minutes.' );\n\t } else if( xhr.responseJSON ){\n\t content += ':',\n\t '<%- element.element_identifier %>',\n\t '',\n\t '' + 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 'click .cancel-create' : function( ev ){\n\t if( typeof this.oncancel === 'function' ){\n\t this.oncancel.call( this );\n\t }\n\t },\n\t 'click .create-collection' : '_clickCreate'//,\n\t },\n\t\n\t // ........................................................................ header\n\t /** expand help */\n\t _clickMoreHelp : function( ev ){\n\t ev.stopPropagation();\n\t this.$( '.main-help' ).addClass( 'expanded' );\n\t this.$( '.more-help' ).hide();\n\t },\n\t /** collapse help */\n\t _clickLessHelp : function( ev ){\n\t ev.stopPropagation();\n\t this.$( '.main-help' ).removeClass( 'expanded' );\n\t this.$( '.more-help' ).show();\n\t },\n\t /** toggle help */\n\t _toggleHelp : function( ev ){\n\t ev.stopPropagation();\n\t this.$( '.main-help' ).toggleClass( 'expanded' );\n\t this.$( '.more-help' ).toggle();\n\t },\n\t\n\t /** show an alert on the top of the interface containing message (alertClass is bootstrap's alert-*) */\n\t _showAlert : function( message, alertClass ){\n\t alertClass = alertClass || 'alert-danger';\n\t this.$( '.main-help' ).hide();\n\t this.$( '.header .alert' )\n\t .attr( 'class', 'alert alert-dismissable' ).addClass( alertClass ).show()\n\t .find( '.alert-message' ).html( message );\n\t },\n\t /** hide the alerts at the top */\n\t _hideAlert : function( message ){\n\t this.$( '.main-help' ).show();\n\t this.$( '.header .alert' ).hide();\n\t },\n\t\n\t // ........................................................................ elements\n\t /** reset all data to the initial state */\n\t reset : function(){\n\t this._instanceSetUp();\n\t this._elementsSetUp();\n\t this.render();\n\t },\n\t\n\t /** deselect all elements */\n\t clearSelectedElements : function( ev ){\n\t this.$( '.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.size() ){\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',\n\t '', _l( 'More help' ), '',\n\t '',\n\t '',\n\t '', _l( 'Less' ), '',\n\t '',\n\t '',\n\t '',\n\t '',\n\t '',\n\t ].join('')),\n\t\n\t /** the middle: element list */\n\t middle : _.template([\n\t '',\n\t '',\n\t _l( 'Start over' ),\n\t '',\n\t '',\n\t _l( 'Clear selected' ),\n\t '',\n\t '',\n\t '',\n\t ''\n\t ].join('')),\n\t\n\t /** creation and cancel controls */\n\t footer : _.template([\n\t '',\n\t '',\n\t\n\t '',\n\t '',\n\t '',\n\t '', _l( 'Name' ), ':',\n\t '',\n\t ''\n\t ].join('')),\n\t\n\t /** help content */\n\t helpContent : _.template([\n\t '',\n\t '',\n\t '',\n\t\n\t '',\n\t '',\n\t '',\n\t '- ',\n\t '
- ', _l( 'Create a single pair' ), ' ',\n\t '
- ', _l( 'Create a list of unpaired datasets' ), ' ',\n\t '
',\n\t '',\n\t '',\n\t '', _l([\n\t 'Collections of datasets are permanent, ordered lists of datasets that can be passed to tools and ',\n\t 'workflows in order to have analyses done on each member of the entire group. This interface allows ',\n\t 'you to create a collection and re-order the final collection.'\n\t ].join( '' )), '
',\n\t '- ',\n\t '
- ', _l([\n\t 'Rename elements in the list by clicking on ',\n\t 'the existing name.'\n\t ].join( '' )), ' ',\n\t '
- ', _l([\n\t 'Discard elements from the final created list by clicking on the ',\n\t '\"Discard\" button.'\n\t ].join( '' )), ' ',\n\t '
- ', _l([\n\t 'Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ',\n\t 'them and you can then move those selected by dragging the ',\n\t 'entire group. Deselect them by clicking them again or by clicking the ',\n\t 'the \"Clear selected\" link.'\n\t ].join( '' )), ' ',\n\t '
- ', _l([\n\t 'Click the \"Start over\" link to begin again as if you had just opened ',\n\t 'the interface.'\n\t ].join( '' )), ' ',\n\t '
- ', _l([\n\t 'Click the \"Cancel\" button to exit the interface.'\n\t ].join( '' )), ' ',\n\t '
',\n\t '', _l([\n\t 'Once your collection is complete, enter a name and ',\n\t 'click \"Create list\".'\n\t ].join( '' )), '
'\n\t ].join('')),\n\t\n\t /** shown in list when all elements are discarded */\n\t invalidElements : _.template([\n\t _l( 'The following selections could not be included due to problems:' ),\n\t '- <% _.each( problems, function( problem ){ %>',\n\t '
- <%- problem.element.name %>: <%- problem.text %> ',\n\t '<% }); %>
- ',\n\t _l( 'No elements left! ' ),\n\t _l( 'Would you like to ' ), '', _l( 'start over' ), '?',\n\t '
'\n\t ].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([\n\t '',\n\t '',\n\t '',\n\t '',\n\t '<% if( _.size( problems ) ){ %>',\n\t _l( 'The following selections could not be included due to problems' ), ':',\n\t '',\n\t '- <% _.each( problems, function( problem ){ %>',\n\t '
- <%- problem.element.name %>: <%- problem.text %> ',\n\t '<% }); %>
',\n\t _l( 'At least one element is needed for the collection' ), '. ',\n\t _l( 'You may need to ' ),\n\t '', _l( 'cancel' ), ' ',\n\t _l( 'and reselect new elements' ), '.',\n\t '',\n\t '',\n\t ''\n\t ].join('')),\n\t },\n\t\n\t // ------------------------------------------------------------------------ misc\n\t /** string rep */\n\t toString : function(){ return 'ListCollectionCreator'; }\n\t});\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\tvar 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\tvar 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//==============================================================================\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\tfunction createListCollection( contents ){\n\t var elements = contents.toJSON(),\n\t promise = listCollectionCreatorModal( elements, {\n\t creationFn : function( elements, name ){\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 );\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\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(3), __webpack_require__(1), __webpack_require__(1)))\n\n/***/ },\n/* 37 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(jQuery, Backbone, $, _) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [\n\t __webpack_require__(48),\n\t __webpack_require__(15),\n\t __webpack_require__(26),\n\t __webpack_require__(6),\n\t __webpack_require__(5)\n\t], __WEBPACK_AMD_DEFINE_RESULT__ = function( LIST_ITEM, STATES, faIconButton, BASE_MVC, _l ){\n\t/* global Backbone */\n\t\n\tvar logNamespace = 'dataset';\n\t/*==============================================================================\n\tTODO:\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\tvar _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\tvar 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 ){ this.logger = this.model.logger = attributes.logger; }\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\n\t // re-rendering on any model changes\n\t this.model.on( 'change', function( model, options ){\n\t // if the model moved into the ready state and is expanded without details, fetch those details now\n\t if( this.model.changedAttributes().state && this.model.inReadyState()\n\t && this.expanded && !this.model.hasDetails() ){\n\t // will render automatically (due to fetch -> change)\n\t this.model.fetch();\n\t\n\t } else {\n\t this.render();\n\t }\n\t }, this );\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 ){ callback.call( view ); }\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 /** Render this HDA, set up ui.\n\t * @param {Number or String} speed jq fx speed\n\t * @returns {Object} this\n\t */\n\t render : function( speed ){\n\t //HACK: hover exit doesn't seem to be called on prev. tooltips when RE-rendering - so: no tooltip hide\n\t // handle that here by removing previous view's tooltips\n\t //this.$el.find(\"[title]\").tooltip( \"destroy\" );\n\t return _super.prototype.render.call( this, speed );\n\t },\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//TODO:?? too complex - possibly move into template\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 )\n\t || ( state === STATES.DISCARDED )\n\t || ( !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\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() )\n\t .prepend( this._renderDetailMessages() );\n\t $details.find( '.display-applications' ).html( this._renderDisplayApplications() );\n\t\n\t//TODO: double tap\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() ){ return ''; }\n\t // render both old and new display apps using the same template\n\t return [\n\t this.templates.displayApplications( this.model.get( 'display_apps' ), this ),\n\t this.templates.displayApplications( this.model.get( 'display_types' ), this )\n\t ].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 });\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//TODO: to (its own) template fn\n\t // don't show anything if the data's been purged\n\t if( this.model.get( 'purged' ) || !this.model.hasData() ){ return null; }\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 $([\n\t '',\n\t '',\n\t ''\n\t ].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 $([\n\t '',\n\t '',\n\t '',\n\t '',\n\t // _l( 'Create a different kind of collection' ),\n\t '',\n\t '',\n\t '',\n\t '',\n\t '',\n\t ''\n\t ].join( '\\n' ));\n\t },\n\t\n\t // ......................................................................... misc\n\t events : _.extend( _.clone( _super.prototype.events ), {\n\t 'click .display-btn' : function( ev ){ this.trigger( 'display', this, ev ); },\n\t 'click .params-btn' : function( ev ){ this.trigger( 'params', this, ev ); },\n\t 'click .download-btn' : function( ev ){ this.trigger( 'download', this, ev ); }\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\tDatasetListItemView.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\" ){ %>',\n\t '- ',\n\t '
- ', _l( 'Download dataset' ), ' ',\n\t _.map( this.model.get( 'meta_files' ), function( meta_file ){\n\t return [\n\t '
- ',\n\t _l( 'Download' ), ' ', meta_file.file_type,\n\t ' '\n\t ].join( '' );\n\t }).join( '\\n' ),\n\t '
',\n\t _l( 'An error occurred setting the metadata for this dataset' ),\n\t '',\n\t '<% } %>'\n\t ]),\n\t error : BASE_MVC.wrapTemplate([\n\t // error during index fetch - show error on dataset\n\t '<% if( model.error ){ %>',\n\t '',\n\t _l( 'There was an error getting the data for this dataset' ), ': <%- model.error %>',\n\t '',\n\t '<% } %>'\n\t ]),\n\t purged : BASE_MVC.wrapTemplate([\n\t '<% if( model.purged ){ %>',\n\t '',\n\t _l( 'This dataset has been deleted and removed from disk' ),\n\t '',\n\t '<% } %>'\n\t ]),\n\t deleted : BASE_MVC.wrapTemplate([\n\t // deleted not purged\n\t '<% if( model.deleted && !model.purged ){ %>',\n\t '',\n\t _l( 'This dataset has been deleted' ),\n\t '',\n\t '<% } %>'\n\t ])\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 '',\n\t\n\t ''\n\t ], 'dataset' );\n\t\n\t var noAccessTemplate = BASE_MVC.wrapTemplate([\n\t '',\n\t '',\n\t '',\n\t '',\n\t\n\t // do not display tags, annotation, display apps, or peek when deleted\n\t '<% if( !dataset.deleted && !dataset.purged ){ %>',\n\t '',\n\t '',\n\t\n\t '',\n\t\n\t '<% if( dataset.peek ){ %>',\n\t '<%= dataset.peek %>
',\n\t '<% } %>',\n\t '<% } %>',\n\t '',\n\t ''\n\t ], 'dataset' );\n\t\n\t//TODO: still toooooooooooooo complex - rework\n\t var summaryTemplates = {};\n\t summaryTemplates[ STATES.OK ] = summaryTemplates[ STATES.FAILED_METADATA ] = BASE_MVC.wrapTemplate([\n\t '<% if( dataset.misc_blurb ){ %>',\n\t '',\n\t _l( 'You do not have permission to view this dataset' ),\n\t '',\n\t '',\n\t '<%- dataset.misc_blurb %>',\n\t '',\n\t '<% } %>',\n\t\n\t '<% if( dataset.file_ext ){ %>',\n\t '',\n\t '',\n\t '<%- dataset.file_ext %>',\n\t '',\n\t '<% } %>',\n\t\n\t '<% if( dataset.metadata_dbkey ){ %>',\n\t '',\n\t '',\n\t '',\n\t '<%- dataset.metadata_dbkey %>',\n\t '',\n\t '',\n\t '<% } %>',\n\t\n\t '<% if( dataset.misc_info ){ %>',\n\t '',\n\t '<%- dataset.misc_info %>',\n\t '',\n\t '<% } %>'\n\t ], 'dataset' );\n\t summaryTemplates[ STATES.NEW ] = BASE_MVC.wrapTemplate([\n\t '', _l( 'This is a new dataset and not all of its data are available yet' ), ''\n\t ], 'dataset' );\n\t summaryTemplates[ STATES.NOT_VIEWABLE ] = BASE_MVC.wrapTemplate([\n\t '', _l( 'You do not have permission to view this dataset' ), ''\n\t ], 'dataset' );\n\t summaryTemplates[ STATES.DISCARDED ] = BASE_MVC.wrapTemplate([\n\t '', _l( 'The job creating this dataset was cancelled before completion' ), ''\n\t ], 'dataset' );\n\t summaryTemplates[ STATES.QUEUED ] = BASE_MVC.wrapTemplate([\n\t '', _l( 'This job is waiting to run' ), ''\n\t ], 'dataset' );\n\t summaryTemplates[ STATES.RUNNING ] = BASE_MVC.wrapTemplate([\n\t '', _l( 'This job is currently running' ), ''\n\t ], 'dataset' );\n\t summaryTemplates[ STATES.UPLOAD ] = BASE_MVC.wrapTemplate([\n\t '', _l( 'This dataset is currently uploading' ), ''\n\t ], 'dataset' );\n\t summaryTemplates[ STATES.SETTING_METADATA ] = BASE_MVC.wrapTemplate([\n\t '', _l( 'Metadata is being auto-detected' ), ''\n\t ], 'dataset' );\n\t summaryTemplates[ STATES.PAUSED ] = BASE_MVC.wrapTemplate([\n\t '', _l( 'This job is paused. Use the \"Resume Paused Jobs\" in the history menu to resume' ), ''\n\t ], 'dataset' );\n\t summaryTemplates[ STATES.ERROR ] = BASE_MVC.wrapTemplate([\n\t '<% if( !dataset.purged ){ %>',\n\t '<%- dataset.misc_blurb %>',\n\t '<% } %>',\n\t '', _l( 'An error occurred with this dataset' ), ':',\n\t '<%- dataset.misc_info %>'\n\t ], 'dataset' );\n\t summaryTemplates[ STATES.EMPTY ] = BASE_MVC.wrapTemplate([\n\t '', _l( 'No data' ), ': <%- dataset.misc_blurb %>'\n\t ], 'dataset' );\n\t summaryTemplates.unknown = BASE_MVC.wrapTemplate([\n\t 'Error: unknown dataset state: \"<%- dataset.state %>\"'\n\t ], '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 ){ %>',\n\t '',\n\t _l( 'The job creating this dataset has been resubmitted' ),\n\t '',\n\t '<% } %>'\n\t ])\n\t };\n\t\n\t // this is applied to both old and new style display apps\n\t var displayApplicationsTemplate = BASE_MVC.wrapTemplate([\n\t '<% _.each( apps, function( app ){ %>',\n\t '',\n\t '<%- app.label %> ',\n\t '',\n\t '<% _.each( app.links, function( link ){ %>',\n\t '\" href=\"<%- link.href %>\">',\n\t '<% print( _l( link.text ) ); %>',\n\t ' ',\n\t '<% }); %>',\n\t '',\n\t '',\n\t '<% }); %>'\n\t ], 'apps' );\n\t\n\t return _.extend( {}, _super.prototype.templates, {\n\t warnings : warnings,\n\t details : detailsTemplate,\n\t noAccess : noAccessTemplate,\n\t summaries : summaryTemplates,\n\t detailMessages : detailMessageTemplates,\n\t displayApplications : displayApplicationsTemplate\n\t });\n\t}());\n\t\n\t\n\t// ============================================================================\n\t return {\n\t DatasetListItemView : DatasetListItemView\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1), __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 38 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/*\n\t This class maps the form dom to an api compatible javascript dictionary.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [ __webpack_require__(4) ], __WEBPACK_AMD_DEFINE_RESULT__ = function( Utils ) {\n\t var Manager = Backbone.Model.extend({\n\t initialize: function( app ) {\n\t this.app = app;\n\t },\n\t\n\t /** Creates a checksum.\n\t */\n\t checksum: function() {\n\t var sum = '';\n\t var self = this;\n\t this.app.section.$el.find( '.section-row' ).each( function() {\n\t var id = $(this).attr( 'id' );\n\t var field = self.app.field_list[ id ];\n\t if ( field ) {\n\t sum += id + ':' + JSON.stringify( field.value && field.value() ) + ':' + field.collapsed + ';';\n\t }\n\t });\n\t return sum;\n\t },\n\t\n\t /** Convert dom into a dictionary of flat id/value pairs used e.g. on job submission.\n\t */\n\t create: function() {\n\t var self = this;\n\t\n\t // get raw dictionary from dom\n\t var dict = {};\n\t this._iterate( this.app.section.$el, dict );\n\t\n\t // add to result dictionary\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 };\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 ) { return a - b; });\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 return matchIds( model.inputs, this.flat_dict, callback );\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 /** Match context\n\t * @param{dict} inputs - Dictionary of input elements\n\t * @param{dict} key - Reference key which is matched to an input name e.g. data_ref\n\t * @param{dict} callback - Called with matched context i.e. callback( input, referenced_input )\n\t */\n\t var matchContext = function( inputs, key, callback, context ) {\n\t context = $.extend( true, {}, context );\n\t _.each( inputs, function ( input ) {\n\t input && input.type && ( context[ input.name ] = input );\n\t });\n\t _.each( inputs, function ( input ) {\n\t if ( _.isObject( input ) ) {\n\t if ( input.type && context[ input[ key ] ] ) {\n\t callback ( input, context[ input[ key ] ] );\n\t } else {\n\t matchContext( input, key, callback, context );\n\t }\n\t }\n\t });\n\t };\n\t\n\t /** Matches a tool model to a dictionary, indexed with flat ids\n\t * @param{dict} inputs - Dictionary of input elements\n\t * @param{dict} mapping - Dictionary containing flat ids\n\t * @param{dict} callback - Called with the mapped dictionary object and corresponding model node\n\t */\n\t var matchIds = function( inputs, mapping, callback ) {\n\t var result = {};\n\t var self = this;\n\t function search ( id, head ) {\n\t for ( var i in head ) {\n\t var node = head[ i ];\n\t var index = node.name;\n\t id != '' && ( index = id + '|' + index );\n\t switch ( node.type ) {\n\t case 'repeat':\n\t for ( var j in node.cache ) {\n\t search ( index + '_' + j, node.cache[ j ] );\n\t }\n\t break;\n\t case 'conditional':\n\t var selectedCase = matchCase( node, node.test_param && node.test_param.value );\n\t selectedCase != -1 && search ( index, node.cases[ selectedCase ].inputs );\n\t break;\n\t case 'section':\n\t search ( index, node.inputs );\n\t break;\n\t default:\n\t var mapped = mapping[ index ];\n\t mapped && callback( mapped, node );\n\t }\n\t }\n\t }\n\t search( '', inputs );\n\t return result;\n\t };\n\t\n\t return {\n\t Manager : Manager,\n\t matchIds : matchIds,\n\t matchContext : matchContext\n\t }\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 39 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone) {/**\n\t This class creates a form input element wrapper\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [], __WEBPACK_AMD_DEFINE_RESULT__ = function() {\n\t return Backbone.View.extend({\n\t initialize: function(app, options) {\n\t this.app = app;\n\t this.field = options.field;\n\t\n\t // set text labels and icons for collapsible button\n\t this.text_enable = app.options.text_enable || 'Enable';\n\t this.text_disable = app.options.text_disable || 'Disable';\n\t this.cls_enable = app.options.cls_enable || 'fa fa-caret-square-o-down';\n\t this.cls_disable = app.options.cls_disable || 'fa fa-caret-square-o-up';\n\t\n\t // set element\n\t this.setElement(this._template(options));\n\t\n\t // link elements\n\t this.$field = this.$('.ui-form-field');\n\t this.$preview = this.$('.ui-form-preview');\n\t this.$collapsible = this.$('.ui-form-collapsible');\n\t this.$collapsible_icon = this.$('.ui-form-collapsible').find('.icon');\n\t this.$error_text = this.$('.ui-form-error-text');\n\t this.$error = this.$('.ui-form-error');\n\t this.$backdrop = this.$('.ui-form-backdrop');\n\t\n\t // add field element\n\t this.$field.prepend(this.field.$el);\n\t\n\t // decide wether to expand or collapse fields\n\t this.field.collapsed = options.collapsible_value !== undefined && JSON.stringify( options.value ) == JSON.stringify( options.collapsible_value );\n\t\n\t // refresh view\n\t this._refresh();\n\t\n\t // add collapsible hide/show\n\t var self = this;\n\t this.$collapsible.on('click', function() {\n\t self.field.collapsed = !self.field.collapsed;\n\t self._refresh();\n\t });\n\t },\n\t\n\t /** Disable input element\n\t */\n\t disable: function( silent ) {\n\t this.$backdrop.show();\n\t silent && this.$backdrop.css({ 'opacity': 0, 'cursor': 'default' } );\n\t },\n\t\n\t /** Set error text\n\t */\n\t error: function(text) {\n\t this.$error_text.html(text);\n\t this.$error.show();\n\t this.$el.addClass('ui-error');\n\t },\n\t\n\t /** Reset this view\n\t */\n\t reset: function() {\n\t this.$error.hide();\n\t this.$el.removeClass('ui-error');\n\t },\n\t\n\t /** Refresh element\n\t */\n\t _refresh: function() {\n\t this.$collapsible_icon.removeClass().addClass('icon');\n\t if (!this.field.collapsed) {\n\t this.$field.fadeIn('fast');\n\t this.$preview.hide();\n\t this._tooltip(this.text_disable, this.cls_disable);\n\t } else {\n\t this.$field.hide();\n\t this.$preview.show();\n\t this._tooltip(this.text_enable, this.cls_enable);\n\t }\n\t this.app.trigger('change');\n\t },\n\t\n\t /** Set tooltip text\n\t */\n\t _tooltip: function(title, cls) {\n\t this.$collapsible_icon.addClass(cls)\n\t .tooltip({ placement: 'bottom' })\n\t .attr('data-original-title', title)\n\t .tooltip('fixTitle').tooltip('hide');\n\t },\n\t\n\t /** Main Template\n\t */\n\t _template: function(options) {\n\t var tmp = '' +\n\t '' +\n\t '' +\n\t '' +\n\t '';\n\t if ( !options.disabled && options.collapsible_value !== undefined ) {\n\t tmp += '' +\n\t '' +\n\t '' + options.label +\n\t '';\n\t } else {\n\t tmp += options.label;\n\t }\n\t tmp += '';\n\t tmp += '';\n\t return tmp;\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2)))\n\n/***/ },\n/* 40 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $) {/**\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),\n\t __webpack_require__(7),\n\t __webpack_require__(43),\n\t __webpack_require__(56),\n\t __webpack_require__(55),\n\t __webpack_require__(52)], __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 '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 },\n\t\n\t // initialize\n\t initialize: function(app, options) {\n\t this.app = app;\n\t },\n\t\n\t /** Returns an input field for a given field type\n\t */\n\t create: function(input_def) {\n\t // add regular/default value if missing\n\t if (input_def.value === undefined) {\n\t input_def.value = null;\n\t }\n\t if (input_def.default_value === undefined) {\n\t input_def.default_value = input_def.value;\n\t }\n\t\n\t // create field wrapper\n\t var field = null;\n\t var fieldClass = this.types[input_def.type];\n\t if (fieldClass && typeof(this[fieldClass]) === 'function') {\n\t field = this[fieldClass].call(this, input_def);\n\t }\n\t\n\t // match unavailable field types\n\t if (!field) {\n\t this.app.incompatible = true;\n\t if (input_def.options) {\n\t field = this._fieldSelect(input_def);\n\t } else {\n\t field = this._fieldText(input_def);\n\t }\n\t Galaxy.emit.debug('form-parameters::_addRow()', 'Auto matched field type (' + input_def.type + ').');\n\t }\n\t\n\t // set initial field value\n\t input_def.value !== undefined && ( field.value( input_def.value ) );\n\t return field;\n\t },\n\t\n\t /** Data input field\n\t */\n\t _fieldData: function(input_def) {\n\t var self = this;\n\t return new SelectContent.View(this.app, {\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 data : input_def.options,\n\t onchange : function() {\n\t self.app.trigger('change');\n\t }\n\t });\n\t },\n\t\n\t /** Select/Checkbox/Radio options field\n\t */\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 // configure options fields\n\t var options = [];\n\t for (var i in input_def.options) {\n\t var option = input_def.options[i];\n\t options.push({\n\t label: option[0],\n\t 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 }\n\t\n\t // create select field\n\t var self = this;\n\t return new SelectClass.View({\n\t id : 'field-' + input_def.id,\n\t data : options,\n\t error_text : input_def.error_text || 'No options available',\n\t optional : input_def.optional && input_def.default_value === null,\n\t multiple : input_def.multiple,\n\t optional : input_def.optional,\n\t searchable : input_def.searchable,\n\t onchange : function() {\n\t self.app.trigger('change');\n\t }\n\t });\n\t },\n\t\n\t /** Drill down options field\n\t */\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 var self = this;\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 onchange : function() {\n\t self.app.trigger('change');\n\t }\n\t });\n\t },\n\t\n\t /** Text input field\n\t */\n\t _fieldText: function(input_def) {\n\t // field replaces e.g. a select field\n\t if (input_def.options) {\n\t input_def.area = input_def.multiple;\n\t if (!Utils.validate(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\n\t // create input element\n\t var self = this;\n\t return new Ui.Input({\n\t id : 'field-' + input_def.id,\n\t area : input_def.area,\n\t onchange : function() {\n\t self.app.trigger('change');\n\t }\n\t });\n\t },\n\t\n\t /** Slider field\n\t */\n\t _fieldSlider: function(input_def) {\n\t var self = this;\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 : function() {\n\t self.app.trigger('change');\n\t }\n\t });\n\t },\n\t\n\t /** Hidden field\n\t */\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 */\n\t _fieldBoolean: function(input_def) {\n\t var self = this;\n\t return new Ui.RadioButton.View({\n\t id : 'field-' + input_def.id,\n\t data : [ { label : 'Yes', value : 'true' },\n\t { label : 'No', value : 'false' }],\n\t onchange : function() {\n\t self.app.trigger('change');\n\t }\n\t });\n\t },\n\t\n\t /** Color picker field\n\t */\n\t _fieldColor: function(input_def) {\n\t var self = this;\n\t return new ColorPicker({\n\t id : 'field-' + input_def.id,\n\t onchange : function() {\n\t self.app.trigger('change');\n\t }\n\t });\n\t },\n\t\n\t /** Library dataset field\n\t */\n\t _fieldLibrary: function(input_def) {\n\t var self = this;\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 : function() {\n\t self.app.trigger('change');\n\t }\n\t });\n\t },\n\t\n\t /** FTP file field\n\t */\n\t _fieldFtp: function(input_def) {\n\t var self = this;\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 : function() {\n\t self.app.trigger('change');\n\t }\n\t });\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 41 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(17), __webpack_require__(11), __webpack_require__(7)], __WEBPACK_AMD_DEFINE_RESULT__ = function(Utils, Table, Portlet, Ui) {\n\t\n\t/** This class creates a ui component which enables the dynamic creation of portlets\n\t*/\n\tvar View = Backbone.View.extend({\n\t /** Initialize\n\t */\n\t initialize : function(options) {\n\t this.options = Utils.merge(options, {\n\t title : 'Section',\n\t empty_text : 'Not available.',\n\t max : null,\n\t min : null\n\t });\n\t this.setElement('');\n\t var self = this;\n\t\n\t // create button\n\t this.button_new = new Ui.ButtonIcon({\n\t icon : 'fa-plus',\n\t title : 'Insert ' + options.title_new,\n\t tooltip : 'Add new ' + options.title_new + ' block',\n\t floating: 'clear',\n\t onclick : function() {\n\t if (options.onnew) {\n\t options.onnew();\n\t }\n\t }\n\t });\n\t\n\t // create table\n\t this.table = new Table.View({\n\t cls : 'ui-table-plain',\n\t content : ''\n\t });\n\t this.$el.append(this.table.$el);\n\t this.$el.append($('').append(this.button_new.$el));\n\t\n\t // reset list\n\t this.list = {};\n\t this.n = 0;\n\t },\n\t\n\t /** Number of repeat blocks\n\t */\n\t size: function() {\n\t return this.n;\n\t },\n\t\n\t /** Add new repeat block\n\t */\n\t add: function(options) {\n\t if (!options.id || this.list[options.id]) {\n\t Galaxy.emit.debug('form-repeat::add()', 'Duplicate repeat block id.');\n\t return;\n\t }\n\t this.n++;\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',\n\t onclick : function() {\n\t if (options.ondel) {\n\t options.ondel();\n\t }\n\t }\n\t });\n\t var portlet = new Portlet.View({\n\t id : options.id,\n\t title : 'placeholder',\n\t cls : 'ui-portlet-repeat',\n\t operations : {\n\t button_delete : button_delete\n\t }\n\t });\n\t portlet.append(options.$el);\n\t portlet.$el.addClass('section-row');\n\t this.list[options.id] = portlet;\n\t this.table.add(portlet.$el);\n\t this.table.append('row_' + options.id, true);\n\t if (this.options.max > 0 && this.n >= this.options.max) {\n\t this.button_new.disable();\n\t }\n\t this._refresh();\n\t },\n\t\n\t /** Delete repeat block\n\t */\n\t del: function(id) {\n\t if (!this.list[id]) {\n\t Galaxy.emit.debug('form-repeat::del()', 'Invalid repeat block id.');\n\t return;\n\t }\n\t this.n--;\n\t var table_row = this.table.get('row_' + id);\n\t table_row.remove();\n\t delete this.list[id];\n\t this.button_new.enable();\n\t this._refresh();\n\t },\n\t\n\t /** Hides add/del options\n\t */\n\t hideOptions: function() {\n\t this.button_new.$el.hide();\n\t _.each( this.list, function( portlet ) {\n\t portlet.hideOperation('button_delete');\n\t });\n\t if( _.isEmpty( this.list ) ) {\n\t this.$el.append( $('').addClass( 'ui-form-info' ).html( this.options.empty_text ) );\n\t }\n\t },\n\t\n\t /** Refresh view\n\t */\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 if (this.n > this.options.min) {\n\t portlet.showOperation('button_delete');\n\t } else {\n\t portlet.hideOperation('button_delete');\n\t }\n\t }\n\t }\n\t});\n\t\n\treturn {\n\t View : View\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\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 42 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, jQuery, _, $) {/**\n\t This class creates a form section and populates it with input elements. It also handles repeat blocks and conditionals by recursively creating new sub sections.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4),\n\t __webpack_require__(17),\n\t __webpack_require__(7),\n\t __webpack_require__(11),\n\t __webpack_require__(41),\n\t __webpack_require__(39),\n\t __webpack_require__(40)], __WEBPACK_AMD_DEFINE_RESULT__ = function(Utils, Table, Ui, Portlet, Repeat, InputElement, Parameters) {\n\t var View = Backbone.View.extend({\n\t initialize: function(app, options) {\n\t this.app = app;\n\t this.inputs = options.inputs;\n\t\n\t // fix table style\n\t options.cls = 'ui-table-plain';\n\t\n\t // add table class for tr tag\n\t // this assist in transforming the form into a json structure\n\t options.cls_tr = 'section-row';\n\t\n\t // create/render views\n\t this.table = new Table.View(options);\n\t this.parameters = new Parameters(app, options);\n\t this.setElement(this.table.$el);\n\t this.render();\n\t },\n\t\n\t /** Render section view\n\t */\n\t render: function() {\n\t this.table.delAll();\n\t for (var i in this.inputs) {\n\t this.add(this.inputs[i]);\n\t }\n\t },\n\t\n\t /** Add a new input element\n\t */\n\t add: function(input) {\n\t var self = this;\n\t var input_def = jQuery.extend(true, {}, input);\n\t input_def.id = input.id = Utils.uid();\n\t\n\t // add to sequential list of inputs\n\t this.app.input_list[input_def.id] = input_def;\n\t\n\t // identify field type\n\t var type = input_def.type;\n\t switch(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 */\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.options.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.options.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_id = input_def.id + '-section-' + i;\n\t var section_row = self.table.get(section_id);\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_id = input_def.id + '-section-' + i;\n\t var sub_section = new View(this.app, {\n\t inputs : input_def.cases[i].inputs\n\t });\n\t sub_section.$el.addClass('ui-table-section');\n\t this.table.add(sub_section.$el);\n\t this.table.append(sub_section_id);\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 */\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 title_new : input_def.title || '',\n\t min : input_def.min,\n\t max : input_def.max,\n\t onnew : function() {\n\t create(input_def.inputs);\n\t 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, {\n\t inputs : inputs\n\t });\n\t repeat.add({\n\t id : sub_section_id,\n\t $el : sub_section.$el,\n\t ondel : function() {\n\t repeat.del(sub_section_id);\n\t self.app.trigger('change');\n\t }\n\t });\n\t }\n\t\n\t //\n\t // add parsed/minimum number of repeat blocks\n\t //\n\t var n_min = input_def.min;\n\t var n_cache = _.size(input_def.cache);\n\t for (var i = 0; i < Math.max(n_cache, n_min); i++) {\n\t var inputs = null;\n\t if (i < n_cache) {\n\t inputs = input_def.cache[i];\n\t } else {\n\t inputs = input_def.inputs;\n\t }\n\t create(inputs);\n\t }\n\t\n\t // hide options\n\t this.app.options.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.table.add(input_element.$el);\n\t this.table.append(input_def.id);\n\t },\n\t\n\t /** Add a customized section\n\t */\n\t _addSection: function(input_def) {\n\t var self = this;\n\t\n\t // create sub section\n\t var sub_section = new View(self.app, {\n\t inputs : input_def.inputs\n\t });\n\t\n\t // delete button\n\t var button_visible = new Ui.ButtonIcon({\n\t icon : 'fa-eye-slash',\n\t tooltip : 'Show/hide section',\n\t cls : 'ui-button-icon-plain'\n\t });\n\t\n\t // create portlet for sub section\n\t var portlet = new Portlet.View({\n\t title : input_def.title || input_def.name,\n\t cls : 'ui-portlet-section',\n\t collapsible : true,\n\t collapsed : true,\n\t operations : {\n\t button_visible: button_visible\n\t }\n\t });\n\t portlet.append( sub_section.$el );\n\t portlet.append( $( '' ).addClass( 'ui-form-info' ).html( input_def.help ) );\n\t portlet.setOperation( 'button_visible', function() {\n\t if( portlet.collapsed ) {\n\t portlet.expand();\n\t } else {\n\t portlet.collapse();\n\t }\n\t });\n\t\n\t // add expansion event handler\n\t portlet.on( 'expanded', function() {\n\t button_visible.setIcon( 'fa-eye' );\n\t });\n\t portlet.on( 'collapsed', function() {\n\t button_visible.setIcon( 'fa-eye-slash' );\n\t });\n\t this.app.on( 'expand', function( input_id ) {\n\t ( portlet.$( '#' + input_id ).length > 0 ) && portlet.expand();\n\t });\n\t\n\t // show sub section if requested\n\t input_def.expanded && portlet.expand();\n\t\n\t // create table row\n\t this.table.add(portlet.$el);\n\t this.table.append(input_def.id);\n\t },\n\t\n\t /** Add a single input field element\n\t */\n\t _addRow: function(input_def) {\n\t var id = input_def.id;\n\t var field = this.parameters.create(input_def);\n\t this.app.field_list[id] = field;\n\t var input_element = new InputElement(this.app, {\n\t name : input_def.name,\n\t label : input_def.label || input_def.name,\n\t value : input_def.value,\n\t default_value : input_def.default_value,\n\t text_value : input_def.text_value || input_def.value,\n\t collapsible_value : input_def.collapsible_value,\n\t collapsible_preview : input_def.collapsible_preview,\n\t help : input_def.help,\n\t argument : input_def.argument,\n\t disabled : input_def.disabled,\n\t field : field\n\t });\n\t this.app.element_list[id] = input_element;\n\t this.table.add(input_element.$el);\n\t this.table.append(id);\n\t input_def.hidden && this.table.get(id).hide();\n\t return field;\n\t }\n\t });\n\t\n\t return {\n\t View: View\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ },\n/* 43 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(7), __webpack_require__(31)], __WEBPACK_AMD_DEFINE_RESULT__ = function(Utils, Ui, Tabs) {\n\t// hda/hdca content selector ui element\n\tvar View = Backbone.View.extend({\n\t // initialize\n\t initialize : function(app, options) {\n\t // link app and options\n\t this.app = app;\n\t this.options = options;\n\t\n\t // track current history elements\n\t this.history = {};\n\t\n\t\n\t // link this\n\t var self = this;\n\t\n\t // add element\n\t this.setElement('';\n\t if (options.help) {\n\t tmp += options.help;\n\t if (options.argument && options.help.indexOf('(' + options.argument + ')') == -1) {\n\t tmp += ' (' + options.argument + ')';\n\t }\n\t }\n\t tmp += '' +\n\t '' +\n\t '';\n\t if ( options.collapsible_preview ) {\n\t tmp += '' + options.text_value + '';\n\t }\n\t tmp += '');\n\t\n\t // list of select fieldsFormSection\n\t this.list = {};\n\t\n\t // radio button options\n\t var radio_buttons = [];\n\t\n\t // identify selector type\n\t if (options.type == 'data_collection') {\n\t this.mode = 'collection';\n\t } else {\n\t if (options.multiple) {\n\t this.mode = 'multiple';\n\t } else {\n\t this.mode = 'single';\n\t }\n\t }\n\t\n\t // set initial state\n\t this.current = this.mode;\n\t this.list = {};\n\t\n\t // error messages\n\t var extensions = Utils.textify(options.extensions);\n\t var hda_error = 'No dataset available.';\n\t if (extensions) {\n\t hda_error = 'No ' + extensions + ' dataset available.';\n\t }\n\t var hdca_error = 'No dataset list available.';\n\t if (extensions) {\n\t hdca_error = 'No ' + extensions + ' dataset collection available.';\n\t }\n\t\n\t // add single dataset selector\n\t if (this.mode == 'single') {\n\t radio_buttons.push({\n\t icon : 'fa-file-o',\n\t value : 'single',\n\t tooltip : 'Single dataset'\n\t });\n\t this.select_single = new Ui.Select.View({\n\t optional : options.optional,\n\t error_text : hda_error,\n\t onchange : function() {\n\t self.trigger('change');\n\t }\n\t });\n\t this.list['single'] = {\n\t field: this.select_single,\n\t type : 'hda'\n\t };\n\t }\n\t\n\t // add multiple dataset selector\n\t if (this.mode == 'single' || this.mode == 'multiple') {\n\t radio_buttons.push({\n\t icon : 'fa-files-o',\n\t value : 'multiple',\n\t tooltip : 'Multiple datasets'\n\t });\n\t this.select_multiple = new Ui.Select.View({\n\t multiple : true,\n\t searchable : false,\n\t optional : options.optional,\n\t error_text : hda_error,\n\t onchange : function() {\n\t self.trigger('change');\n\t }\n\t });\n\t this.list['multiple'] = {\n\t field: this.select_multiple,\n\t type : 'hda'\n\t };\n\t }\n\t\n\t // add collection selector\n\t if (this.mode == 'single' || this.mode == 'multiple' || this.mode == 'collection') {\n\t radio_buttons.push({\n\t icon : 'fa-folder-o',\n\t value : 'collection',\n\t tooltip : 'Dataset collection'\n\t });\n\t var multiple = this.mode == 'multiple';\n\t this.select_collection = new Ui.Select.View({\n\t error_text : hdca_error,\n\t multiple : multiple,\n\t searchable : false,\n\t optional : options.optional,\n\t onchange : function() {\n\t self.trigger('change');\n\t }\n\t });\n\t this.list['collection'] = {\n\t field: this.select_collection,\n\t type : 'hdca'\n\t };\n\t }\n\t\n\t // create button\n\t this.button_type = new Ui.RadioButton.View({\n\t value : this.current,\n\t data : radio_buttons,\n\t onchange: function(value) {\n\t self.current = value;\n\t self.refresh();\n\t self.trigger('change');\n\t }\n\t });\n\t\n\t // add batch mode information\n\t this.$batch = $(this.template_batch());\n\t\n\t // number of radio buttons\n\t var n_buttons = _.size(this.list);\n\t\n\t // add button to dom\n\t var button_width = 0;\n\t if (n_buttons > 1) {\n\t this.$el.append(this.button_type.$el);\n\t button_width = Math.max(0, _.size(this.list) * 35) + 'px';\n\t }\n\t\n\t // append field elements\n\t for (var i in this.list) {\n\t this.$el.append(this.list[i].field.$el.css({\n\t 'margin-left': button_width\n\t }));\n\t }\n\t\n\t // append batch message\n\t this.$el.append(this.$batch.css({\n\t 'margin-left': button_width\n\t }));\n\t\n\t // update options\n\t this.update(options.data);\n\t\n\t // set initial value\n\t if (this.options.value !== undefined) {\n\t this.value(this.options.value);\n\t }\n\t\n\t // refresh view\n\t this.refresh();\n\t\n\t // add change event. fires on trigger\n\t this.on('change', function() {\n\t if (options.onchange) {\n\t options.onchange(self.value());\n\t }\n\t });\n\t },\n\t\n\t /** Indicate that select fields are being updated */\n\t wait: function() {\n\t for (var i in this.list) {\n\t this.list[i].field.wait();\n\t }\n\t },\n\t\n\t /** Indicate that the options update has been completed */\n\t unwait: function() {\n\t for (var i in this.list) {\n\t this.list[i].field.unwait();\n\t }\n\t },\n\t\n\t /** Update content selector */\n\t update: function(options) {\n\t // update a particular select field\n\t var self = this;\n\t function _update(field, options) {\n\t if (field) {\n\t // identify available options\n\t var select_options = [];\n\t for (var i in options) {\n\t var item = options[i];\n\t select_options.push({\n\t label: item.hid + ': ' + item.name,\n\t value: item.id\n\t });\n\t // backup to local history\n\t self.history[item.id + '_' + item.src] = item;\n\t }\n\t // update field\n\t field.update(select_options);\n\t }\n\t }\n\t\n\t // update available options\n\t _update(this.select_single, options.hda);\n\t _update(this.select_multiple, options.hda);\n\t _update(this.select_collection, options.hdca);\n\t },\n\t\n\t /** Return the currently selected dataset values */\n\t value : function (new_value) {\n\t // update current value\n\t if (new_value !== undefined) {\n\t if (new_value && new_value.values) {\n\t try {\n\t // create list with values\n\t var list = [];\n\t for (var i in new_value.values) {\n\t list.push(new_value.values[i].id);\n\t }\n\t\n\t // identify suitable select field\n\t if (new_value && new_value.values.length > 0 && new_value.values[0].src == 'hdca') {\n\t this.current = 'collection';\n\t this.select_collection.value(list);\n\t } else {\n\t if (this.mode == 'multiple') {\n\t this.current = 'multiple';\n\t this.select_multiple.value(list);\n\t } else {\n\t this.current = 'single';\n\t this.select_single.value(list[0]);\n\t }\n\t }\n\t } catch (err) {\n\t Galaxy.emit.debug('tools-select-content::value()', 'Skipped.');\n\t }\n\t } else {\n\t for (var i in this.list) {\n\t this.list[i].field.value(null);\n\t }\n\t }\n\t }\n\t\n\t // refresh view\n\t this.refresh();\n\t\n\t // validate value\n\t var id_list = this._select().value();\n\t if (id_list === null) {\n\t return null;\n\t }\n\t\n\t // transform into an array\n\t if (!(id_list instanceof Array)) {\n\t id_list = [id_list];\n\t }\n\t\n\t // check if value exists\n\t if (id_list.length === 0) {\n\t return null;\n\t }\n\t\n\t // prepare result dict\n\t var result = {\n\t batch : this._batch(),\n\t values : []\n\t }\n\t\n\t // append to dataset ids\n\t for (var i in id_list) {\n\t var details = this.history[id_list[i] + '_' + this.list[this.current].type];\n\t if (details) {\n\t result.values.push(details);\n\t } else {\n\t return null;\n\t }\n\t }\n\t\n\t // sort by history ids\n\t result.values.sort(function(a, b){\n\t return a.hid - b.hid;\n\t });\n\t\n\t // return\n\t return result;\n\t },\n\t\n\t /** Refreshes data selection view */\n\t refresh: function() {\n\t this.button_type.value(this.current);\n\t for (var i in this.list) {\n\t var $el = this.list[i].field.$el;\n\t if (this.current == i) {\n\t $el.show();\n\t } else {\n\t $el.hide();\n\t }\n\t }\n\t if (this._batch()) {\n\t this.$batch.show();\n\t } else {\n\t this.$batch.hide();\n\t }\n\t },\n\t\n\t /** Assists in selecting the current field */\n\t _select: function() {\n\t return this.list[this.current].field;\n\t },\n\t\n\t /** Assists in identifying the batch mode */\n\t _batch: function() {\n\t if (this.current == 'collection') {\n\t var hdca = this.history[this._select().value() + '_hdca'];\n\t if (hdca && hdca.map_over_type) {\n\t return true;\n\t }\n\t }\n\t if (this.current != 'single') {\n\t if (this.mode == 'single') {\n\t return true;\n\t }\n\t }\n\t return false;\n\t },\n\t\n\t /** Batch message template */\n\t template_batch: function() {\n\t return '' +\n\t '' +\n\t 'This is a batch mode input field. A separate job will be triggered for each dataset.' +\n\t '';\n\t }\n\t});\n\t\n\treturn {\n\t View: View\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\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3)))\n\n/***/ },\n/* 44 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, _, $) {/**\n\t This is the main class of the form plugin. It is referenced as 'app' in all lower level modules.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(11), __webpack_require__(7), __webpack_require__(42), __webpack_require__(38)], __WEBPACK_AMD_DEFINE_RESULT__ = function(Utils, Portlet, Ui, FormSection, FormData) {\n\t return Backbone.View.extend({\n\t initialize: function(options) {\n\t this.options = Utils.merge(options, {\n\t initial_errors : false,\n\t cls : 'ui-portlet-limited',\n\t icon : ''\n\t });\n\t this.modal = ( parent.Galaxy && parent.Galaxy.modal ) || new Ui.Modal.View();\n\t this.setElement('');\n\t this.render();\n\t },\n\t\n\t /** Update available options */\n\t update: function(new_model){\n\t var self = this;\n\t this.data.matchModel(new_model, function(input_id, node) {\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 // backup new options\n\t input.options = node.options;\n\t\n\t // get/update field\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({\n\t 'label': opt[0],\n\t 'value': opt[1]\n\t });\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 if (active) {\n\t field.wait();\n\t } else {\n\t field.unwait();\n\t }\n\t }\n\t }\n\t },\n\t\n\t /** Highlight and scroll to input element (currently only used for error notifications)\n\t */\n\t highlight: function (input_id, message, silent) {\n\t // get input field\n\t var input_element = this.element_list[input_id];\n\t\n\t // check input element\n\t if (input_element) {\n\t // mark error\n\t input_element.error(message || 'Please verify this parameter.');\n\t\n\t // trigger expand event for parent containers\n\t this.trigger('expand', input_id);\n\t\n\t // scroll to first input element\n\t if (!silent) {\n\t if (self==top) {\n\t var $panel = this.$el.parents().filter(function() {\n\t return $(this).css('overflow') == 'auto';\n\t }).first();\n\t $panel.animate({ scrollTop : $panel.scrollTop() + input_element.$el.offset().top - 50 }, 500);\n\t } else {\n\t $('html, body').animate({ scrollTop : input_element.$el.offset().top - 20 }, 500);\n\t }\n\t }\n\t }\n\t },\n\t\n\t /** Highlights errors\n\t */\n\t errors: function(options) {\n\t // hide previous error statements\n\t this.trigger('reset');\n\t\n\t // highlight all errors\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 */\n\t render: function() {\n\t // link this\n\t var self = this;\n\t\n\t // reset events\n\t this.off('change');\n\t this.off('reset');\n\t\n\t // reset field list, which contains the input field elements\n\t this.field_list = {};\n\t\n\t // reset sequential input definition list, which contains the input definitions as provided from the api\n\t this.input_list = {};\n\t\n\t // reset input element list, which contains the dom elements of each input element (includes also the input field)\n\t this.element_list = {};\n\t\n\t // creates a json data structure from the input form\n\t this.data = new FormData.Manager(this);\n\t\n\t // create ui elements\n\t this._renderForm();\n\t\n\t // refresh data\n\t this.data.create();\n\t\n\t // show errors on startup\n\t if (this.options.initial_errors) {\n\t this.errors(this.options);\n\t }\n\t\n\t // add listener which triggers on checksum change\n\t var current_check = this.data.checksum();\n\t this.on('change', function() {\n\t var new_check = self.data.checksum();\n\t if (new_check != current_check) {\n\t current_check = new_check;\n\t self.options.onchange && self.options.onchange();\n\t }\n\t });\n\t\n\t // add reset listener\n\t this.on('reset', function() {\n\t for (var i in this.element_list) {\n\t this.element_list[i].reset();\n\t }\n\t });\n\t return this;\n\t },\n\t\n\t /** Renders the UI elements required for the form\n\t */\n\t _renderForm: function() {\n\t // create message view\n\t this.message = new Ui.Message();\n\t\n\t // create tool form section\n\t this.section = new FormSection.View(this, {\n\t inputs : this.options.inputs\n\t });\n\t\n\t // remove tooltips\n\t $( '.tooltip' ).remove();\n\t\n\t // create portlet\n\t this.portlet = new Portlet.View({\n\t icon : this.options.icon,\n\t title : this.options.title,\n\t cls : this.options.cls,\n\t operations : this.options.operations,\n\t buttons : this.options.buttons,\n\t collapsible : this.options.collapsible,\n\t collapsed : this.options.collapsed\n\t });\n\t\n\t // append message\n\t this.portlet.append(this.message.$el.addClass('ui-margin-top'));\n\t\n\t // append tool section\n\t this.portlet.append(this.section.$el);\n\t\n\t // start form\n\t this.$el.empty();\n\t this.$el.append(this.portlet.$el);\n\t\n\t // show message if available in model\n\t if (this.options.message) {\n\t this.message.update({\n\t persistent : true,\n\t status : 'warning',\n\t message : this.options.message\n\t });\n\t }\n\t\n\t // log\n\t Galaxy.emit.debug('form-view::initialize()', 'Completed');\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(3), __webpack_require__(1)))\n\n/***/ },\n/* 45 */\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__ = [\n\t __webpack_require__(35),\n\t __webpack_require__(46),\n\t __webpack_require__(5)\n\t], __WEBPACK_AMD_DEFINE_RESULT__ = function( DC_MODEL, HISTORY_CONTENT, _l ){\n\t/*==============================================================================\n\t\n\tModels for DatasetCollections contained within a history.\n\t\n\tTODO:\n\t these might be compactable to one class if some duplication with\n\t collection-model is used.\n\t\n\t==============================================================================*/\n\tvar hcontentMixin = HISTORY_CONTENT.HistoryContentMixin,\n\t ListDC = DC_MODEL.ListDatasetCollection,\n\t PairDC = DC_MODEL.PairDatasetCollection,\n\t ListPairedDC = DC_MODEL.ListPairedDatasetCollection;\n\t\n\t//==============================================================================\n\t/** Override to post to contents route w/o id. */\n\tfunction 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//==============================================================================\n\t/** @class Backbone model for List Dataset Collection within a History.\n\t */\n\tvar 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 initialize : function( model, options ){\n\t ListDC.prototype.initialize.call( this, model, options );\n\t hcontentMixin.initialize.call( this, model, options );\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 ([ 'HistoryListDatasetCollection(', this.get( 'name' ), ')' ].join( '' ));\n\t }\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\tvar 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 initialize : function( model, options ){\n\t PairDC.prototype.initialize.call( this, model, options );\n\t hcontentMixin.initialize.call( this, model, options );\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 ([ 'HistoryPairDatasetCollection(', this.get( 'name' ), ')' ].join( '' ));\n\t }\n\t});\n\t\n\t\n\t//==============================================================================\n\t/** @class Backbone model for List of Pairs Dataset Collection within a History.\n\t * @constructs\n\t */\n\tvar HistoryListPairedDatasetCollection = ListPairedDC.extend( hcontentMixin ).extend(\n\t/** @lends HistoryListPairedDatasetCollection.prototype */{\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 initialize : function( model, options ){\n\t ListPairedDC.prototype.initialize.call( this, model, options );\n\t hcontentMixin.initialize.call( this, model, options );\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 ([ 'HistoryListPairedDatasetCollection(', this.get( 'name' ), ')' ].join( '' ));\n\t }\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 };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3)))\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, jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [\n\t __webpack_require__(15),\n\t __webpack_require__(6),\n\t __webpack_require__(5)\n\t], __WEBPACK_AMD_DEFINE_RESULT__ = function( STATES, BASE_MVC, _l ){\n\t\n\tvar logNamespace = 'history';\n\t//==============================================================================\n\t/** How the type_id attribute is built for the history's mixed contents collection */\n\tvar typeIdStr = function _typeIdStr( type, id ){\n\t return [ type, id ].join( '-' );\n\t};\n\t\n\t//==============================================================================\n\t/** @class Mixin for HistoryContents content (HDAs, HDCAs).\n\t */\n\tvar HistoryContentMixin = {\n\t//TODO:?? into true Backbone.Model?\n\t\n\t /** default attributes for a model */\n\t defaults : {\n\t /** parent (containing) history */\n\t history_id : null,\n\t /** some content_type (HistoryContents can contain mixed model classes) */\n\t history_content_type: null,\n\t /** indicating when/what order the content was generated in the context of the history */\n\t hid : null,\n\t /** whether the user wants the content shown (visible) */\n\t visible : true\n\t },\n\t\n\t // ........................................................................ mixed content element\n\t//TODO: there's got to be a way to move this into HistoryContents - if we can do that, this class might not be needed\n\t // In order to be part of a MIXED bbone collection, we can't rely on the id\n\t // (which may collide btwn models of different classes)\n\t // Build a new id (type_id) that prefixes the history_content_type so the bbone collection can differentiate\n\t idAttribute : 'type_id',\n\t\n\t /** override constructor to build type_id and insert into original attributes */\n\t constructor : function( attrs, options ){\n\t attrs.type_id = typeIdStr( attrs.history_content_type, attrs.id );\n\t this.debug( 'HistoryContentMixin.constructor:', attrs.type_id );\n\t Backbone.Model.apply( this, arguments );\n\t },\n\t\n\t /** object level fn for building the type_id string */\n\t _typeIdStr : function(){\n\t return typeIdStr( this.get( 'history_content_type' ), this.get( 'id' ) );\n\t },\n\t\n\t /** add listener to re-create type_id when the id changes */\n\t initialize : function( attrs, options ){\n\t this.on( 'change:id', this._createTypeId );\n\t },\n\t\n\t /** set the type_id in the model attributes */\n\t _createTypeId : function(){\n\t this.set( 'type_id', this._typeIdStr() );\n\t },\n\t\n\t /** override because backbone tests boolean( idAttribute ), but it's not an empty string even for new models\n\t * due to our use of type_id.\n\t */\n\t isNew : function(){\n\t return !this.get( 'id' );\n\t },\n\t\n\t // ........................................................................ common queries\n\t /** the more common alias of visible */\n\t hidden : function(){\n\t return !this.get( 'visible' );\n\t },\n\t\n\t /** based on show_deleted, show_hidden (gen. from the container control),\n\t * would this ds show in the list of ds's?\n\t * @param {Boolean} show_deleted are we showing deleted hdas?\n\t * @param {Boolean} show_hidden are we showing hidden hdas?\n\t */\n\t isVisible : function( show_deleted, show_hidden ){\n\t//TODO:?? Another unfortunate name collision\n\t var isVisible = true;\n\t if( ( !show_deleted )\n\t && ( this.get( 'deleted' ) || this.get( 'purged' ) ) ){\n\t isVisible = false;\n\t }\n\t if( ( !show_hidden )\n\t && ( !this.get( 'visible' ) ) ){\n\t isVisible = false;\n\t }\n\t return isVisible;\n\t },\n\t\n\t // ........................................................................ ajax\n\t//TODO: global\n\t//TODO: these are probably better done on the leaf classes\n\t /** history content goes through the 'api/histories' API */\n\t urlRoot: Galaxy.root + 'api/histories/',\n\t\n\t /** full url spec. for this content */\n\t url : function(){\n\t var url = this.urlRoot + this.get( 'history_id' ) + '/contents/'\n\t + this.get('history_content_type') + 's/' + this.get( 'id' );\n\t return url;\n\t },\n\t\n\t /** save this content as not visible */\n\t hide : function( options ){\n\t if( !this.get( 'visible' ) ){ return jQuery.when(); }\n\t return this.save( { visible: false }, options );\n\t },\n\t /** save this content as visible */\n\t unhide : function( options ){\n\t if( this.get( 'visible' ) ){ return jQuery.when(); }\n\t return this.save( { visible: true }, options );\n\t },\n\t\n\t // ........................................................................ misc\n\t /** String representation */\n\t toString : function(){\n\t var nameAndId = this.get( 'id' ) || '';\n\t if( this.get( 'name' ) ){\n\t nameAndId = this.get( 'hid' ) + ' :\"' + this.get( 'name' ) + '\",' + nameAndId;\n\t }\n\t return 'HistoryContent(' + nameAndId + ')';\n\t }\n\t};\n\t\n\t\n\t//==============================================================================\n\t//TODO: needed?\n\t/** @class (Concrete/non-mixin) base model for content items.\n\t */\n\tvar HistoryContent = Backbone.Model\n\t .extend( BASE_MVC.LoggableMixin )\n\t .extend( HistoryContentMixin )\n\t .extend({ _logNamespace : logNamespace });\n\t\n\t\n\t//==============================================================================\n\t return {\n\t typeIdStr : typeIdStr,\n\t HistoryContentMixin : HistoryContentMixin,\n\t HistoryContent : HistoryContent\n\t };\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\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) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [\n\t __webpack_require__(46),\n\t __webpack_require__(97),\n\t __webpack_require__(45),\n\t __webpack_require__(6),\n\t __webpack_require__(5)\n\t], __WEBPACK_AMD_DEFINE_RESULT__ = function( HISTORY_CONTENT, HDA_MODEL, HDCA_MODEL, BASE_MVC, _l ){\n\t\n\tvar logNamespace = 'history';\n\t//==============================================================================\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\tvar HistoryContents = Backbone.Collection\n\t .extend( BASE_MVC.LoggableMixin )\n\t .extend(/** @lends HistoryContents.prototype */{\n\t//TODO:?? may want to inherit from some MixedModelCollection\n\t//TODO:?? also consider inheriting from a 'DatasetList'\n\t//TODO: can we decorate the mixed models using the model fn below (instead of having them build their own type_id)?\n\t\n\t _logNamespace : logNamespace,\n\t\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//TODO: can we move the type_id stuff here?\n\t //attrs.type_id = typeIdStr( attrs );\n\t\n\t if( attrs.history_content_type === \"dataset\" ) {\n\t return new HDA_MODEL.HistoryDatasetAssociation( attrs, options );\n\t\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 }\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 return { validationError : 'Unknown collection_type: ' + attrs.history_content_type };\n\t }\n\t return { validationError : 'Unknown history_content_type: ' + attrs.history_content_type };\n\t },\n\t\n\t /** Set up.\n\t * @see Backbone.Collection#initialize\n\t */\n\t initialize : function( models, options ){\n\t options = options || {};\n\t//TODO: could probably use the contents.history_id instead\n\t this.historyId = options.historyId;\n\t //this._setUpListeners();\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 this.on( 'all', function(){\n\t this.debug( this + '.event:', arguments );\n\t });\n\t },\n\t\n\t /** root api url */\n\t urlRoot : Galaxy.root + 'api/histories',\n\t /** complete api url */\n\t url : function(){\n\t return this.urlRoot + '/' + this.historyId + '/contents';\n\t },\n\t\n\t // ........................................................................ common queries\n\t /** Get the ids of every item in this collection\n\t * @returns array of encoded ids\n\t */\n\t ids : function(){\n\t//TODO: is this still useful since type_id\n\t return this.map( function( item ){ return item.get('id'); });\n\t },\n\t\n\t /** Get contents that are not ready\n\t * @returns array of content models\n\t */\n\t notReady : function(){\n\t return this.filter( function( content ){\n\t return !content.inReadyState();\n\t });\n\t },\n\t\n\t /** Get the id of every model in this collection not in a 'ready' state (running).\n\t * @returns an array of model ids\n\t * @see HistoryDatasetAssociation#inReadyState\n\t */\n\t running : function(){\n\t var idList = [];\n\t this.each( function( item ){\n\t var isRunning = !item.inReadyState();\n\t if( isRunning ){\n\t//TODO: is this still correct since type_id\n\t idList.push( item.get( 'id' ) );\n\t }\n\t });\n\t return idList;\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 return _.first( this.filter( function( content ){ return content.get( 'hid' ) === hid; }) );\n\t },\n\t\n\t //TODO:?? this may belong in the containing view\n\t /** Get every 'shown' model in this collection based on show_deleted/hidden\n\t * @param {Boolean} show_deleted are we showing deleted content?\n\t * @param {Boolean} show_hidden are we showing hidden content?\n\t * @returns array of content models\n\t * @see HistoryDatasetAssociation#isVisible\n\t */\n\t getVisible : function( show_deleted, show_hidden, filters ){\n\t filters = filters || [];\n\t //this.debug( 'filters:', filters );\n\t // always filter by show deleted/hidden first\n\t this.debug( 'checking isVisible' );\n\t var filteredHdas = new HistoryContents( this.filter( function( item ){\n\t return item.isVisible( show_deleted, show_hidden );\n\t }));\n\t\n\t _.each( filters, function( filterFn ){\n\t if( !_.isFunction( filterFn ) ){ return; }\n\t filteredHdas = new HistoryContents( filteredHdas.filter( filterFn ) );\n\t });\n\t return filteredHdas;\n\t },\n\t\n\t /** return a new contents collection of only hidden items */\n\t hidden : function(){\n\t function filterFn( c ){ return c.hidden(); }\n\t return new HistoryContents( this.filter( filterFn ) );\n\t },\n\t\n\t /** return a new contents collection of only hidden items */\n\t deleted : function(){\n\t function filterFn( c ){ return c.get( 'deleted' ); }\n\t return new HistoryContents( this.filter( filterFn ) );\n\t },\n\t\n\t /** return true if any contents don't have details */\n\t haveDetails : function(){\n\t return this.all( function( content ){ return content.hasDetails(); });\n\t },\n\t\n\t // ........................................................................ ajax\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 = ( options.data )?( _.extend( options.data, detailsFlag ) ):( detailsFlag );\n\t return this.fetch( options );\n\t },\n\t\n\t /** using a queue, perform ajaxFn on each of the models in this collection */\n\t ajaxQueue : function( ajaxFn, options ){\n\t var deferred = jQuery.Deferred(),\n\t startingLength = this.length,\n\t responses = [];\n\t\n\t if( !startingLength ){\n\t deferred.resolve([]);\n\t return deferred;\n\t }\n\t\n\t // use reverse order (stylistic choice)\n\t var ajaxFns = this.chain().reverse().map( function( content, i ){\n\t return function(){\n\t var xhr = ajaxFn.call( content, options );\n\t // if successful, notify using the deferred to allow tracking progress\n\t xhr.done( function( response ){\n\t deferred.notify({ curr: i, total: startingLength, response: response, model: content });\n\t });\n\t // (regardless of previous error or success) if not last ajax call, shift and call the next\n\t // if last fn, resolve deferred\n\t xhr.always( function( response ){\n\t responses.push( response );\n\t if( ajaxFns.length ){\n\t ajaxFns.shift()();\n\t } else {\n\t deferred.resolve( responses );\n\t }\n\t });\n\t };\n\t }).value();\n\t // start the queue\n\t ajaxFns.shift()();\n\t\n\t return deferred;\n\t },\n\t\n\t isCopyable : function( contentsJSON ){\n\t var copyableModelClasses = [\n\t 'HistoryDatasetAssociation',\n\t 'HistoryDatasetCollectionAssociation'\n\t ];\n\t return ( ( _.isObject( contentsJSON ) && contentsJSON.id )\n\t && ( _.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 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.post( this.url(), {\n\t content : id,\n\t source : contentType,\n\t type : type\n\t })\n\t .done( function( response ){\n\t collection.add([ response ]);\n\t })\n\t .fail( function( error, status, message ){\n\t collection.trigger( 'error', collection, xhr, {},\n\t 'Error copying contents', { type: type, id: id, source: contentType });\n\t });\n\t return xhr;\n\t },\n\t\n\t // ........................................................................ sorting/filtering\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 /** override to ensure type id is set */\n\t set : function( models, options ){\n\t models = _.isArray( models )? models : [ models ];\n\t _.each( models, function( model ){\n\t if( !model.type_id || !model.get || !model.get( 'type_id' ) ){\n\t model.type_id = HISTORY_CONTENT.typeIdStr( model.history_content_type, model.id );\n\t }\n\t });\n\t Backbone.Collection.prototype.set.call( this, models, options );\n\t },\n\t\n\t /** */\n\t createHDCA : function( elementIdentifiers, collectionType, name, options ){\n\t //precondition: elementIdentifiers is an array of plain js objects\n\t // in the proper form to create the collectionType\n\t var contents = this,\n\t typeToModel = {\n\t list : HDCA_MODEL.HistoryListDatasetCollection,\n\t paired : HDCA_MODEL.HistoryPairDatasetCollection\n\t },\n\t hdca = new (typeToModel[ collectionType ])({\n\t history_id : this.historyId,\n\t name : name,\n\t // should probably be able to just send in a bunch of json here and restruct per class\n\t element_identifiers : elementIdentifiers\n\t });\n\t // do I even need to use new above, can I just pass the attrs here\n\t return hdca.save()\n\t .done( function( response ){\n\t contents.add( hdca );\n\t })\n\t .fail( function( xhr, status, message ){\n\t contents.trigger( 'error', xhr, status, message );\n\t });\n\t },\n\t\n\t\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 /** debugging */\n\t print : function(){\n\t var contents = this;\n\t contents.each( function( c ){\n\t contents.debug( c );\n\t if( c.elements ){\n\t contents.debug( '\\t elements:', c.elements );\n\t }\n\t });\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//==============================================================================\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\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(3), __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, $, _, jQuery) {!(__WEBPACK_AMD_DEFINE_ARRAY__ = [\n\t __webpack_require__(6),\n\t __webpack_require__(5)\n\t], __WEBPACK_AMD_DEFINE_RESULT__ = function( BASE_MVC, _l ){\n\t\n\tvar 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\tvar 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 $( view ).queue( 'fx', [\n\t function( next ){ this.$el.fadeOut( speed, next ); },\n\t function( next ){\n\t view._swapNewRender( $newRender );\n\t next();\n\t },\n\t function( next ){ this.$el.fadeIn( speed, next ); },\n\t function( next ){\n\t this.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()\n\t .attr( 'class', _.isFunction( this.className )? this.className(): this.className )\n\t .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({\n\t duration : view.fxSpeed,\n\t step: function(){\n\t view.trigger( 'expanding', view );\n\t },\n\t complete: function(){\n\t view.trigger( 'expanded', view );\n\t }\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.$details().slideUp({\n\t duration : view.fxSpeed,\n\t step: function(){\n\t view.trigger( 'collapsing', view );\n\t },\n\t complete: function(){\n\t view.trigger( 'collapsed', view );\n\t }\n\t });\n\t }\n\t\n\t});\n\t\n\t\n\t//==============================================================================\n\t/** A view that is displayed in some larger list/grid/collection.\n\t * Inherits from Expandable, Selectable, Draggable.\n\t * The DOM contains warnings, a title bar, and a series of primary action controls.\n\t * Primary actions are meant to be easily accessible item functions (such as delete)\n\t * that are rendered in the title bar.\n\t *\n\t * Details are rendered when the user clicks the title bar or presses enter/space when\n\t * the title bar is in focus.\n\t *\n\t * Designed as a base class for history panel contents - but usable elsewhere (I hope).\n\t */\n\tvar ListItemView = ExpandableView.extend(\n\t BASE_MVC.mixin( BASE_MVC.SelectableViewMixin, BASE_MVC.DraggableViewMixin, {\n\t\n\t//TODO: that's a little contradictory\n\t tagName : 'div',\n\t className : 'list-item',\n\t\n\t /** Set up the base class and all mixins */\n\t initialize : function( attributes ){\n\t ExpandableView.prototype.initialize.call( this, attributes );\n\t BASE_MVC.SelectableViewMixin.initialize.call( this, attributes );\n\t BASE_MVC.DraggableViewMixin.initialize.call( this, attributes );\n\t this._setUpListeners();\n\t },\n\t\n\t /** event listeners */\n\t _setUpListeners : function(){\n\t // hide the primary actions in the title bar when selectable and narrow\n\t this.on( 'selectable', function( isSelectable ){\n\t if( isSelectable ){\n\t this.$( '.primary-actions' ).hide();\n\t } else {\n\t this.$( '.primary-actions' ).show();\n\t }\n\t }, this );\n\t //this.on( 'all', function( event ){\n\t // this.log( event );\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, $newRender );\n\t if( this.selectable ){ this.showSelector( 0 ); }\n\t if( this.draggable ){ this.draggableOn(); }\n\t return this.$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\n\t // dragging - don't work, originalEvent === null\n\t //'dragstart .dataset-title-bar' : 'dragStartHandler',\n\t //'dragend .dataset-title-bar' : 'dragEndHandler'\n\t\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, KEYCODE_RETURN = 13;\n\t if( event && ( event.type === 'keydown' )\n\t &&( 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\tListItemView.prototype.templates = (function(){\n\t//TODO: move to require text! plugin\n\t\n\t var elTemplato = BASE_MVC.wrapTemplate([\n\t '',\n\t // errors, messages, etc.\n\t '',\n\t\n\t // multi-select checkbox\n\t ''\n\t ]);\n\t\n\t var warnings = {};\n\t\n\t var titleBarTemplate = BASE_MVC.wrapTemplate([\n\t // adding a tabindex here allows focusing the title bar and the use of keydown to expand the dataset display\n\t '',\n\t '',\n\t '',\n\t // space for title bar buttons - gen. floated to the right\n\t '',\n\t '',\n\t\n\t // expandable area for more details\n\t '',\n\t '',\n\t//TODO: prob. belongs in dataset-list-item\n\t '',\n\t ''\n\t ], 'element' );\n\t\n\t var subtitleTemplate = BASE_MVC.wrapTemplate([\n\t // override this\n\t ''\n\t ]);\n\t\n\t var detailsTemplate = BASE_MVC.wrapTemplate([\n\t // override this\n\t ''\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//==============================================================================\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\tvar 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//TODO: hackish\n\t if( this.foldoutStyle === 'drilldown' ){ this.expanded = false; }\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//TODO:?? override to exclude foldout scope?\n\t //$ : function( selector ){\n\t // var $found = ListItemView.prototype.$.call( this, selector );\n\t // return $found;\n\t //},\n\t\n\t /** in this override, attach the foldout panel when rendering details */\n\t _renderDetails : function(){\n\t//TODO: hackish\n\t if( this.foldoutStyle === 'drilldown' ){ return $(); }\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//TODO: hack\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()\n\t .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.foldout.on( '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\tFoldoutListItemView.prototype.templates = (function(){\n\t\n\t//TODO:?? unnecessary?\n\t // use element identifier\n\t var detailsTemplate = BASE_MVC.wrapTemplate([\n\t '',\n\t '<%- element.name %>',\n\t '',\n\t '',\n\t '',\n\t // override with more info (that goes above the panel)\n\t ''\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//==============================================================================\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\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3), __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($) {/**\n\t This is the base class of the tool form plugin. This class is e.g. inherited by the regular and the workflow tool form.\n\t*/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(60), __webpack_require__(7), __webpack_require__(44),\n\t __webpack_require__(23), __webpack_require__(21), __webpack_require__(33)], __WEBPACK_AMD_DEFINE_RESULT__ = function(Utils, Deferred, Ui, FormBase, ToolTemplate, CitationModel, CitationView) {\n\t return FormBase.extend({\n\t initialize: function(options) {\n\t var self = this;\n\t FormBase.prototype.initialize.call(this, options);\n\t this.deferred = new Deferred();\n\t if (options.inputs) {\n\t this._buildForm(options);\n\t options.needs_update && this.deferred.execute( function( process ) {\n\t self._updateModel( process );\n\t });\n\t } else {\n\t this.deferred.execute(function(process) {\n\t self._buildModel(process, options, true);\n\t });\n\t }\n\t },\n\t\n\t /** Wait for deferred build processes before removal */\n\t remove: function() {\n\t var self = this;\n\t this.$el.hide();\n\t this.deferred.execute(function(){\n\t FormBase.prototype.remove.call(self);\n\t Galaxy.emit.debug('tool-form-base::remove()', '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.options = Utils.merge(options, this.options);\n\t this.options = Utils.merge({\n\t icon : ( (options.icon === undefined) && 'fa-wrench' ) || '',\n\t title : '' + options.name + ' ' + options.description + ' (Galaxy Version ' + options.version + ')',\n\t operations : this._operations(),\n\t onchange : function() {\n\t self.deferred.reset();\n\t self.deferred.execute(function(process) {\n\t self._updateModel(process);\n\t });\n\t }\n\t }, this.options);\n\t this.options.customize && this.options.customize( this.options );\n\t this.render();\n\t if ( !this.options.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 */\n\t _buildModel: function(process, options, hide_message) {\n\t var self = this;\n\t this.options.id = options.id;\n\t this.options.version = options.version;\n\t\n\t // build request url\n\t var build_url = '';\n\t var build_data = {};\n\t if ( options.job_id ) {\n\t build_url = Galaxy.root + 'api/jobs/' + options.job_id + '/build_for_rerun';\n\t } else {\n\t build_url = Galaxy.root + 'api/tools/' + options.id + '/build';\n\t if ( Galaxy.params && Galaxy.params.tool_id == options.id ) {\n\t build_data = $.extend( {}, Galaxy.params );\n\t options.version && ( build_data[ 'tool_version' ] = options.version );\n\t }\n\t }\n\t\n\t // get initial model\n\t Utils.request({\n\t type : 'GET',\n\t url : build_url,\n\t data : build_data,\n\t success : function(new_model) {\n\t self._buildForm(new_model['tool_model'] || new_model);\n\t !hide_message && self.message.update({\n\t status : 'success',\n\t message : 'Now you are using \\'' + self.options.name + '\\' version ' + self.options.version + ', id \\'' + self.options.id + '\\'.',\n\t persistent : false\n\t });\n\t Galaxy.emit.debug('tool-form-base::initialize()', 'Initial tool model ready.', new_model);\n\t process.resolve();\n\t\n\t },\n\t error : function(response) {\n\t var error_message = ( response && response.err_msg ) || 'Uncaught error.';\n\t if ( self.$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.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::initialize()', 'Initial tool model request failed.', response);\n\t process.reject();\n\t }\n\t });\n\t },\n\t\n\t /** Request a new model for an already created tool form and updates the form inputs\n\t */\n\t _updateModel: function(process) {\n\t // link this\n\t var self = this;\n\t var model_url = this.options.update_url || Galaxy.root + 'api/tools/' + this.options.id + '/build';\n\t var current_state = {\n\t tool_id : this.options.id,\n\t tool_version : this.options.version,\n\t inputs : $.extend(true, {}, self.data.create())\n\t }\n\t this.wait(true);\n\t\n\t // log tool state\n\t Galaxy.emit.debug('tool-form-base::_updateModel()', 'Sending current state.', current_state);\n\t\n\t // post job\n\t Utils.request({\n\t type : 'POST',\n\t url : model_url,\n\t data : current_state,\n\t success : function(new_model) {\n\t self.update(new_model['tool_model'] || new_model);\n\t self.options.update && self.options.update(new_model);\n\t self.wait(false);\n\t Galaxy.emit.debug('tool-form-base::_updateModel()', 'Received new model.', new_model);\n\t process.resolve();\n\t },\n\t error : function(response) {\n\t Galaxy.emit.debug('tool-form-base::_updateModel()', 'Refresh request failed.', response);\n\t process.reject();\n\t }\n\t });\n\t },\n\t\n\t /** Create tool operation menu\n\t */\n\t _operations: function() {\n\t var self = this;\n\t var options = this.options;\n\t\n\t // button for version selection\n\t var versions_button = new Ui.ButtonMenu({\n\t icon : 'fa-cubes',\n\t title : (!options.narrow && 'Versions') || null,\n\t tooltip : 'Select another tool version'\n\t });\n\t if (!options.sustain_version && options.versions && options.versions.length > 1) {\n\t for (var i in options.versions) {\n\t var version = options.versions[i];\n\t if (version != options.version) {\n\t versions_button.addMenu({\n\t title : 'Switch to ' + version,\n\t version : version,\n\t icon : 'fa-cube',\n\t onclick : function() {\n\t // here we update the tool version (some tools encode the version also in the id)\n\t var id = options.id.replace(options.version, this.version);\n\t var version = this.version;\n\t // queue model request\n\t self.deferred.reset();\n\t self.deferred.execute(function(process) {\n\t self._buildModel(process, {id: id, version: version})\n\t });\n\t }\n\t });\n\t }\n\t }\n\t } else {\n\t versions_button.$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 tooltip : 'Ask a question about this tool (Biostar)',\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 tooltip : 'Search help for this tool (Biostar)',\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 tooltip : 'Share this tool',\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 tooltip : 'Download this tool',\n\t onclick : function() {\n\t window.location.href = Galaxy.root + 'api/tools/' + options.id + '/download';\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 tooltip : 'Display tool requirements',\n\t onclick : function() {\n\t if (!this.visible) {\n\t this.visible = true;\n\t self.message.update({\n\t persistent : true,\n\t message : ToolTemplate.requirements(options),\n\t status : 'info'\n\t });\n\t } else {\n\t this.visible = false;\n\t self.message.update({\n\t message : ''\n\t });\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 tooltip : 'Access the repository',\n\t onclick : function() {\n\t window.open(options.sharable_url);\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 */\n\t _footer: function() {\n\t var options = this.options;\n\t var $el = $( '' ).append( ToolTemplate.help( 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}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t\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(Backbone, $) {/**\n\t * Model, view, and controller objects for Galaxy tools and tool panel.\n\t */\n\t\n\t !(__WEBPACK_AMD_DEFINE_ARRAY__ = [\n\t __webpack_require__(3),\n\t __webpack_require__(20),\n\t __webpack_require__(14),\n\t __webpack_require__(22),\n\t __webpack_require__(64),\n\t __webpack_require__(65),\n\t __webpack_require__(63),\n\t __webpack_require__(66),\n\t\n\t], __WEBPACK_AMD_DEFINE_RESULT__ = function(_, util, data, ToolForm, tool_form_template, tool_link_template, panel_section_template, tool_search_template) {\n\t\n\t/**\n\t * Mixin for tracking model visibility.\n\t */\n\tvar VisibilityMixin = {\n\t hidden: false,\n\t\n\t show: function() {\n\t this.set(\"hidden\", false);\n\t },\n\t\n\t hide: function() {\n\t this.set(\"hidden\", true);\n\t },\n\t\n\t toggle: function() {\n\t this.set(\"hidden\", !this.get(\"hidden\"));\n\t },\n\t\n\t is_visible: function() {\n\t return !this.attributes.hidden;\n\t }\n\t\n\t};\n\t\n\t/**\n\t * A tool parameter.\n\t */\n\tvar ToolParameter = Backbone.Model.extend({\n\t defaults: {\n\t name: null,\n\t label: null,\n\t type: null,\n\t value: null,\n\t html: null,\n\t num_samples: 5\n\t },\n\t\n\t initialize: function(options) {\n\t this.attributes.html = unescape(this.attributes.html);\n\t },\n\t\n\t copy: function() {\n\t return new ToolParameter(this.toJSON());\n\t },\n\t\n\t set_value: function(value) {\n\t this.set('value', value || '');\n\t }\n\t});\n\t\n\tvar ToolParameterCollection = Backbone.Collection.extend({\n\t model: ToolParameter\n\t});\n\t\n\t/**\n\t * A data tool parameter.\n\t */\n\tvar DataToolParameter = ToolParameter.extend({});\n\t\n\t/**\n\t * An integer tool parameter.\n\t */\n\tvar IntegerToolParameter = ToolParameter.extend({\n\t set_value: function(value) {\n\t this.set('value', parseInt(value, 10));\n\t },\n\t\n\t /**\n\t * Returns samples from a tool input.\n\t */\n\t get_samples: function() {\n\t return d3.scale.linear()\n\t .domain([this.get('min'), this.get('max')])\n\t .ticks(this.get('num_samples'));\n\t }\n\t});\n\t\n\tvar FloatToolParameter = IntegerToolParameter.extend({\n\t set_value: function(value) {\n\t this.set('value', parseFloat(value));\n\t }\n\t});\n\t\n\t/**\n\t * A select tool parameter.\n\t */\n\tvar SelectToolParameter = ToolParameter.extend({\n\t /**\n\t * Returns tool options.\n\t */\n\t get_samples: function() {\n\t return _.map(this.get('options'), function(option) {\n\t return option[0];\n\t });\n\t }\n\t});\n\t\n\t// Set up dictionary of parameter types.\n\tToolParameter.subModelTypes = {\n\t 'integer': IntegerToolParameter,\n\t 'float': FloatToolParameter,\n\t 'data': DataToolParameter,\n\t 'select': SelectToolParameter\n\t};\n\t\n\t/**\n\t * A Galaxy tool.\n\t */\n\tvar Tool = Backbone.Model.extend({\n\t // Default attributes.\n\t defaults: {\n\t id: null,\n\t name: null,\n\t description: null,\n\t target: null,\n\t inputs: [],\n\t outputs: []\n\t },\n\t\n\t urlRoot: Galaxy.root + 'api/tools',\n\t\n\t initialize: function(options) {\n\t\n\t // Set parameters.\n\t this.set('inputs', new ToolParameterCollection(_.map(options.inputs, function(p) {\n\t var p_class = ToolParameter.subModelTypes[p.type] || ToolParameter;\n\t return new p_class(p);\n\t })));\n\t },\n\t\n\t /**\n\t *\n\t */\n\t toJSON: function() {\n\t var rval = Backbone.Model.prototype.toJSON.call(this);\n\t\n\t // Convert inputs to JSON manually.\n\t rval.inputs = this.get('inputs').map(function(i) { return i.toJSON(); });\n\t return rval;\n\t },\n\t\n\t /**\n\t * Removes inputs of a particular type; this is useful because not all inputs can be handled by\n\t * client and server yet.\n\t */\n\t remove_inputs: function(types) {\n\t var tool = this,\n\t incompatible_inputs = tool.get('inputs').filter( function(input) {\n\t return ( types.indexOf( input.get('type') ) !== -1);\n\t });\n\t tool.get('inputs').remove(incompatible_inputs);\n\t },\n\t\n\t /**\n\t * Returns object copy, optionally including only inputs that can be sampled.\n\t */\n\t copy: function(only_samplable_inputs) {\n\t var copy = new Tool(this.toJSON());\n\t\n\t // Return only samplable inputs if flag is set.\n\t if (only_samplable_inputs) {\n\t var valid_inputs = new Backbone.Collection();\n\t copy.get('inputs').each(function(input) {\n\t if (input.get_samples()) {\n\t valid_inputs.push(input);\n\t }\n\t });\n\t copy.set('inputs', valid_inputs);\n\t }\n\t\n\t return copy;\n\t },\n\t\n\t apply_search_results: function(results) {\n\t ( _.indexOf(results, this.attributes.id) !== -1 ? this.show() : this.hide() );\n\t return this.is_visible();\n\t },\n\t\n\t /**\n\t * Set a tool input's value.\n\t */\n\t set_input_value: function(name, value) {\n\t this.get('inputs').find(function(input) {\n\t return input.get('name') === name;\n\t }).set('value', value);\n\t },\n\t\n\t /**\n\t * Set many input values at once.\n\t */\n\t set_input_values: function(inputs_dict) {\n\t var self = this;\n\t _.each(_.keys(inputs_dict), function(input_name) {\n\t self.set_input_value(input_name, inputs_dict[input_name]);\n\t });\n\t },\n\t\n\t /**\n\t * Run tool; returns a Deferred that resolves to the tool's output(s).\n\t */\n\t run: function() {\n\t return this._run();\n\t },\n\t\n\t /**\n\t * Rerun tool using regions and a target dataset.\n\t */\n\t rerun: function(target_dataset, regions) {\n\t return this._run({\n\t action: 'rerun',\n\t target_dataset_id: target_dataset.id,\n\t regions: regions\n\t });\n\t },\n\t\n\t /**\n\t * Returns input dict for tool's inputs.\n\t */\n\t get_inputs_dict: function() {\n\t var input_dict = {};\n\t this.get('inputs').each(function(input) {\n\t input_dict[input.get('name')] = input.get('value');\n\t });\n\t return input_dict;\n\t },\n\t\n\t /**\n\t * Run tool; returns a Deferred that resolves to the tool's output(s).\n\t * NOTE: this method is a helper method and should not be called directly.\n\t */\n\t _run: function(additional_params) {\n\t // Create payload.\n\t var payload = _.extend({\n\t tool_id: this.id,\n\t inputs: this.get_inputs_dict()\n\t }, additional_params);\n\t\n\t // Because job may require indexing datasets, use server-side\n\t // deferred to ensure that job is run. Also use deferred that\n\t // resolves to outputs from tool.\n\t var run_deferred = $.Deferred(),\n\t ss_deferred = new util.ServerStateDeferred({\n\t ajax_settings: {\n\t url: this.urlRoot,\n\t data: JSON.stringify(payload),\n\t dataType: \"json\",\n\t contentType: 'application/json',\n\t type: \"POST\"\n\t },\n\t interval: 2000,\n\t success_fn: function(response) {\n\t return response !== \"pending\";\n\t }\n\t });\n\t\n\t // Run job and resolve run_deferred to tool outputs.\n\t $.when(ss_deferred.go()).then(function(result) {\n\t run_deferred.resolve(new data.DatasetCollection(result));\n\t });\n\t return run_deferred;\n\t }\n\t});\n\t_.extend(Tool.prototype, VisibilityMixin);\n\t\n\t/**\n\t * Tool view.\n\t */\n\tvar ToolView = Backbone.View.extend({\n\t\n\t});\n\t\n\t/**\n\t * Wrap collection of tools for fast access/manipulation.\n\t */\n\tvar ToolCollection = Backbone.Collection.extend({\n\t model: Tool\n\t});\n\t\n\t/**\n\t * Label or section header in tool panel.\n\t */\n\tvar ToolSectionLabel = Backbone.Model.extend(VisibilityMixin);\n\t\n\t/**\n\t * Section of tool panel with elements (labels and tools).\n\t */\n\tvar ToolSection = Backbone.Model.extend({\n\t defaults: {\n\t elems: [],\n\t open: false\n\t },\n\t\n\t clear_search_results: function() {\n\t _.each(this.attributes.elems, function(elt) {\n\t elt.show();\n\t });\n\t\n\t this.show();\n\t this.set(\"open\", false);\n\t },\n\t\n\t apply_search_results: function(results) {\n\t var all_hidden = true,\n\t cur_label;\n\t _.each(this.attributes.elems, function(elt) {\n\t if (elt instanceof ToolSectionLabel) {\n\t cur_label = elt;\n\t cur_label.hide();\n\t }\n\t else if (elt instanceof Tool) {\n\t if (elt.apply_search_results(results)) {\n\t all_hidden = false;\n\t if (cur_label) {\n\t cur_label.show();\n\t }\n\t }\n\t }\n\t });\n\t\n\t if (all_hidden) {\n\t this.hide();\n\t }\n\t else {\n\t this.show();\n\t this.set(\"open\", true);\n\t }\n\t }\n\t});\n\t_.extend(ToolSection.prototype, VisibilityMixin);\n\t\n\t/**\n\t * Tool search that updates results when query is changed. Result value of null\n\t * indicates that query was not run; if not null, results are from search using\n\t * query.\n\t */\n\tvar ToolSearch = Backbone.Model.extend({\n\t defaults: {\n\t search_hint_string: \"search tools\",\n\t min_chars_for_search: 3,\n\t spinner_url: \"\",\n\t clear_btn_url: \"\",\n\t search_url: \"\",\n\t visible: true,\n\t query: \"\",\n\t results: null,\n\t // ESC (27) will clear the input field and tool search filters\n\t clear_key: 27\n\t },\n\t\n\t urlRoot: Galaxy.root + 'api/tools',\n\t\n\t initialize: function() {\n\t this.on(\"change:query\", this.do_search);\n\t },\n\t\n\t /**\n\t * Do the search and update the results.\n\t */\n\t do_search: function() {\n\t var query = this.attributes.query;\n\t\n\t // If query is too short, do not search.\n\t if (query.length < this.attributes.min_chars_for_search) {\n\t this.set(\"results\", null);\n\t return;\n\t }\n\t\n\t // Do search via AJAX.\n\t var q = query;\n\t // Stop previous ajax-request\n\t if (this.timer) {\n\t clearTimeout(this.timer);\n\t }\n\t // Start a new ajax-request in X ms\n\t $(\"#search-clear-btn\").hide();\n\t $(\"#search-spinner\").show();\n\t var self = this;\n\t this.timer = setTimeout(function () {\n\t // log the search to analytics if present\n\t if ( typeof ga !== 'undefined' ) {\n\t ga( 'send', 'pageview', Galaxy.root + '?q=' + q );\n\t }\n\t $.get( self.urlRoot, { q: q }, function (data) {\n\t self.set(\"results\", data);\n\t $(\"#search-spinner\").hide();\n\t $(\"#search-clear-btn\").show();\n\t }, \"json\" );\n\t }, 400 );\n\t },\n\t\n\t clear_search: function() {\n\t this.set(\"query\", \"\");\n\t this.set(\"results\", null);\n\t }\n\t\n\t});\n\t_.extend(ToolSearch.prototype, VisibilityMixin);\n\t\n\t/**\n\t * Tool Panel.\n\t */\n\tvar ToolPanel = Backbone.Model.extend({\n\t\n\t initialize: function(options) {\n\t this.attributes.tool_search = options.tool_search;\n\t this.attributes.tool_search.on(\"change:results\", this.apply_search_results, this);\n\t this.attributes.tools = options.tools;\n\t this.attributes.layout = new Backbone.Collection( this.parse(options.layout) );\n\t },\n\t\n\t /**\n\t * Parse tool panel dictionary and return collection of tool panel elements.\n\t */\n\t parse: function(response) {\n\t // Recursive function to parse tool panel elements.\n\t var self = this,\n\t // Helper to recursively parse tool panel.\n\t parse_elt = function(elt_dict) {\n\t var type = elt_dict.model_class;\n\t // There are many types of tools; for now, anything that ends in 'Tool'\n\t // is treated as a generic tool.\n\t if ( type.indexOf('Tool') === type.length - 4 ) {\n\t return self.attributes.tools.get(elt_dict.id);\n\t }\n\t else if (type === 'ToolSection') {\n\t // Parse elements.\n\t var elems = _.map(elt_dict.elems, parse_elt);\n\t elt_dict.elems = elems;\n\t return new ToolSection(elt_dict);\n\t }\n\t else if (type === 'ToolSectionLabel') {\n\t return new ToolSectionLabel(elt_dict);\n\t }\n\t };\n\t\n\t return _.map(response, parse_elt);\n\t },\n\t\n\t clear_search_results: function() {\n\t this.get('layout').each(function(panel_elt) {\n\t if (panel_elt instanceof ToolSection) {\n\t panel_elt.clear_search_results();\n\t }\n\t else {\n\t // Label or tool, so just show.\n\t panel_elt.show();\n\t }\n\t });\n\t },\n\t\n\t apply_search_results: function() {\n\t var results = this.get('tool_search').get('results');\n\t if (results === null) {\n\t this.clear_search_results();\n\t return;\n\t }\n\t\n\t var cur_label = null;\n\t this.get('layout').each(function(panel_elt) {\n\t if (panel_elt instanceof ToolSectionLabel) {\n\t cur_label = panel_elt;\n\t cur_label.hide();\n\t }\n\t else if (panel_elt instanceof Tool) {\n\t if (panel_elt.apply_search_results(results)) {\n\t if (cur_label) {\n\t cur_label.show();\n\t }\n\t }\n\t }\n\t else {\n\t // Starting new section, so clear current label.\n\t cur_label = null;\n\t panel_elt.apply_search_results(results);\n\t }\n\t });\n\t }\n\t});\n\t\n\t/**\n\t * View classes for Galaxy tools and tool panel.\n\t *\n\t * Views use precompiled Handlebars templates for rendering. Views update as needed\n\t * based on (a) model/collection events and (b) user interactions; in this sense,\n\t * they are controllers are well and the HTML is the real view in the MVC architecture.\n\t */\n\t\n\t/**\n\t * Base view that handles visibility based on model's hidden attribute.\n\t */\n\tvar BaseView = Backbone.View.extend({\n\t initialize: function() {\n\t this.model.on(\"change:hidden\", this.update_visible, this);\n\t this.update_visible();\n\t },\n\t update_visible: function() {\n\t ( this.model.attributes.hidden ? this.$el.hide() : this.$el.show() );\n\t }\n\t});\n\t\n\t/**\n\t * Link to a tool.\n\t */\n\tvar ToolLinkView = BaseView.extend({\n\t tagName: 'div',\n\t\n\t render: function() {\n\t // create element\n\t var $link = $('');\n\t $link.append(tool_link_template(this.model.toJSON()));\n\t\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 }\n\t else if ( this.model.get( 'model_class' ) === 'Tool' ) { // regular tools\n\t var self = this;\n\t $link.find('a').on('click', function(e) {\n\t e.preventDefault();\n\t var form = new ToolForm.View( { id : self.model.id, version : self.model.get('version') } );\n\t form.deferred.execute(function() {\n\t Galaxy.app.display( form );\n\t });\n\t });\n\t }\n\t\n\t // add element\n\t this.$el.append($link);\n\t return this;\n\t }\n\t});\n\t\n\t/**\n\t * Panel label/section header.\n\t */\n\tvar ToolSectionLabelView = BaseView.extend({\n\t tagName: 'div',\n\t className: 'toolPanelLabel',\n\t\n\t render: function() {\n\t this.$el.append( $(\"\").text(this.model.attributes.text) );\n\t return this;\n\t }\n\t});\n\t\n\t/**\n\t * Panel section.\n\t */\n\tvar ToolSectionView = BaseView.extend({\n\t tagName: 'div',\n\t className: 'toolSectionWrapper',\n\t\n\t initialize: function() {\n\t BaseView.prototype.initialize.call(this);\n\t this.model.on(\"change:open\", this.update_open, this);\n\t },\n\t\n\t render: function() {\n\t // Build using template.\n\t this.$el.append( panel_section_template(this.model.toJSON()) );\n\t\n\t // Add tools to section.\n\t var section_body = this.$el.find(\".toolSectionBody\");\n\t _.each(this.model.attributes.elems, function(elt) {\n\t if (elt instanceof Tool) {\n\t var tool_view = new ToolLinkView({model: elt, className: \"toolTitle\"});\n\t tool_view.render();\n\t section_body.append(tool_view.$el);\n\t }\n\t else if (elt instanceof ToolSectionLabel) {\n\t var label_view = new ToolSectionLabelView({model: elt});\n\t label_view.render();\n\t section_body.append(label_view.$el);\n\t }\n\t else {\n\t // TODO: handle nested section bodies?\n\t }\n\t });\n\t return this;\n\t },\n\t\n\t events: {\n\t 'click .toolSectionTitle > a': 'toggle'\n\t },\n\t\n\t /**\n\t * Toggle visibility of tool section.\n\t */\n\t toggle: function() {\n\t this.model.set(\"open\", !this.model.attributes.open);\n\t },\n\t\n\t /**\n\t * Update whether section is open or close.\n\t */\n\t update_open: function() {\n\t (this.model.attributes.open ?\n\t this.$el.children(\".toolSectionBody\").slideDown(\"fast\") :\n\t this.$el.children(\".toolSectionBody\").slideUp(\"fast\")\n\t );\n\t }\n\t});\n\t\n\tvar ToolSearchView = Backbone.View.extend({\n\t tagName: 'div',\n\t id: 'tool-search',\n\t className: 'bar',\n\t\n\t events: {\n\t 'click': 'focus_and_select',\n\t 'keyup :input': 'query_changed',\n\t 'click #search-clear-btn': 'clear'\n\t },\n\t\n\t render: function() {\n\t this.$el.append( tool_search_template(this.model.toJSON()) );\n\t if (!this.model.is_visible()) {\n\t this.$el.hide();\n\t }\n\t this.$el.find('[title]').tooltip();\n\t return this;\n\t },\n\t\n\t focus_and_select: function() {\n\t this.$el.find(\":input\").focus().select();\n\t },\n\t\n\t clear: function() {\n\t this.model.clear_search();\n\t this.$el.find(\":input\").val('');\n\t this.focus_and_select();\n\t return false;\n\t },\n\t\n\t query_changed: function( evData ) {\n\t // check for the 'clear key' (ESC) first\n\t if( ( this.model.attributes.clear_key ) &&\n\t ( this.model.attributes.clear_key === evData.which ) ){\n\t this.clear();\n\t return false;\n\t }\n\t this.model.set(\"query\", this.$el.find(\":input\").val());\n\t }\n\t});\n\t\n\t/**\n\t * Tool panel view. Events triggered include:\n\t * tool_link_click(click event, tool_model)\n\t */\n\tvar ToolPanelView = Backbone.View.extend({\n\t tagName: 'div',\n\t className: 'toolMenu',\n\t\n\t /**\n\t * Set up view.\n\t */\n\t initialize: function() {\n\t this.model.get('tool_search').on(\"change:results\", this.handle_search_results, this);\n\t },\n\t\n\t render: function() {\n\t var self = this;\n\t\n\t // Render search.\n\t var search_view = new ToolSearchView( { model: this.model.get('tool_search') } );\n\t search_view.render();\n\t self.$el.append(search_view.$el);\n\t\n\t // Render panel.\n\t this.model.get('layout').each(function(panel_elt) {\n\t if (panel_elt instanceof ToolSection) {\n\t var section_title_view = new ToolSectionView({model: panel_elt});\n\t section_title_view.render();\n\t self.$el.append(section_title_view.$el);\n\t }\n\t else if (panel_elt instanceof Tool) {\n\t var tool_view = new ToolLinkView({model: panel_elt, className: \"toolTitleNoSection\"});\n\t tool_view.render();\n\t self.$el.append(tool_view.$el);\n\t }\n\t else if (panel_elt instanceof ToolSectionLabel) {\n\t var label_view = new ToolSectionLabelView({model: panel_elt});\n\t label_view.render();\n\t self.$el.append(label_view.$el);\n\t }\n\t });\n\t\n\t // Setup tool link click eventing.\n\t self.$el.find(\"a.tool-link\").click(function(e) {\n\t // Tool id is always the first class.\n\t var\n\t tool_id = $(this).attr('class').split(/\\s+/)[0],\n\t tool = self.model.get('tools').get(tool_id);\n\t\n\t self.trigger(\"tool_link_click\", e, tool);\n\t });\n\t\n\t return this;\n\t },\n\t\n\t handle_search_results: function() {\n\t var results = this.model.get('tool_search').get('results');\n\t if (results && results.length === 0) {\n\t $(\"#search-no-results\").show();\n\t }\n\t else {\n\t $(\"#search-no-results\").hide();\n\t }\n\t }\n\t});\n\t\n\t/**\n\t * View for working with a tool: setting parameters and inputs and executing the tool.\n\t */\n\tvar ToolFormView = Backbone.View.extend({\n\t className: 'toolForm',\n\t\n\t render: function() {\n\t this.$el.children().remove();\n\t this.$el.append( tool_form_template(this.model.toJSON()) );\n\t }\n\t});\n\t\n\t/**\n\t * Integrated tool menu + tool execution.\n\t */\n\tvar IntegratedToolMenuAndView = Backbone.View.extend({\n\t className: 'toolMenuAndView',\n\t\n\t initialize: function() {\n\t this.tool_panel_view = new ToolPanelView({collection: this.collection});\n\t this.tool_form_view = new ToolFormView();\n\t },\n\t\n\t render: function() {\n\t // Render and append tool panel.\n\t this.tool_panel_view.render();\n\t this.tool_panel_view.$el.css(\"float\", \"left\");\n\t this.$el.append(this.tool_panel_view.$el);\n\t\n\t // Append tool form view.\n\t this.tool_form_view.$el.hide();\n\t this.$el.append(this.tool_form_view.$el);\n\t\n\t // On tool link click, show tool.\n\t var self = this;\n\t this.tool_panel_view.on(\"tool_link_click\", function(e, tool) {\n\t // Prevents click from activating link:\n\t e.preventDefault();\n\t // Show tool that was clicked on:\n\t self.show_tool(tool);\n\t });\n\t },\n\t\n\t /**\n\t * Fetch and display tool.\n\t */\n\t show_tool: function(tool) {\n\t var self = this;\n\t tool.fetch().done( function() {\n\t self.tool_form_view.model = tool;\n\t self.tool_form_view.render();\n\t self.tool_form_view.$el.show();\n\t $('#left').width(\"650px\");\n\t });\n\t }\n\t});\n\t\n\t// Exports\n\treturn {\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\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\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(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\tvar 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.size() ){\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.$el.addClass( 'popmenu-wrapper' ).hide()\n\t .css({ position : 'absolute' })\n\t .html( this.template( this.$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 $( this ).children( 'a.popupmenu-option' ).click( function( event ){\n\t option.func.call( menu, event, option );\n\t // We must preventDefault otherwise clicking \"cancel\"\n\t // on a purge or something still navigates and causes\n\t // the action.\n\t event.preventDefault();\n\t // bubble up so that an option click will call the close behavior\n\t });\n\t }\n\t });\n\t }\n\t return this;\n\t },\n\t\n\t template : function( id, options ){\n\t return [\n\t '- ', this._templateOptions( options ), '
- (no options)
';\n\t }\n\t return _.map( options, function( option ){\n\t if( option.divider ){\n\t return '';\n\t } else if( option.header ){\n\t return [ '- ', option.html, '
' ].join( '' );\n\t }\n\t var href = option.href || 'javascript:void(0);',\n\t target = ( option.target )?( ' target=\"' + option.target + '\"' ):( '' ),\n\t check = ( option.checked )?( '' ):( '' );\n\t return [\n\t '- ',\n\t check, option.html,\n\t '
'\n\t ].join( '' );\n\t }).join( '' );\n\t },\n\t\n\t // get the absolute position/offset for the menu\n\t _getShownPosition : function( clickEvent ){\n\t\n\t // display menu horiz. centered on click...\n\t var menuWidth = this.$el.width();\n\t var x = clickEvent.pageX - menuWidth / 2 ;\n\t\n\t // adjust to handle horiz. scroll and window dimensions ( draw entirely on visible screen area )\n\t x = Math.min( x, $( document ).scrollLeft() + $( window ).width() - menuWidth - 5 );\n\t x = Math.max( x, $( document ).scrollLeft() + 5 );\n\t return {\n\t top: clickEvent.pageY,\n\t left: x\n\t };\n\t },\n\t\n\t // bind an event handler to all available frames so that when anything is clicked\n\t // the menu is removed from the DOM and the event handler unbinds itself\n\t _setUpCloseBehavior: function(){\n\t var menu = this;\n\t//TODO: alternately: focus hack, blocking overlay, jquery.blockui\n\t\n\t // function to close popup and unbind itself\n\t function closePopup( event ){\n\t $( document ).off( 'click.close_popup' );\n\t if( window.parent !== window ){\n\t try {\n\t $( window.parent.document ).off( \"click.close_popup\" );\n\t } catch( err ){}\n\t } else {\n\t try {\n\t $( 'iframe#galaxy_main' ).contents().off( \"click.close_popup\" );\n\t } catch( err ){}\n\t }\n\t menu.remove();\n\t }\n\t\n\t $( 'html' ).one( \"click.close_popup\", closePopup );\n\t if( window.parent !== window ){\n\t try {\n\t $( window.parent.document ).find( 'html' ).one( \"click.close_popup\", closePopup );\n\t } catch( err ){}\n\t } else {\n\t try {\n\t $( 'iframe#galaxy_main' ).contents().one( \"click.close_popup\", closePopup );\n\t } catch( err ){}\n\t }\n\t },\n\t\n\t // add a menu option/item at the given index\n\t addItem: function( item, index ){\n\t // append to end if no index\n\t index = ( index >= 0 ) ? index : this.options.length;\n\t this.options.splice( index, 0, item );\n\t return this;\n\t },\n\t\n\t // remove a menu option/item at the given index\n\t removeItem: function( index ){\n\t if( index >=0 ){\n\t this.options.splice( index, 1 );\n\t }\n\t return this;\n\t },\n\t\n\t // search for a menu option by its html\n\t findIndexByHtml: function( html ){\n\t for( var i = 0; i < this.options.length; i++ ){\n\t if( _.has( this.options[i], 'html' ) && ( this.options[i].html === html )){\n\t return i;\n\t }\n\t }\n\t return null;\n\t },\n\t\n\t // search for a menu option by its html\n\t findItemByHtml: function( html ){\n\t return this.options[( this.findIndexByHtml( html ))];\n\t },\n\t\n\t // string representation\n\t toString: function(){\n\t return 'PopupMenu';\n\t }\n\t});\n\t/** shortcut to new for when you don't need to preserve the ref */\n\tPopupMenu.create = function _create( $button, options ){\n\t return new PopupMenu( $button, options );\n\t};\n\t\n\t// -----------------------------------------------------------------------------\n\t// the following class functions are bridges from the original make_popupmenu and make_popup_menus\n\t// to the newer backbone.js PopupMenu\n\t\n\t/** Create a PopupMenu from simple map initial_options activated by clicking button_element.\n\t * Converts initial_options to object array used by PopupMenu.\n\t * @param {jQuery|DOMElement} button_element element which, when clicked, activates menu\n\t * @param {Object} initial_options map of key -> values, where\n\t * key is option text, value is fn to call when option is clicked\n\t * @returns {PopupMenu} the PopupMenu created\n\t */\n\tPopupMenu.make_popupmenu = function( button_element, initial_options ){\n\t var convertedOptions = [];\n\t _.each( initial_options, function( optionVal, optionKey ){\n\t var newOption = { html: optionKey };\n\t\n\t // keys with null values indicate: header\n\t if( optionVal === null ){ // !optionVal? (null only?)\n\t newOption.header = true;\n\t\n\t // keys with function values indicate: a menu option\n\t } else if( jQuery.type( optionVal ) === 'function' ){\n\t newOption.func = optionVal;\n\t }\n\t //TODO:?? any other special optionVals?\n\t // there was no divider option originally\n\t convertedOptions.push( newOption );\n\t });\n\t return new PopupMenu( $( button_element ), convertedOptions );\n\t};\n\t\n\t/** Find all anchors in $parent (using selector) and covert anchors into a PopupMenu options map.\n\t * @param {jQuery} $parent the element that contains the links to convert to options\n\t * @param {String} selector jq selector string to find links\n\t * @returns {Object[]} the options array to initialize a PopupMenu\n\t */\n\t//TODO: lose parent and selector, pass in array of links, use map to return options\n\tPopupMenu.convertLinksToOptions = function( $parent, selector ){\n\t $parent = $( $parent );\n\t selector = selector || 'a';\n\t var options = [];\n\t $parent.find( selector ).each( function( elem, i ){\n\t var option = {}, $link = $( elem );\n\t\n\t // convert link text to the option text (html) and the href into the option func\n\t option.html = $link.text();\n\t if( $link.attr( 'href' ) ){\n\t var linkHref = $link.attr( 'href' ),\n\t linkTarget = $link.attr( 'target' ),\n\t confirmText = $link.attr( 'confirm' );\n\t\n\t option.func = function(){\n\t // if there's a \"confirm\" attribute, throw up a confirmation dialog, and\n\t // if the user cancels - do nothing\n\t if( ( confirmText ) && ( !confirm( confirmText ) ) ){ return; }\n\t\n\t // if there's no confirm attribute, or the user accepted the confirm dialog:\n\t switch( linkTarget ){\n\t // relocate the center panel\n\t case '_parent':\n\t window.parent.location = linkHref;\n\t break;\n\t\n\t // relocate the entire window\n\t case '_top':\n\t window.top.location = linkHref;\n\t break;\n\t\n\t // relocate this panel\n\t default:\n\t window.location = linkHref;\n\t }\n\t };\n\t }\n\t options.push( option );\n\t });\n\t return options;\n\t};\n\t\n\t/** Create a single popupmenu from existing DOM button and anchor elements\n\t * @param {jQuery} $buttonElement the element that when clicked will open the menu\n\t * @param {jQuery} $menuElement the element that contains the anchors to convert into a menu\n\t * @param {String} menuElementLinkSelector jq selector string used to find anchors to be made into menu options\n\t * @returns {PopupMenu} the PopupMenu (Backbone View) that can render, control the menu\n\t */\n\tPopupMenu.fromExistingDom = function( $buttonElement, $menuElement, menuElementLinkSelector ){\n\t $buttonElement = $( $buttonElement );\n\t $menuElement = $( $menuElement );\n\t var options = PopupMenu.convertLinksToOptions( $menuElement, menuElementLinkSelector );\n\t // we're done with the menu (having converted it to an options map)\n\t $menuElement.remove();\n\t return new PopupMenu( $buttonElement, options );\n\t};\n\t\n\t/** Create all popupmenus within a document or a more specific element\n\t * @param {DOMElement} parent the DOM element in which to search for popupmenus to build (defaults to document)\n\t * @param {String} menuSelector jq selector string to find popupmenu menu elements (defaults to \"div[popupmenu]\")\n\t * @param {Function} buttonSelectorBuildFn the function to build the jq button selector.\n\t * Will be passed $menuElement, parent.\n\t * (Defaults to return '#' + $menuElement.attr( 'popupmenu' ); )\n\t * @returns {PopupMenu[]} array of popupmenus created\n\t */\n\tPopupMenu.make_popup_menus = function( parent, menuSelector, buttonSelectorBuildFn ){\n\t parent = parent || document;\n\t // orig. Glx popupmenu menus have a (non-std) attribute 'popupmenu'\n\t // which contains the id of the button that activates the menu\n\t menuSelector = menuSelector || 'div[popupmenu]';\n\t // default to (orig. Glx) matching button to menu by using the popupmenu attr of the menu as the id of the button\n\t buttonSelectorBuildFn = buttonSelectorBuildFn || function( $menuElement, parent ){\n\t return '#' + $menuElement.attr( 'popupmenu' );\n\t };\n\t\n\t // aggregate and return all PopupMenus\n\t var popupMenusCreated = [];\n\t $( parent ).find( menuSelector ).each( function(){\n\t var $menuElement = $( this ),\n\t $buttonElement = $( parent ).find( buttonSelectorBuildFn( $menuElement, parent ) );\n\t popupMenusCreated.push( PopupMenu.fromDom( $buttonElement, $menuElement ) );\n\t $buttonElement.addClass( 'popup' );\n\t });\n\t return popupMenusCreated;\n\t};\n\t\n\t\n\t// =============================================================================\n\t return PopupMenu;\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t\n\t\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1), __webpack_require__(3), __webpack_require__(1)))\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, $) {/** Renders the color picker used e.g. in the tool form **/\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4)], __WEBPACK_AMD_DEFINE_RESULT__ = function( Utils ) {\n\t return Backbone.View.extend({\n\t colors: {\n\t standard: ['c00000','ff0000','ffc000','ffff00','92d050','00b050','00b0f0','0070c0','002060','7030a0'],\n\t base : ['ffffff','000000','eeece1','1f497d','4f81bd','c0504d','9bbb59','8064a2','4bacc6','f79646'],\n\t theme :[['f2f2f2','7f7f7f','ddd9c3','c6d9f0','dbe5f1','f2dcdb','ebf1dd','e5e0ec','dbeef3','fdeada'],\n\t ['d8d8d8','595959','c4bd97','8db3e2','b8cce4','e5b9b7','d7e3bc','ccc1d9','b7dde8','fbd5b5'],\n\t ['bfbfbf','3f3f3f','938953','548dd4','95b3d7','d99694','c3d69b','b2a2c7','92cddc','fac08f'],\n\t ['a5a5a5','262626','494429','17365d','366092','953734','76923c','5f497a','31859b','e36c09'],\n\t ['7f7f7e','0c0c0c','1d1b10','0f243e','244061','632423','4f6128','3f3151','205867','974806']]\n\t },\n\t initialize : function( options ) {\n\t this.options = Utils.merge( options, {} );\n\t this.setElement( this._template() );\n\t\n\t // link components\n\t this.$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.$( '.ui-color-picker-header' );\n\t\n\t // build panel\n\t this._build();\n\t\n\t // hide panel on start up\n\t this.visible = false;\n\t\n\t // set initial value\n\t this.value( this.options.value );\n\t\n\t // link boxes\n\t this.$boxes = this.$( '.ui-color-picker-box' );\n\t\n\t // add event handler\n\t var self = this;\n\t this.$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.$view.fadeOut( 'fast' );\n\t }\n\t } );\n\t },\n\t\n\t // value\n\t value : function ( new_val ) {\n\t if ( new_val !== undefined && new_val !== null ) {\n\t // update color value\n\t this.$value.css( 'background-color', new_val );\n\t \n\t // check selected color in panel\n\t this.$( '.ui-color-picker-box' ).empty();\n\t this.$( this._getValue() ).html( this._templateCheck() );\n\t\n\t // trigger custom event\n\t this.options.onchange && this.options.onchange( new_val );\n\t }\n\t\n\t // return current value\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 panel\n\t _build: function() {\n\t var $content = this._content({\n\t label : 'Theme Colors',\n\t colors : this.colors.base,\n\t padding : 10\n\t });\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 {\n\t 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 line_def[ 'padding' ] = 5;\n\t }\n\t }\n\t line_def[ 'colors' ] = this.colors.theme[ i ];\n\t this._content( line_def );\n\t }\n\t this._content({\n\t label : 'Standard Colors',\n\t colors : this.colors.standard,\n\t padding : 5\n\t });\n\t },\n\t\n\t // create content\n\t _content: function( options ) {\n\t // get parameters\n\t var label = options.label;\n\t var colors = options.colors;\n\t var padding = options.padding;\n\t var top = options.top;\n\t var bottom = options.bottom;\n\t\n\t // create lines\n\t var $content = $( this._templateContent() );\n\t\n\t // set label\n\t var $label = $content.find( '.label' );\n\t if ( options.label ) {\n\t $label.html( options.label );\n\t } else {\n\t $label.hide();\n\t }\n\t\n\t // build line\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 ( 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 ( 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 if (padding) {\n\t $line.css( 'padding-bottom', padding );\n\t }\n\t return $content;\n\t },\n\t\n\t // check icon\n\t _templateCheck: function() {\n\t return '';\n\t },\n\t\n\t // content template\n\t _templateContent: function() {\n\t return '' +\n\t '' +\n\t '' +\n\t '';\n\t },\n\t\n\t // box template\n\t _templateBox: function( color ) {\n\t return '';\n\t },\n\t\n\t // template\n\t _template: function() {\n\t return '' +\n\t '' +\n\t '' +\n\t '' +\n\t 'Select a color' +\n\t '' +\n\t '';\n\t }\n\t });\n\t}.apply(exports, __WEBPACK_AMD_DEFINE_ARRAY__), __WEBPACK_AMD_DEFINE_RESULT__ !== undefined && (module.exports = __WEBPACK_AMD_DEFINE_RESULT__));\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(1)))\n\n/***/ },\n/* 53 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function($) {// dependencies\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(25)], __WEBPACK_AMD_DEFINE_RESULT__ = function(Utils, Options) {\n\t\n\t/**\n\t * This class creates/wraps a drill down element.\n\t */\n\tvar View = Options.BaseIcons.extend({\n\t // initialize\n\t initialize: function(options) {\n\t options.type = options.display || 'checkbox';\n\t options.multiple = (options.display == 'checkbox');\n\t Options.BaseIcons.prototype.initialize.call(this, options);\n\t this.initial = true;\n\t },\n\t\n\t // set expand states for initial value\n\t value: function (new_val) {\n\t var val = Options.BaseIcons.prototype.value.call(this, new_val);\n\t if (this.initial && val !== null && this.header_index) {\n\t this.initial = false;\n\t var values = val;\n\t if (!$.isArray(values)) {\n\t values = [values];\n\t }\n\t for (var i in values) {\n\t var list = this.header_index[values[i]];\n\t for (var j in list) {\n\t this._setState(list[j], true);\n\t }\n\t }\n\t }\n\t return val;\n\t },\n\t\n\t /** Expand/collapse a sub group\n\t */\n\t _setState: function (header_id, is_expanded) {\n\t var $button = this.$('.button-' + header_id);\n\t var $subgroup = this.$('.subgroup-' + header_id);\n\t $button.data('is_expanded', is_expanded);\n\t if (is_expanded) {\n\t $subgroup.fadeIn('fast')\n\t $button.removeClass('fa-plus-square');\n\t $button.addClass('fa-minus-square');\n\t } else {\n\t $subgroup.hide();\n\t $button.removeClass('fa-minus-square');\n\t $button.addClass('fa-plus-square');\n\t }\n\t },\n\t\n\t /** Template to create options tree\n\t */\n\t _templateOptions: function(options) {\n\t // link this\n\t var self = this;\n\t\n\t // link data\n\t this.header_index = {};\n\t \n\t // attach event handler\n\t function attach($el, header_id) {\n\t var $button = $el.find('.button-' + header_id);\n\t $button.on('click', function() {\n\t self._setState(header_id, !$button.data('is_expanded'));\n\t });\n\t }\n\t\n\t // recursive function which iterates through options\n\t function iterate ($tmpl, options, header) {\n\t header = header || [];\n\t for (i in options) {\n\t // current option level in hierarchy\n\t var level = options[i];\n\t\n\t // check for options\n\t var has_options = level.options.length > 0;\n\t\n\t // copy current header list\n\t var new_header = header.slice(0);\n\t\n\t // keep track of header list\n\t self.header_index[level.value] = new_header.slice(0);\n\t\n\t // build template\n\t var $group = $('');\n\t if (has_options) {\n\t // create button and subgroup\n\t var header_id = Utils.uid();\n\t var $button = $('');\n\t var $subgroup = $('');\n\t\n\t // keep track of button and subgroup\n\t new_header.push(header_id);\n\t\n\t // create expandable header section\n\t var $buttongroup = $('');\n\t $buttongroup.append($button);\n\t $buttongroup.append(self._templateOption({\n\t label: level.name,\n\t value: level.value\n\t }));\n\t $group.append($buttongroup);\n\t iterate($subgroup, level.options, new_header);\n\t $group.append($subgroup);\n\t\n\t // attach expand/collapse events\n\t attach($group, header_id);\n\t } else {\n\t // append child options\n\t $group.append(self._templateOption({\n\t label: level.name,\n\t value: level.value\n\t }));\n\t }\n\t $tmpl.append($group);\n\t }\n\t }\n\t\n\t // iterate through options and create dom\n\t var $tmpl = $('');\n\t iterate($tmpl, options);\n\t\n\t // return template\n\t return $tmpl;\n\t },\n\t\n\t /** Template for drill down view\n\t */\n\t _template: function(options) {\n\t return '';\n\t }\n\t});\n\t\n\treturn {\n\t View: View\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\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(1)))\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, $, _) {/**\n\t * This class creates/wraps a default html select field as backbone class.\n\t */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(16)], __WEBPACK_AMD_DEFINE_RESULT__ = function(Utils, Buttons) {\n\tvar View = Backbone.View.extend({\n\t // options\n\t optionsDefault: {\n\t id : Utils.uid(),\n\t cls : 'ui-select',\n\t error_text : 'No options available',\n\t empty_text : 'Nothing selected',\n\t visible : true,\n\t wait : false,\n\t multiple : false,\n\t searchable : true,\n\t optional : false\n\t },\n\t\n\t // initialize\n\t initialize: function(options) {\n\t // link this\n\t var self = this;\n\t\n\t // configure options\n\t this.options = Utils.merge(options, this.optionsDefault);\n\t\n\t // create new element\n\t this.setElement(this._template(this.options));\n\t\n\t // link elements\n\t this.$select = this.$el.find('.select');\n\t this.$icon_dropdown = this.$el.find('.icon-dropdown');\n\t this.$icon_dropdown.on( 'click', function() { self.$select.select2 && self.$select.select2( 'open' ) });\n\t\n\t // allow regular multi-select field to be resized\n\t var minHeight = null;\n\t this.$('.icon-resize').on('mousedown', function(event) {\n\t var currentY = event.pageY;\n\t var currentHeight = self.$select.height();\n\t minHeight = minHeight || currentHeight;\n\t $('#dd-helper').show().on('mousemove', function(event) {\n\t self.$select.height(Math.max(currentHeight + (event.pageY - currentY), minHeight));\n\t }).on('mouseup mouseleave', function() {\n\t $('#dd-helper').hide().off();\n\t });\n\t });\n\t\n\t // multiple select fields have an additional button and other custom properties\n\t if (this.options.multiple) {\n\t // create select all button\n\t if (this.options.searchable) {\n\t this.all_button = new Buttons.ButtonCheck({\n\t onclick: function() {\n\t var new_value = [];\n\t if (self.all_button.value() !== 0) {\n\t new_value = self._availableOptions();\n\t }\n\t self.value(new_value);\n\t self.trigger('change');\n\t }\n\t });\n\t this.$el.prepend(this.all_button.$el);\n\t } else {\n\t this.$el.addClass('ui-select-multiple');\n\t }\n\t this.$select.prop('multiple', true);\n\t this.$icon_dropdown.remove();\n\t }\n\t\n\t // update initial options\n\t this.update(this.options.data);\n\t\n\t // set initial value\n\t if (this.options.value !== undefined) {\n\t this.value(this.options.value);\n\t }\n\t\n\t // show/hide\n\t if (!this.options.visible) {\n\t this.hide();\n\t }\n\t\n\t // wait\n\t if (this.options.wait) {\n\t this.wait();\n\t } else {\n\t this.show();\n\t }\n\t\n\t // add change event. fires only on user activity\n\t this.$select.on('change', function() {\n\t self.trigger('change');\n\t });\n\t\n\t // add change event. fires on trigger\n\t this.on('change', function() {\n\t self.options.onchange && self.options.onchange(this.value());\n\t });\n\t },\n\t\n\t /** Return/Set current selection\n\t */\n\t value: function (new_value) {\n\t // set new value\n\t if (new_value !== undefined) {\n\t if (new_value === null) {\n\t new_value = '__null__';\n\t }\n\t if (this.exists(new_value) || this.options.multiple) {\n\t this.$select.val(new_value);\n\t if (this.$select.select2) {\n\t this.$select.select2('val', new_value);\n\t }\n\t }\n\t }\n\t // get current value\n\t var current = this._getValue();\n\t if (this.all_button) {\n\t this.all_button.value($.isArray(current) && current.length || 0, this._size());\n\t }\n\t return current;\n\t },\n\t\n\t /** Return the first select option\n\t */\n\t first: function() {\n\t var options = this.$select.find('option').first();\n\t if (options.length > 0) {\n\t return options.val();\n\t } else {\n\t return null;\n\t }\n\t },\n\t\n\t /** Return the label/text of the current selection\n\t */\n\t text: function () {\n\t return this.$select.find('option:selected').text();\n\t },\n\t\n\t /** Show the select field\n\t */\n\t show: function() {\n\t this.unwait();\n\t this.$select.show();\n\t this.$el.show();\n\t },\n\t\n\t /** Hide the select field\n\t */\n\t hide: function() {\n\t this.$el.hide();\n\t },\n\t\n\t /** Show a spinner indicating that the select options are currently loaded\n\t */\n\t wait: function() {\n\t this.$icon_dropdown.removeClass();\n\t this.$icon_dropdown.addClass('icon-dropdown fa fa-spinner fa-spin');\n\t },\n\t\n\t /** Hide spinner indicating that the request has been completed\n\t */\n\t unwait: function() {\n\t this.$icon_dropdown.removeClass();\n\t this.$icon_dropdown.addClass('icon-dropdown fa fa-caret-down');\n\t },\n\t\n\t /** Returns true if the field is disabled\n\t */\n\t disabled: function() {\n\t return this.$select.is(':disabled');\n\t },\n\t\n\t /** Enable the select field\n\t */\n\t enable: function() {\n\t this.$select.prop('disabled', false);\n\t },\n\t\n\t /** Disable the select field\n\t */\n\t disable: function() {\n\t this.$select.prop('disabled', true);\n\t },\n\t\n\t /** Update all available options at once\n\t */\n\t update: function(options) {\n\t // backup current value\n\t var current = this._getValue();\n\t\n\t // remove all options\n\t this.$select.find('option').remove();\n\t\n\t // add optional field\n\t if (!this.options.multiple && this.options.optional) {\n\t this.$select.append(this._templateOption({value : '__null__', label : this.options.empty_text}));\n\t }\n\t\n\t // add new options\n\t for (var key in options) {\n\t this.$select.append(this._templateOption(options[key]));\n\t }\n\t\n\t // count remaining entries\n\t if (this._size() == 0) {\n\t // disable select field\n\t this.disable();\n\t\n\t // create placeholder\n\t this.$select.append(this._templateOption({value : '__null__', label : this.options.error_text}));\n\t } else {\n\t // enable select field\n\t this.enable();\n\t }\n\t\n\t // update to searchable field (in this case select2)\n\t if (this.options.searchable) {\n\t this.$select.select2('destroy');\n\t this.$select.select2({ closeOnSelect: !this.options.multiple });\n\t this.$( '.select2-container .select2-search input' ).off( 'blur' );\n\t }\n\t\n\t // set previous value\n\t this.value(current);\n\t\n\t // check if any value was set\n\t if (this._getValue() === null && !(this.options.multiple && this.options.optional)) {\n\t this.value(this.first());\n\t }\n\t },\n\t\n\t /** Set the custom onchange callback function\n\t */\n\t setOnChange: function(callback) {\n\t this.options.onchange = callback;\n\t },\n\t\n\t /** Check if a value is an existing option\n\t */\n\t exists: function(value) {\n\t return this.$select.find('option[value=\"' + value + '\"]').length > 0;\n\t },\n\t\n\t /** Get current value from dom\n\t */\n\t _getValue: function() {\n\t var val = this.$select.val();\n\t if (!Utils.validate(val)) {\n\t return null;\n\t }\n\t return val;\n\t },\n\t\n\t /** Returns all currently available options\n\t */\n\t _availableOptions: function() {\n\t var available = [];\n\t this.$select.find('option').each(function(i, e){\n\t available.push($(e).attr('value'));\n\t });\n\t return available;\n\t },\n\t\n\t /** Number of available options\n\t */\n\t _size: function() {\n\t return this.$select.find('option').length;\n\t },\n\t\n\t /** Template for select options\n\t */\n\t _templateOption: function(options) {\n\t return '';\n\t },\n\t\n\t /** Template for select view\n\t */\n\t _template: function(options) {\n\t return '' +\n\t ''\n\t '' +\n\t '