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p=e.View.extend(u.default.LoggableMixin).extend({_logNamespace:"list",viewClass:l.default.ListItemView,collectionClass:e.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:(0,f.default)("This list is empty"),noneFoundMsg:(0,f.default)("No matching items found"),searchPlaceholder:(0,f.default)("search"),initialize:function(e,t){e=e||{},e.logger&&(this.logger=e.logger),this.log(this+".initialize:",e),this.fxSpeed=n.has(e,"fxSpeed")?e.fxSpeed:this.fxSpeed,this.filters=[],this.searchFor=e.searchFor||"",this.selecting=void 0===e.selecting||e.selecting,this.selected=e.selected||[],this.lastSelected=null,this.dragItems=e.dragItems||!1,this.viewClass=e.viewClass||this.viewClass,this.views=[],this.collection=e.collection||this._createDefaultCollection(),this.filters=e.filters||[],this.$scrollContainer=e.$scrollContainer||this.$scrollContainer,this.title=e.title||"",this.subtitle=e.subtitle||"",this._setUpListeners()},_setUpListeners:function(){return this.off(),this.on({error:function(e,t,i,n,s){console.error(e,t,i,n,s)},loading:function(){this._showLoadingIndicator("loading...",40)},"loading-done":function(){this._hideLoadingIndicator(40)}}),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this._setUpCollectionListeners(),this._setUpViewListeners(),this},_createDefaultCollection:function(){return new this.collectionClass([])},_setUpCollectionListeners:function(){return this.log(this+"._setUpCollectionListeners",this.collection),this.stopListening(this.collection),this.listenTo(this.collection,{error:function(e,t,i,n,s){this.trigger("error",e,t,i,n,s)},update:function(e,t){var i=t.changes;return t.renderAll||i.added.length+i.removed.length>1?this.renderItems():1===i.added.length?this.addItemView(n.first(i.added),e,t):1===i.removed.length?this.removeItemView(n.first(i.removed),e,t):void 0}}),this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners"),this.on({"view:selected":function(e,t){if(t&&t.shiftKey&&this.lastSelected){var i=this.viewFromModelId(this.lastSelected);i&&this.selectRange(e,i)}else t&&t.altKey&&!this.selecting&&this.showSelectors();this.selected.push(e.model.id),this.lastSelected=e.model.id},"view:de-selected":function(e,t){this.selected=n.without(this.selected,e.model.id)}})},render:function(e){this.log(this+".render",e);var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var e=s(this.templates.el({},this));return this._renderControls(e),this._renderTitle(e),this._renderSubtitle(e),this._renderSearch(e),this.renderItems(e),e},_renderControls:function(e){this.debug(this+"(ListPanel)._renderControls");var t=s(this.templates.controls({},this));return e.find(".controls").replaceWith(t),t},_renderTitle:function(e){},_renderSubtitle:function(e){},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;i.log("_queueNewRender:",e,t),s(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",this.className).append(e.children()),this.selecting&&this.showSelectors(0),this},_setUpBehaviors:function(e){return e=e||this.$el,this.$controls(e).find("[title]").tooltip(),this._renderMultiselectActionMenu(e),this},_renderMultiselectActionMenu:function(e){e=e||this.$el;var t=e.find(".list-action-menu"),i=this.multiselectActions();if(!i.length)return t.empty();var n=s(['"].join("")),a=i.map(function(e){var t=['",'','','',"
"]),controls:u.default.wrapTemplate(['','
"])}}();var m=p.extend({modelCollectionKey:"contents",initialize:function(e){p.prototype.initialize.call(this,e),this.selecting=void 0!==e.selecting&&e.selecting,this.setModel(this.model,e)},setModel:function(e,t){if(t=t||{},this.debug(this+".setModel:",e,t),this.freeModel(),this.freeViews(),e){var i=this.model?this.model.get("id"):null;this.model=e,this.logger&&(this.model.logger=this.logger),this._setUpModelListeners(),this.stopListening(this.collection),this.collection=this.model[this.modelCollectionKey]||t.collection||this._createDefaultCollection(),this._setUpCollectionListeners(),i&&e.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.listenTo(this.model,"error",function(){var e=Array.prototype.slice.call(arguments,0);e.unshift("error"),this.trigger.apply(this,e)},this),this.logger&&this.listenTo(this.model,"all",function(e){this.info(this+"(model)",e,arguments)}),this},_renderControls:function(e){this.debug(this+"(ModelListPanel)._renderControls");var t=this.model?this.model.toJSON():{},i=s(this.templates.controls(t,this));return e.find(".controls").replaceWith(i),i},toString:function(){return"ModelListPanel("+this.model+")"}});m.prototype.templates=function(){var e=u.default.wrapTemplate(['','
",'<%- view.title %>
',"<%- view.subtitle %>
','','','','',"
",'','
","','",'","
",'","','
"]);return n.extend(n.clone(p.prototype.templates),{controls:e})}(),t.default={ListPanel:p,ModelListPanel:m}}).call(t,i(2),i(1),i(0))},function(e,t,i){"use strict";function n(e,t){function i(e){o(this).parent().children("input").val("").trigger("searchInput.clear").blur(),t.onclear()}function n(e,n){if(!n)return i();o(this).trigger("search.search",n),"function"==typeof t.onfirstsearch&&u?(u=!1,t.onfirstsearch(n)):t.onsearch(n)}function s(){return['"].join("")}var r=27,d=13,c=o(e),u=!0,h={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onfirstsearch:null,onsearch:function(e){},minSearchLen:0,escWillClear:!0,oninit:function(){}};return"string"===a.default.type(t)?("toggle-loading"===t&&function(){c.find(".search-loading").toggle(),c.find(".search-clear").toggle()}(),c):("object"===a.default.type(t)&&(t=a.default.extend(!0,{},h,t)),c.addClass("search-input").prepend([function(){return o(s()).focus(function(e){o(this).select()}).keyup(function(e){if(e.preventDefault(),e.stopPropagation(),e.which===r&&t.escWillClear)i.call(this,e);else{var s=o(this).val();(e.which===d||t.minSearchLen&&s.length>=t.minSearchLen)&&n.call(this,e,s)}}).val(t.initialVal)}(),function(){return o([''].join("")).tooltip({placement:"bottom"}).click(function(e){i.call(this,e)})}(),function(){return o([''].join("")).hide().tooltip({placement:"bottom"})}()]))}var s=i(0),a=function(e){return e&&e.__esModule?e:{default:e}}(s),o=a.default,l=window._l||function(e){return e};a.default.fn.extend({searchInput:function(e){return this.each(function(){return n(this,e)})}})},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(17),a=n(s),o=i(4),l=n(o),r=i(58),d=n(r),c=i(3),u=n(c),h=a.default.DatasetListItemView,f=h.extend({className:h.prototype.className+" history-content",initialize:function(e,t){h.prototype.initialize.call(this,e,t)},toString:function(){return"HDAListItemView("+(this.model?""+this.model:"(no model)")+")"}});f.prototype.templates=function(){var t=function(t){return'\n \n "},i=e.extend({},h.prototype.templates.warnings,{hidden:l.default.wrapTemplate(["<% if( !dataset.visible ){ %>",'","<% } %>"],"dataset")});return e.extend({},h.prototype.templates,{titleBar:t,warnings:i})}(),t.default={HDAListItemView:f}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(8),a=n(s),o=i(33),l=n(o),r=i(59),d=n(r),c=i(4),u=(n(c),i(58)),h=n(u),f=i(3),p=n(f),m=l.default.DCListItemView,g=m.extend({className:m.prototype.className+" history-content",_setUpListeners:function(){var e=this;m.prototype._setUpListeners.call(this);var t=function(t,i){e.render()};this.model.jobStatesSummary&&this.listenTo(this.model.jobStatesSummary,"change",t),this.listenTo(this.model,{"change:tags change:visible change:state":t})},_getFoldoutPanelClass:function(){return d.default.CollectionView},_swapNewRender:function(e){m.prototype._swapNewRender.call(this,e);var t,i=this.model.jobStatesSummary;t=i?i.new()?"loading":i.errored()?"error":i.terminal()?"ok":i.running()?"running":"queued":this.model.get("job_source_id")?"loading":this.model.get("populated_state")?a.default.OK:a.default.RUNNING,this.$el.addClass("state-"+t);var n=this.stateDescription();return this.$(".state-description").html(n),this.$el},stateDescription:function(){var e=this.model,t=(e.get("element_count"),e.get("job_source_type")),i=(this.model.get("collection_type"),d.default.collectionTypeDescription(e)),n=d.default.collectionDescription(e),s=e.jobStatesSummary;if(t&&"Job"!=t){if(s&&s.hasDetails()){var a=s.new(),o=a?null:s.jobCount();if(a)return'\n ','
",'<%- model.name %>
',"<%- view.subtitle %>
','','','','',"
",'','
","','",'","
",'","\n Creating jobs...\n ';if(s.errored()){return"a "+i+" with "+s.numInError()+" / "+o+" jobs in error"}if(s.terminal())return n;var l=s.states().running||0,r=s.states().ok||0,c=r/(1*o),u=l/(1*o),h=1-c-u;return'\n
\n '+(o&&o>1?o+" jobs":"a job")+" generating a "+i+'\n \n \n '}return'\n
\n Loading job data for '+i+'...\n '}return n},toString:function(){return"HDCAListItemView("+(this.model?""+this.model:"(no model)")+")"}});g.prototype.templates=function(){var t=e.extend({},m.prototype.templates.warnings,{hidden:function(e){e.visible||(0,p.default)("This collection has been hidden")}}),i=function(t){return'\n \n "};return e.extend({},m.prototype.templates,{warnings:t,titleBar:i})}(),t.default={HDCAListItemView:g}}).call(t,i(1))},,function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(67),l=a(o),r=i(42),d=a(r),c=i(9),u=a(c),h=i(5),f=a(h),p=e.View.extend({el:"body",className:"full-content",_panelids:["left","right"],initialize:function(t){var i=this;this.config=n.defaults(t.config||{},{message_box_visible:!1,message_box_content:"",message_box_class:"info",show_inactivity_warning:!1,inactivity_box_content:""}),Galaxy.modal=this.modal=new u.default.View,Galaxy.display=this.display=function(e){e.title?(f.default.setWindowTitle(e.title),e.allow_title_display=!1):(f.default.setWindowTitle(),e.allow_title_display=!0),i.center.display(e)},Galaxy.router=this.router=t.Router&&new t.Router(i,t),this.masthead=new l.default.View(this.config),this.center=new d.default.CenterPanel,this.$el.attr("scroll","no"),this.$el.html(this._template()),this.$("#masthead").replaceWith(this.masthead.$el),this.$("#center").append(this.center.$el),this.$el.append(this.masthead.frame.$el),this.$el.append(this.modal.$el),this.$messagebox=this.$("#messagebox"),this.$inactivebox=this.$("#inactivebox"),this.panels={},n.each(this._panelids,function(e){var n=e.charAt(0).toUpperCase()+e.slice(1),s=t[n];if(s){var a=new s(i,t);i[a.toString()]=a,i.panels[e]=new d.default.SidePanel({id:e,el:i.$("#"+e),view:a})}}),this.render(),this.router&&e.history.start({root:Galaxy.root,pushState:!0})},render:function(){return s(".select2-hidden-accessible").remove(),this.masthead.render(),this.renderMessageBox(),this.renderInactivityBox(),this.renderPanels(),this._checkCommunicationServerOnline(),this},renderMessageBox:function(){if(this.config.message_box_visible){var e=this.config.message_box_content||"",t=this.config.message_box_class||"info";this.$el.addClass("has-message-box"),this.$messagebox.attr("class","panel-"+t+"-message").html(e).toggle(!!e).show()}else this.$el.removeClass("has-message-box"),this.$messagebox.hide();return this},renderInactivityBox:function(){if(this.config.show_inactivity_warning){var e=this.config.inactivity_box_content||"",t=s("").attr("href",Galaxy.root+"user/resend_verification").text("Resend verification");this.$el.addClass("has-inactivity-box"),this.$inactivebox.html(e+" ").append(t).toggle(!!e).show()}else this.$el.removeClass("has-inactivity-box"),this.$inactivebox.hide();return this},renderPanels:function(){var e=this;return n.each(this._panelids,function(t){var i=e.panels[t];i?i.render():(e.$("#center").css(t,0),e.$("#"+t).hide())}),this},_template:function(){return['d)return 1}for(var c,u,h=0,f=Math.max(o.length,l.length);hu)return 1}return 0}Object.defineProperty(t,"__esModule",{value:!0}),t.default=n},function(e,t,i){"use strict";var n=i(0),s=function(e){return e&&e.__esModule?e:{default:e}}(n),a=s.default;s.default.fn.extend({hoverhighlight:function(e,t){return e=e||"body",this.length?(a(this).each(function(){var i=a(this),n=i.data("target");n&&i.mouseover(function(i){a(n,e).css({background:t})}).mouseout(function(e){a(n).css({background:""})})}),this):this}})},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(9),l=a(o),r=i(36),d=a(r),c=i(3),u=a(c),h={defaultName:e.template("Copy of '<%- name %>'"),title:e.template((0,u.default)("Copying history")+' "<%- name %>"'),submitLabel:(0,u.default)("Copy"),errorMessage:(0,u.default)("History could not be copied."),progressive:(0,u.default)("Copying history"),activeLabel:(0,u.default)("Copy only the active, non-deleted datasets"),allLabel:(0,u.default)("Copy all datasets including deleted ones"),anonWarning:(0,u.default)("As an anonymous user, unless you login or register, you will lose your current history ")+(0,u.default)("after copying this history. "),_template:e.template(["<% if( isAnon ){ %>",'","<% } %>",""].join("")),_showAjaxIndicator:function(){var e='
","=c?l.push(e.createPair.call(this,{listA:n,indexA:a,listB:s,indexB:o.index})):a+=1,!n.length||!s.length)return l}return this.debug("paired:",JSON.stringify(l,null," ")),this.debug("autopair _strategy ---------------------------"),l}}function r(e,t){var i=e.toJSON();return b(i,{historyId:e.historyId,defaultHideSourceItems:t})}Object.defineProperty(t,"__esModule",{value:!0});var d=i(99),c=o(d),u=i(53),h=o(u),f=i(52),p=o(f),m=i(4),g=o(m),_=i(3),v=o(_);i(54);var w=e.View.extend(g.default.LoggableMixin).extend({_logNamespace:"collections",tagName:"li",className:"dataset paired",initialize:function(e){this.pair=e.pair||{}},template:n.template(['<%- pair.forward.name %>','','<%- pair.name %>',"",'<%- pair.reverse.name %>'].join("")),render:function(){this.dragStartHandler=n.bind(this._dragstart,this),this.dragEndHandler=n.bind(this._dragend,this);var e=this.$el.attr("draggable",!0).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container").get(0);return e.addEventListener("dragstart",this.dragStartHandler,!1),e.addEventListener("dragend",this.dragEndHandler,!1),this},events:{dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(e){e.currentTarget.style.opacity="0.4",e.originalEvent&&(e=e.originalEvent),e.dataTransfer.effectAllowed="move",e.dataTransfer.setData("text/plain",JSON.stringify(this.pair)),this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(e){e.currentTarget.style.opacity="1.0",this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(e){this.$el.parent().trigger(e)},toString:function(){return"PairView("+this.pair.name+")"}}),y=e.View.extend(g.default.LoggableMixin).extend(p.default.CollectionCreatorMixin).extend({_logNamespace:"collections",className:"list-of-pairs-collection-creator collection-creator flex-row-container",initialize:function(e){this.metric("PairedCollectionCreator.initialize",e),e=n.defaults(e,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:!0,strategy:"lcs",matchPercentage:.9,twoPassAutopairing:!0}),this.initialList=e.datasets,this.historyId=e.historyId,this.filters=this.commonFilters[e.filters]||this.commonFilters[this.DEFAULT_FILTERS],n.isArray(e.filters)&&(this.filters=e.filters),this.automaticallyPair=e.automaticallyPair,this.strategy=this.strategies[e.strategy]||this.strategies[this.DEFAULT_STRATEGY],n.isFunction(e.strategy)&&(this.strategy=e.strategy),this.matchPercentage=e.matchPercentage,this.twoPassAutopairing=e.twoPassAutopairing,this.removeExtensions=!0,this.oncancel=e.oncancel,this.oncreate=e.oncreate,this.autoscrollDist=e.autoscrollDist||24,this.unpairedPanelHidden=!1,this.pairedPanelHidden=!1,this.$dragging=null,this.blocking=!1,this._setUpCommonSettings(e),this._setUpBehaviors(),this._dataSetUp()},commonFilters:{illumina:["_1","_2"],Rs:["_R1","_R2"]},DEFAULT_FILTERS:"illumina",strategies:{simple:"autopairSimple",lcs:"autopairLCS",levenshtein:"autopairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[],this.unpaired=[],this.selectedIds=[],this._sortInitialList(),this._ensureIds(),this.unpaired=this.initialList.slice(0),this.automaticallyPair&&(this.autoPair(),this.once("rendered:initial",function(){this.trigger("autopair")}))},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(e){return e.sort(function(e,t){return(0,h.default)(e.name,t.name)}),e},_ensureIds:function(){return this.initialList.forEach(function(e){e.hasOwnProperty("id")||(e.id=n.uniqueId())}),this.initialList},_splitByFilters:function(){function e(e,t){return t.test(e.name)}var t=this.filters.map(function(e){return new RegExp(e)}),i=[[],[]];return this.unpaired.forEach(function(n){t.forEach(function(t,s){e(n,t)&&i[s].push(n)})}),i},_addToUnpaired:function(e){var t=this;this.unpaired.splice(function i(n,s){if(n===s)return n;var a=Math.floor((s-n)/2)+n,o=(0,h.default)(e.name,t.unpaired[a].name);if(o<0)return i(n,a);if(o>0)return i(a+1,s);for(;t.unpaired[a]&&t.unpaired[a].name===e.name;)a++;return a}(0,this.unpaired.length),0,e)},autoPair:function(e){var t=this._splitByFilters(),i=[];return this.twoPassAutopairing&&(i=this.autopairSimple({listA:t[0],listB:t[1]}),t=this._splitByFilters()),e=e||this.strategy,t=this._splitByFilters(),i=i.concat(this[e].call(this,{listA:t[0],listB:t[1]}))},autopairSimple:l({scoreThreshold:function(){return.6},match:function(e){return e=e||{},e.matchTo===e.possible?{index:e.index,score:1}:e.bestMatch}}),autopairLevenshtein:l({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var t=(0,c.default)(e.matchTo,e.possible),i=1-t/Math.max(e.matchTo.length,e.possible.length);return i>e.bestMatch.score?{index:e.index,score:i}:e.bestMatch}}),autopairLCS:l({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var t=this._naiveStartingAndEndingLCS(e.matchTo,e.possible).length,i=t/Math.max(e.matchTo.length,e.possible.length);return i>e.bestMatch.score?{index:e.index,score:i}:e.bestMatch}}),_naiveStartingAndEndingLCS:function(e,t){for(var i="",n="",s=0,a=0;s=0&&a>=0&&e[s]===t[a];)n=[e[s],n].join(""),s-=1,a-=1;return i+n},_pair:function(e,t,i){i=i||{},this.debug("_pair:",e,t);var s=this._createPair(e,t,i.name);return this.paired.push(s),this.unpaired=n.without(this.unpaired,e,t),i.silent||this.trigger("pair:new",s),s},_createPair:function(e,t,i){if(!e||!t||e===t)throw new Error("Bad pairing: "+[JSON.stringify(e),JSON.stringify(t)]);return i=i||this._guessNameForPair(e,t),{forward:e,name:i,reverse:t}},_guessNameForPair:function(e,t,i){i=void 0!==i?i:this.removeExtensions;var n=e.name,s=t.name,a=this._naiveStartingAndEndingLCS(n.replace(new RegExp(this.filters[0]),""),s.replace(new RegExp(this.filters[1]),""));if(i){var o=a.lastIndexOf(".");if(o>0){var l=a.slice(o,a.length);a=a.replace(l,""),n=n.replace(l,""),s=s.replace(l,"")}}return a||n+" & "+s},_unpair:function(e,t){if(t=t||{},!e)throw new Error("Bad pair: "+JSON.stringify(e));return this.paired=n.without(this.paired,e),this._addToUnpaired(e.forward),this._addToUnpaired(e.reverse),t.silent||this.trigger("pair:unpair",[e]),e},unpairAll:function(){for(var e=[];this.paired.length;)e.push(this._unpair(this.paired[0],{silent:!0}));this.trigger("pair:unpair",e)},_pairToJSON:function(e,t){return t=t||"hda",{collection_type:"paired",src:"new_collection",name:e.name,element_identifiers:[{name:"forward",id:e.forward.id,src:t},{name:"reverse",id:e.reverse.id,src:t}]}},createList:function(e){var t=this,i=Galaxy.root+"api/histories/"+this.historyId+"/contents/dataset_collections",a={type:"dataset_collection",collection_type:"list:paired",hide_source_items:t.hideOriginals||!1,name:n.escape(e||t.$(".collection-name").val()),element_identifiers:t.paired.map(function(e){return t._pairToJSON(e)})};return 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i=this.collection.get(e);i.set({percentage:100,status:"error",info:t}),this.ui_button.model.set({percentage:this._uploadPercentage(100,i.get("file_size")),status:"danger"}),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.error++,this.render()},_eventComplete:function(){this.collection.each(function(e){"queued"==e.get("status")&&e.set("status","init")}),this.counter.running=0,this.render()},_eventRemove:function(e){var t=e.get("status");"success"==t?this.counter.success--:"error"==t?this.counter.error--:this.counter.announce--,this.uploadbox.remove(e.id),this.render()},_eventFtp:function(){if(this.ftp.visible)this.ftp.hide();else{this.ftp.empty();var e=this;this.ftp.append(new p.default({collection:this.collection,ftp_upload_site:this.ftp_upload_site,onadd:function(t){return e.uploadbox.add([{mode:"ftp",name:t.path,size:t.size,path:t.path}])},onremove:function(t){e.collection.remove(t)}}).$el),this.ftp.show()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(0!=this.counter.announce&&0==this.counter.running){var e=this;this.upload_size=0,this.upload_completed=0,this.collection.each(function(t){"init"==t.get("status")&&(t.set("status","queued"),e.upload_size+=t.get("file_size"))}),this.ui_button.model.set({percentage:0,status:"success"}),this.counter.running=this.counter.announce,this.history_id=this.app.currentHistory(),this._uploadFtp(),this.uploadbox.start(),this.render()}},_eventStop:function(){this.counter.running>0&&(this.ui_button.model.set("status","info"),s(".upload-top-info").html("Queue will pause after completing the current 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e=this.model.attributes;this.$title.html(s.escape(e.file_name)),this.$size.html(d.default.bytesToString(e.file_size)),this.$mode.removeClass().addClass("upload-mode").addClass("text-primary"),"new"==e.file_mode?(this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$mode.addClass("fa fa-edit")):"local"==e.file_mode?this.$mode.addClass("fa fa-laptop"):"ftp"==e.file_mode&&this.$mode.addClass("fa fa-folder-open-o")},_refreshExtension:function(){this.select_extension.value(this.model.get("extension"))},_refreshGenome:function(){this.select_genome.value(this.model.get("genome"))},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("Failed: "+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));this.$progress_bar.css({width:e+"%"}),this.$percentage.html(100!=e?e+"%":"Adding to 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","=c?l.push(e.createPair.call(this,{listA:n,indexA:a,listB:s,indexB:o.index})):a+=1,!n.length||!s.length)return l}return this.debug("paired:",JSON.stringify(l,null," ")),this.debug("autopair _strategy ---------------------------"),l}}function r(e,t){var i=e.toJSON();return b(i,{historyId:e.historyId,defaultHideSourceItems:t})}Object.defineProperty(t,"__esModule",{value:!0});var d=i(99),c=o(d),u=i(53),h=o(u),f=i(52),p=o(f),m=i(4),g=o(m),_=i(3),v=o(_);i(54);var w=e.View.extend(g.default.LoggableMixin).extend({_logNamespace:"collections",tagName:"li",className:"dataset paired",initialize:function(e){this.pair=e.pair||{}},template:n.template(['<%- pair.forward.name %>','','<%- pair.name %>',"",'<%- pair.reverse.name %>'].join("")),render:function(){this.dragStartHandler=n.bind(this._dragstart,this),this.dragEndHandler=n.bind(this._dragend,this);var e=this.$el.attr("draggable",!0).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container").get(0);return e.addEventListener("dragstart",this.dragStartHandler,!1),e.addEventListener("dragend",this.dragEndHandler,!1),this},events:{dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(e){e.currentTarget.style.opacity="0.4",e.originalEvent&&(e=e.originalEvent),e.dataTransfer.effectAllowed="move",e.dataTransfer.setData("text/plain",JSON.stringify(this.pair)),this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(e){e.currentTarget.style.opacity="1.0",this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(e){this.$el.parent().trigger(e)},toString:function(){return"PairView("+this.pair.name+")"}}),y=e.View.extend(g.default.LoggableMixin).extend(p.default.CollectionCreatorMixin).extend({_logNamespace:"collections",className:"list-of-pairs-collection-creator collection-creator 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e.sort(function(e,t){return(0,h.default)(e.name,t.name)}),e},_ensureIds:function(){return this.initialList.forEach(function(e){e.hasOwnProperty("id")||(e.id=n.uniqueId())}),this.initialList},_splitByFilters:function(){function e(e,t){return t.test(e.name)}var t=this.filters.map(function(e){return new RegExp(e)}),i=[[],[]];return this.unpaired.forEach(function(n){t.forEach(function(t,s){e(n,t)&&i[s].push(n)})}),i},_addToUnpaired:function(e){var t=this;this.unpaired.splice(function i(n,s){if(n===s)return n;var a=Math.floor((s-n)/2)+n,o=(0,h.default)(e.name,t.unpaired[a].name);if(o<0)return i(n,a);if(o>0)return i(a+1,s);for(;t.unpaired[a]&&t.unpaired[a].name===e.name;)a++;return a}(0,this.unpaired.length),0,e)},autoPair:function(e){var t=this._splitByFilters(),i=[];return this.twoPassAutopairing&&(i=this.autopairSimple({listA:t[0],listB:t[1]}),t=this._splitByFilters()),e=e||this.strategy,t=this._splitByFilters(),i=i.concat(this[e].call(this,{listA:t[0],listB:t[1]}))},autopairSimple:l({scoreThreshold:function(){return.6},match:function(e){return e=e||{},e.matchTo===e.possible?{index:e.index,score:1}:e.bestMatch}}),autopairLevenshtein:l({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var t=(0,c.default)(e.matchTo,e.possible),i=1-t/Math.max(e.matchTo.length,e.possible.length);return i>e.bestMatch.score?{index:e.index,score:i}:e.bestMatch}}),autopairLCS:l({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var t=this._naiveStartingAndEndingLCS(e.matchTo,e.possible).length,i=t/Math.max(e.matchTo.length,e.possible.length);return i>e.bestMatch.score?{index:e.index,score:i}:e.bestMatch}}),_naiveStartingAndEndingLCS:function(e,t){for(var i="",n="",s=0,a=0;s=0&&a>=0&&e[s]===t[a];)n=[e[s],n].join(""),s-=1,a-=1;return i+n},_pair:function(e,t,i){i=i||{},this.debug("_pair:",e,t);var s=this._createPair(e,t,i.name);return this.paired.push(s),this.unpaired=n.without(this.unpaired,e,t),i.silent||this.trigger("pair:new",s),s},_createPair:function(e,t,i){if(!e||!t||e===t)throw new Error("Bad pairing: "+[JSON.stringify(e),JSON.stringify(t)]);return i=i||this._guessNameForPair(e,t),{forward:e,name:i,reverse:t}},_guessNameForPair:function(e,t,i){i=void 0!==i?i:this.removeExtensions;var n=e.name,s=t.name,a=this._naiveStartingAndEndingLCS(n.replace(new RegExp(this.filters[0]),""),s.replace(new RegExp(this.filters[1]),""));if(i){var o=a.lastIndexOf(".");if(o>0){var l=a.slice(o,a.length);a=a.replace(l,""),n=n.replace(l,""),s=s.replace(l,"")}}return a||n+" & "+s},_unpair:function(e,t){if(t=t||{},!e)throw new Error("Bad pair: "+JSON.stringify(e));return this.paired=n.without(this.paired,e),this._addToUnpaired(e.forward),this._addToUnpaired(e.reverse),t.silent||this.trigger("pair:unpair",[e]),e},unpairAll:function(){for(var e=[];this.paired.length;)e.push(this._unpair(this.paired[0],{silent:!0}));this.trigger("pair:unpair",e)},_pairToJSON:function(e,t){return t=t||"hda",{collection_type:"paired",src:"new_collection",name:e.name,element_identifiers:[{name:"forward",id:e.forward.id,src:t},{name:"reverse",id:e.reverse.id,src:t}]}},createList:function(e){var t=this,i=Galaxy.root+"api/histories/"+this.historyId+"/contents/dataset_collections",a={type:"dataset_collection",collection_type:"list:paired",hide_source_items:t.hideOriginals||!1,name:n.escape(e||t.$(".collection-name").val()),element_identifiers:t.paired.map(function(e){return t._pairToJSON(e)})};return 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o=i(3),l=a(o),r=i(5),d=(a(r),i(49)),c=a(d),u=i(256),h=a(u),f=i(91),p=a(f),m=i(92),g=a(m),_=i(27),v=a(_),w=i(12),y=a(w),b=i(6),x=a(b),$=i(257),C=a($);i(93),t.default=e.View.extend({upload_size:0,collection:new c.default.Collection,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ui_button=e.ui_button,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.$uploadbox=this.$(".upload-box"),this.$uploadtable=this.$(".upload-table"),this.btnLocal=new x.default.Button({id:"btn-local",title:(0,l.default)("Choose local file"),onclick:function(){t.uploadbox.select()},icon:"fa fa-laptop"}),this.btnFtp=new x.default.Button({id:"btn-ftp",title:(0,l.default)("Choose FTP file"),onclick:function(){t._eventFtp()},icon:"fa fa-folder-open-o"}),this.btnCreate=new 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y.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome,onchange:function(e){t._changeGenome(e)}}),this.loader=new C.default({$container:this.$uploadbox,collection:this.collection,new_content:function(e){var i=new h.default(t,{model:e});return t.$uploadtable.find("> tbody:first").append(i.$el),i.render(),i}}),this.collection.on("remove",function(e){t._eventRemove(e)}),this.render()},render:function(){var e="";e=0==this.counter.announce?this.uploadbox.compatible()?" 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Add more files or click 'Start' to proceed.":"Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining.",this.$(".upload-top-info").html(e);var t=0==this.counter.running&&this.counter.announce+this.counter.success+this.counter.error>0,i=0==this.counter.running&&this.counter.announce>0,n=0==this.counter.running,s=this.counter.announce+this.counter.success+this.counter.error>0;this.btnReset[t?"enable":"disable"](),this.btnStart[i?"enable":"disable"](),this.btnStart.$el[i?"addClass":"removeClass"]("btn-primary"),this.btnStop[this.counter.running>0?"enable":"disable"](),this.btnLocal[n?"enable":"disable"](),this.btnFtp[n?"enable":"disable"](),this.btnCreate[n?"enable":"disable"](),this.btnFtp.$el[this.ftp_upload_site?"show":"hide"](),this.$(".upload-table")[s?"show":"hide"](),this.$(".upload-helper")[s?"hide":"show"]()},_eventAnnounce:function(e,t){this.counter.announce++;var i=new c.default.Model({id:e,file_name:t.name,file_size:t.size,file_mode:t.mode||"local",file_path:t.path,file_data:t});this.render(),this.collection.add(i)},_eventProgress:function(e,t){var i=this.collection.get(e);i.set("percentage",t),this.ui_button.model.set("percentage",this._uploadPercentage(t,i.get("file_size")))},_eventSuccess:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"success"}),this.ui_button.model.set("percentage",this._uploadPercentage(100,i.get("file_size"))),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.success++,this.render(),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"error",info:t}),this.ui_button.model.set({percentage:this._uploadPercentage(100,i.get("file_size")),status:"danger"}),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.error++,this.render()},_eventComplete:function(){this.collection.each(function(e){"queued"==e.get("status")&&e.set("status","init")}),this.counter.running=0,this.render()},_eventRemove:function(e){var t=e.get("status");"success"==t?this.counter.success--:"error"==t?this.counter.error--:this.counter.announce--,this.uploadbox.remove(e.id),this.render()},_eventFtp:function(){if(this.ftp.visible)this.ftp.hide();else{this.ftp.empty();var e=this;this.ftp.append(new p.default({collection:this.collection,ftp_upload_site:this.ftp_upload_site,onadd:function(t){return e.uploadbox.add([{mode:"ftp",name:t.path,size:t.size,path:t.path}])},onremove:function(t){e.collection.remove(t)}}).$el),this.ftp.show()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(0!=this.counter.announce&&0==this.counter.running){var e=this;this.upload_size=0,this.upload_completed=0,this.collection.each(function(t){"init"==t.get("status")&&(t.set("status","queued"),e.upload_size+=t.get("file_size"))}),this.ui_button.model.set({percentage:0,status:"success"}),this.counter.running=this.counter.announce,this.history_id=this.app.currentHistory(),this._uploadFtp(),this.uploadbox.start(),this.render()}},_eventStop:function(){this.counter.running>0&&(this.ui_button.model.set("status","info"),s(".upload-top-info").html("Queue will pause after completing the current 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e=this,t=[];this.collection.each(function(i){"queued"==i.get("status")&&"ftp"==i.get("file_mode")&&(e.uploadbox.remove(i.id),t.push(i))}),t.length>0&&s.uploadpost({data:this.app.toData(t),url:this.app.options.nginx_upload_path,success:function(i){n.each(t,function(t){e._eventSuccess(t.id)})},error:function(i){n.each(t,function(t){e._eventError(t.id,i)})}})},_uploadPercentage:function(e,t){return(this.upload_completed+e*t)/this.upload_size},_template:function(){return''}})}).call(t,i(2),i(1),i(0))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),l=a(o),r=i(5),d=a(r),c=i(49),u=(a(c),i(90)),h=a(u),f=i(27),p=a(f),m=i(12),g=a(m);t.default=e.View.extend({status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template(t.model)),this.$mode=this.$(".upload-mode"),this.$title=this.$(".upload-title"),this.$text=this.$(".upload-text"),this.$size=this.$(".upload-size"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$text_content=this.$(".upload-text-content"),this.$settings=this.$(".upload-settings"),this.$symbol=this.$(".upload-symbol"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.settings=new p.default.View({title:(0,l.default)("Upload configuration"),container:this.$(".upload-settings"),placement:"bottom"});var s=this.app.select_genome.value(),a=this.app.select_extension.value();this.select_genome=new 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e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=n(5),s=a(o),l=n(306),c=a(l),d=e.Model.extend({initialize:function(e,t){this.app=e,this.element=t.element,this.input_terminals={},this.output_terminals={},this.errors={},this.workflow_outputs=[]},getWorkflowOutput:function(e){return i.findWhere(this.workflow_outputs,{output_name:e})},isWorkflowOutput:function(e){return void 0!==this.getWorkflowOutput(e)},removeWorkflowOutput:function(e){for(;this.isWorkflowOutput(e);)this.workflow_outputs.splice(this.getWorkflowOutput(e),1)},addWorkflowOutput:function(e,t){if(!this.isWorkflowOutput(e)){var n={output_name:e};return t&&(n.label=t),this.workflow_outputs.push(n),!0}return!1},labelWorkflowOutput:function(e,t){var n=!1,i=null;if(this.isWorkflowOutput(e)){var r=this.getWorkflowOutput(e);i=r.label,r.label=t,n=i!=t}else n=this.addWorkflowOutput(e,t);return n&&(this.app.workflow.updateOutputLabel(i,t),this.markChanged(),this.nodeView.redrawWorkflowOutputs()),n},connectedOutputTerminals:function(){return this._connectedTerminals(this.output_terminals)},_connectedTerminals:function(e){var t=[];return r.each(e,function(e,n){n.connectors.length>0&&t.push(n)}),t},hasConnectedOutputTerminals:function(){var e=this.output_terminals;for(var t in e)if(e[t].connectors.length>0)return!0;return!1},connectedMappedInputTerminals:function(){return this._connectedMappedTerminals(this.input_terminals)},hasConnectedMappedInputTerminals:function(){var e=this.input_terminals;for(var t in e){var n=e[t];if(n.connectors.length>0&&n.isMappedOver())return!0}return!1},_connectedMappedTerminals:function(e){var t=[];return r.each(e,function(e,n){n.mapOver().isCollection&&n.connectors.length>0&&t.push(n)}),t},mappedInputTerminals:function(){return this._mappedTerminals(this.input_terminals)},_mappedTerminals:function(e){var t=[];return r.each(e,function(e,n){n.mapOver().isCollection&&t.push(n)}),t},hasMappedOverInputTerminals:function(){var e=!1;return i.each(this.input_terminals,function(t){t.mapOver().isCollection&&(e=!0)}),e},redraw:function(){r.each(this.input_terminals,function(e,t){t.redraw()}),r.each(this.output_terminals,function(e,t){t.redraw()})},clone:function(){var e=this,t={name:this.name,label:this.label,annotation:this.annotation,post_job_actions:this.post_job_actions},n=this.app.workflow.create_node(this.type,this.name,this.content_id);s.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:{type:this.type,tool_id:this.content_id,inputs:this.tool_state},success:function(i){var r=Object.assign({},i,t);n.init_field_data(r),n.update_field_data(r),e.app.workflow.activate_node(n)}})},destroy:function(){r.each(this.input_terminals,function(e,t){t.destroy()}),r.each(this.output_terminals,function(e,t){t.destroy()}),this.app.workflow.remove_node(this),r(this.element).remove()},make_active:function(){r(this.element).addClass("toolForm-active")},make_inactive:function(){var e=this.element.get(0);!function(t){t.removeChild(e),t.appendChild(e)}(e.parentNode),r(e).removeClass("toolForm-active")},init_field_data:function(e){e.type&&(this.type=e.type),this.name=e.name,this.config_form=e.config_form,this.tool_version=this.config_form&&this.config_form.version,this.tool_state=e.tool_state,this.errors=e.errors,this.tooltip=e.tooltip?e.tooltip:"",this.annotation=e.annotation,this.post_job_actions=e.post_job_actions?e.post_job_actions:{},this.label=e.label,this.uuid=e.uuid,this.workflow_outputs=e.workflow_outputs?e.workflow_outputs:[];var t=this,n=new c.default({el:this.element[0],node:t});t.nodeView=n,r.each(e.data_inputs,function(e,t){n.addDataInput(t)}),e.data_inputs.length>0&&e.data_outputs.length>0&&n.addRule(),r.each(e.data_outputs,function(e,t){n.addDataOutput(t)}),n.render(),this.app.workflow.node_changed(this,!0)},update_field_data:function(e){var t=this,n=t.nodeView,a=[];if(r.each(n.outputViews,function(t,n){var r=n.output.name,o=e.data_outputs,s=!1;i.each(o,function(e){e.name==r&&(s=!0)}),!1===s&&a.push(r)}),i.each(a,function(e){i.each(n.outputViews[e].terminalElement.terminal.connectors,function(e){e&&e.destroy()}),n.outputViews[e].remove(),delete n.outputViews[e],delete t.output_terminals[e]}),r.each(t.workflow_outputs,function(e,n){n&&!t.output_terminals[n.output_name]&&t.workflow_outputs.splice(e,1)}),r.each(e.data_outputs,function(e,i){n.outputViews[i.name]?(t.output_terminals[i.name].datatypes=i.extensions,t.output_terminals[i.name].destroyInvalidConnections()):n.addDataOutput(i)}),this.tool_state=e.tool_state,this.config_form=e.config_form,this.tool_version=this.config_form&&this.config_form.version,this.errors=e.errors,this.annotation=e.annotation,this.label=e.label,"post_job_actions"in e){var o=e.post_job_actions;this.post_job_actions=o||{}}t.nodeView.renderToolErrors();var s=n.$("div.inputs"),l=n.newInputsDiv(),c={};i.each(e.data_inputs,function(e){var n=t.nodeView.addDataInput(e,l);c[e.name]=n}),i.each(i.difference(i.values(n.terminalViews),i.values(c)),function(e){e.el.terminal.destroy()}),n.terminalViews=c,t.nodeView.render(),1==e.data_outputs.length&&"collection_type"in e.data_outputs[0]&&n.updateDataOutput(e.data_outputs[0]),s.replaceWith(l),"workflow_outputs"in e&&(this.workflow_outputs=e.workflow_outputs?e.workflow_outputs:[]),this.markChanged(),this.redraw()},error:function(e){var t=r(this.element).find(".toolFormBody");t.find("div").remove();var n="![]()
").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png").click(function(){var e=t.output.name;i.isWorkflowOutput(e)?(i.removeWorkflowOutput(e),t.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png")):(i.addWorkflowOutput(e),t.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png")),window.workflow_globals.workflow.has_changes=!0,window.workflow_globals.canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Mark dataset as a workflow output. All unmarked datasets will be hidden."}),this.$el.css({top:"50%",margin:"-8px 0px 0px 0px",right:8}),this.$el.show(),this.resetImage()},resetImage:function(){this.node.isWorkflowOutput(this.output.name)?this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png"):this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-outline.png")},hoverImage:function(){this.$("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small-yellow.png")}});t.default={DataInputView:i,DataOutputView:r}}).call(t,n(2),n(0))},function(e,t,n){"use strict";(function(e,i){function r(e){return e&&e.__esModule?e:{default:e}}function a(e){var t=e.model.attributes,n=t.workflow,i=t.node;t.inputs.unshift({type:"text",name:"__annotation",label:"Annotation",fixed:!0,value:i.annotation,area:!0,help:"Add an annotation or notes to this step. Annotations are available when a workflow is viewed."}),t.inputs.unshift({type:"text",name:"__label",label:"Label",value:i.label,help:(0,d.default)("Add a step label."),fixed:!0,onchange:function(t){var r=!1;for(var a in n.nodes){var o=n.nodes[a];if(o.label&&o.label==t&&o.id!=i.id){r=!0;break}}var s=e.data.match("__label");e.element_list[s].model.set("error_text",r&&"Duplicate label. Please fix this before saving the workflow."),e.trigger("change")}})}function o(e,t,n,i){var r=i.node.post_job_actions;t=t||[],t.push(e);for(var a in e.inputs){var s=e.inputs[a];if(s.action){if(s.name="pja__"+n+"__"+s.action,s.pja_arg&&(s.name+="__"+s.pja_arg),s.payload)for(var l in s.payload)s.payload[s.name+"__"+l]=s.payload[l],delete s.payload[l];var c=r[s.action+n];if(c){for(var d in t)t[d].expanded=!0;s.pja_arg?s.value=c.action_arguments&&c.action_arguments[s.pja_arg]||s.value:s.value="true"}}s.inputs&&o(s,t.slice(0),n,i)}}function s(e,t){var n=[],i=[],r=t.datatypes,a=t.node,s=t.workflow;for(var l in r)n.push({0:r[l],1:r[l]});for(l in a.input_terminals)i.push(a.input_terminals[l].name);n.sort(function(e,t){return e.label>t.label?1:e.labelhere for more information. Valid inputs are: '+i.join(", ")+"."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:n,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"tags",label:"Add Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{action:"RemoveTagDatasetAction",pja_arg:"tags",label:"Remove Tags",type:"text",value:"",ignore:"",help:"This action will remove tags for the dataset."},{title:(0,d.default)("Assign columns"),type:"section",flat:!0,inputs:[{action:"ColumnSetAction",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};return o(u,[],e,t),u}function l(e){var t=e.model.attributes,n=t.inputs,i=t.node,r=i.post_job_actions,a=i.output_terminals&&Object.keys(i.output_terminals)[0];if(a){n.push({name:"pja__"+a+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(r["EmailAction"+a])),ignore:"false",help:(0,d.default)("An email notification will be sent when the job has completed."),payload:{host:window.location.host}}),n.push({name:"pja__"+a+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(r["DeleteIntermediatesAction"+a])),ignore:"false",help:"Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs."});for(var o in i.output_terminals)n.push(s(o,t))}}Object.defineProperty(t,"__esModule",{value:!0});var c=n(3),d=r(c),u=n(5),h=r(u),f=n(13),p=r(f),g=n(81),m=r(g),_=e.View.extend({initialize:function(e){var t=this,n=e.node;this.form=new p.default(h.default.merge(e,{onchange:function(){h.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:{id:n.id,type:n.type,content_id:n.content_id,inputs:t.form.data.create()},success:function(e){n.update_field_data(e)}})}})),a(this.form),this.form.render()}}),v=e.View.extend({initialize:function(e){var t=this,n=e.node;this.form=new m.default(h.default.merge(e,{text_enable:"Set in Advance",text_disable:"Set at Runtime",narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",initialmodel:function(e,n){t._customize(n),e.resolve()},buildmodel:function(e,t){t.model.get("postchange")(e,t)},postchange:function(e,r){var a=r.model.attributes,o={tool_id:a.id,tool_version:a.version,type:"tool",inputs:i.extend(!0,{},r.data.create())};Galaxy.emit.debug("tool-form-workflow::postchange()","Sending current state.",o),h.default.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:o,success:function(i){r.model.set(i.config_form),t._customize(r),r.update(i.config_form),r.errors(i.config_form),n.update_field_data(i),Galaxy.emit.debug("tool-form-workflow::postchange()","Received new model.",i),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form-workflow::postchange()","Refresh request failed.",t),e.reject()}})}}))},_customize:function(e){var t=e.model.attributes;h.default.deepeach(t.inputs,function(e){e.type&&(-1!=["data","data_collection"].indexOf(e.type)?(e.type="hidden",e.info="Data input '"+e.name+"' ("+h.default.textify(e.extensions)+")",e.value={__class__:"RuntimeValue"}):e.fixed||(e.collapsible_value={__class__:"RuntimeValue"},e.is_workflow=e.options&&0===e.options.length||-1!=["integer","float"].indexOf(e.type)))}),h.default.deepeach(t.inputs,function(e){"conditional"===e.type&&(e.test_param.collapsible_value=void 0)}),l(e),a(e)}});t.default={Default:_,Tool:v}}).call(t,n(2),n(0))},function(e,t,n){"use strict";(function(e,i){function r(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=n(3),s=a(o),l=n(1),c=r(l),d=n(312),u=r(d),h=n(24),f=a(h),p=n(5),g=a(p),m=n(46),_=a(m),v=n(44),y=a(v);n(77);var b=e.Model.extend({is_visible:function(e,t){var n=e.getBoundingClientRect(),r=i("svg")[0].getBoundingClientRect();return!(n.right<0||n.left>r.right||n.bottom<0||n.top>r.bottom)}}),w={drawTicks:function(e,t,n,i,r){var a=e.append("g").selectAll("g").data(t).enter().append("g").selectAll("g").data(n).enter().append("g").attr("class","tick").attr("transform",function(e){return"rotate("+(180*e.angle/Math.PI-90)+")translate("+e.radius+",0)"}),o=[],s=[],l=function(e){return e.angle>Math.PI?"end":null};return r?(o=[0,0,0,-4],s=[4,0,"",".35em"],l=null):(o=[1,0,4,0],s=[0,4,".35em",""]),a.append("line").attr("x1",o[0]).attr("y1",o[1]).attr("x2",o[2]).attr("y1",o[3]).style("stroke","#000"),a.append("text").attr("x",s[0]).attr("y",s[1]).attr("dx",s[2]).attr("dy",s[3]).attr("text-anchor",l).attr("transform",i).text(function(e){return e.label})},formatNum:function(e,t){if(void 0===t&&(t=2),null===e)return null;var n=null;if(Math.abs(e)<1)n=e.toPrecision(t);else{var i=Math.round(e.toPrecision(t));e=Math.abs(e),e<1e3?n=i:e<1e6?n=Math.round((i/1e3).toPrecision(3)).toFixed(0)+"K":e<1e9&&(n=Math.round((i/1e6).toPrecision(3)).toFixed(0)+"M")}return n}},x=e.Model.extend({}),k=e.View.extend({className:"circster",initialize:function(e){this.genome=e.genome,this.label_arc_height=50,this.scale=1,this.circular_views=null,this.chords_views=null,this.model.get("drawables").on("add",this.add_track,this),this.model.get("drawables").on("remove",this.remove_track,this);var t=this.model.get("config");t.get("arc_dataset_height").on("change:value",this.update_track_bounds,this),t.get("track_gap").on("change:value",this.update_track_bounds,this)},get_circular_tracks:function(){return this.model.get("drawables").filter(function(e){return"DiagonalHeatmapTrack"!==e.get("track_type")})},get_chord_tracks:function(){return this.model.get("drawables").filter(function(e){return"DiagonalHeatmapTrack"===e.get("track_type")})},get_tracks_bounds:function(){var e=this.get_circular_tracks(),t=this.model.get("config").get_value("arc_dataset_height"),n=this.model.get("config").get_value("track_gap"),i=Math.min(this.$el.width(),this.$el.height())-20,r=i/2-e.length*(t+n)+n-this.label_arc_height,a=u.range(r,i/2,t+n);return c.map(a,function(e){return[e,e+t]})},render:function(){var e=this,t=e.$el.width(),n=e.$el.height(),i=this.get_circular_tracks(),r=this.get_chord_tracks(),a=e.model.get("config").get_value("total_gap"),o=this.get_tracks_bounds(),s=u.select(e.$el[0]).append("svg").attr("width",t).attr("height",n).attr("pointer-events","all").append("svg:g").call(u.behavior.zoom().on("zoom",function(){var t=d.event.scale;s.attr("transform","translate("+d.event.translate+") scale("+t+")"),e.scale!==t&&(e.zoom_drag_timeout&&clearTimeout(e.zoom_drag_timeout),e.zoom_drag_timeout=setTimeout(function(){},400))})).attr("transform","translate("+t/2+","+n/2+")").append("svg:g").attr("class","tracks");this.circular_views=i.map(function(t,n){var i=new T({el:s.append("g")[0],track:t,radius_bounds:o[n],genome:e.genome,total_gap:a});return i.render(),i}),this.chords_views=r.map(function(t){var n=new E({el:s.append("g")[0],track:t,radius_bounds:o[0],genome:e.genome,total_gap:a});return n.render(),n});var l=this.circular_views[this.circular_views.length-1].radius_bounds[1],c=[l,l+this.label_arc_height];this.label_track_view=new C({el:s.append("g")[0],track:new x,radius_bounds:c,genome:e.genome,total_gap:a}),this.label_track_view.render()},add_track:function(e){var t=this.model.get("config").get_value("total_gap");if("DiagonalHeatmapTrack"===e.get("track_type")){var n=this.circular_views[0].radius_bounds,i=new E({el:u.select("g.tracks").append("g")[0],track:e,radius_bounds:n,genome:this.genome,total_gap:t});i.render(),this.chords_views.push(i)}else{var r=this.get_tracks_bounds();c.each(this.circular_views,function(e,t){e.update_radius_bounds(r[t])}),c.each(this.chords_views,function(e){e.update_radius_bounds(r[0])});var a=this.circular_views.length,o=new T({el:u.select("g.tracks").append("g")[0],track:e,radius_bounds:r[a],genome:this.genome,total_gap:t});o.render(),this.circular_views.push(o)}},remove_track:function(e,t,n){var i=this.circular_views[n.index];this.circular_views.splice(n.index,1),i.$el.remove();var r=this.get_tracks_bounds();c.each(this.circular_views,function(e,t){e.update_radius_bounds(r[t])})},update_track_bounds:function(){var e=this.get_tracks_bounds();c.each(this.circular_views,function(t,n){t.update_radius_bounds(e[n])}),c.each(this.chords_views,function(t){t.update_radius_bounds(e[0])})}}),M=e.View.extend({tagName:"g",initialize:function(e){this.bg_stroke="#ddd",this.loading_bg_fill="#ffc",this.bg_fill="#ddd",this.total_gap=e.total_gap,this.track=e.track,this.radius_bounds=e.radius_bounds,this.genome=e.genome,this.chroms_layout=this._chroms_layout(),this.data_bounds=[],this.scale=1,this.parent_elt=u.select(this.$el[0])},get_fill_color:function(){var e=this.track.get("config").get_value("block_color");return e||(e=this.track.get("config").get_value("color")),e},render:function(){var e=this.parent_elt,t=this.chroms_layout,n=u.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),r=e.selectAll("g").data(t).enter().append("svg:g"),a=r.append("path").attr("d",n).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);a.append("title").text(function(e){return e.data.chrom});var o=this,s=o.track.get("data_manager"),l=!s||s.data_is_ready();i.when(l).then(function(){i.when(o._render_data(e)).then(function(){a.style("fill",o.bg_fill),o.render_labels()})})},render_labels:function(){},update_radius_bounds:function(e){this.radius_bounds=e;var t=u.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1e3).attr("d",t),this._transition_chrom_data(),this._transition_labels()},update_scale:function(e){var t=this.scale;if(this.scale=e,!(e<=t)){var n=this,r=new b;return 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null===e}),o=e.get("config").get_value("color");n.each(function(e,t){u.select(this).transition().duration(1e3).style("stroke",o).style("fill",o).attr("d",a[t])})})}},_transition_labels:function(){},_update_data_bounds:function(e){this.data_bounds=e||this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome)),this._transition_chrom_data()},_render_data:function(e){var t=this,n=this.chroms_layout,r=this.track,a=i.Deferred();return i.when(r.get("data_manager").get_genome_wide_data(this.genome)).then(function(i){t.data_bounds=t.get_data_bounds(i),r.get("config").set_value("min_value",t.data_bounds[0],{silent:!0}),r.get("config").set_value("max_value",t.data_bounds[1],{silent:!0});var o=c.zip(n,i);c.each(o,function(n){var i=n[0],r=n[1];return t._render_chrom_data(e,i,r)});var s=t.get_fill_color();t.parent_elt.selectAll("path.chrom-data").style("stroke",s).style("fill",s),a.resolve(e)}),a},_render_chrom_data:function(e,t,n){},_get_path_function:function(e,t){},_chroms_layout:function(){var e=this.genome.get_chroms_info(),t=u.layout.pie().value(function(e){return e.len}).sort(null),n=t(e),i=2*Math.PI*this.total_gap/e.length;return c.map(n,function(e,t){var n=e.endAngle-i;return e.endAngle=n>e.startAngle?n:e.startAngle,e})}}),C=M.extend({initialize:function(e){M.prototype.initialize.call(this,e),this.innerRadius=this.radius_bounds[0],this.radius_bounds[0]=this.radius_bounds[1],this.bg_stroke="#fff",this.bg_fill="#fff",this.min_arc_len=.05},_render_data:function(e){var t=this,n=e.selectAll("g");n.selectAll("path").attr("id",function(e){return"label-"+e.data.chrom}),n.append("svg:text").filter(function(e){return e.endAngle-e.startAngle>t.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("class","chrom-label").attr("xlink:href",function(e){return"#label-"+e.data.chrom}).attr("startOffset","25%").text(function(e){return e.data.chrom});var i=function(e){var n=(e.endAngle-e.startAngle)/e.value,i=u.range(0,e.value,25e6).map(function(i,r){return{radius:t.innerRadius,angle:i*n+e.startAngle,label:0===r?0:r%3?null:t.formatNum(i)}});return i.length<4&&(i[i.length-1].label=t.formatNum(Math.round((i[i.length-1].angle-e.startAngle)/n))),i},r=function(e){return e.angle>Math.PI?"rotate(180)translate(-16)":null},a=c.filter(this.chroms_layout,function(e){return e.endAngle-e.startAngle>t.min_arc_len});this.drawTicks(this.parent_elt,a,i,r)}});c.extend(C.prototype,w);var S=M.extend({initialize:function(e){M.prototype.initialize.call(this,e);var t=this.track.get("config");t.get("min_value").on("change:value",this._update_min_max,this),t.get("max_value").on("change:value",this._update_min_max,this),t.get("color").on("change:value",this._transition_chrom_data,this)},_update_min_max:function(){var e=this.track.get("config"),t=[e.get_value("min_value"),e.get_value("max_value")];this._update_data_bounds(t),this.parent_elt.selectAll(".min_max").text(function(e,n){return t[n]})},_quantile:function(e,t){return e.sort(u.ascending),u.quantile(e,t)},_render_chrom_data:function(e,t,n){var i=this._get_path_function(t,n);return i?e.datum(n.data).append("path").attr("class","chrom-data").attr("chrom",t.data.chrom).attr("d",i):null},_get_path_function:function(e,t){if("string"==typeof t||!t.data||0===t.data.length)return null;var n=u.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(!0),i=u.scale.linear().domain([0,t.data.length]).range([e.startAngle,e.endAngle]),r=u.svg.line.radial().interpolate("linear").radius(function(e){return n(e[1])}).angle(function(e,t){return i(t)});return u.svg.area.radial().interpolate(r.interpolate()).innerRadius(n(0)).outerRadius(r.radius()).angle(r.angle())},render_labels:function(){var e=this,t=function(){return"rotate(90)"},n=this.drawTicks(this.parent_elt,[this.chroms_layout[0]],this._data_bounds_ticks_fn(),t,!0).classed("min_max",!0);c.each(n,function(t){i(t).click(function(){new _.default.ConfigSettingCollectionView({collection:e.track.get("config")}).render_in_modal("Configure Track")})})},_transition_labels:function(){if(0!==this.data_bounds.length){var e=this,t=c.filter(this.chroms_layout,function(e){return e.endAngle-e.startAngle>.08}),n=c.filter(t,function(e,t){return t%3==0}),i=c.flatten(c.map(n,function(t){return 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e=this.get("history_content_type"),t=this.get("history_id"),i=this.get("id"),n=""+this.urlRoot+t+"/contents/"+e+"s/"+i;return"dataset_collection"==e&&(n=n+"?view=element-reference&fuzzy_count="+l),n},hide:function(t){return this.get("visible")?this.save({visible:!1},t):e.when()},unhide:function(t){return this.get("visible")?e.when():this.save({visible:!0},t)},toString:function(){return[this.get("type_id"),this.get("hid"),this.get("name")].join(":")}};t.default={HistoryContentMixin:r}}).call(t,i(0))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var i={_validationWarning:function(e,t){"name"===e&&(e=this.$(".collection-name").add(this.$(".collection-name-prompt")),this.$(".collection-name").focus().select()),t?(e=e||this.$(".validation-warning"),e.removeClass("validation-warning")):e.addClass("validation-warning")},_changeHideOriginals:function(e){this.hideOriginals=this.$(".hide-originals").prop("checked")},_changeName:function(e){this._validationWarning("name",!!this._getName())},_nameCheckForEnter:function(e){13!==e.keyCode||this.blocking||this._clickCreate()},_getName:function(){return e.escape(this.$(".collection-name").val())},_clickMoreHelp:function(e){e.stopPropagation(),this.$(".main-help").addClass("expanded"),this.$(".more-help").hide()},_clickLessHelp:function(e){e.stopPropagation(),this.$(".main-help").removeClass("expanded"),this.$(".more-help").show()},_toggleHelp:function(e){e.stopPropagation(),this.$(".main-help").toggleClass("expanded"),this.$(".more-help").toggle()},_showAlert:function(e,t){t=t||"alert-danger",this.$(".main-help").hide(),this.$(".header .alert").attr("class","alert alert-dismissable").addClass(t).show().find(".alert-message").html(e)},_hideAlert:function(e){this.$(".main-help").show(),this.$(".header .alert").hide()},_cancelCreate:function(e){"function"==typeof this.oncancel&&this.oncancel.call(this)},_clickCreate:function(e){var t=this._getName();t?this.blocking||this.createList(t):this._validationWarning("name")},_setUpCommonSettings:function(e){this.hideOriginals=e.defaultHideSourceItems||!1},_renderFooter:function(t,i){var n=this,s=this.$(".footer").empty().html(this.templates.footer());return e.each(this.footerSettings,function(e,t){n.$(t).prop("checked",n[e])}),"function"==typeof this.oncancel&&this.$(".cancel-create.btn").show(),s},_creatorTemplates:{main:e.template(['','',''].join(""))}};t.default={CollectionCreatorMixin:i}}).call(t,i(1))},function(e,t,i){"use strict";function n(e,t){var i=/(-?[0-9\.]+)/g,n=e.toString().toLowerCase()||"",s=t.toString().toLowerCase()||"",a=String.fromCharCode(0),o=n.replace(i,a+"$1"+a).split(a),l=s.replace(i,a+"$1"+a).split(a),r=new Date(n).getTime(),d=r?new Date(s).getTime():null;if(d){if(r'+this.progressive+"...
";this.modal.$(".modal-body").empty().append(e).css({"margin-top":"8px"})},dialog:function(t,i,a){function o(){var e=t.$("#copy-modal-title").val();if(!e)return void t.$(".invalid-title").show();var n="copy-all"===t.$('input[name="copy-what"]:checked').val();t.$("button").prop("disabled",!0),l._showAjaxIndicator(),i.copy(!0,e,n).done(function(e){r.resolve(e)}).fail(function(t,s,a){var o={name:e,copyAllDatasets:n};d.default.ajaxErrorModal(i,t,o,l.errorMessage),r.rejectWith(r,arguments)}).done(function(){m&&t.hide()})}a=a||{};var l=this,r=n.Deferred(),c=a.nameFn||this.defaultName,h=c({name:i.get("name")}),f=a.allDatasets?"copy-all":"copy-non-deleted",p=!!e.isUndefined(a.allowAll)||a.allowAll,m=!!e.isUndefined(a.autoClose)||a.autoClose;this.modal=t;var g=a.closing_callback;return t.show(e.extend(a,{title:this.title({name:i.get("name")}),body:s(l._template({name:h,isAnon:Galaxy.user.isAnonymous(),allowAll:p,copyWhat:f,activeLabel:this.activeLabel,allLabel:this.allLabel,anonWarning:this.anonWarning})),buttons:e.object([[(0,u.default)("Cancel"),function(){t.hide()}],[this.submitLabel,o]]),height:"auto",closing_events:!0,closing_callback:function(e){e&&r.reject({cancelled:!0}),g&&g(e)}})),t.$("#copy-modal-title").focus().select(),t.$("#copy-modal-title").on("keydown",function(e){13===e.keyCode&&(e.preventDefault(),o())}),r}},f=e.extend({},h,{defaultName:e.template("imported: <%- name %>"),title:e.template((0,u.default)("Importing history")+' "<%- name %>"'),submitLabel:(0,u.default)("Import"),errorMessage:(0,u.default)("History could not be imported."),progressive:(0,u.default)("Importing history"),activeLabel:(0,u.default)("Import only the active, non-deleted datasets"),allLabel:(0,u.default)("Import all datasets including deleted ones"),anonWarning:(0,u.default)("As an anonymous user, unless you login or register, you will lose your current history ")+(0,u.default)("after importing this history. ")}),p=function(e,t){t=t||{};var i=window.parent.Galaxy.modal||new l.default.View({});return t.useImport?f.dialog(i,e,t):h.dialog(i,e,t)};t.default=p}).call(t,i(1),i(0),i(0))},function(e,t,i){"use strict";(function(e){function n(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}Object.defineProperty(t,"__esModule",{value:!0});var s=i(1),a=n(s),o=i(2),l=n(o),r=i(4),d=function(e){return e&&e.__esModule?e:{default:e}}(r),c=l.Collection.extend({initialize:function(e,t){l.Collection.prototype.initialize.call(this,e,t),this.setOrder(t.order||this.order,{silent:!0})},_setUpListeners:function(){return this.on({"changed-order":this.sort})},fetch:function(e){return e=this._buildFetchOptions(e),Galaxy.debug("fetch options:",e),l.Collection.prototype.fetch.call(this,e)},_buildFetchOptions:function(e){e=a.clone(e)||{};var t=this;e.traditional=!0,e.data=e.data||t._buildFetchData(e),Galaxy.debug("data:",e.data);var i=this._buildFetchFilters(e);return Galaxy.debug("filters:",i),a.isEmpty(i)||a.extend(e.data,this._fetchFiltersToAjaxData(i)),Galaxy.debug("data:",e.data),e},_buildFetchData:function(e){var t={};return this.order&&(t.order=this.order),a.defaults(a.pick(e,this._fetchParams),t)},_fetchParams:["order","limit","offset","view","keys"],_buildFetchFilters:function(e){return a.clone(e.filters||{})},_fetchFiltersToAjaxData:function(e){var t={q:[],qv:[]};return a.each(e,function(e,i){void 0!==e&&""!==e&&(!0===e&&(e="True"),!1===e&&(e="False"),null===e&&(e="None"),t.q.push(i),t.qv.push(e))}),t},reset:function(e,t){return this.allFetched=!1,l.Collection.prototype.reset.call(this,e,t)},order:null,comparators:{update_time:d.default.buildComparator("update_time",{ascending:!1}),"update_time-asc":d.default.buildComparator("update_time",{ascending:!0}),create_time:d.default.buildComparator("create_time",{ascending:!1}),"create_time-asc":d.default.buildComparator("create_time",{ascending:!0})},setOrder:function(e,t){t=t||{};var i=this,n=i.comparators[e];if(a.isUndefined(n))throw new Error("unknown order: "+e);if(n!==i.comparator)return i.order=e,i.comparator=n,t.silent||i.trigger("changed-order",t),i}}),u=c.extend({limitPerPage:500,initialize:function(e,t){c.prototype.initialize.call(this,e,t),this.currentPage=t.currentPage||0},getTotalItemCount:function(){return this.length},shouldPaginate:function(){return this.getTotalItemCount()>=this.limitPerPage},getLastPage:function(){return Math.floor(this.getTotalItemCount()/this.limitPerPage)},getPageCount:function(){return this.getLastPage()+1},getPageLimitOffset:function(e){return e=this.constrainPageNum(e),{limit:this.limitPerPage,offset:e*this.limitPerPage}},constrainPageNum:function(e){return Math.max(0,Math.min(e,this.getLastPage()))},fetchPage:function(e,t){var i=this;return e=i.constrainPageNum(e),i.currentPage=e,t=a.defaults(t||{},i.getPageLimitOffset(e)),i.trigger("fetching-more"),i.fetch(t).always(function(){i.trigger("fetching-more-done")})},fetchCurrentPage:function(e){return this.fetchPage(this.currentPage,e)},fetchPrevPage:function(e){return this.fetchPage(this.currentPage-1,e)},fetchNextPage:function(e){return this.fetchPage(this.currentPage+1,e)}}),h=c.extend({limitOnFirstFetch:null,limitPerFetch:100,initialize:function(e,t){c.prototype.initialize.call(this,e,t),this.limitOnFirstFetch=t.limitOnFirstFetch||this.limitOnFirstFetch,this.limitPerFetch=t.limitPerFetch||this.limitPerFetch,this.allFetched=!1,this.lastFetched=t.lastFetched||0},_buildFetchOptions:function(e){return e.remove=e.remove||!1,c.prototype._buildFetchOptions.call(this,e)},fetchFirst:function(e){return Galaxy.debug("ControlledFetchCollection.fetchFirst:",e),e=e?a.clone(e):{},this.allFetched=!1,this.lastFetched=0,this.fetchMore(a.defaults(e,{reset:!0,limit:this.limitOnFirstFetch}))},fetchMore:function(t){Galaxy.debug("ControlledFetchCollection.fetchMore:",t),t=a.clone(t||{});var i=this;if(Galaxy.debug("fetchMore, options.reset:",t.reset),!t.reset&&i.allFetched)return e.when();t.reset?t.offset=0:void 0===t.offset&&(t.offset=i.lastFetched);var n=t.limit=t.limit||i.limitPerFetch||null;return Galaxy.debug("fetchMore, limit:",n,"offset:",t.offset),i.trigger("fetching-more"),i.fetch(t).always(function(){i.trigger("fetching-more-done")}).done(function(e){var t=a.isArray(e)?e.length:0;i.lastFetched+=t,Galaxy.debug("fetchMore, lastFetched:",i.lastFetched),(!n||t'):this.$list().find(".contents-loading-indicator").remove()},renderItems:function(e){e=e||this.$el;var t=this.$list(e);n(".tooltip").remove(),t.empty(),this.views=[];var i=this._filterCollection();return i.length?(this._renderPagination(e),this.views=this._renderSomeItems(i,t)):e.find("> .controls .list-pagination").empty(),this._renderEmptyMessage(e).toggle(!i.length),this.trigger("views:ready",this.views),this.views},_renderPagination:function(e){var t=e.find("> .controls .list-pagination");return this.searchFor||!this.model.contents.shouldPaginate()?t.empty():(t.html(this.templates.pagination({current:this.model.contents.currentPage+1,last:this.model.contents.getLastPage()+1},this)),t.find("select.pages").tooltip(),t)},_renderSomeItems:function(e,t){var i=this,n=[];return t.append(e.map(function(e){var t=i._createItemView(e);return n.push(t),i._renderItemView$el(t)})),n},_filterItem:function(e){var t=this.model.contents;return(t.includeHidden||!e.hidden())&&(t.includeDeleted||!e.isDeletedOrPurged())&&k.prototype._filterItem.call(this,e)},_getItemViewClass:function(e){var t=e.get("history_content_type");switch(t){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+t)},_getItemViewOptions:function(t){var i=k.prototype._getItemViewOptions.call(this,t);return e.extend(i,{linkTarget:this.linkTarget,expanded:this.model.contents.storage.isExpanded(t.id),hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(e){var t=this;return k.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{expanded:function(e){t.model.contents.storage.addExpanded(e.model)},collapsed:function(e){t.model.contents.storage.removeExpanded(e.model)}})},collapseAll:function(){this.model.contents.storage.clearExpanded(),k.prototype.collapseAll.call(this)},getSelectedModels:function(){var e=k.prototype.getSelectedModels.call(this);return e.historyId=this.collection.historyId,e},events:e.extend(e.clone(k.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click > .controls .prev":"_clickPrevPage","click > .controls .next":"_clickNextPage","change > .controls .pages":"_changePageSelect","click .messages [class$=message]":"clearMessages"}),_clickPrevPage:function(e){this.model.stopPolling(),this.model.contents.fetchPrevPage()},_clickNextPage:function(e){this.model.stopPolling(),this.model.contents.fetchNextPage()},_changePageSelect:function(e){this.model.stopPolling();var t=n(e.currentTarget).val();this.model.contents.fetchPage(t)},toggleShowDeleted:function(e,t){e=void 0!==e?e:!this.model.contents.includeDeleted;var i=this.model.contents;return i.setIncludeDeleted(e,t),this.trigger("show-deleted",e),i.fetchCurrentPage({renderAll:!0}),e},toggleShowHidden:function(e,t,i){e=void 0!==e?e:!this.model.contents.includeHidden;var n=this.model.contents;return n.setIncludeHidden(e,i),this.trigger("show-hidden",e),n.fetchCurrentPage({renderAll:!0}),e},_firstSearch:function(e){var t=this;if(this.log("onFirstSearch",e),this.model.contents.haveSearchDetails())return void this.searchItems(e);this.$("> .controls .search-input").searchInput("toggle-loading"),this.searchFor=e;this.model.contents.progressivelyFetchDetails({silent:!0}).progress(function(e,i,n){t.renderItems(),t.trigger("search:loading-progress",i,n)}).always(function(){t.$el.find("> .controls .search-input").searchInput("toggle-loading")}).done(function(){t.searchItems(e,"force")})},clearSearch:function(e){var t=this;return this.searchFor?(this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.model.contents.fetchCurrentPage({silent:!0}).done(function(){t.renderItems()}),this):this},errorHandler:function(t,i,n){if(!i||0!==i.status||0!==i.readyState){if(this.error(t,i,n),e.isString(t)&&e.isString(i)){var s=t,a=i;return v.default.errorModal(s,a,n)}return i&&502===i.status?v.default.badGatewayErrorModal():v.default.ajaxErrorModal(t,i,n)}},clearMessages:function(t){return(e.isUndefined(t)?this.$messages().children('[class$="message"]'):n(t.currentTarget)).fadeOut(this.fxSpeed,function(){n(this).remove()}),this},scrollToHid:function(t){return this.scrollToItem(e.first(this.viewsWhereModel({hid:t})))},ordinalIndicator:function(e){var t=""+e;switch(t.charAt(t.length-1)){case"1":return t+"st";case"2":return t+"nd";case"3":return t+"rd";default:return t+"th"}},toString:function(){return"HistoryView("+(this.model?this.model.get("name"):"")+")"}});S.prototype.templates=function(){var t=function(){return'
\n \n
'},i=x.default.wrapTemplate(['','
"],"history"),n=x.default.wrapTemplate(['','",''],"pages");return e.extend(e.clone(k.prototype.templates),{el:t,controls:i,pagination:n})}(),t.default={HistoryView:S}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e){function i(t){return''+e.escape(t.slice(5))+""}function n(t){var n=e.filter(e.uniq(t.tags),function(e){return 0===e.indexOf("name:")}),s=e.sortBy(n).map(i);return'\n "}Object.defineProperty(t,"__esModule",{value:!0}),t.default={nametagTemplate:n}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}function s(e){var t=e.get("collection_type");return"list"==t?(0,f.default)("list"):"paired"==t?(0,f.default)("dataset pair"):"list:paired"==t?(0,f.default)("list of pairs"):(0,f.default)("nested list")}function a(e){var t=e.get("element_count"),i="a "+s(e);if(t){var n;1==t?n="with 1 item":t&&(n="with "+t+" items"),i=i+" "+(0,f.default)(n)}return i}Object.defineProperty(t,"__esModule",{value:!0});var o=i(38),l=n(o),r=i(29),d=(n(r),i(33)),c=n(d),u=i(4),h=(n(u),i(3)),f=n(h),p=l.default.ModelListPanel,m=p.extend({_logNamespace:"collections",className:p.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:c.default.DatasetDCEListItemView,modelCollectionKey:"elements",initialize:function(e){p.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,this.panelStack=[],this.parentName=e.parentName,this.foldoutStyle=e.foldoutStyle||"foldout",this.downloadUrl=Galaxy.root+"api/dataset_collections/"+this.model.attributes.id+"/download"},getNestedDCDCEViewClass:function(){return c.default.NestedDCDCEListItemView.extend({foldoutPanelClass:m})},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;this.handleWarning(e),i.log("_queueNewRender:",e,t),i._swapNewRender(e),i.trigger("rendered",i)},handleWarning:function(e){var t=this.views.length,i=this.model.get("element_count");if(i&&i!==t){var n=(0,f.default)("displaying only "+t+" of "+i+" items");e.find(".elements-warning").html('")}},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(e){switch(e.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.getNestedDCDCEViewClass()}throw new TypeError("Unknown element type:",e.get("element_type"))},_getItemViewOptions:function(t){var i=p.prototype._getItemViewOptions.call(this,t);return e.extend(i,{linkTarget:this.linkTarget,hasUser:this.hasUser,foldoutStyle:this.foldoutStyle})},_setUpItemViewListeners:function(e){var t=this;return p.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}}),this},_expandDrilldownPanel:function(e){this.panelStack.push(e),this.$("> .controls").add(this.$list()).hide(),e.parentName=this.model.get("name"),this.$el.append(e.render().$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.render()},events:{"click .navigation .back":"close"},close:function(e){this.remove(),this.trigger("close")},toString:function(){return"CollectionView("+(this.model?this.model.get("name"):"")+")"}});m.prototype.templates=function(){var t=function(t,i){var n=a(i.model);return'\n ','
",'','<%- history.name %>
',"<%- history.nice_size %>
','','",'','','','',"
",'','
",'',"','",'","
",'","\n \n
'};return e.extend(e.clone(p.prototype.templates),{controls:t})}(),t.default={collectionTypeDescription:s,collectionDescription:a,CollectionView:m}}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(8),o=s(a),l=i(17),r=s(l),d=i(22),c=s(d),u=i(61),h=s(u),f=i(10),p=s(f),m=i(4),g=s(m),_=i(3),v=s(_),w=r.default.DatasetListItemView,y=w.extend({initialize:function(e){w.prototype.initialize.call(this,e),this.hasUser=e.hasUser,this.purgeAllowed=e.purgeAllowed||!1,this.tagsEditorShown=e.tagsEditorShown||!1,this.annotationEditorShown=e.annotationEditorShown||!1},_renderPrimaryActions:function(){var e=w.prototype._renderPrimaryActions.call(this);return this.model.get("state")===o.default.NOT_VIEWABLE?e:w.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){var t=this;if(this.model.get("state")===o.default.DISCARDED||!this.model.get("accessible"))return null;var i=this.model.get("purged"),n=this.model.get("deleted"),s={title:(0,v.default)("Edit attributes"),href:Galaxy.root+"datasets/edit?dataset_id="+this.model.attributes.id,faIcon:"fa-pencil",classes:"edit-btn",onclick:function(e){Galaxy.router&&(e.preventDefault(),Galaxy.router.push("datasets/edit",{dataset_id:t.model.attributes.id}))}};return n||i?(s.disabled=!0,i?s.title=(0,v.default)("Cannot edit attributes of datasets removed from disk"):n&&(s.title=(0,v.default)("Undelete dataset to edit attributes"))):e.contains([o.default.UPLOAD,o.default.NEW],this.model.get("state"))&&(s.disabled=!0,s.title=(0,v.default)("This dataset is not yet editable")),(0,p.default)(s)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var e=this,t=this.model.isDeletedOrPurged();return(0,p.default)({title:t?(0,v.default)("Dataset is already deleted"):(0,v.default)("Delete"),disabled:t,faIcon:"fa-times",classes:"delete-btn",onclick:function(){e.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},_renderDetails:function(){var t=w.prototype._renderDetails.call(this),i=this.model.get("state");return!this.model.isDeletedOrPurged()&&e.contains([o.default.OK,o.default.FAILED_METADATA],i)&&(this._renderTags(t),this._renderAnnotation(t),this._makeDbkeyEditLink(t)),this._setUpBehaviors(t),t},_renderToolHelpButton:function(){var e=this.model.attributes.dataset_id,t=this.model.attributes.creating_job,i=this,s=function(t){var s='\n
\n '+(e.escape(t.name)||e.escape(t.element_identifier))+'
\n \n '+n+'\n
\n \n
\n \n \n \n \n \n
\n ';t.name&&t.help?(s+="Tool help for "+t.name+"
",s+=t.help):s+="Tool help is unavailable for this dataset.
",s+="
",i.$el.find(".details").append(n.parseHTML(s))},a=function(e){n.ajax({url:Galaxy.root+"api/tools/"+e.tool_id+"/build"}).done(function(e){s(e)}).fail(function(){s({})})};return null===Galaxy.user.id?null:(0,p.default)({title:(0,v.default)("Tool Help"),classes:"icon-btn",href:"#",faIcon:"fa-question",onclick:function(){i.$el.find(".toolhelp").length>0?i.$el.find(".toolhelp").toggle():n.ajax({url:Galaxy.root+"api/jobs/"+t}).done(function(e){a(e)}).fail(function(){console.log('Failed at recovering job information from the Galaxy API for job id "'+t+'".')})}})},_renderSecondaryActions:function(){var e=w.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case o.default.UPLOAD:case o.default.NOT_VIEWABLE:return e;case o.default.ERROR:return e.unshift(this._renderErrButton()),e.concat([this._renderRerunButton(),this._renderToolHelpButton()]);case o.default.OK:case o.default.FAILED_METADATA:return e.concat([this._renderRerunButton(),this._renderVisualizationsButton(),this._renderToolHelpButton()])}return e.concat([this._renderRerunButton(),this._renderToolHelpButton()])},_renderErrButton:function(){var e=this;return(0,p.default)({title:(0,v.default)("View or report this error"),href:Galaxy.root+"datasets/error?dataset_id="+this.model.attributes.id,classes:"report-error-btn",faIcon:"fa-bug",onclick:function(t){Galaxy.router&&(t.preventDefault(),Galaxy.router.push("datasets/error",{dataset_id:e.model.attributes.id}))}})},_renderRerunButton:function(){var e=this.model.get("creating_job");if(this.model.get("rerunnable"))return(0,p.default)({title:(0,v.default)("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(t){Galaxy.router&&(t.preventDefault(),Galaxy.router.push("/",{job_id:e}))}})},_renderVisualizationsButton:function(){var t=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||e.isEmpty(t))return null;if(!e.isObject(t[0]))return this.warn("Visualizations have been switched off"),null;var i=n(this.templates.visualizations(t,this));return i.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(i.find(".visualization-link").addBack(".visualization-link")),i},_addScratchBookFn:function(e){e.click(function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:(0,v.default)("Visualization"),url:n(this).attr("href")}),e.preventDefault(),e.stopPropagation())})},_renderTags:function(e){if(this.hasUser){var t=this;this.tagsEditor=new c.default.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.tagsEditorShown=!0},onhide:function(){t.tagsEditorShown=!1},$activator:(0,p.default)({title:(0,v.default)("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(e){if(this.hasUser){var t=this;this.annotationEditor=new h.default.AnnotationEditor({model:this.model,el:e.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.annotationEditorShown=!0},onhide:function(){t.annotationEditorShown=!1},$activator:(0,p.default)({title:(0,v.default)("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(e){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var t=n('?').attr("href",this.model.urls.edit).attr("target","_top");e.find(".dbkey .value").replaceWith(t)}},events:e.extend(e.clone(w.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(e){this.trigger("edit",this,e)},"click .delete-btn":function(e){this.trigger("delete",this,e)},"click .rerun-btn":function(e){this.trigger("rerun",this,e)},"click .report-err-btn":function(e){this.trigger("report-err",this,e)},"click .visualization-btn":function(e){this.trigger("visualize",this,e)},"click .dbkey a":function(e){this.trigger("edit",this,e)}}),_clickUndeleteLink:function(e){return this.model.undelete(),!1},_clickPurgeLink:function(e){return confirm((0,v.default)("This will permanently remove the data in your dataset. Are you sure?"))&&this.model.purge(),!1},toString:function(){return"HDAEditView("+(this.model?""+this.model:"(no model)")+")"}});y.prototype.templates=function(){var t=e.extend({},w.prototype.templates.warnings,{failed_metadata:g.default.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','","<% } %>"],"dataset"),deleted:g.default.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'","<% } %>"],"dataset")}),i=g.default.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'",s+=t.help):s+="Tool help is unavailable for this dataset.
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','','',"",'","
","<% } %>"],"visualizations");return e.extend({},w.prototype.templates,{warnings:t,visualizations:i})}(),t.default={DatasetListItemEdit:y}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(4),o=s(a),l=i(3),r=s(l);i(15);var d=e.View.extend(o.default.LoggableMixin).extend(o.default.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(e){e=e||{},this.tooltipConfig=e.tooltipConfig||{placement:"bottom"},this.listenTo(this.model,"change:annotation",function(){this.render()}),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.$el.html(this._template()),this.$annotation().make_text_editable({use_textarea:!0,on_finish:function(t){e.$annotation().text(t),e.model.save({annotation:t},{silent:!0}).fail(function(){e.$annotation().text(e.model.previous("annotation"))})}}),this},_template:function(){var e=this.model.get("annotation");return['",'',n.escape(e),"
"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off(),this.stopListening(this.model),e.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",""+this.model,")"].join("")}});t.default={AnnotationEditor:d}}).call(t,i(2),i(1))},,,,,,,,,function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var n=i(2),s=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(n),a=i(32),o=function(e){return e&&e.__esModule?e:{default:e}}(a),l=["new","queued","running"],r=["error","deleted"],d=s.Model.extend({url:function(){return Galaxy.root+"api/histories/"+this.attributes.history_id+"/contents/dataset_collections/"+this.attributes.collection_id+"/jobs_summary"},hasDetails:function(){return this.has("populated_state")},new:function(){return!this.hasDetails()||"new"==this.get("populated_state")},errored:function(){return"error"===this.get("populated_state")||this.anyWithStates(r)},states:function(){return this.get("states")||{}},anyWithState:function(e){return(this.states()[e]||0)>0},anyWithStates:function(e){var t=this.states();for(var i in e)if((t[e[i]]||0)>0)return!0;return!1},numWithStates:function(e){var t=this.states(),i=0;for(var n in e)i+=t[e[n]]||0;return i},numInError:function(){return this.numWithStates(r)},running:function(){return this.anyWithState("running")},terminal:function(){return!this.new()&&!this.anyWithStates(l)},jobCount:function(){var e=this.states(),t=0;for(var i in e)t+=e[i];return t},toString:function(){return"JobStatesSummary(id="+this.get("id")+")"}}),c=s.Collection.extend({model:d,initialize:function(){this.updateTimeoutId=null,this.active=!0},url:function(){var e=this.models.filter(function(e){return!e.terminal()}),t=e.map(function(e){return e.get("id")}).join(","),i=e.map(function(e){return e.get("model")}).join(",");return Galaxy.root+"api/histories/"+this.historyId+"/jobs_summary?ids="+t+"&types="+i},monitor:function(){var e=this;if(this.clearUpdateTimeout(),this.active){var t=function(){e.updateTimeoutId=setTimeout(function(){e.monitor()},2e3)},i=this.models.filter(function(e){return!e.terminal()});if(i.length,!1){var n=i.map(function(e){return function(){return e.fetch()}});return new o.default.AjaxQueue(n).done(t)}i.length>0?this.fetch({remove:!1}).done(t):t()}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},toString:function(){return"JobStatesSummaryCollection()"}});t.default={JobStatesSummary:d,JobStatesSummaryCollection:c,FETCH_STATE_ON_ADD:!1}},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(57),l=a(o),r=i(16),d=(a(r),i(8)),c=(a(d),i(37)),u=a(c),h=i(72),f=a(h),p=i(96),m=a(p),g=i(22),_=a(g),v=i(61),w=a(v),y=i(28),b=a(y),x=i(73),$=a(x),C=i(74),k=a(C),S=i(10),T=a(S),P=i(47),D=(a(P),i(4)),E=a(D),A=i(3),M=a(A);i(15);var I=l.default.HistoryView,j=I.extend({HDAViewClass:f.default.HDAListItemEdit,HDCAViewClass:m.default.HDCAListItemEdit,initialize:function(e){e=e||{},I.prototype.initialize.call(this,e),this.tagsEditor=null,this.dragItems=!0,this.annotationEditor=null,this.purgeAllowed=e.purgeAllowed||!1,this.annotationEditorShown=e.annotationEditorShown||!1,this.tagsEditorShown=e.tagsEditorShown||!1},_setUpListeners:function(){return I.prototype._setUpListeners.call(this),this.on({"droptarget:drop":function(e,t){this.dataDropped(t),this.dropTargetOff()},"view:attached view:removed":function(){this._renderCounts()},"search:loading-progress":this._renderSearchProgress,"search:searching":this._renderSearchFindings})},_setUpModelListeners:function(){return I.prototype._setUpModelListeners.call(this),this.listenTo(this.model,"change:size",this.updateHistoryDiskSize),this},_setUpCollectionListeners:function(){return I.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"change:deleted":this._handleItemDeletedChange,"change:visible":this._handleItemVisibleChange,"change:purged":function(e){this.model.fetch()},"fetching-deleted":function(e){this.$("> .controls .deleted-count").html(""+(0,M.default)("loading...")+"")},"fetching-hidden":function(e){this.$("> .controls .hidden-count").html(""+(0,M.default)("loading...")+"")},"fetching-deleted-done fetching-hidden-done":this._renderCounts}),this},_buildNewRender:function(){var e=I.prototype._buildNewRender.call(this);return this.model?(Galaxy&&Galaxy.user&&Galaxy.user.id&&Galaxy.user.id===this.model.get("user_id")&&(this._renderTags(e),this._renderAnnotation(e)),e):e},updateHistoryDiskSize:function(){this.$(".history-size").text(this.model.get("nice_size"))},renderItems:function(e){var t=I.prototype.renderItems.call(this,e);return this.searchFor?this._renderSearchFindings(e):this._renderCounts(e),t},_renderCounts:function(t){t=t instanceof e?t:this.$el;var i=this.templates.counts(this.model.toJSON(),this);return t.find("> .controls .subtitle").html(i)},_renderTags:function(e){var t=this;this.tagsEditor=new _.default.TagsEditor({model:this.model,el:e.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDATagEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDATagEditors(!1,t.fxSpeed)},$activator:(0,T.default)({title:(0,M.default)("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".controls .actions"))})},_renderAnnotation:function(e){var t=this;this.annotationEditor=new w.default.AnnotationEditor({model:this.model,el:e.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDAAnnotationEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDAAnnotationEditors(!1,t.fxSpeed)},$activator:(0,T.default)({title:(0,M.default)("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".controls .actions"))})},_setUpBehaviors:function(e){if(e=e||this.$el,I.prototype._setUpBehaviors.call(this,e),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.model.get("user_id")){var t=this;e.find("> .controls .name").attr("title",(0,M.default)("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(e){var i=t.model.get("name");e&&e!==i?(t.$el.find("> .controls .name").text(e),t.model.save({name:e}).fail(function(){t.$el.find("> .controls .name").text(t.model.previous("name"))})):t.$el.find("> .controls .name").text(i)}})}},multiselectActions:function(){var e=this,t=[{html:(0,M.default)("Hide datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.hide;e.getSelectedModels().ajaxQueue(t)}},{html:(0,M.default)("Unhide datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.unhide;e.getSelectedModels().ajaxQueue(t)}},{html:(0,M.default)("Delete datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.delete;e.getSelectedModels().ajaxQueue(t)}},{html:(0,M.default)("Undelete datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.undelete;e.getSelectedModels().ajaxQueue(t)}}];return e.purgeAllowed&&t.push({html:(0,M.default)("Permanently delete datasets"),func:function(){if(confirm((0,M.default)("This will permanently remove the data in your datasets. Are you sure?"))){var t=u.default.HistoryDatasetAssociation.prototype.purge;e.getSelectedModels().ajaxQueue(t)}}}),t=t.concat(e._collectionActions())},_collectionActions:function(){var e=this;return[{html:(0,M.default)("Build Dataset List"),func:function(){e.buildCollection("list")}},{html:(0,M.default)("Build Dataset Pair"),func:function(){e.buildCollection("paired")}},{html:(0,M.default)("Build List of Dataset Pairs"),func:function(){e.buildCollection("list:paired")}}]},buildCollection:function(e,t,i){var n,s=this,t=t||s.getSelectedModels(),i=i||!1;"list"==e?n=b.default.createListCollection:"paired"==e?n=$.default.createPairCollection:"list:paired"==e?n=k.default.createListOfPairsCollection:console.warn("Unknown collectionType encountered "+e),n(t,i).done(function(){s.model.refresh()})},_getItemViewOptions:function(e){var t=I.prototype._getItemViewOptions.call(this,e);return n.extend(t,{purgeAllowed:this.purgeAllowed,tagsEditorShown:this.tagsEditor&&!this.tagsEditor.hidden,annotationEditorShown:this.annotationEditor&&!this.annotationEditor.hidden}),t},_handleItemDeletedChange:function(e){e.get("deleted")?this._handleItemDeletion(e):this._handleItemUndeletion(e),this._renderCounts()},_handleItemDeletion:function(e){var t=this.model.get("contents_active");t.deleted+=1,t.active-=1,this.model.contents.includeDeleted||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUndeletion:function(e){var t=this.model.get("contents_active");t.deleted-=1,this.model.contents.includeDeleted||(t.active-=1),this.model.set("contents_active",t)},_handleItemVisibleChange:function(e){e.hidden()?this._handleItemHidden(e):this._handleItemUnhidden(e),this._renderCounts()},_handleItemHidden:function(e){var t=this.model.get("contents_active");t.hidden+=1,t.active-=1,this.model.contents.includeHidden||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUnhidden:function(e){var t=this.model.get("contents_active");t.hidden-=1,this.model.contents.includeHidden||(t.active-=1),this.model.set("contents_active",t)},toggleHDATagEditors:function(e,t){n.each(this.views,function(i){i.tagsEditor&&i.tagsEditor.toggle(e,t)})},toggleHDAAnnotationEditors:function(e,t){n.each(this.views,function(i){i.annotationEditor&&i.annotationEditor.toggle(e,t)})},events:n.extend(n.clone(I.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(e){this.toggleShowDeleted()},"click .toggle-hidden-link":function(e){this.toggleShowHidden()}}),_renderSearchProgress:function(e,t){var i=e+t;return this.$("> .controls .subtitle").html(["",(0,M.default)("Searching "),i,"/",this.model.contentsShown(),""].join(""))},_renderSearchFindings:function(t){t=t instanceof e?t:this.$el;var i=this.templates.found(this.model.toJSON(),this);return t.find("> .controls .subtitle").html(i),this},dropTargetOn:function(){if(this.dropTarget)return this;this.dropTarget=!0;var e={dragenter:n.bind(this.dragenter,this),dragover:n.bind(this.dragover,this),dragleave:n.bind(this.dragleave,this),drop:n.bind(this.drop,this)},t=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),t]);for(var i in e)e.hasOwnProperty(i)&&t.on(i,e[i]);return this},_renderDropTarget:function(){return this.$(".history-drop-target").remove(),s("").addClass("history-drop-target")},_renderDropTargetHelp:function(){return this.$(".history-drop-target-help").remove(),s("").addClass("history-drop-target-help").text((0,M.default)("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget)return this;this.dropTarget=!1;var e=this.$(".history-drop-target").get(0);for(var t in this._dropHandlers)this._dropHandlers.hasOwnProperty(t)&&e.off(t,this._dropHandlers[t]);return this.$(".history-drop-target").remove(),this.$(".history-drop-target-help").remove(),this},dropTargetToggle:function(){return this.dropTarget?this.dropTargetOff():this.dropTargetOn(),this},dragenter:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","2px solid black")},dragover:function(e){e.preventDefault(),e.stopPropagation()},dragleave:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","1px dashed black")},drop:function(e){e.preventDefault();var t=this,i=e.originalEvent.dataTransfer,n=i.getData("text");i.dropEffect="move";try{n=JSON.parse(n)}catch(e){t.warn("error parsing JSON from drop:",n)}return t.trigger("droptarget:drop",e,n,t),!1},dataDropped:function(t){var i=this;return n.isObject(t)&&"HistoryDatasetAssociation"===t.model_class&&t.id?0!==i.contents.currentPage?i.contents.fetchPage(0).then(function(){return i.model.contents.copy(t.id)}):i.model.contents.copy(t.id):e.when()},toString:function(){return"HistoryViewEdit("+(this.model?this.model.get("name"):"")+")"}});j.prototype.templates=function(){var e=E.default.wrapTemplate(["<% var shown = Math.max( view.views.length, history.contents_active.active ) %>","<% if( shown ){ %>",'',"<%- shown %> ",(0,M.default)("shown"),"","<% } %>","<% if( history.contents_active.deleted ){ %>",'',"<% if( view.model.contents.includeDeleted ){ %>",'',(0,M.default)("hide deleted"),"","<% } else { %>","<%- history.contents_active.deleted %> ",'',(0,M.default)("deleted"),"","<% } %>","","<% } %>","<% if( history.contents_active.hidden ){ %>",'',"<% if( view.model.contents.includeHidden ){ %>",'',(0,M.default)("hide hidden"),"","<% } else { %>","<%- history.contents_active.hidden %> ",'',(0,M.default)("hidden"),"","<% } %>","","<% } %>"],"history"),t=E.default.wrapTemplate([(0,M.default)("Found")," <%- view.views.length %>, ","<% if( history.contents_active.deleted ){ %>","<% if( view.model.contents.includeDeleted ){ %>",'',(0,M.default)("hide deleted"),", ","<% } else { %>",'',(0,M.default)("show deleted"),", ","<% } %>","<% } %>","<% if( history.contents_active.hidden ){ %>","<% if( view.model.contents.includeHidden ){ %>",'',(0,M.default)("hide hidden"),"","<% } else { %>",'',(0,M.default)("show hidden"),"","<% } %>","<% } %>"],"history");return n.extend(n.clone(I.prototype.templates),{counts:e,found:t})}(),t.default={HistoryViewEdit:j}}).call(t,i(0),i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(60),o=s(a),l=i(40),r=s(l),d=i(4),c=s(d),u=i(3),h=s(u),f=o.default.DatasetListItemEdit,p=f.extend({className:f.prototype.className+" history-content",_fetchModelDetails:function(){var t=this;return t.model.inReadyState()&&!t.model.hasDetails()?t.model.fetch({silent:!0}):t.model.has("rerunnable")?e.when():t.model.fetch({silent:!0,data:{keys:["rerunnable","creating_job"].join(",")}})},events:n.extend(n.clone(f.prototype.events),{"click .unhide-link":function(e){return this.model.unhide(),!1}}),toString:function(){return"HDAListItemEdit("+(this.model?""+this.model:"(no model)")+")"}});p.prototype.templates=function(){var e=n.extend({},f.prototype.templates.warnings,{hidden:c.default.wrapTemplate(["<% if( !dataset.visible ){ %>",'","<% } %>"],"dataset")});return n.extend({},f.prototype.templates,{titleBar:r.default.HDAListItemView.prototype.templates.titleBar,warnings:e})}(),t.default={HDAListItemEdit:p}}).call(t,i(0),i(1))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}function o(e,t){var i=e.toJSON();return v(i,{defaultHideSourceItems:t,creationFn:function(t,i,n){return t=[{name:"forward",src:"hda",id:t[0].id},{name:"reverse",src:"hda",id:t[1].id}],e.createHDCA(t,"paired",i,n)}})}Object.defineProperty(t,"__esModule",{value:!0});var l=i(28),r=a(l),d=i(20),c=a(d),u=i(4),h=a(u),f=i(3),p=a(f),m=e.View.extend(h.default.LoggableMixin).extend({_logNamespace:"collections",tagName:"li",className:"collection-element",initialize:function(e){this.element=e.element||{},this.identifier=e.identifier},render:function(){return this.$el.attr("data-element-id",this.element.id).html(this.template({identifier:this.identifier,element:this.element})),this},template:n.template(['<%- identifier %>','<%- element.name %>'].join("")),destroy:function(){this.off(),this.$el.remove()},toString:function(){return"DatasetCollectionElementView()"}}),g=r.default.ListCollectionCreator,_=g.extend({elementViewClass:m,collectionClass:c.default.HistoryDatasetCollection,className:"pair-collection-creator collection-creator flex-row-container",_mangleDuplicateNames:function(){},render:function(e,t){return 2===this.workingElements.length?g.prototype.render.call(this,e,t):this._renderInvalid(e,t)},_renderList:function(e,t){var i=this,a=s(""),o=i.$list();n.each(this.elementViews,function(e){e.destroy(),i.removeElementView(e)}),a.append(i._createForwardElementView().$el),a.append(i._createReverseElementView().$el),o.empty().append(a.children()),n.invoke(i.elementViews,"render")},_createForwardElementView:function(){return this._createElementView(this.workingElements[0],{identifier:"forward"})},_createReverseElementView:function(){return this._createElementView(this.workingElements[1],{identifier:"reverse"})},_createElementView:function(e,t){var i=new this.elementViewClass(n.extend(t,{element:e}));return this.elementViews.push(i),i},swap:function(){this.workingElements=[this.workingElements[1],this.workingElements[0]],this._renderList()},events:n.extend(n.clone(g.prototype.events),{"click .swap":"swap"}),templates:n.extend(n.clone(g.prototype.templates),{middle:n.template(['",'',"
"].join("")),helpContent:n.template(["",(0,p.default)(["Pair collections are permanent collections containing two datasets: one forward and one reverse. ","Often these are forward and reverse reads. The pair collections can be passed to tools and ","workflows in order to have analyses done on both datasets. This interface allows ","you to create a pair, name it, and swap which is forward and which reverse."].join("")),"
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- ",(0,p.default)(['Click the "Swap" link to make your forward dataset the reverse ',"and the reverse dataset forward."].join(""))," ","
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e={};Galaxy.user.attributes.preferences&&"extra_user_preferences"in Galaxy.user.attributes.preferences&&(e=JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences));var t="use_cached_job|use_cached_job_checkbox"in e&&e["use_cached_job|use_cached_job_checkbox"];this.display_use_cached_job_checkbox="true"===t,this.display_use_cached_job_checkbox&&(this.job_options_form=new m.default({cls:"ui-portlet-narrow",title:"Job re-use Options",inputs:[{type:"conditional",name:"use_cached_job",test_param:{name:"check",label:"BETA: Attempt to reuse jobs with identical parameters?",type:"boolean",value:"false",help:"This may skip executing jobs that you have already run."}}]}),this._append(this.$steps,this.job_options_form.$el))},_renderStep:function(e){var t=this,i=null;this.deferred.execute(function(a){if(t.$steps.addClass("ui-steps"),"tool"==e.step_type)e.postchange=function(t,i){var s={tool_id:e.id,tool_version:e.version,inputs:n.extend(!0,{},i.data.create())};i.wait(!0),Galaxy.emit.debug("tool-form-composite::postchange()","Sending current state.",s),d.default.request({type:"POST",url:Galaxy.root+"api/tools/"+e.id+"/build",data:s,success:function(e){i.update(e),i.wait(!1),Galaxy.emit.debug("tool-form-composite::postchange()","Received new model.",e),t.resolve()},error:function(e){Galaxy.emit.debug("tool-form-composite::postchange()","Refresh request failed.",e),t.reject()}})},i=new w.default(e),e.post_job_actions&&e.post_job_actions.length&&i.portlet.append(n("").addClass("ui-form-element-disabled").append(n("").addClass("ui-form-title").html("Job Post Actions")).append(n("").addClass("ui-form-preview").html(s.reduce(e.post_job_actions,function(e,t){return e+" "+t.short_str},""))));else{var o=-1!=["data_input","data_collection_input"].indexOf(e.step_type);s.each(e.inputs,function(e){e.flavor="module",e.hide_label=o}),i=new m.default(d.default.merge({title:e.fixed_title,onchange:function(){s.each(t.links[e.index],function(e){t._refreshStep(e)})},inputs:e.inputs&&e.inputs.length>0?e.inputs:[{type:"hidden",name:"No options available.",ignore:null}]},e))}t.forms[e.index]=i,t._append(t.$steps,i.$el),t._refresh(),e.needs_refresh&&t._refreshStep(e),i.portlet[t.show_progress?"disable":"enable"](),t.show_progress&&t.execute_btn.model.set({wait:!0,wait_text:"Preparing...",percentage:100*(e.index+1)/t.steps.length}),Galaxy.emit.debug("tool-form-composite::initialize()",e.index+" : Workflow step state ready.",e),setTimeout(function(){a.resolve()},0)})},_refreshStep:function(e){var t=this,i=this.forms[e.index];i?(s.each(t.parms[e.index],function(e,n){if(e.step_linked||e.wp_linked){var a=i.field_list[i.data.match(n)];if(a){var o=void 0;if(e.step_linked)o={values:[]},s.each(e.step_linked,function(e){if(t._isDataStep(e)){var i=t.forms[e.index].data.create().input;i&&s.each(i.values,function(e){o.values.push(e)})}}),!e.multiple&&o.values.length>0&&(o={values:[o.values[0]]});else if(e.wp_linked){o=e.value;for(var l,r=/\$\{(.+?)\}/g;l=r.exec(e.value);){var d=t.wp_form.field_list[t.wp_form.data.match(l[1])],c=d&&d.value();c&&(o=o.split(l[0]).join(c))}}void 0!==o&&a.value(o)}}}),i.trigger("change")):e.needs_refresh=!0},_refreshHistory:function(){var e=this,t=parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.model;this._refresh_history&&clearTimeout(this._refresh_history),t&&t.refresh().success(function(){0===t.numOfUnfinishedShownContents()&&(e._refresh_history=setTimeout(function(){e._refreshHistory()},t.UPDATE_DELAY))})},_execute:function(){var e=this;this.show_progress=!0,this._enabled(!1),this.deferred.execute(function(t){setTimeout(function(){t.resolve(),e._submit()},0)})},_submit:function(){var e=this,t=this.history_form.data.create(),i={new_history_name:t["new_history|name"]?t["new_history|name"]:null,history_id:t["new_history|name"]?null:this.model.get("history_id"),replacement_params:this.wp_form?this.wp_form.data.create():{},parameters:{},parameters_normalized:!0,batch:!0};this.display_use_cached_job_checkbox&&(i.use_cached_job="true"===this.job_options_form.data.create()["use_cached_job|check"]);var s=!0;for(var a in this.forms){var o=this.forms[a],r=o.data.create(),c=e.steps[a],u=c.step_index;o.trigger("reset");for(var h in r){var f=r[h],p=o.data.match(h),m=(o.field_list[p],o.input_list[p]);if(!m.step_linked){if(!(s=this._isDataStep(c)?f&&f.values&&f.values.length>0:m.optional||m.is_workflow&&""!==f||!m.is_workflow&&null!==f)){o.highlight(p);break}i.parameters[u]=i.parameters[u]||{},i.parameters[u][h]=r[h]}}if(!s)break}s?(Galaxy.emit.debug("tool-form-composite::submit()","Validation 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failed"),body:e._templateError(i,t&&t.err_msg),buttons:{Close:function(){e.modal.hide()}}})},complete:function(){e._enabled(!0)}})):(e._enabled(!0),Galaxy.emit.debug("tool-form-composite::submit()","Validation failed.",i))},_append:function(e,t){e.append("").append(t)},_enabled:function(e){this.execute_btn.model.set({wait:!e,wait_text:"Sending...",percentage:-1}),this.wp_form&&this.wp_form.portlet[e?"enable":"disable"](),this.history_form&&this.history_form.portlet[e?"enable":"disable"](),s.each(this.forms,function(t){t&&t.portlet[e?"enable":"disable"]()})},_isDataStep:function(e){for(var t=n.isArray(e)?e:[e],i=0;i','','',"
","','',e.title,"","
"].join("")},_templateAllWorkflow:function(e){return['','',e.title,"","
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"].join("")},_template:function(){return['','",'','','
"].join("")},toString:function(){return"toolPanel"}}));t.default=h}).call(t,i(2),i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),a=n(s),o=i(5),l=n(o),r=i(9),d=n(r),c=i(78),u=n(c),h=i(254),f=n(h),p=i(255),m=n(p),g=i(258),_=n(g),v=i(260),w=n(v);t.default=e.View.extend({options:{nginx_upload_path:"",ftp_upload_site:"n/a",default_genome:"?",default_extension:"auto",height:500,width:900,auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."}},list_extensions:[],list_genomes:[],initialize:function(e){var t=this;this.options=l.default.merge(e,this.options),this.ui_button=new f.default.View({onclick:function(e){e.preventDefault(),t.show()},onunload:function(){var e=t.ui_button.model.get("percentage",0);if(e>0&&e<100)return"Several uploads are queued."}}),this.setElement(this.ui_button.$el);var t=this;l.default.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(e){for(var i in e)t.list_extensions.push({id:e[i].extension,text:e[i].extension,description:e[i].description,description_url:e[i].description_url,composite_files:e[i].composite_files});t.list_extensions.sort(function(e,t){var i=e.text&&e.text.toLowerCase(),n=t.text&&t.text.toLowerCase();return i>n?1:i',"",(0,c.default)("Workflows"),"","
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","Drop files here
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
0%
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
0%
Drop files here
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
0%
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Import Galaxy workflow
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Dataset Error
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this.allFetched=!1,l.Collection.prototype.reset.call(this,e,t)},order:null,comparators:{update_time:d.default.buildComparator("update_time",{ascending:!1}),"update_time-asc":d.default.buildComparator("update_time",{ascending:!0}),create_time:d.default.buildComparator("create_time",{ascending:!1}),"create_time-asc":d.default.buildComparator("create_time",{ascending:!0})},setOrder:function(e,t){t=t||{};var i=this,n=i.comparators[e];if(a.isUndefined(n))throw new Error("unknown order: "+e);if(n!==i.comparator)return i.order=e,i.comparator=n,t.silent||i.trigger("changed-order",t),i}}),u=c.extend({limitPerPage:500,initialize:function(e,t){c.prototype.initialize.call(this,e,t),this.currentPage=t.currentPage||0},getTotalItemCount:function(){return this.length},shouldPaginate:function(){return this.getTotalItemCount()>=this.limitPerPage},getLastPage:function(){return Math.floor(this.getTotalItemCount()/this.limitPerPage)},getPageCount:function(){return this.getLastPage()+1},getPageLimitOffset:function(e){return e=this.constrainPageNum(e),{limit:this.limitPerPage,offset:e*this.limitPerPage}},constrainPageNum:function(e){return Math.max(0,Math.min(e,this.getLastPage()))},fetchPage:function(e,t){var i=this;return e=i.constrainPageNum(e),i.currentPage=e,t=a.defaults(t||{},i.getPageLimitOffset(e)),i.trigger("fetching-more"),i.fetch(t).always(function(){i.trigger("fetching-more-done")})},fetchCurrentPage:function(e){return this.fetchPage(this.currentPage,e)},fetchPrevPage:function(e){return this.fetchPage(this.currentPage-1,e)},fetchNextPage:function(e){return this.fetchPage(this.currentPage+1,e)}}),h=c.extend({limitOnFirstFetch:null,limitPerFetch:100,initialize:function(e,t){c.prototype.initialize.call(this,e,t),this.limitOnFirstFetch=t.limitOnFirstFetch||this.limitOnFirstFetch,this.limitPerFetch=t.limitPerFetch||this.limitPerFetch,this.allFetched=!1,this.lastFetched=t.lastFetched||0},_buildFetchOptions:function(e){return e.remove=e.remove||!1,c.prototype._buildFetchOptions.call(this,e)},fetchFirst:function(e){return Galaxy.debug("ControlledFetchCollection.fetchFirst:",e),e=e?a.clone(e):{},this.allFetched=!1,this.lastFetched=0,this.fetchMore(a.defaults(e,{reset:!0,limit:this.limitOnFirstFetch}))},fetchMore:function(t){Galaxy.debug("ControlledFetchCollection.fetchMore:",t),t=a.clone(t||{});var i=this;if(Galaxy.debug("fetchMore, options.reset:",t.reset),!t.reset&&i.allFetched)return e.when();t.reset?t.offset=0:void 0===t.offset&&(t.offset=i.lastFetched);var n=t.limit=t.limit||i.limitPerFetch||null;return Galaxy.debug("fetchMore, limit:",n,"offset:",t.offset),i.trigger("fetching-more"),i.fetch(t).always(function(){i.trigger("fetching-more-done")}).done(function(e){var t=a.isArray(e)?e.length:0;i.lastFetched+=t,Galaxy.debug("fetchMore, lastFetched:",i.lastFetched),(!n||t'):this.$list().find(".contents-loading-indicator").remove()},renderItems:function(e){e=e||this.$el;var t=this.$list(e);n(".tooltip").remove(),t.empty(),this.views=[];var i=this._filterCollection();return i.length?(this._renderPagination(e),this.views=this._renderSomeItems(i,t)):e.find("> .controls .list-pagination").empty(),this._renderEmptyMessage(e).toggle(!i.length),this.trigger("views:ready",this.views),this.views},_renderPagination:function(e){var t=e.find("> .controls .list-pagination");return this.searchFor||!this.model.contents.shouldPaginate()?t.empty():(t.html(this.templates.pagination({current:this.model.contents.currentPage+1,last:this.model.contents.getLastPage()+1},this)),t.find("select.pages").tooltip(),t)},_renderSomeItems:function(e,t){var i=this,n=[];return t.append(e.map(function(e){var t=i._createItemView(e);return n.push(t),i._renderItemView$el(t)})),n},_filterItem:function(e){var t=this.model.contents;return(t.includeHidden||!e.hidden())&&(t.includeDeleted||!e.isDeletedOrPurged())&&k.prototype._filterItem.call(this,e)},_getItemViewClass:function(e){var t=e.get("history_content_type");switch(t){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+t)},_getItemViewOptions:function(t){var i=k.prototype._getItemViewOptions.call(this,t);return e.extend(i,{linkTarget:this.linkTarget,expanded:this.model.contents.storage.isExpanded(t.id),hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(e){var t=this;return k.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{expanded:function(e){t.model.contents.storage.addExpanded(e.model)},collapsed:function(e){t.model.contents.storage.removeExpanded(e.model)}})},collapseAll:function(){this.model.contents.storage.clearExpanded(),k.prototype.collapseAll.call(this)},getSelectedModels:function(){var e=k.prototype.getSelectedModels.call(this);return e.historyId=this.collection.historyId,e},events:e.extend(e.clone(k.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click > .controls .prev":"_clickPrevPage","click > .controls .next":"_clickNextPage","change > .controls .pages":"_changePageSelect","click .messages [class$=message]":"clearMessages"}),_clickPrevPage:function(e){this.model.stopPolling(),this.model.contents.fetchPrevPage()},_clickNextPage:function(e){this.model.stopPolling(),this.model.contents.fetchNextPage()},_changePageSelect:function(e){this.model.stopPolling();var t=n(e.currentTarget).val();this.model.contents.fetchPage(t)},toggleShowDeleted:function(e,t){e=void 0!==e?e:!this.model.contents.includeDeleted;var i=this.model.contents;return i.setIncludeDeleted(e,t),this.trigger("show-deleted",e),i.fetchCurrentPage({renderAll:!0}),e},toggleShowHidden:function(e,t,i){e=void 0!==e?e:!this.model.contents.includeHidden;var n=this.model.contents;return n.setIncludeHidden(e,i),this.trigger("show-hidden",e),n.fetchCurrentPage({renderAll:!0}),e},_firstSearch:function(e){var t=this;if(this.log("onFirstSearch",e),this.model.contents.haveSearchDetails())return void this.searchItems(e);this.$("> .controls .search-input").searchInput("toggle-loading"),this.searchFor=e;this.model.contents.progressivelyFetchDetails({silent:!0}).progress(function(e,i,n){t.renderItems(),t.trigger("search:loading-progress",i,n)}).always(function(){t.$el.find("> .controls .search-input").searchInput("toggle-loading")}).done(function(){t.searchItems(e,"force")})},clearSearch:function(e){var t=this;return this.searchFor?(this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.model.contents.fetchCurrentPage({silent:!0}).done(function(){t.renderItems()}),this):this},errorHandler:function(t,i,n){if(!i||0!==i.status||0!==i.readyState){if(this.error(t,i,n),e.isString(t)&&e.isString(i)){var s=t,a=i;return v.default.errorModal(s,a,n)}return i&&502===i.status?v.default.badGatewayErrorModal():v.default.ajaxErrorModal(t,i,n)}},clearMessages:function(t){return(e.isUndefined(t)?this.$messages().children('[class$="message"]'):n(t.currentTarget)).fadeOut(this.fxSpeed,function(){n(this).remove()}),this},scrollToHid:function(t){return this.scrollToItem(e.first(this.viewsWhereModel({hid:t})))},ordinalIndicator:function(e){var t=""+e;switch(t.charAt(t.length-1)){case"1":return t+"st";case"2":return t+"nd";case"3":return t+"rd";default:return t+"th"}},toString:function(){return"HistoryView("+(this.model?this.model.get("name"):"")+")"}});S.prototype.templates=function(){var t=function(){return'
\n \n
'},i=x.default.wrapTemplate(['','
"],"history"),n=x.default.wrapTemplate(['','",''],"pages");return e.extend(e.clone(k.prototype.templates),{el:t,controls:i,pagination:n})}(),t.default={HistoryView:S}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e){function i(t){return''+e.escape(t.slice(5))+""}function n(t){var n=e.filter(e.uniq(t.tags),function(e){return 0===e.indexOf("name:")}),s=e.sortBy(n).map(i);return'\n "}Object.defineProperty(t,"__esModule",{value:!0}),t.default={nametagTemplate:n}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}function s(e){var t=e.get("collection_type");return"list"==t?(0,f.default)("list"):"paired"==t?(0,f.default)("dataset pair"):"list:paired"==t?(0,f.default)("list of pairs"):(0,f.default)("nested list")}function a(e){var t=e.get("element_count"),i="a "+s(e);if(t){var n;1==t?n="with 1 item":t&&(n="with "+t+" items"),i=i+" "+(0,f.default)(n)}return i}Object.defineProperty(t,"__esModule",{value:!0});var o=i(38),l=n(o),r=i(29),d=(n(r),i(33)),c=n(d),u=i(4),h=(n(u),i(3)),f=n(h),p=l.default.ModelListPanel,m=p.extend({_logNamespace:"collections",className:p.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:c.default.DatasetDCEListItemView,modelCollectionKey:"elements",initialize:function(e){p.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,this.panelStack=[],this.parentName=e.parentName,this.foldoutStyle=e.foldoutStyle||"foldout",this.downloadUrl=Galaxy.root+"api/dataset_collections/"+this.model.attributes.id+"/download"},getNestedDCDCEViewClass:function(){return c.default.NestedDCDCEListItemView.extend({foldoutPanelClass:m})},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;this.handleWarning(e),i.log("_queueNewRender:",e,t),i._swapNewRender(e),i.trigger("rendered",i)},handleWarning:function(e){var t=this.views.length,i=this.model.get("element_count");if(i&&i!==t){var n=(0,f.default)("displaying only "+t+" of "+i+" items");e.find(".elements-warning").html('")}},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(e){switch(e.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.getNestedDCDCEViewClass()}throw new TypeError("Unknown element type:",e.get("element_type"))},_getItemViewOptions:function(t){var i=p.prototype._getItemViewOptions.call(this,t);return e.extend(i,{linkTarget:this.linkTarget,hasUser:this.hasUser,foldoutStyle:this.foldoutStyle})},_setUpItemViewListeners:function(e){var t=this;return p.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}}),this},_expandDrilldownPanel:function(e){this.panelStack.push(e),this.$("> .controls").add(this.$list()).hide(),e.parentName=this.model.get("name"),this.$el.append(e.render().$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.render()},events:{"click .navigation .back":"close"},close:function(e){this.remove(),this.trigger("close")},toString:function(){return"CollectionView("+(this.model?this.model.get("name"):"")+")"}});m.prototype.templates=function(){var t=function(t,i){var n=a(i.model);return'\n ','
",'','<%- history.name %>
',"<%- history.nice_size %>
','','",'','','','',"
",'','
",'',"','",'","
",'","\n \n
'};return e.extend(e.clone(p.prototype.templates),{controls:t})}(),t.default={collectionTypeDescription:s,collectionDescription:a,CollectionView:m}}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(8),o=s(a),l=i(17),r=s(l),d=i(22),c=s(d),u=i(61),h=s(u),f=i(10),p=s(f),m=i(4),g=s(m),_=i(3),v=s(_),w=r.default.DatasetListItemView,y=w.extend({initialize:function(e){w.prototype.initialize.call(this,e),this.hasUser=e.hasUser,this.purgeAllowed=e.purgeAllowed||!1,this.tagsEditorShown=e.tagsEditorShown||!1,this.annotationEditorShown=e.annotationEditorShown||!1},_renderPrimaryActions:function(){var e=w.prototype._renderPrimaryActions.call(this);return this.model.get("state")===o.default.NOT_VIEWABLE?e:w.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){var t=this;if(this.model.get("state")===o.default.DISCARDED||!this.model.get("accessible"))return null;var i=this.model.get("purged"),n=this.model.get("deleted"),s={title:(0,v.default)("Edit attributes"),href:Galaxy.root+"datasets/edit?dataset_id="+this.model.attributes.id,faIcon:"fa-pencil",classes:"edit-btn",onclick:function(e){Galaxy.router&&(e.preventDefault(),Galaxy.router.push("datasets/edit",{dataset_id:t.model.attributes.id}))}};return n||i?(s.disabled=!0,i?s.title=(0,v.default)("Cannot edit attributes of datasets removed from disk"):n&&(s.title=(0,v.default)("Undelete dataset to edit attributes"))):e.contains([o.default.UPLOAD,o.default.NEW],this.model.get("state"))&&(s.disabled=!0,s.title=(0,v.default)("This dataset is not yet editable")),(0,p.default)(s)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var e=this,t=this.model.isDeletedOrPurged();return(0,p.default)({title:t?(0,v.default)("Dataset is already deleted"):(0,v.default)("Delete"),disabled:t,faIcon:"fa-times",classes:"delete-btn",onclick:function(){e.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},_renderDetails:function(){var t=w.prototype._renderDetails.call(this),i=this.model.get("state");return!this.model.isDeletedOrPurged()&&e.contains([o.default.OK,o.default.FAILED_METADATA],i)&&(this._renderTags(t),this._renderAnnotation(t),this._makeDbkeyEditLink(t)),this._setUpBehaviors(t),t},_renderToolHelpButton:function(){var e=this.model.attributes.dataset_id,t=this.model.attributes.creating_job,i=this,s=function(t){var s='\n
\n '+(e.escape(t.name)||e.escape(t.element_identifier))+'
\n \n '+n+'\n
\n \n
\n \n \n \n \n \n
\n ';t.name&&t.help?(s+="Tool help for "+t.name+"
",s+=t.help):s+="Tool help is unavailable for this dataset.
",s+="
",i.$el.find(".details").append(n.parseHTML(s))},a=function(e){n.ajax({url:Galaxy.root+"api/tools/"+e.tool_id+"/build"}).done(function(e){s(e)}).fail(function(){s({})})};return null===Galaxy.user.id?null:(0,p.default)({title:(0,v.default)("Tool Help"),classes:"icon-btn",href:"#",faIcon:"fa-question",onclick:function(){i.$el.find(".toolhelp").length>0?i.$el.find(".toolhelp").toggle():n.ajax({url:Galaxy.root+"api/jobs/"+t}).done(function(e){a(e)}).fail(function(){console.log('Failed at recovering job information from the Galaxy API for job id "'+t+'".')})}})},_renderSecondaryActions:function(){var e=w.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case o.default.UPLOAD:case o.default.NOT_VIEWABLE:return e;case o.default.ERROR:return e.unshift(this._renderErrButton()),e.concat([this._renderRerunButton(),this._renderToolHelpButton()]);case o.default.OK:case o.default.FAILED_METADATA:return e.concat([this._renderRerunButton(),this._renderVisualizationsButton(),this._renderToolHelpButton()])}return e.concat([this._renderRerunButton(),this._renderToolHelpButton()])},_renderErrButton:function(){var e=this;return(0,p.default)({title:(0,v.default)("View or report this error"),href:Galaxy.root+"datasets/error?dataset_id="+this.model.attributes.id,classes:"report-error-btn",faIcon:"fa-bug",onclick:function(t){Galaxy.router&&(t.preventDefault(),Galaxy.router.push("datasets/error",{dataset_id:e.model.attributes.id}))}})},_renderRerunButton:function(){var e=this.model.get("creating_job");if(this.model.get("rerunnable"))return(0,p.default)({title:(0,v.default)("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(t){Galaxy.router&&(t.preventDefault(),Galaxy.router.push("/",{job_id:e}))}})},_renderVisualizationsButton:function(){var t=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||e.isEmpty(t))return null;if(!e.isObject(t[0]))return this.warn("Visualizations have been switched off"),null;var i=n(this.templates.visualizations(t,this));return i.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(i.find(".visualization-link").addBack(".visualization-link")),i},_addScratchBookFn:function(e){e.click(function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:(0,v.default)("Visualization"),url:n(this).attr("href")}),e.preventDefault(),e.stopPropagation())})},_renderTags:function(e){if(this.hasUser){var t=this;this.tagsEditor=new c.default.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.tagsEditorShown=!0},onhide:function(){t.tagsEditorShown=!1},$activator:(0,p.default)({title:(0,v.default)("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(e){if(this.hasUser){var t=this;this.annotationEditor=new h.default.AnnotationEditor({model:this.model,el:e.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.annotationEditorShown=!0},onhide:function(){t.annotationEditorShown=!1},$activator:(0,p.default)({title:(0,v.default)("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(e){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var t=n('?').attr("href",this.model.urls.edit).attr("target","_top");e.find(".dbkey .value").replaceWith(t)}},events:e.extend(e.clone(w.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(e){this.trigger("edit",this,e)},"click .delete-btn":function(e){this.trigger("delete",this,e)},"click .rerun-btn":function(e){this.trigger("rerun",this,e)},"click .report-err-btn":function(e){this.trigger("report-err",this,e)},"click .visualization-btn":function(e){this.trigger("visualize",this,e)},"click .dbkey a":function(e){this.trigger("edit",this,e)}}),_clickUndeleteLink:function(e){return this.model.undelete(),!1},_clickPurgeLink:function(e){return confirm((0,v.default)("This will permanently remove the data in your dataset. Are you sure?"))&&this.model.purge(),!1},toString:function(){return"HDAEditView("+(this.model?""+this.model:"(no model)")+")"}});y.prototype.templates=function(){var t=e.extend({},w.prototype.templates.warnings,{failed_metadata:g.default.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','","<% } %>"],"dataset"),deleted:g.default.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'","<% } %>"],"dataset")}),i=g.default.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'",s+=t.help):s+="Tool help is unavailable for this dataset.
",s+="
','','',"",'","
","<% } %>"],"visualizations");return e.extend({},w.prototype.templates,{warnings:t,visualizations:i})}(),t.default={DatasetListItemEdit:y}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(4),o=s(a),l=i(3),r=s(l);i(15);var d=e.View.extend(o.default.LoggableMixin).extend(o.default.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(e){e=e||{},this.tooltipConfig=e.tooltipConfig||{placement:"bottom"},this.listenTo(this.model,"change:annotation",function(){this.render()}),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.$el.html(this._template()),this.$annotation().make_text_editable({use_textarea:!0,on_finish:function(t){e.$annotation().text(t),e.model.save({annotation:t},{silent:!0}).fail(function(){e.$annotation().text(e.model.previous("annotation"))})}}),this},_template:function(){var e=this.model.get("annotation");return['",'',n.escape(e),"
"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off(),this.stopListening(this.model),e.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",""+this.model,")"].join("")}});t.default={AnnotationEditor:d}}).call(t,i(2),i(1))},,,,,,,,,function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var n=i(2),s=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(n),a=i(32),o=function(e){return e&&e.__esModule?e:{default:e}}(a),l=["new","queued","running"],r=["error","deleted"],d=s.Model.extend({url:function(){return Galaxy.root+"api/histories/"+this.attributes.history_id+"/contents/dataset_collections/"+this.attributes.collection_id+"/jobs_summary"},hasDetails:function(){return 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e.get("id")}).join(","),i=e.map(function(e){return e.get("model")}).join(",");return Galaxy.root+"api/histories/"+this.historyId+"/jobs_summary?ids="+t+"&types="+i},monitor:function(){var e=this;if(this.clearUpdateTimeout(),this.active){var t=function(){e.updateTimeoutId=setTimeout(function(){e.monitor()},2e3)},i=this.models.filter(function(e){return!e.terminal()});if(i.length,!1){var n=i.map(function(e){return function(){return e.fetch()}});return new o.default.AjaxQueue(n).done(t)}i.length>0?this.fetch({remove:!1}).done(t):t()}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},toString:function(){return"JobStatesSummaryCollection()"}});t.default={JobStatesSummary:d,JobStatesSummaryCollection:c,FETCH_STATE_ON_ADD:!1}},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var 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Are you sure?"))){var t=u.default.HistoryDatasetAssociation.prototype.purge;e.getSelectedModels().ajaxQueue(t)}}}),t=t.concat(e._collectionActions())},_collectionActions:function(){var e=this;return[{html:(0,M.default)("Build Dataset List"),func:function(){e.buildCollection("list")}},{html:(0,M.default)("Build Dataset Pair"),func:function(){e.buildCollection("paired")}},{html:(0,M.default)("Build List of Dataset Pairs"),func:function(){e.buildCollection("list:paired")}}]},buildCollection:function(e,t,i){var n,s=this,t=t||s.getSelectedModels(),i=i||!1;"list"==e?n=b.default.createListCollection:"paired"==e?n=$.default.createPairCollection:"list:paired"==e?n=k.default.createListOfPairsCollection:console.warn("Unknown collectionType encountered "+e),n(t,i).done(function(){s.model.refresh()})},_getItemViewOptions:function(e){var t=I.prototype._getItemViewOptions.call(this,e);return n.extend(t,{purgeAllowed:this.purgeAllowed,tagsEditorShown:this.tagsEditor&&!this.tagsEditor.hidden,annotationEditorShown:this.annotationEditor&&!this.annotationEditor.hidden}),t},_handleItemDeletedChange:function(e){e.get("deleted")?this._handleItemDeletion(e):this._handleItemUndeletion(e),this._renderCounts()},_handleItemDeletion:function(e){var t=this.model.get("contents_active");t.deleted+=1,t.active-=1,this.model.contents.includeDeleted||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUndeletion:function(e){var t=this.model.get("contents_active");t.deleted-=1,this.model.contents.includeDeleted||(t.active-=1),this.model.set("contents_active",t)},_handleItemVisibleChange:function(e){e.hidden()?this._handleItemHidden(e):this._handleItemUnhidden(e),this._renderCounts()},_handleItemHidden:function(e){var t=this.model.get("contents_active");t.hidden+=1,t.active-=1,this.model.contents.includeHidden||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUnhidden:function(e){var t=this.model.get("contents_active");t.hidden-=1,this.model.contents.includeHidden||(t.active-=1),this.model.set("contents_active",t)},toggleHDATagEditors:function(e,t){n.each(this.views,function(i){i.tagsEditor&&i.tagsEditor.toggle(e,t)})},toggleHDAAnnotationEditors:function(e,t){n.each(this.views,function(i){i.annotationEditor&&i.annotationEditor.toggle(e,t)})},events:n.extend(n.clone(I.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(e){this.toggleShowDeleted()},"click .toggle-hidden-link":function(e){this.toggleShowHidden()}}),_renderSearchProgress:function(e,t){var i=e+t;return this.$("> .controls .subtitle").html(["",(0,M.default)("Searching "),i,"/",this.model.contentsShown(),""].join(""))},_renderSearchFindings:function(t){t=t instanceof e?t:this.$el;var i=this.templates.found(this.model.toJSON(),this);return t.find("> .controls .subtitle").html(i),this},dropTargetOn:function(){if(this.dropTarget)return this;this.dropTarget=!0;var e={dragenter:n.bind(this.dragenter,this),dragover:n.bind(this.dragover,this),dragleave:n.bind(this.dragleave,this),drop:n.bind(this.drop,this)},t=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),t]);for(var i in e)e.hasOwnProperty(i)&&t.on(i,e[i]);return this},_renderDropTarget:function(){return this.$(".history-drop-target").remove(),s("").addClass("history-drop-target")},_renderDropTargetHelp:function(){return this.$(".history-drop-target-help").remove(),s("").addClass("history-drop-target-help").text((0,M.default)("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget)return this;this.dropTarget=!1;var e=this.$(".history-drop-target").get(0);for(var t in this._dropHandlers)this._dropHandlers.hasOwnProperty(t)&&e.off(t,this._dropHandlers[t]);return this.$(".history-drop-target").remove(),this.$(".history-drop-target-help").remove(),this},dropTargetToggle:function(){return this.dropTarget?this.dropTargetOff():this.dropTargetOn(),this},dragenter:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","2px solid black")},dragover:function(e){e.preventDefault(),e.stopPropagation()},dragleave:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","1px dashed black")},drop:function(e){e.preventDefault();var t=this,i=e.originalEvent.dataTransfer,n=i.getData("text");i.dropEffect="move";try{n=JSON.parse(n)}catch(e){t.warn("error parsing JSON from drop:",n)}return t.trigger("droptarget:drop",e,n,t),!1},dataDropped:function(t){var i=this;return n.isObject(t)&&"HistoryDatasetAssociation"===t.model_class&&t.id?0!==i.contents.currentPage?i.contents.fetchPage(0).then(function(){return i.model.contents.copy(t.id)}):i.model.contents.copy(t.id):e.when()},toString:function(){return"HistoryViewEdit("+(this.model?this.model.get("name"):"")+")"}});j.prototype.templates=function(){var e=E.default.wrapTemplate(["<% var shown = Math.max( view.views.length, history.contents_active.active ) %>","<% if( shown ){ %>",'',"<%- shown %> ",(0,M.default)("shown"),"","<% } %>","<% if( history.contents_active.deleted ){ %>",'',"<% if( view.model.contents.includeDeleted ){ %>",'',(0,M.default)("hide deleted"),"","<% } else { %>","<%- history.contents_active.deleted %> ",'',(0,M.default)("deleted"),"","<% } %>","","<% } %>","<% if( history.contents_active.hidden ){ %>",'',"<% if( view.model.contents.includeHidden ){ %>",'',(0,M.default)("hide hidden"),"","<% } else { %>","<%- history.contents_active.hidden %> ",'',(0,M.default)("hidden"),"","<% } %>","","<% } %>"],"history"),t=E.default.wrapTemplate([(0,M.default)("Found")," <%- view.views.length %>, ","<% if( history.contents_active.deleted ){ %>","<% if( view.model.contents.includeDeleted ){ %>",'',(0,M.default)("hide deleted"),", ","<% } else { %>",'',(0,M.default)("show deleted"),", ","<% } %>","<% } %>","<% if( history.contents_active.hidden ){ %>","<% if( view.model.contents.includeHidden ){ %>",'',(0,M.default)("hide hidden"),"","<% } else { %>",'',(0,M.default)("show hidden"),"","<% } %>","<% } %>"],"history");return n.extend(n.clone(I.prototype.templates),{counts:e,found:t})}(),t.default={HistoryViewEdit:j}}).call(t,i(0),i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(60),o=s(a),l=i(40),r=s(l),d=i(4),c=s(d),u=i(3),h=s(u),f=o.default.DatasetListItemEdit,p=f.extend({className:f.prototype.className+" history-content",_fetchModelDetails:function(){var t=this;return t.model.inReadyState()&&!t.model.hasDetails()?t.model.fetch({silent:!0}):t.model.has("rerunnable")?e.when():t.model.fetch({silent:!0,data:{keys:["rerunnable","creating_job"].join(",")}})},events:n.extend(n.clone(f.prototype.events),{"click .unhide-link":function(e){return this.model.unhide(),!1}}),toString:function(){return"HDAListItemEdit("+(this.model?""+this.model:"(no model)")+")"}});p.prototype.templates=function(){var e=n.extend({},f.prototype.templates.warnings,{hidden:c.default.wrapTemplate(["<% if( !dataset.visible ){ %>",'","<% } %>"],"dataset")});return n.extend({},f.prototype.templates,{titleBar:r.default.HDAListItemView.prototype.templates.titleBar,warnings:e})}(),t.default={HDAListItemEdit:p}}).call(t,i(0),i(1))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}function o(e,t){var i=e.toJSON();return v(i,{defaultHideSourceItems:t,creationFn:function(t,i,n){return 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o={};s.each(e.output_connections,function(e){n.step_index===e.input_step_index&&(o[e.input_name]=e)}),s.each(t.parms[a],function(t,n){var s=o[n];s&&(t.type="hidden",t.help=t.step_linked?t.help+", ":"",t.help+="Output dataset '"+s.output_name+"' from step "+(parseInt(i)+1),t.step_linked=t.step_linked||[],t.step_linked.push({index:e.index,step_type:e.step_type}))})})});var i=0;this.wp_inputs={},s.each(this.steps,function(i,n){s.each(t.parms[n],function(t,n){e(t.value,function(e){e.links.push(i),t.wp_linked=!0,t.type="text",t.backdrop=!0,t.style="ui-form-wp-target"})}),s.each(i.post_job_actions,function(t){s.each(t.action_arguments,function(t){e(t,function(){})})})}),s.each(this.steps,function(e,i){if("tool"==e.step_type){var n=!0;_.default.visitInputs(e.inputs,function(i,s,a){var 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e={};Galaxy.user.attributes.preferences&&"extra_user_preferences"in Galaxy.user.attributes.preferences&&(e=JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences));var t="use_cached_job|use_cached_job_checkbox"in e&&e["use_cached_job|use_cached_job_checkbox"];this.display_use_cached_job_checkbox="true"===t,this.display_use_cached_job_checkbox&&(this.job_options_form=new m.default({cls:"ui-portlet-narrow",title:"Job re-use Options",inputs:[{type:"conditional",name:"use_cached_job",test_param:{name:"check",label:"BETA: Attempt to reuse jobs with identical parameters?",type:"boolean",value:"false",help:"This may skip executing jobs that you have already run."}}]}),this._append(this.$steps,this.job_options_form.$el))},_renderStep:function(e){var t=this,i=null;this.deferred.execute(function(a){if(t.$steps.addClass("ui-steps"),"tool"==e.step_type)e.postchange=function(t,i){var s={tool_id:e.id,tool_version:e.version,inputs:n.extend(!0,{},i.data.create())};i.wait(!0),Galaxy.emit.debug("tool-form-composite::postchange()","Sending current state.",s),d.default.request({type:"POST",url:Galaxy.root+"api/tools/"+e.id+"/build",data:s,success:function(e){i.update(e),i.wait(!1),Galaxy.emit.debug("tool-form-composite::postchange()","Received new model.",e),t.resolve()},error:function(e){Galaxy.emit.debug("tool-form-composite::postchange()","Refresh request failed.",e),t.reject()}})},i=new w.default(e),e.post_job_actions&&e.post_job_actions.length&&i.portlet.append(n("").addClass("ui-form-element-disabled").append(n("").addClass("ui-form-title").html("Job Post Actions")).append(n("").addClass("ui-form-preview").html(s.reduce(e.post_job_actions,function(e,t){return e+" "+t.short_str},""))));else{var o=-1!=["data_input","data_collection_input"].indexOf(e.step_type);s.each(e.inputs,function(e){e.flavor="module",e.hide_label=o}),i=new m.default(d.default.merge({title:e.fixed_title,onchange:function(){s.each(t.links[e.index],function(e){t._refreshStep(e)})},inputs:e.inputs&&e.inputs.length>0?e.inputs:[{type:"hidden",name:"No options available.",ignore:null}]},e))}t.forms[e.index]=i,t._append(t.$steps,i.$el),t._refresh(),e.needs_refresh&&t._refreshStep(e),i.portlet[t.show_progress?"disable":"enable"](),t.show_progress&&t.execute_btn.model.set({wait:!0,wait_text:"Preparing...",percentage:100*(e.index+1)/t.steps.length}),Galaxy.emit.debug("tool-form-composite::initialize()",e.index+" : Workflow step state ready.",e),setTimeout(function(){a.resolve()},0)})},_refreshStep:function(e){var t=this,i=this.forms[e.index];i?(s.each(t.parms[e.index],function(e,n){if(e.step_linked||e.wp_linked){var a=i.field_list[i.data.match(n)];if(a){var o=void 0;if(e.step_linked)o={values:[]},s.each(e.step_linked,function(e){if(t._isDataStep(e)){var i=t.forms[e.index].data.create().input;i&&s.each(i.values,function(e){o.values.push(e)})}}),!e.multiple&&o.values.length>0&&(o={values:[o.values[0]]});else if(e.wp_linked){o=e.value;for(var l,r=/\$\{(.+?)\}/g;l=r.exec(e.value);){var d=t.wp_form.field_list[t.wp_form.data.match(l[1])],c=d&&d.value();c&&(o=o.split(l[0]).join(c))}}void 0!==o&&a.value(o)}}}),i.trigger("change")):e.needs_refresh=!0},_refreshHistory:function(){var e=this,t=parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.model;this._refresh_history&&clearTimeout(this._refresh_history),t&&t.refresh().success(function(){0===t.numOfUnfinishedShownContents()&&(e._refresh_history=setTimeout(function(){e._refreshHistory()},t.UPDATE_DELAY))})},_execute:function(){var e=this;this.show_progress=!0,this._enabled(!1),this.deferred.execute(function(t){setTimeout(function(){t.resolve(),e._submit()},0)})},_submit:function(){var e=this,t=this.history_form.data.create(),i={new_history_name:t["new_history|name"]?t["new_history|name"]:null,history_id:t["new_history|name"]?null:this.model.get("history_id"),replacement_params:this.wp_form?this.wp_form.data.create():{},parameters:{},parameters_normalized:!0,batch:!0};this.display_use_cached_job_checkbox&&(i.use_cached_job="true"===this.job_options_form.data.create()["use_cached_job|check"]);var s=!0;for(var a in this.forms){var o=this.forms[a],r=o.data.create(),c=e.steps[a],u=c.step_index;o.trigger("reset");for(var h in r){var f=r[h],p=o.data.match(h),m=(o.field_list[p],o.input_list[p]);if(!m.step_linked){if(!(s=this._isDataStep(c)?f&&f.values&&f.values.length>0:m.optional||m.is_workflow&&""!==f||!m.is_workflow&&null!==f)){o.highlight(p);break}i.parameters[u]=i.parameters[u]||{},i.parameters[u][h]=r[h]}}if(!s)break}s?(Galaxy.emit.debug("tool-form-composite::submit()","Validation complete.",i),d.default.request({type:"POST",url:Galaxy.root+"api/workflows/"+this.model.id+"/invocations",data:i,success:function(t){if(Galaxy.emit.debug("tool-form-composite::submit","Submission successful.",t),e.$el.children().hide(),e.$el.append(e._templateSuccess(t)),n.isArray(t)&&t.length>0){e.$el.append(n("",{id:"webhook-view"}));new $.default.WebhookView({urlRoot:Galaxy.root+"api/webhooks/workflow",toolId:i.tool_id,toolVersion:i.tool_version})}e._refreshHistory()},error:function(t){Galaxy.emit.debug("tool-form-composite::submit","Submission failed.",t);var n=!1;if(t&&t.err_data)for(var s in e.forms){var a=e.forms[s],o=t.err_data[a.model.get("step_index")];if(o){var r=a.data.matchResponse(o);for(var d in r){a.highlight(d,r[d]),n=!0;break}}}n||e.modal.show({title:(0,l.default)("Workflow submission failed"),body:e._templateError(i,t&&t.err_msg),buttons:{Close:function(){e.modal.hide()}}})},complete:function(){e._enabled(!0)}})):(e._enabled(!0),Galaxy.emit.debug("tool-form-composite::submit()","Validation failed.",i))},_append:function(e,t){e.append("").append(t)},_enabled:function(e){this.execute_btn.model.set({wait:!e,wait_text:"Sending...",percentage:-1}),this.wp_form&&this.wp_form.portlet[e?"enable":"disable"](),this.history_form&&this.history_form.portlet[e?"enable":"disable"](),s.each(this.forms,function(t){t&&t.portlet[e?"enable":"disable"]()})},_isDataStep:function(e){for(var t=n.isArray(e)?e:[e],i=0;i','','',"
","','',e.title,"","
"].join("")},_templateAllWorkflow:function(e){return['','',e.title,"","
"].join("")},_templateWorkflowLink:function(e){return['','',e.title,"","
"].join("")},_template:function(){return['','",'','','
"].join("")},toString:function(){return"toolPanel"}}));t.default=h}).call(t,i(2),i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),a=n(s),o=i(5),l=n(o),r=i(9),d=n(r),c=i(78),u=n(c),h=i(254),f=n(h),p=i(255),m=n(p),g=i(258),_=n(g),v=i(260),w=n(v);t.default=e.View.extend({options:{nginx_upload_path:"",ftp_upload_site:"n/a",default_genome:"?",default_extension:"auto",height:500,width:900,auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."}},list_extensions:[],list_genomes:[],initialize:function(e){var t=this;this.options=l.default.merge(e,this.options),this.ui_button=new f.default.View({onclick:function(e){e.preventDefault(),t.show()},onunload:function(){var e=t.ui_button.model.get("percentage",0);if(e>0&&e<100)return"Several uploads are queued."}}),this.setElement(this.ui_button.$el);var t=this;l.default.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(e){for(var i in e)t.list_extensions.push({id:e[i].extension,text:e[i].extension,description:e[i].description,description_url:e[i].description_url,composite_files:e[i].composite_files});t.list_extensions.sort(function(e,t){var i=e.text&&e.text.toLowerCase(),n=t.text&&t.text.toLowerCase();return i>n?1:i',"",(0,c.default)("Workflows"),"","
",'','',"
","Drop files here
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
0%
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
0%
Drop files here
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
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'+e.description+"
Length Format
The length format is two-column, separated by whitespace, of the form:
chrom/contig length of chrom/contig
For example, the first few entries of mm9.len are as follows:
chr1 197195432\nchr2 181748087\nchr3 159599783\nchr4 155630120\nchr5 152537259
Trackster uses this information to populate the select box for chrom/contig, andto set the maximum basepair of the track browser. You may either upload a .len fileof this format (Len File option), or directly enter the information into the box (Len Entry option).
"},_templateFasta:function(){return"FASTA format
This is a multi-fasta file from your current history that provides the genomesequences for each chromosome/contig in your build.
Here is a snippet from an example multi-fasta file:
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'},_templateHeader:function(){return'"+this.model.get("plural")+" shared with you by others
| Title | Owner |
|---|
'+this._templateActions()+'
You have no workflows.
'},_templateActionButtons:function(){return''},_templateWorkflowTable:function(){return'| Name | Tags | Owner | # of Steps | Published | Show in tools panel |
|---|
'+(0,m.default)("Your workflows")+"
Import Galaxy workflow
Click the link above to visit myExperiment and browse for Galaxy workflows.
Dataset Error
"),e.$el.append("An error occured while running the tool "+i.tool_id+".
"),e.$el.append("Tool execution generated the following messages:
"),e.$el.append(''+i.stderr+""),e.$el.append("
Report This Error"),e.$el.append("
Usually the local Galaxy administrators regularly review errors that occur on the server. However, if you would like to provide additional information (such as what you were trying to do when the error occurred) and a contact e-mail address, we will be better able to investigate your problem and get back to you.
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diff --git a/static/scripts/bundled/extended.bundled.js b/static/scripts/bundled/extended.bundled.js
index e0f8e3d3225..3343dad6506 100644
--- a/static/scripts/bundled/extended.bundled.js
+++ b/static/scripts/bundled/extended.bundled.js
@@ -48,4 +48,4 @@ s=n,l=e("",{css:{position:"absolute",top:"-200px",left:i?"0px":"-1000px",
// the check will work anyway, as when moving the node will be loaded first and checked again
if(v === 'i' && !ins.is_loaded(p)) { }
*/
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- "+a+"
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s=n.Model.extend({initialize:function(e){this.mapOver=e.mapOver||a,this.terminal=e.terminal,this.terminal.terminalMapping=this},disableMapOver:function(){this.setMapOver(a)},setMapOver:function(e){this.mapOver=e,this.trigger("change")}}),l=n.Model.extend({initialize:function(e){this.element=e.element,this.connectors=[]},connect:function(e){this.connectors.push(e),this.node&&this.node.markChanged()},disconnect:function(t){this.connectors.splice(e.inArray(t,this.connectors),1),this.node&&(this.node.markChanged(),this.resetMappingIfNeeded())},redraw:function(){e.each(this.connectors,function(e,t){t.redraw()})},destroy:function(){e.each(this.connectors.slice(),function(e,t){t.destroy()})},destroyInvalidConnections:function(){i.each(this.connectors,function(e){e&&e.destroyIfInvalid()})},setMapOver:function(e){this.multiple||this.mapOver().equal(e)||(this.terminalMapping.setMapOver(e),i.each(this.node.output_terminals,function(t){t.setMapOver(e)}))},mapOver:function(){return 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t=e.handle2;t&&(t.resetMappingIfNeeded(),e.destroyIfInvalid())})}}),d=l.extend({initialize:function(e){l.prototype.initialize.call(this,e),this.update(e.input)},canAccept:function(e){return!this._inputFilled()&&this.attachable(e)},resetMappingIfNeeded:function(){this.mapOver().isCollection&&((this.node.hasConnectedMappedInputTerminals()||!this.node.hasConnectedOutputTerminals())&&this.resetMapping())},resetMapping:function(){this.terminalMapping.disableMapOver(),this.node.hasMappedOverInputTerminals()||i.each(this.node.output_terminals,function(e){e.resetMapping()})},connected:function(){return 0!==this.connectors.length},_inputFilled:function(){return!!this.connected()&&(!this.multiple||!!this._collectionAttached())},_collectionAttached:function(){if(this.connected()){var e=this.connectors[0].handle1;return!!e&&!!(e.isCollection||e.isMappedOver()||e.datatypes.indexOf("input_collection")>0)}return!1},_mappingConstraints:function(){if(!this.node)return[];var e=this.mapOver();if(e.isCollection)return[e];var t=[];return this.node.hasConnectedOutputTerminals()?t.push(i.first(i.values(this.node.output_terminals)).mapOver()):i.each(this.node.connectedMappedInputTerminals(),function(e){t.push(e.mapOver())}),t},_producesAcceptableDatatype:function(e){for(var t in this.datatypes){var n=this.datatypes[t];if("input"==n)return!0;var i=[];if(i=i.concat(e.datatypes),e.node.post_job_actions)for(var r in e.node.post_job_actions){var a=e.node.post_job_actions[r];"ChangeDatatypeAction"!=a.action_type||""!==a.output_name&&a.output_name!=e.name||!a.action_arguments||i.push(a.action_arguments.newtype)}for(var o in i){var s=i[o];if("input"==s||"_sniff_"==s||"input_collection"==s||window.workflow_globals.app.isSubType(i[o],n))return!0}}return!1},_otherCollectionType:function(e){var t=a;e.isCollection&&(t=e.collectionType);var n=e.mapOver();return n.isCollection&&(t=n.append(t)),t}}),u=d.extend({update:function(e){this.datatypes=e.extensions,this.multiple=e.multiple,this.collection=!1},connect:function(e){d.prototype.connect.call(this,e);var t=e.handle1;if(t){var n=this._otherCollectionType(t);n.isCollection&&this.setMapOver(n)}},attachable:function(e){var t=this._otherCollectionType(e),n=this.mapOver();if(t.isCollection){if(this.multiple)return!(this.connected()&&!this._collectionAttached())&&(1==t.rank&&this._producesAcceptableDatatype(e));if(n.isCollection&&n.canMatch(t))return this._producesAcceptableDatatype(e);return!!this._mappingConstraints().every(i.bind(t.canMatch,t))&&this._producesAcceptableDatatype(e)}return!n.isCollection&&this._producesAcceptableDatatype(e)}}),h=d.extend({update:function(e){this.multiple=!1,this.collection=!0,this.datatypes=e.extensions;var t=[];e.collection_types?i.each(e.collection_types,function(e){t.push(new r(e))}):t.push(o),this.collectionTypes=t},connect:function(e){d.prototype.connect.call(this,e);var t=e.handle1;if(t){var n=this._effectiveMapOver(t);this.setMapOver(n)}},_effectiveMapOver:function(e){var t=this.collectionTypes,n=this._otherCollectionType(e);if(!i.some(t,function(e){return e.canMatch(n)}))for(var r in t){var o=t[r];if(n.canMapOver(o)){var s=n.effectiveMapOver(o);if(s!=a)return s}}return a},_effectiveCollectionTypes:function(){var e=this.mapOver();return i.map(this.collectionTypes,function(t){return e.append(t)})},attachable:function(e){var t=this._otherCollectionType(e);if(t.isCollection){var n=this._effectiveCollectionTypes(),r=this.mapOver();if(i.some(n,function(e){return e.canMatch(t)}))return this._producesAcceptableDatatype(e);if(r.isCollection)return!1;if(i.some(this.collectionTypes,function(e){return t.canMapOver(e)})){var a=this._effectiveMapOver(e);if(!a.isCollection)return!1;if(this._mappingConstraints().every(a.canMatch))return this._producesAcceptableDatatype(e)}}return!1}}),f=l.extend({initialize:function(e){if(l.prototype.initialize.call(this,e),this.datatypes=e.datatypes,e.collection_type)this.collectionType=new r(e.collection_type);else{e.collection_type_source||console.log("Warning: No collection type or collection type source defined."),this.collectionType=o}this.isCollection=!0},update:function(e){var t;if(e.collection_type)t=new r(e.collection_type);else{e.collection_type_source||console.log("Warning: No collection type or collection type source defined."),t=o}t.collectionType!=this.collectionType.collectionType&&i.each(this.connectors,function(e){e.destroy()}),this.collectionType=t}});t.default={InputTerminal:u,OutputTerminal:c,InputCollectionTerminal:h,OutputCollectionTerminal:f,TerminalMapping:s,CollectionTypeDescription:r,NULL_COLLECTION_TYPE_DESCRIPTION:a,ANY_COLLECTION_TYPE_DESCRIPTION:o}}).call(t,n(0),n(2),n(1))},function(e,t,n){"use 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").addClass("tracks"),this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var t=this;this.model.get("tracks").each(function(e){e.get("track").view=t}),this.config=x.default.ConfigSettingCollection.from_models_and_saved_values([{key:"name",label:"Name",type:"text",default_value:""},{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"},{key:"block_color",label:"Block color",type:"color"},{key:"reverse_strand_color",label:"Antisense strand color",type:"color"}],{})},render:function(){var e=new L({model:this.model.get("parameter_tree")});i("#left").append(e.$el);var t=this,n=t.model.get("regions"),r=i("").text(e.toString()))}),r.children().first().attr("colspan",2);var a=i(" " style="display:none;" data-id="<%- library.get("id") %>">',"<% if(!edit_mode) { %>",'<% if(library.get("deleted")) { %>','<%- library.get("name") %> ',"<% } else { %>",'"><%- library.get("name") %> ',"<% } %>",'<% if(library.get("description")) { %>','<% if( (library.get("description")).length> 80 ) { %>','"><%= _.escape(library.get("description")).substring(0, 80) + "..." %> ',"<% } else { %>",'<%= _.escape(library.get("description"))%> ',"<% } %>","<% } else { %>",""><%= _.escape(library.get("synopsis")).substring(0, 120) + "..." %> ',"<% } else { %>",'<%= _.escape(library.get("synopsis"))%> ',"<% } %>","<% } else { %>","','<% if( (library.get("public")) && (library.get("deleted") === false) ) { %>',' ',"<% }%>",'','/permissions">','','','','" class="fa fa-ban fa-lg">',''," "," "].join(""))}});t.default={LibraryRowView:s}}).call(t,n(2),n(0),n(1))},function(e,t,n){"use strict";(function(e,i,r){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=n(3),s=a(o),l=n(7),c=a(l),d=n(18),u=a(d),h=e.View.extend({el:"#center",defaults:{search_term:""},events:{"click #create_new_library_btn":"createLibraryFromModal","click #include_deleted_chk":"includeDeletedChecked","click #exclude_restricted_chk":"excludeRestrictedChecked","click .page_size_prompt":"showPageSizePrompt","keyup .library-search-input":"searchLibraries"},initialize:function(e){this.options=i.defaults(this.options||{},e,this.defaults),this.render()},render:function(){var e=this.templateToolBar(),t=!1,n=!0;Galaxy.user&&(t=Galaxy.user.isAdmin(),n=Galaxy.user.isAnonymous()),this.$el.html(e({admin_user:t,anon_user:n})),t&&(this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted"),this.$el.find("#exclude_restricted_chk")[0].checked=Galaxy.libraries.preferences.get("without_restricted"))},renderPaginator:function(e){this.options=i.extend(this.options,e);var t=this.templatePaginator();this.$el.find("#library_paginator").html(t({show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_libraries_count:this.options.total_libraries_count,libraries_shown:this.options.libraries_shown,library_page_size:Galaxy.libraries.preferences.get("library_page_size")}))},createLibraryFromModal:function(e){e.preventDefault(),e.stopPropagation();var t=this;this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:(0,s.default)("Create New Library"),body:this.templateNewLibraryInModal(),buttons:{Create:function(){t.createNewLibrary()},Close:function(){t.modal.hide()}}})},createNewLibrary:function(){var e=this.serializeNewLibrary();if(this.validateNewLibrary(e)){var t=new u.default.Library,n=this;t.save(e,{success:function(e){Galaxy.libraries.libraryListView.collection.add(e),n.modal.hide(),n.clearLibraryModal(),Galaxy.libraries.libraryListView.render(),c.default.success("Library created.")},error:function(e,t){void 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",'Getting Started
- Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.
- Adjust the tree by using parameter inputs to select min, max, and number of samples
- Run the tool with different settings by clicking on tree nodes
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0!==t.responseJSON?s.default.error(t.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}}):s.default.error("An error occurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}})},render:function(e){this.options=i.extend(this.options,e);var t=this.templateFolder();r(".tooltip").hide();var n,a=this.folderContainer.attributes.metadata.full_path;if(n=1===a.length?0:a[a.length-2][0],this.$el.html(t({path:this.folderContainer.attributes.metadata.full_path,parent_library_id:this.folderContainer.attributes.metadata.parent_library_id,id:this.options.id,upper_folder_id:n,order:this.current_sort_order})),this.options.dataset_id){var o=i.findWhere(self.rowViews,{id:this.options.dataset_id});o?o.showDatasetDetails():s.default.error("Requested dataset not found. Showing folder instead.")}else(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.paginate();r("#center [data-toggle]").tooltip(),r("#center").css("overflow","auto")},paginate:function(e){this.options=i.extend(this.options,e),(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.options.total_items_count=this.folder_container.get("folder").models.length,this.options.page_count=Math.ceil(this.options.total_items_count/Galaxy.libraries.preferences.get("folder_page_size"));var t=Galaxy.libraries.preferences.get("folder_page_size")*(this.options.show_page-1),n=null;n=this.folder_container.get("folder").models.slice(t,t+Galaxy.libraries.preferences.get("folder_page_size")),this.options.items_shown=n.length,Galaxy.libraries.preferences.get("folder_page_size")*this.options.show_page>this.options.total_items_count+Galaxy.libraries.preferences.get("folder_page_size")&&(n=[]),Galaxy.libraries.folderToolbarView.renderPaginator(this.options),this.collection.reset(n)},rePaint:function(e){this.options=i.extend(this.options,e),this.removeAllRows(),this.renderAll(),this.checkEmptiness()},addAll:function(e){i.each(e,function(e){Galaxy.libraries.folderListView.collection.add(e,{current_sort_order:!1})}),r("#center [data-toggle]").tooltip(),this.checkEmptiness(),this.postRender()},postRender:function(){var e=this.folderContainer.attributes.metadata;e.contains_file_or_folder=void 0!==this.collection.findWhere({type:"file"})||void 0!==this.collection.findWhere({type:"folder"}),Galaxy.libraries.folderToolbarView.configureElements(e)},renderAll:function(){var e=this;i.each(this.collection.models.reverse(),function(t){e.renderOne(t)}),this.postRender()},renderOne:function(e){this.options.contains_file_or_folder=!0,e.set("folder_id",this.id);var t=new u.default.FolderRowView({model:e});this.rowViews[e.get("id")]=t,this.$el.find("#first_folder_item").after(t.el)},removeOne:function(e){this.$el.find("tr").filter(function(){return r(this).data("id")&&r(this).data("id")===e.id}).remove()},removeAllRows:function(){r(".library-row").remove()},checkEmptiness:function(){0===this.$el.find(".dataset_row").length&&0===this.$el.find(".folder_row").length?this.$el.find(".empty-folder-message").show():this.$el.find(".empty-folder-message").hide()},sortColumnClicked:function(e){e.preventDefault(),this.current_sort_order="asc"===this.current_sort_order?"desc":"asc",this.current_sort_key=e.currentTarget.className.replace("sort-folder-",""),this.collection.sortFolder(this.current_sort_key,this.current_sort_order),this.renderSortIcon()},selectAll:function(e){var t=e.target.checked,n=this;r(":checkbox","#folder_list_body").each(function(){this.checked=t;var e=r(this).closest("tr");t?n.makeDarkRow(e):n.makeWhiteRow(e)})},selectClickedRow:function(e){var t,n,i="";t=r(e.target).closest("tr"),"input"===e.target.localName?(i=e.target,n="input"):"td"===e.target.localName&&(i=t.find(":checkbox")[0],n="td"),i.checked?"td"===n?(i.checked="",this.makeWhiteRow(t)):"input"===n&&this.makeDarkRow(t):"td"===n?(i.checked="selected",this.makeDarkRow(t)):"input"===n&&this.makeWhiteRow(t)},makeDarkRow:function(e){e.removeClass("light").addClass("dark"),e.find("a").removeClass("light").addClass("dark"),e.find(".fa-file-o").removeClass("fa-file-o").addClass("fa-file"),e.find(".fa-folder-o").removeClass("fa-folder-o").addClass("fa-folder")},makeWhiteRow:function(e){e.removeClass("dark").addClass("light"),e.find("a").removeClass("dark").addClass("light"),e.find(".fa-file").removeClass("fa-file").addClass("fa-file-o"),e.find(".fa-folder").removeClass("fa-folder").addClass("fa-folder-o")},renderSortIcon:function(){"asc"===this.current_sort_order?(r('[class*="sort-icon"]').removeClass("fa-sort-alpha-desc").removeClass("fa-sort-alpha-asc"),r(".sort-icon-"+this.current_sort_key).addClass("fa-sort-alpha-asc")):r(".sort-icon-"+this.current_sort_key).addClass("fa-sort-alpha-desc")},templateFolder:function(){return i.template(['",'',"",'
",'"].join(""))}});t.default={FolderListView:h}}).call(t,n(2),n(1),n(0))},function(e,t,n){"use strict";(function(e,i,r){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=n(7),s=a(o),l=n(18),c=a(l),d=n(138),u=a(d),h=e.View.extend({events:{"click .undelete_dataset_btn":"undeleteDataset","click .undelete_folder_btn":"undeleteFolder","click .edit_folder_btn":"startModifications","click .cancel_folder_btn":"cancelModifications","click .save_folder_btn":"saveModifications"},defaults:{type:null,visibility_config:{edit_folder_btn:!1,save_folder_btn:!1,cancel_folder_btn:!1,permission_folder_btn:!1},edit_mode:!1},initialize:function(e){this.options=i.defaults(e||{},this.defaults),this.render(this.options)},render:function(e){this.options=i.extend(this.options,e);var t=this.options.model,n=null;return"folder"===t.get("type")||"LibraryFolder"===t.get("model_class")?(this.options.type="folder",this.prepareButtons(t),n=t.get("deleted")?this.templateRowDeletedFolder():this.templateRowFolder()):"file"===t.get("type")||"LibraryDatasetDatasetAssociation"===t.get("model_class")||"LibraryDataset"===t.get("model_class")?(this.options.type="file",n=t.get("deleted")?this.templateRowDeletedFile():this.templateRowFile()):(Galaxy.emit.error("Unknown library item type found."),Galaxy.emit.error(t.get("type")||t.get("model_class"))),this.setElement(n({content_item:t,edit_mode:this.options.edit_mode,button_config:this.options.visibility_config})),this.$el.show(),this},prepareButtons:function(e){var t=this.options.visibility_config;!1===this.options.edit_mode?(t.save_folder_btn=!1,t.cancel_folder_btn=!1,!0===e.get("deleted")?(t.edit_folder_btn=!1,t.permission_folder_btn=!1):!1===e.get("deleted")&&(t.save_folder_btn=!1,t.cancel_folder_btn=!1,!0===e.get("can_modify")&&(t.edit_folder_btn=!0),!0===e.get("can_manage")&&(t.permission_folder_btn=!0))):!0===this.options.edit_mode&&(t.edit_folder_btn=!1,t.permission_folder_btn=!1,t.save_folder_btn=!0,t.cancel_folder_btn=!0),this.options.visibility_config=t},showDatasetDetails:function(){Galaxy.libraries.datasetView=new u.default.LibraryDatasetView({id:this.id})},undeleteDataset:function(e){r(".tooltip").hide();var t=this,n=r(e.target).closest("tr").data("id"),i=Galaxy.libraries.folderListView.collection.get(n);i.url=i.urlRoot+i.id+"?undelete=true",i.destroy({success:function(e,i){Galaxy.libraries.folderListView.collection.remove(n);var r=new c.default.Item(i);Galaxy.libraries.folderListView.collection.add(r),Galaxy.libraries.folderListView.collection.sortFolder("name","asc"),s.default.success("Dataset undeleted. Click this to see it.","",{onclick:function(){var e=t.model.get("folder_id");window.location=Galaxy.root+"library/list#folders/"+e+"/datasets/"+t.id}})},error:function(e,t){void 0!==t.responseJSON?s.default.error("Dataset was not undeleted. "+t.responseJSON.err_msg):s.default.error("An error occured! Dataset was not undeleted. Please try again.")}})},undeleteFolder:function(e){r(".tooltip").hide();var t=r(e.target).closest("tr").data("id"),n=Galaxy.libraries.folderListView.collection.get(t);n.url=n.urlRoot+n.id+"?undelete=true",n.destroy({success:function(e,n){Galaxy.libraries.folderListView.collection.remove(t);var i=new c.default.FolderAsModel(n);Galaxy.libraries.folderListView.collection.add(i),Galaxy.libraries.folderListView.collection.sortFolder("name","asc"),s.default.success("Folder undeleted.")},error:function(e,t){void 0!==t.responseJSON?s.default.error("Folder was not undeleted. "+t.responseJSON.err_msg):s.default.error("An error occured! Folder was not undeleted. Please try again.")}})},startModifications:function(){this.options.edit_mode=!0,this.repaint()},cancelModifications:function(){this.options.edit_mode=!1,this.repaint()},saveModifications:function(){var e=Galaxy.libraries.folderListView.collection.get(this.$el.data("id")),t=!1,n=this.$el.find(".input_folder_name").val();if(void 0!==n&&n!==e.get("name")){if(!(n.length>2))return void s.default.warning("Folder name has to be at least 3 characters long.");e.set("name",n),t=!0}var i=this.$el.find(".input_folder_description").val();if(void 0!==i&&i!==e.get("description")&&(e.set("description",i),t=!0),t){var r=this;e.save(null,{patch:!0,success:function(e){r.options.edit_mode=!1,r.repaint(e),s.default.success("Changes to folder saved.")},error:function(e,t){void 0!==t.responseJSON?s.default.error(t.responseJSON.err_msg):s.default.error("An error occured while attempting to update the folder.")}})}else this.options.edit_mode=!1,this.repaint(e),s.default.info("Nothing has changed.")},repaint:function(){r(".tooltip").hide();var e=this.$el;this.render(),e.replaceWith(this.$el),this.$el.find("[data-toggle]").tooltip()},templateRowFolder:function(){return i.template(['',"",''," ",'",'<%- content_item.get("name") %>'," ","",'<%- content_item.get("description") %>'," ","<% } else if(edit_mode){ %>",'folder ","",'<%= _.escape(content_item.get("update_time")) %>'," ","","<% if(edit_mode) { %>",'",'","<% } else if (!edit_mode){%>",'",'','","","<% } %>"," "," "].join(""))},templateRowFile:function(){return i.template(['',"",''," ",'',''," ","",'/datasets/<%- content_item.id %>" class="library-dataset">','<%- content_item.get("name") %>',""," ",'<%- content_item.get("message") %> ','<%= _.escape(content_item.get("file_ext")) %> ','<%= _.escape(content_item.get("file_size")) %> ','<%= _.escape(content_item.get("update_time")) %> ',"",'<% if ( content_item.get("state") !== "ok" ) { %>','<%= _.escape(content_item.get("state")) %>',"<% } %>"," ","",'<% if (content_item.get("is_unrestricted")) { %>','',"<% } %>",'<% if (content_item.get("is_private")) { %>','',"<% } %>",'<% if ((content_item.get("is_unrestricted") === false) && (content_item.get("is_private") === false)) { %>','',"<% } %>",'<% if (content_item.get("can_manage")) { %>','/datasets/<%- content_item.id %>/permissions">','","","<% } %>"," "," "].join(""))},templateRowDeletedFile:function(){return i.template(['',"",''," ","','<%- content_item.get("name") %>'," ","",'<%- content_item.get("message") %>'," ","",'<%= _.escape(content_item.get("file_ext")) %>'," ","",'<%= _.escape(content_item.get("file_size")) %>'," ","",'<%= _.escape(content_item.get("update_time")) %>'," ","",'<% if ( content_item.get("state") !== "ok" ) { %>','<%= _.escape(content_item.get("state")) %>',"<% } %>"," ","",'','"," "," "].join(""))},templateRowDeletedFolder:function(){return i.template(['',"",''," ","','<%- content_item.get("name") %>'," ","",'<%- content_item.get("description") %>'," ","","folder"," ","",'<%= _.escape(content_item.get("update_time")) %>'," ","",'','"," "," "].join(""))}});t.default={FolderRowView:h}}).call(t,n(2),n(1),n(0))},function(e,t,n){"use strict";(function(e,i){function r(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=n(7),o=r(a),s=n(18),l=r(s),c=n(320),d=r(c),u=n(1),h=r(u),f=e.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},defaults:{page_count:null,show_page:null,all_fetched:!1},initialize:function(e){this.options=h.default.defaults(this.options||{},e,this.defaults);var t=this;this.modal=null,this.collection=new l.default.Libraries,this.collection.url=this.collection.urlRoot+"?deleted=false",this.collection.fetch({success:function(){t.render()},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occurred.")}})},render:function(e){this.options=h.default.extend(this.options,e),this.setElement("#libraries_element");var t=this.templateLibraryList(),n=null,r=null,a=function(e){return!0===e.get("public")};if(i(".tooltip").hide(),void 0!==e&&(r=void 0!==e.models?e.models:null),null!==this.collection&&null===r)this.sortLibraries(),n=Galaxy.libraries.preferences.get("with_deleted")?this.collection.models:this.collection.where({deleted:!1}),Galaxy.libraries.preferences.get("without_restricted")&&(n=h.default.filter(n,a));else if(null!==r){if(Galaxy.libraries.preferences.get("with_deleted"))n=r;else{var o=function(e){return!1===e.get("deleted")};n=h.default.filter(r,o)}Galaxy.libraries.preferences.get("without_restricted")&&(n=h.default.filter(n,a))}else n=[];(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.options.total_libraries_count=n.length;var s=Galaxy.libraries.preferences.get("library_page_size")*(this.options.show_page-1);this.options.page_count=Math.ceil(this.options.total_libraries_count/Galaxy.libraries.preferences.get("library_page_size")),this.options.total_libraries_count>0&&sthis.options.total_libraries_count+Galaxy.libraries.preferences.get("library_page_size")&&(n=[]),this.$el.html(t({length:1,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options),this.renderRows(n)):(this.$el.html(t({length:0,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options)),i("#center [data-toggle]").tooltip(),i("#center").css("overflow","auto")},fetchDeleted:function(){if(this.options.all_fetched)this.render();else{var e=this;this.collection.url=this.collection.urlRoot+"?deleted=true",this.collection.fetch({remove:!1,success:function(){e.options.all_fetched=!0,e.render()},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occurred.")}})}},renderRows:function(e){for(var t=0;t',"<% if(length === 0) { %>","<% if(search_term.length > 0) { %>","',"",'
","<% }%>","
"].join(""))}});t.default={LibraryListView:f}}).call(t,n(2),n(0))},function(e,t,n){"use strict";(function(e,i,r){Object.defineProperty(t,"__esModule",{value:!0});var a=n(7),o=function(e){return e&&e.__esModule?e:{default:e}}(a),s=e.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library"},edit_mode:!1,element_visibility_config:{upload_library_btn:!1,edit_library_btn:!1,permission_library_btn:!1,save_library_btn:!1,cancel_library_btn:!1,delete_library_btn:!1,undelete_library_btn:!1},initialize:function(e){this.render(e)},render:function(e){void 0===e&&(e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))),this.prepareButtons(e);var t=this.templateRow();return this.setElement(t({library:e,button_config:this.element_visibility_config,edit_mode:this.edit_mode})),this.$el.show(),this},repaint:function(e){i(".tooltip").hide();var t=this.$el;this.render(),t.replaceWith(this.$el),this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){var t=this.element_visibility_config;!1===this.edit_mode?(t.save_library_btn=!1,t.cancel_library_btn=!1,t.delete_library_btn=!1,!0===e.get("deleted")?(t.undelete_library_btn=!0,t.upload_library_btn=!1,t.edit_library_btn=!1,t.permission_library_btn=!1):!1===e.get("deleted")&&(t.save_library_btn=!1,t.cancel_library_btn=!1,t.undelete_library_btn=!1,!0===e.get("can_user_add")&&(t.upload_library_btn=!0),!0===e.get("can_user_modify")&&(t.edit_library_btn=!0),!0===e.get("can_user_manage")&&(t.permission_library_btn=!0))):!0===this.edit_mode&&(t.upload_library_btn=!1,t.edit_library_btn=!1,t.permission_library_btn=!1,t.save_library_btn=!0,t.cancel_library_btn=!0,t.delete_library_btn=!0,t.undelete_library_btn=!1),this.element_visibility_config=t},edit_button_clicked:function(){this.edit_mode=!0,this.repaint()},cancel_library_modification:function(){this.edit_mode=!1,this.repaint()},save_library_modification:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=!1,n=this.$el.find(".input_library_name").val();if(void 0!==n&&n!==e.get("name")){if(!(n.length>2))return void o.default.warning("Library name has to be at least 3 characters long.");e.set("name",n),t=!0}var i=this.$el.find(".input_library_description").val();void 0!==i&&i!==e.get("description")&&(e.set("description",i),t=!0);var r=this.$el.find(".input_library_synopsis").val();if(void 0!==r&&r!==e.get("synopsis")&&(e.set("synopsis",r),t=!0),t){var a=this;e.save(null,{patch:!0,success:function(e){a.edit_mode=!1,a.repaint(e),o.default.success("Changes to library saved.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured while attempting to update the library.")}})}else this.edit_mode=!1,this.repaint(e),o.default.info("Nothing has changed.")},delete_library:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=this;e.destroy({success:function(e){e.set("deleted",!0),Galaxy.libraries.libraryListView.collection.add(e),t.edit_mode=!1,!1===Galaxy.libraries.preferences.get("with_deleted")?(i(".tooltip").hide(),t.repaint(e),t.$el.remove()):!0===Galaxy.libraries.preferences.get("with_deleted")&&t.repaint(e),o.default.success("Library has been marked deleted.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured during deleting the library.")}})},undelete_library:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=this;e.url=e.urlRoot+e.id+"?undelete=true",e.destroy({success:function(e){e.set("deleted",!1),Galaxy.libraries.libraryListView.collection.add(e),t.edit_mode=!1,t.repaint(e),o.default.success("Library has been undeleted.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured while undeleting the library.")}})},templateRow:function(){return r.template(['| ',' | ',' | name | ','description | ','data type | ','size | ','time updated (UTC) | ','state | ','',"",'',' |
|---|---|---|---|---|---|---|---|---|
| ",'" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..'," | ",""," | "," | "," | "," | "," | "," | "," | "," |
","There are no libraries matching your search. Try different keyword.","
","<% } else{ %>","","There are no libraries visible to you here. If you expected some to show up please consult the",' library security wikipage',' or visit the Galaxy support site.',"
","<% }%>","<% } else{ %>",'| ','',"name","",''," | ",'description | ','synopsis | ','',"",'',""," |
|---|
','
"].join(""))},templatePaginator:function(){return i.template(['','
",'','","
","',"
","- ',"<% if ( ( show_page - 1 ) > 0 ) { %>","<% if ( ( show_page - 1 ) > page_count ) { %>",'
- ','
- <% print( show_page - 1 ) %> ',"<% } else { %>",'
- ','
- <% print( show_page - 1 ) %> ',"<% } %>","<% } else { %>",'
- ','
- <% print( show_page - 1 ) %> ',"<% } %>",'
- ','<% print( show_page ) %>'," ","<% if ( ( show_page ) < page_count ) { %>",'
- <% print( show_page + 1 ) %> ','
- ',"<% } else { %>",'
- <% print( show_page + 1 ) %> ','
- ',"<% } %>","
',"","
"].join(""))}});t.default={LibraryToolbarView:h}}).call(t,n(2),n(1),n(0))},function(e,t,n){"use strict";(function(e,i,r,a){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=n(3),l=o(s),c=n(5),d=o(c),u=n(7),h=o(u),f=n(18),p=o(f),g=n(12),m=o(g),_=n(28),v=o(_),y=n(73),b=o(y),w=n(74),x=o(w),k=n(20),M=o(k);n(139);var C=e.View.extend({el:"#center",events:{"click .toolbtn-create-folder":"createFolderFromModal","click .toolbtn-bulk-import":"importToHistoryModal","click .include-deleted-datasets-chk":"checkIncludeDeleted","click .toolbtn-bulk-delete":"deleteSelectedItems","click .toolbtn-show-locinfo":"showLocInfo","click .page-size-prompt":"showPageSizePrompt","click .toolbtn-collection-import":"showCollectionSelect"},defaults:{can_add_library_item:!1,contains_file_or_folder:!1,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(e){this.options=i.defaults(e||{},this.defaults),this.fetchExtAndGenomes(),this.render()},render:function(e){this.options=i.extend(this.options,e);var t=this.templateToolBar(),n={id:this.options.id,is_admin:!1,is_anonym:!0,mutiple_add_dataset_options:!1};Galaxy.user&&(n.is_admin=Galaxy.user.isAdmin(),n.is_anonym=Galaxy.user.isAnonymous(),null===Galaxy.config.user_library_import_dir&&!1===Galaxy.config.allow_library_path_paste&&null===Galaxy.config.library_import_dir||(n.mutiple_add_dataset_options=!0)),this.$el.html(t(n))},renderPaginator:function(e){this.options=i.extend(this.options,e);var 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| ",'"><%= category.get("name") %>'," | ",'<%= category.get("description") %> | ','<%= category.get("repositories") %> | ',"
','
",'Repositories in <%= category.get("name") %>
','',"','
"].join(""))});t.default={Category:d}}).call(t,n(2),n(1),n(0))},function(e,t,n){"use strict";(function(e,i,r){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=n(34),s=a(o),l=n(139),c=(a(l),n(5)),d=a(c),u=n(9),h=a(u),f=n(13),p=a(f),g=n(35),m=a(g),_=e.View.extend({el:"#center",initialize:function(e){this.options=i.defaults(this.options||{},this.defaults),this.model=new s.default.RepositoryCollection,this.listenTo(this.model,"sync",this.render);var t=e.tool_shed.replace(/\//g,"%2f");this.model.url+="?tool_shed_url="+t+"&repository_id="+e.repository_id,this.model.tool_shed_url=e.tool_shed.replace(/%2f/g,"/"),this.model.tool_shed=t,this.model.category=e.repository_id,this.model.fetch()},render:function(e){var t=this.templateRepoDetails,n=this.model.models[0];this.options={repository:n.get("repository"),tool_shed:this.model.tool_shed,queue:m.default.queueLength()};var a=Object.keys(this.options.repository.metadata).sort(function(e,t){return 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e=this;r("#changeset").on("change",function(){e.options.current_changeset=r("#changeset").find("option:selected").text(),e.options.current_metadata=e.options.repository.metadata[e.options.current_changeset],e.checkInstalled(e.options.current_metadata),e.reDraw(e.options)}),r("#tool_panel_section_select").on("change",function(){e.tpsSelection()}),r("#install_repository").on("click",function(t){r("#repository_installation");t.preventDefault();var n={};n.repositories=JSON.stringify([[r("#install_repository").attr("data-tsrid"),r("#changeset").find("option:selected").val()]]),n.tool_shed_repository_ids=JSON.stringify([r("#install_repository").attr("data-tsrid")]),n.tool_shed_url=e.model.tool_shed_url,n.install_tool_dependencies=r("#install_tool_dependencies").val(),n.install_repository_dependencies=r("#install_repository_dependencies").val(),n.install_resolver_dependencies=r("#install_resolver_dependencies").val();e.panelSelect(n);n.tool_panel_section=JSON.stringify(e.panelSelect(n)),n.shed_tool_conf=r("select[name='shed_tool_conf']").find("option:selected").val(),n.changeset=r("#changeset").find("option:selected").val();var i=r("#repository_installation").attr("action");e.prepareInstall(n,i)}),r("#queue_install").on("click",function(t){e.options.current_changeset=r("#changeset").find("option:selected").text(),e.options.current_metadata=e.options.repository.metadata[e.options.current_changeset];var n=(e.options.current_changeset,{});i.each(Object.keys(e.options.current_metadata),function(t){n[t]||(n[t]=e.options.current_metadata[t])}),n.install_tool_dependencies=r("#install_tool_dependencies").val(),n.install_repository_dependencies=r("#install_repository_dependencies").val(),n.install_resolver_dependencies=r("#install_resolver_dependencies").val(),n.tool_panel_section=JSON.stringify(e.panelSelect({})),n.shed_tool_conf=r("select[name='shed_tool_conf']").find("option:selected").val(),n.tool_shed_url=e.model.tool_shed_url,"/"==n.tool_shed_url.substr(-1)&&(n.tool_shed_url=n.tool_shed_url.substr(0,n.tool_shed_url.length-1)),m.default.addToQueue(n),e.checkInstalled(n)}),r(".tool_panel_section_picker").on("change",function(){r(this).find("option:selected").val()==r("#tool_panel_section_select").find("option:selected").val()?r(this).attr("default","active"):r(this).removeAttr("default")}),r(function(){r("#repository_dependencies").jstree()}),r(".tool_form").on("click",function(){var t=r(this).attr("data-guid"),n=(r(this).attr("data-clean"),r(this).attr("data-name")),i=r(this).attr("data-desc"),a=e.model.tool_shed_url,o=r("#repository_details").attr("data-tsrid"),s=r("#changeset").find("option:selected").val(),l=Galaxy.root+"api/tool_shed/tool_json",c={guid:t,tool_shed_url:a,tsr_id:o,changeset:s};r.get(l,c,function(e){e.cls="ui-portlet-plain";var t=new p.default(e);d.default.deepeach(e.inputs,function(e){e.type&&-1!=["data","data_collection"].indexOf(e.type)&&(e.type="hidden",e.info="Data input '"+e.name+"' ("+d.default.textify(e.extensions)+")")});var r=new h.default.View,a=""+n+" "+i;r.show({closing_events:!0,title:a,body:t.$el,buttons:{Close:function(){r.hide()}}})})})},checkInstalled:function(e){var t=this,n={name:e.name,owner:e.owner},i=!1;t.repoQueued(e);r.get(Galaxy.root+"api/tool_shed_repositories",n,function(n){for(var a=0;a','","
",'','','',"
","
","| Owner | ','Name | ',"Synopsis | ",'Type | ',"
|---|---|---|---|
| <%= repository.owner %> | ","",'"," | ","<%= repository.description %> | ","<%= repository.type %> | ","
Repository information for <%= repository.name %> from <%= repository.owner %>
','',"','","
"].join("")),templateRepoDependencies:i.template(['Repository Dependencies
','',"
"].join("")),templateRepoDependency:i.template(['- ","
- Repository installation requires the following","<% if (has_repository_dependencies) { %>","<% _.each(repository_dependencies, function(dependency) { %>","<% dependency.repository_dependency_template = repository_dependency_template; %>","<%= repository_dependency_template(dependency) %>","<% }); %>","<% } %>"," ","
- ',"<% _.each(repository_dependencies, function(dependency) { %>","<% dependency.repository_dependency_template = repository_dependency_template; %>","<%= repository_dependency_template(dependency) %>","<% }); %>","
Shed tool configuration file:
','','
"].join("")),templateToolDependency:i.template(["<% if (has_repository_dependencies) { %>","<% _.each(repository_dependencies, function(dependency) { %>","<% if (dependency.includes_tool_dependencies) { %>","<% dependency.tool_dependency_template = tool_dependency_template %>","<%= tool_dependency_template(dependency) %>","<% } %>","<% }); %>","<% } %>"].join("")),templateGlobalSectionCreate:i.template(['','",'
","Select the file whose tool_path setting you want used for installing repositories.
',"','
"].join("")),templateGlobalSectionSelect:i.template(['','','','
","',"Add a new tool panel section to contain the installed tools (optional).","
","','
"].join("")),templateToolSectionCreate:i.template(['Tool Panel Section
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","','",'','
","',"Select an existing tool panel section to contain the installed tools (optional).","
","','','',"
"].join("")),templateToolSectionSelect:i.template(['','",'','',"
"].join("")),templatePanelSelectOptions:i.template(["<% _.each(sections, function(section) { %>",'',"<% }); %>"].join(""))});t.default={RepoDetails:_}}).call(t,n(2),n(1),n(0))},function(e,t,n){"use strict";(function(e,i,r){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=n(3),s=a(o),l=n(34),c=a(l),d=n(35),u=a(d),h=e.View.extend({el:"#center",defaults:[{}],initialize:function(e){var t=this;this.model=new c.default.RepoQueue,this.listenTo(this.model,"sync",this.render),this.model.fetch(),t.render()},render:function(e){var t=this,n=t.templateRepoQueue,r=t.model.models;t.$el.html(n({title:(0,s.default)("Repository Installation Queue"),repositories:r,queue:u.default.queueLength()})),i("#center").css("overflow","auto"),t.bindEvents()},bindEvents:function(){var t=this;i(".install_one").on("click",function(){var e=t.loadFromQueue(i(this).attr("data-repokey"));t.installFromQueue(e,i(this).attr("data-repokey"))}),i(".remove_one").on("click",function(){var e=i(this).attr("data-repokey"),t=JSON.parse(localStorage.repositories);if(t.hasOwnProperty(e)){var n=t[e].repository.id;delete t[e],i("#queued_repository_"+n).remove()}localStorage.repositories=JSON.stringify(t)}),i("#clear_queue").on("click",function(){localStorage.repositories="{}"}),i("#from_workflow").on("click",function(){e.history.navigate("workflows",{trigger:!0,replace:!0})})},installFromQueue:function(t,n){var r=Object();r.install_tool_dependencies=t.install_tool_dependencies,r.install_repository_dependencies=t.install_repository_dependencies,r.install_resolver_dependencies=t.install_resolver_dependencies,r.tool_panel_section=t.tool_panel_section,r.shed_tool_conf=t.shed_tool_conf,r.repositories=JSON.stringify([[t.repository.id,t.changeset_revision]]),r.tool_shed_repository_ids=JSON.stringify([t.repository.id]),r.tool_shed_url=n.split("|")[0],r.changeset=t.changeset_revision;var a=Galaxy.root+"api/tool_shed_repositories/install?async=True";if(i("#queued_repository_"+t.repository.id).remove(),localStorage.repositories){void 0===n&&(n=u.default.queueKey(t));var o=JSON.parse(localStorage.repositories);o.hasOwnProperty(n)&&(delete o[n],localStorage.repositories=JSON.stringify(o))}i.post(a,r,function(t){var n=JSON.parse(t),r=n.repositories,a="status/r/"+r.join("|");i.post(Galaxy.root+"admin_toolshed/install_repositories",n,function(e){console.log("Initializing repository installation succeeded")}),e.history.navigate(a,{trigger:!0,replace:!0})})},loadFromQueue:function(e){var t=JSON.parse(localStorage.repositories);if(t.hasOwnProperty(e))return t[e]},reDraw:function(e){this.$el.empty(),this.initialize(e),this.model.fetch(),this.render(e)},templateRepoQueue:r.template(['','
",'<%= title %>
','',"','','',"
",'',"
"].join(""))});t.default={RepoQueueView:h}}).call(t,n(2),n(0),n(1))},function(e,t,n){"use strict";(function(e,i,r){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=n(3),s=a(o),l=n(34),c=a(l),d=n(35),u=a(d),h=e.View.extend({el:"#center",initialize:function(e){this.options=i.defaults(this.options||[{}],e,this.defaults),this.model=new c.default.RepoStatus,this.listenTo(this.model,"sync",this.render),this.model.url+="?repositories="+this.options.repositories.join("|"),this.model.fetch(),this.timer=setInterval(function(e){var t=["installed","error"],n=!0;i.some(e.model.models,function(e){repo_id=e.get("id");var i=e.get("status").toLowerCase();if(-1===t.indexOf(i))return n=!1,!0}),n?clearInterval(e.timer):e.model.fetch()},2e3,this)},close:function(){clearInterval(this.timer)},render:function(e){this.options=i.extend(this.options,e);var t=this.templateRepoStatus;this.$el.html(t({title:(0,s.default)("Repository Status"),repositories:this.model.models,queue:u.default.queueLength()})),r("#center").css("overflow","auto"),this.bindEvents()},bindEvents:function(){},reDraw:function(e){this.$el.empty(),this.initialize(e)},templateRepoStatus:i.template(['| Name | ','Owner | ','Revision | ','ToolShed | ','Install | ',''," |
|---|---|---|---|---|---|
| <%= repository.get("repository").name %> | ','<%= repository.get("repository").owner %> | ','<%= repository.get("changeset_revision") %> | ','<%= repository.get("tool_shed_url") %> | ','','" type="submit" id="install_repository_<%= repository.get("id") %>" name="install_repository" value="Install now" />'," | ",'','" type="submit" id="unqueue_repository_<%= repository.get("id") %>" name="unqueue_repository" value="Remove from queue" />'," | ","
','
",'",'<%= title %>
','',"| Name | ','Description | ','Owner | ','Revision | ','Installation Status | ',"
|---|---|---|---|---|
| ",' ','"," "," | ","",' ','"," "," | ","",' ','"," "," | ","",' ','"," "," | ","",' ','"," "," | ","
','
",'",'<%= title %>
','',"| Workflows | ','Tool IDs | ','Shed | ','Name | ','Owner | ','Actions | ',"
|---|---|---|---|---|---|
','
| ",'','
| ",'<%= workflow.get("shed") %> | ','<%= workflow.get("repository") %> | ','<%= workflow.get("owner") %> | ','','
| ","
"+u.TOOLS+" |
"+u.IFRAME+u.STATUS+" |
",{"Make link":function(){var t=e(s._options.hrefSelector).val()||"",n=e(".wym_id").val()||"",i=e(s._options.titleSelector).val()||"";if(t||n){s._exec(u.CREATE_LINK,l);var r=e("a[href="+l+"]",s._doc.body);r.attr(u.HREF,t).attr(u.TITLE,i).attr("id",n),0===r.text().indexOf("wym-")&&r.text(i)}hide_modal()},Cancel:function(){hide_modal()}},{},o)}if(t==u.DIALOG_IMAGE)return s._selected_image&&(e(s._options.dialogImageSelector+" "+s._options.srcSelector).val(e(s._selected_image).attr(u.SRC)),e(s._options.dialogImageSelector+" "+s._options.titleSelector).val(e(s._selected_image).attr(u.TITLE)),e(s._options.dialogImageSelector+" "+s._options.altSelector).val(e(s._selected_image).attr(u.ALT))),void show_modal("Image","
",{Insert:function(){var t=e(s._options.srcSelector).val();t.length>0&&(s._exec(u.INSERT_IMAGE,l),e("img[src$="+l+"]",s._doc.body).attr(u.SRC,t).attr(u.TITLE,e(s._options.titleSelector).val()).attr(u.ALT,e(s._options.altSelector).val())),hide_modal()},Cancel:function(){hide_modal()}});if(t==u.DIALOG_TABLE&&show_modal("Table","
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"+WYMeditor.CONTAINERS+WYMeditor.CLASSES+"
"+WYMeditor.HTML+WYMeditor.IFRAME+WYMeditor.STATUS+"
"+WYMeditor.LOGO+"
{Tools}
- "+WYMeditor.TOOLS_ITEMS+"
{Containers}
- "+WYMeditor.CONTAINERS_ITEMS+"
{Classes}
- "+WYMeditor.CLASSES_ITEMS+"