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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.$scrollContainer,this.title=e.title||"",this.subtitle=e.subtitle||"",this._setUpListeners()},_setUpListeners:function(){return 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"].join(""))});t.default={RepoStatus:h}}).call(t,n(2),n(1),n(0))},328:function(e,t,n){"use strict";(function(e,i,r){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=n(3),s=a(o),l=n(18),c=a(l),d=n(19),u=a(d),h=e.View.extend({el:"#center",defaults:[{}],initialize:function(e){var t=this;this.model=new c.default.WorkflowTools,this.listenTo(this.model,"sync",this.render),this.model.fetch(),t.render()},render:function(e){var t=this,n=t.templateWorkflows,r=t.model.models;t.$el.html(n({title:(0,s.default)("Workflows Missing Tools"),workflows:r,queue:u.default.queueLength()})),i("#center").css("overflow","auto"),t.bindEvents()},bindEvents:function(){var t,n=this;i(".show_wf_repo").on("click",function(){var n=i(this).attr("data-toolids"),r=i(this).attr("data-shed"),a=Galaxy.root+"api/tool_shed/repository",o={tool_ids:n};i.get(a,o,function(n){t=n.repository.id;var i="repository/s/"+r.replace(/:/g,"%3a").replace(/\//g,"%2f")+"/r/"+n.repository.id;e.history.navigate(i,{trigger:!0,replace:!0})})}),i(".queue_wf_repo").on("click",function(){var e=i(this),n=e.attr("data-toolids"),r=e.attr("data-shed"),a=Galaxy.root+"api/tool_shed/repository",o={tool_ids:n};i.get(a,o,function(n){t=n.repository.id,o={tool_shed_url:r,repository_id:t},i.get(a,o,function(t){var n=Object.keys(t.repository.metadata),i=n[0],a=t.repository.metadata[i];a.tool_shed_url=r,u.default.addToQueue(a),e.remove()})})}),i("#from_workflow").on("click",n.loadWorkflows)},reDraw:function(e){this.$el.empty(),this.initialize(e)},templateWorkflows:r.template(['','',"
\n Loading job data for '+i+'...\n '}return n},toString:function(){return"HDCAListItemView("+(this.model?""+this.model:"(no model)")+")"}});g.prototype.templates=function(){var t=e.extend({},m.prototype.templates.warnings,{hidden:function(e){e.visible||(0,p.default)("This collection has been hidden")}}),i=function(t){return'\n \n "};return e.extend({},m.prototype.templates,{warnings:t,titleBar:i})}(),t.default={HDCAListItemView:g}}).call(t,i(1))},,function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(67),l=a(o),r=i(42),d=a(r),c=i(9),u=a(c),h=i(5),f=a(h),p=e.View.extend({el:"body",className:"full-content",_panelids:["left","right"],initialize:function(t){var i=this;this.config=n.defaults(t.config||{},{message_box_visible:!1,message_box_content:"",message_box_class:"info",show_inactivity_warning:!1,inactivity_box_content:""}),Galaxy.modal=this.modal=new u.default.View,Galaxy.display=this.display=function(e){e.title?(f.default.setWindowTitle(e.title),e.allow_title_display=!1):(f.default.setWindowTitle(),e.allow_title_display=!0),i.center.display(e)},Galaxy.router=this.router=t.Router&&new t.Router(i,t),this.masthead=new l.default.View(this.config),this.center=new d.default.CenterPanel,this.$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(3),l=a(o),r=i(4),d=a(r),c=i(88),u=a(c),h=i(6),f=a(h),p=i(11),m=a(p),g=i(91),_=a(g),v=i(46),y=a(v),w=i(8),b=a(w),x=i(35),C=a(x),$=i(62),k=a($),S=e.View.extend({initialize:function(t){var i=this;this.modal=parent.Galaxy.modal||new b.default.View,this.model=t&&t.model||new e.Model(t),this.deferred=new u.default,this.setElement(n("").addClass("ui-form-composite").append(this.$message=n("")).append(this.$header=n("")).append(this.$steps=n(""))),n("body").append(this.$el),this._configure(),this.render(),n(window).resize(function(){i._refresh()})},_refresh:function(e){var t=s.reduce(this.$el.children(),function(e,t){return e+n(t).outerHeight()},0)-this.$steps.height()+90;this.$steps.css("height",n(window).height()-t)},_configure:function(){function e(e,n){for(var s,a=/\$\{(.+?)\}/g;s=a.exec(String(e));){var o=s[1];n(t.wp_inputs[o]=t.wp_inputs[o]||{label:o,name:o,type:"text",color:"hsl( "+100*++i+", 70%, 30% )",style:"ui-form-wp-source",links:[]})}}var t=this;this.forms=[],this.steps=[],this.links=[],this.parms=[],s.each(this.model.get("steps"),function(e,i){Galaxy.emit.debug("tool-form-composite::initialize()",i+" : Preparing workflow step.");var n=k.default[e.step_type],a=parseInt(i+1)+": "+(e.step_label||e.step_name);e.annotation&&(a+=" - 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The workflow may still run, but any new options will have default values. Please review the messages below to make a decision about whether the changes will affect your analysis.",status:"warning",persistent:!0,fade:!1}).$el);var e=this.model.get("step_version_changes");e&&e.length>0&&this.$message.append(new f.default.Message({message:"Some tools are being executed with different versions compared to those available when this workflow was last saved because the other versions are not or no longer available on this Galaxy instance. To upgrade your workflow and dismiss this message simply edit the workflow and re-save it.",status:"warning",persistent:!0,fade:!1}).$el)},_renderParameters:function(){var e=this;this.wp_form=null,s.isEmpty(this.wp_inputs)||(this.wp_form=new m.default({title:"Workflow Parameters",inputs:this.wp_inputs,cls:"ui-portlet-narrow",onchange:function(){s.each(e.wp_form.input_list,function(t,i){s.each(t.links,function(t){e._refreshStep(t)})})}}),this._append(this.$steps.empty(),this.wp_form.$el))},_renderHistory:function(){this.history_form=new m.default({cls:"ui-portlet-narrow",title:"History Options",inputs:[{type:"conditional",name:"new_history",test_param:{name:"check",label:"Send results to a new history",type:"boolean",value:"false",help:""},cases:[{value:"true",inputs:[{name:"name",label:"History name",type:"text",value:this.model.get("name")}]}]}]}),this._append(this.$steps,this.history_form.$el)},_renderStep:function(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 y.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 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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},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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"+(JSON.stringify(t)||""))).append(n("").text(JSON.stringify(e,null,4)))}});t.default={View:S}}).call(t,i(2),i(0),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(8),l=a(o),r=i(113),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. 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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.$el;var t=e.find(".list-action-menu"),i=this.multiselectActions();if(!i.length)return t.empty();var n=s(['"].join("")),a=i.map(function(e){var t=['',e.html," "].join("");return s(t).click(function(t){return t.preventDefault(),e.func(t)})});return n.find("ul").append(a),t.replaceWith(n),n},multiselectActions:function(){return[]},$scrollContainer:function(e){return(e||this.$el).parent().parent()},$controls:function(e){return(e||this.$el).find("> .controls")},$list:function(e){return(e||this.$el).find("> .list-items")},$messages:function(e){return(e||this.$el).find("> .controls .messages")},$emptyMessage:function(e){return(e||this.$el).find("> .empty-message")},renderItems:function(e){e=e||this.$el;var t=this;t.log(this+".renderItems",e);var i=t.$list(e);t.freeViews();var n=t._filterCollection();return t.views=n.map(function(e){return t._createItemView(e)}),i.empty(),t.views.length&&t._attachItems(e),t._renderEmptyMessage(e).toggle(!t.views.length),t.trigger("views:ready",t.views),t.views},_filterCollection:function(){var e=this;return e.collection.filter(n.bind(e._filterItem,e))},_filterItem:function(e){var t=this;return n.every(t.filters.map(function(t){return t.call(e)}))&&(!t.searchFor||e.matchesAll(t.searchFor))},_createItemView:function(e){var t=this._getItemViewClass(e),i=n.extend(this._getItemViewOptions(e),{model:e}),s=new t(i);return this._setUpItemViewListeners(s),s},_destroyItemView:function(e){this.stopListening(e),this.views=n.without(this.views,e)},_destroyItemViews:function(e){var t=this;return t.views.forEach(function(e){t.stopListening(e)}),t.views=[],t},freeViews:function(){return this._destroyItemViews()},_getItemViewClass:function(e){return this.viewClass},_getItemViewOptions:function(e){return{fxSpeed:this.fxSpeed,expanded:!1,selectable:this.selecting,selected:n.contains(this.selected,e.id),draggable:this.dragItems}},_setUpItemViewListeners:function(e){var t=this;return this.listenTo(e,"all",function(){var e=Array.prototype.slice.call(arguments,0);e[0]="view:"+e[0],t.trigger.apply(t,e)}),this.listenTo(e,"draggable:dragstart",function(e,t){var i={},n=this.getSelectedModels();i=n.length?n.toJSON():[t.model.toJSON()],e.dataTransfer.setData("text",JSON.stringify(i))},this),t},_attachItems:function(e){var t=this;return this.$list(e).append(this.views.map(function(e){return t._renderItemView$el(e)})),this},_renderItemView$el:function(e){return e.render(0).$el},_renderEmptyMessage:function(e){this.debug("_renderEmptyMessage",e,this.searchFor);var t=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(e).text(t)},expandAll:function(){n.each(this.views,function(e){e.expand()})},collapseAll:function(){n.each(this.views,function(e){e.collapse()})},addItemView:function(e,t,i){var n=this,a=n._filterCollection().indexOf(e);if(-1!==a){var o=n._createItemView(e);return s(o).queue("fx",[function(e){n.$emptyMessage().is(":visible")?n.$emptyMessage().fadeOut(n.fxSpeed,e):e()},function(e){n._attachView(o,a),e()}]),o}},_attachView:function(e,t,i){i=!!n.isUndefined(i)||i,t=t||0;var s=this;return s.views.splice(t,0,e),s._insertIntoListAt(t,s._renderItemView$el(e).hide()),s.trigger("view:attached",e),i?e.$el.slideDown(s.fxSpeed,function(){s.trigger("view:attached:rendered")}):(e.$el.show(),s.trigger("view:attached:rendered")),e},_insertIntoListAt:function(e,t){var i=this.$list();return 0===e?i.prepend(t):i.children().eq(e-1).after(t),t},removeItemView:function(e,t,i){var a=this,o=n.find(a.views,function(t){return t.model===e});if(o)return a.views=n.without(a.views,o),a.trigger("view:removed",o),s({}).queue("fx",[function(e){o.$el.fadeOut(a.fxSpeed,e)},function(e){o.remove(),a.trigger("view:removed:rendered"),a.views.length?e():a._renderEmptyMessage().fadeIn(a.fxSpeed,e)}]),o},viewFromModelId:function(e){return n.find(this.views,function(t){return t.model.id===e})},viewFromModel:function(e){return e?this.viewFromModelId(e.id):void 0},viewsWhereModel:function(e){return this.views.filter(function(t){return n.isMatch(t.model.attributes,e)})},viewRange:function(e,t){if(e===t)return e?[e]:[];var i=this.views.indexOf(e),n=this.views.indexOf(t);return-1===i||-1===n?i===n?[]:-1===i?[t]:[e]:i .controls .search-query");return i.val()!==e&&i.val(e),this},clearSearch:function(e){return this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.renderItems(),this},THROTTLE_SELECTOR_FX_AT:20,showSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!0,this.$(".list-actions").slideDown(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,n.each(this.views,function(t){t.showSelector(e)})},hideSelectors:function(e){e=void 0!==e?e:this.fxSpeed,this.selecting=!1,this.$(".list-actions").slideUp(e),e=this.views.length>=this.THROTTLE_SELECTOR_FX_AT?0:e,n.each(this.views,function(t){t.hideSelector(e)}),this.selected=[],this.lastSelected=null},toggleSelectors:function(){this.selecting?this.hideSelectors():this.showSelectors()},selectAll:function(e){n.each(this.views,function(t){t.select(e)})},deselectAll:function(e){this.lastSelected=null,n.each(this.views,function(t){t.deselect(e)})},selectRange:function(e,t){var i=this.viewRange(e,t);return n.each(i,function(e){e.select()}),i},getSelectedViews:function(){return n.filter(this.views,function(e){return e.selected})},getSelectedModels:function(){return new this.collection.constructor(n.map(this.getSelectedViews(),function(e){return e.model}))},_showLoadingIndicator:function(e,t,i){this.debug("_showLoadingIndicator",this.indicator,e,t,i),t=void 0!==t?t:this.fxSpeed,this.indicator||(this.indicator=new d.default(this.$el),this.debug("\t created",this.indicator)),this.$el.is(":visible")?(this.$el.fadeOut(t),this.indicator.show(e,t,i)):this.indicator.show(0,i)},_hideLoadingIndicator:function(e,t){this.debug("_hideLoadingIndicator",this.indicator,e,t),e=void 0!==e?e:this.fxSpeed,this.indicator&&this.indicator.hide(e,t)},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(e,t){return t=t||0,this.$scrollContainer().animate({scrollTop:e},t),this},scrollToTop:function(e){return this.scrollTo(0,e)},scrollToItem:function(e,t){return this},scrollToId:function(e,t){return this.scrollToItem(this.viewFromModelId(e),t)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});p.prototype.templates=function(){return{el:u.default.wrapTemplate(["" 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))},317: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(13),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 0!==t.responseJSON?c.default.error(t.responseJSON.err_msg):c.default.error("An error occured.")}})}else c.default.error("Library's name is missing.");return!1},showPageSizePrompt:function(e){e.preventDefault();var t=prompt("How many libraries per page do you want to see?",Galaxy.libraries.preferences.get("library_page_size"));null!=t&&t==parseInt(t)&&(Galaxy.libraries.preferences.set({library_page_size:parseInt(t)}),Galaxy.libraries.libraryListView.render({show_page:1}))},clearLibraryModal:function(){r("input[name='Name']").val(""),r("input[name='Description']").val(""),r("input[name='Synopsis']").val("")},serializeNewLibrary:function(){return{name:r("input[name='Name']").val(),description:r("input[name='Description']").val(),synopsis:r("input[name='Synopsis']").val()}},validateNewLibrary:function(e){return""!==e.name},includeDeletedChecked:function(e){e.target.checked?(Galaxy.libraries.preferences.set({with_deleted:!0}),Galaxy.libraries.libraryListView.fetchDeleted()):(Galaxy.libraries.preferences.set({with_deleted:!1}),Galaxy.libraries.libraryListView.render())},excludeRestrictedChecked:function(e){e.target.checked?Galaxy.libraries.preferences.set({without_restricted:!0}):Galaxy.libraries.preferences.set({without_restricted:!1}),Galaxy.libraries.libraryListView.render()},searchLibraries:function(e){var t=r(".library-search-input").val();this.options.search_term=t,Galaxy.libraries.libraryListView.searchLibraries(t)},templateToolBar:function(){return i.template(['t.id?1:e.id=0;d--){var u=l[d].trim();0!==u.length&&c.push(u)}this.initChainCallControl({length:c.length,action:"adding_datasets"}),this.chainCallImportingFolders({paths:c,preserve_dirs:e,link_data:t,space_to_tab:n,to_posix_lines:i,source:"admin_path",file_type:o,tag_using_filenames:a,dbkey:s})}else h.default.info("Please enter a path relative to Galaxy root.")},initChainCallControl:function(e){var t;switch(e.action){case"adding_datasets":t=this.templateAddingDatasetsProgressBar(),this.modal.$el.find(".modal-body").html(t({folder_name:this.options.folder_name}));break;case"deleting_datasets":t=this.templateDeletingItemsProgressBar(),this.modal.$el.find(".modal-body").html(t());break;case"to_history":t=this.templateImportIntoHistoryProgressBar(),this.modal.$el.find(".modal-body").html(t({history_name:e.history_name}));break;default:Galaxy.emit.error("Wrong action specified.","datalibs")}this.progress=0,this.progressStep=100/e.length,this.options.chain_call_control.total_number=e.length,this.options.chain_call_control.failed_number=0},importFromJstreePath:function(e,t){var n=r("#jstree_browser").jstree().get_selected(!0),a=i.filter(n,function(e){return 0==e.state.disabled}),o=this.modal.$el.find(".preserve-checkbox").is(":checked"),s=this.modal.$el.find(".link-checkbox").is(":checked"),l=this.modal.$el.find(".spacetab-checkbox").is(":checked"),c=this.modal.$el.find(".posix-checkbox").is(":checked"),d=this.select_extension.value(),u=this.select_genome.value(),f=this.modal.$el.find(".tag-files").is(":checked"),p=a[0].type,_=[];if(a.length<1)h.default.info("Please select some items first.");else{this.modal.disableButton("Import");for(var g=a.length-1;g>=0;g--)void 0!==a[g].li_attr.full_path&&_.push(a[g].li_attr.full_path);if(this.initChainCallControl({length:_.length,action:"adding_datasets"}),"folder"===p){var m=t.source+"_folder";this.chainCallImportingFolders({paths:_,preserve_dirs:o,link_data:s,space_to_tab:l,to_posix_lines:c,source:m,file_type:d,dbkey:u,tag_using_filenames:f})}else if("file"===p){var m=t.source+"_file";this.chainCallImportingUserdirFiles({paths:_,file_type:d,dbkey:u,link_data:s,space_to_tab:l,to_posix_lines:c,source:m,tag_using_filenames:f})}}},fetchAndDisplayHistoryContents:function(e){var t=new p.default.HistoryContents({id:e}),n=this;t.fetch({success:function(t){var i=n.templateHistoryContents();n.histories.get(e).set({contents:t}),n.modal.$el.find("#selected_history_content").html(i({history_contents:t.models.reverse()})),n.modal.$el.find(".history-import-select-all").bind("click",function(){r("#selected_history_content [type=checkbox]").prop("checked",!0)}),n.modal.$el.find(".history-import-unselect-all").bind("click",function(){r("#selected_history_content [type=checkbox]").prop("checked",!1)})},error:function(e,t){void 0!==t.responseJSON?h.default.error(t.responseJSON.err_msg):h.default.error("An error occurred.")}})},addAllDatasetsFromHistory:function(){var e=this.modal.$el.find("#selected_history_content").find(":checked"),t=[],n=[],i=[];if(e.length<1)h.default.info("You must select some datasets first.");else{this.modal.disableButton("Add"),e.each(function(){var e=r(this).closest("li").data("id");if(e){var i=r(this).closest("li").data("name");t.push(e),n.push(i)}});for(var a=t.length-1;a>=0;a--){var o=t[a],s=new p.default.Item;s.url=Galaxy.root+"api/folders/"+this.options.id+"/contents","collection"===n[a]?s.set({from_hdca_id:o}):s.set({from_hda_id:o}),i.push(s)}this.initChainCallControl({length:i.length,action:"adding_datasets"}),this.chainCallAddingHdas(i)}},chainCallImportingIntoHistory:function(e,t){var n=this,i=e.pop();if(void 0===i)return 0===this.options.chain_call_control.failed_number?h.default.success("Selected datasets imported into history. Click this to start analyzing it.","",{onclick:function(){window.location=Galaxy.root}}):this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number?h.default.error("There was an error and no datasets were imported into history."):this.options.chain_call_control.failed_number=0;s--){var c=new p.default.Item({id:e[s]});o.push(c)}for(var s=t.length-1;s>=0;s--){var d=new p.default.FolderAsModel({id:t[s]});o.push(d)}this.options.chain_call_control.total_number=a,this.chainCallDeletingItems(o)}},showLocInfo:function(){var e=null,t=this;null!==Galaxy.libraries.libraryListView?(e=Galaxy.libraries.libraryListView.collection.get(this.options.parent_library_id),this.showLocInfoModal(e)):(e=new p.default.Library({id:this.options.parent_library_id}),e.fetch({success:function(){t.showLocInfoModal(e)},error:function(e,t){void 0!==t.responseJSON?h.default.error(t.responseJSON.err_msg):h.default.error("An error occurred.")}}))},showLocInfoModal:function(e){var t=this,n=this.templateLocInfoInModal();this.modal=Galaxy.modal,this.modal.show({closing_events:!0,title:(0,l.default)("Location Details"),body:n({library:e,options:t.options}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(e){switch(e.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back(),h.default.error("Invalid import source.")}},showPageSizePrompt:function(e){e.preventDefault();var t=prompt("How many items per page do you want to see?",Galaxy.libraries.preferences.get("folder_page_size"));null!=t&&t==parseInt(t)&&(Galaxy.libraries.preferences.set({folder_page_size:parseInt(t)}),Galaxy.libraries.folderListView.render({id:this.options.id,show_page:1}))},findCheckedRows:function(){return r("#folder_list_body").find(":checked")},templateToolBar:function(){return i.template(['
","=0;n--)t.push(e[n].id);return t},savePermissions:function(e){var t=this,n=this._extractIds(this.accessSelectObject.$el.select2("data")),i=this._extractIds(this.addSelectObject.$el.select2("data")),a=this._extractIds(this.manageSelectObject.$el.select2("data")),o=this._extractIds(this.modifySelectObject.$el.select2("data"));r.post(Galaxy.root+"api/libraries/"+t.id+"/permissions?action=set_permissions",{"access_ids[]":n,"add_ids[]":i,"manage_ids[]":a,"modify_ids[]":o}).done(function(e){t.showPermissions({fetched_permissions:e}),s.default.success("Permissions saved.")}).fail(function(){s.default.error("An error occurred while attempting to set library permissions.")})},templateLibraryPermissions:function(){return i.template(['=0;n--)t.push(e[n].id);return t},savePermissions:function(e){var t=this,n=this._extractIds(this.addSelectObject.$el.select2("data")),i=this._extractIds(this.manageSelectObject.$el.select2("data")),a=this._extractIds(this.modifySelectObject.$el.select2("data"));r.post(Galaxy.root+"api/folders/"+t.id+"/permissions?action=set_permissions",{"add_ids[]":n,"manage_ids[]":i,"modify_ids[]":a}).done(function(e){t.showPermissions({fetched_permissions:e}),s.default.success("Permissions saved.")}).fail(function(){s.default.error("An error occurred while attempting to set folder permissions.")})},templateFolderPermissions:function(){return i.template(['','
",'','','','','','','','',"
",''].join("")},toString:function(){return"PageLayoutView"},_checkCommunicationServerOnline:function(){var e=window.Galaxy.config.communication_server_host,t=window.Galaxy.config.communication_server_port,i=window.Galaxy.user.attributes.preferences,n=s("#show-chat-online");i&&-1!=["1","true"].indexOf(i.communication_server)?s.ajax({url:e+":"+t}).success(function(e){null!==window.Galaxy.user.id&&"hidden"===n.css("visibility")&&n.css("visibility","visible")}).error(function(e){n.css("visibility","hidden")}):n.css("visibility","hidden")}});t.default={View:p}}).call(t,i(2),i(1),i(0))},,,,,,function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var i=e.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_name:"",file_mode:"",file_size:0,file_type:null,file_path:"",file_data:null,percentage:0,space_to_tab:!1,to_posix_lines:!0,enabled:!0},reset:function(e){this.clear().set(this.defaults).set(e)}}),n=e.Collection.extend({model:i});t.default={Model:i,Collection:n}}).call(t,i(2))},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(8),l=a(o),r=i(4),d=a(r),c=i(3),u=a(c),h=d.default.SearchableModelMixin,f=e.Model.extend(d.default.LoggableMixin).extend(d.default.mixin(h,{_logNamespace:"dataset",defaults:{state:l.default.NEW,deleted:!1,purged:!1,name:"(unnamed dataset)",accessible:!0,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(e,t){this.debug(this+"(Dataset).initialize",e,t),
//!! this state is not in trans.app.model.Dataset.states - set it here -
-this.get("accessible")||this.set("state",l.default.NOT_VIEWABLE),this.urls=this._generateUrls(),this._setUpListeners()},_generateUrls:function(){var e=this.get("id");if(!e)return{};var t={purge:"datasets/"+e+"/purge_async",display:"datasets/"+e+"/display/?preview=True",edit:"datasets/edit?dataset_id="+e,download:"datasets/"+e+"/display"+this._downloadQueryParameters(),report_error:"dataset/errors?id="+e,rerun:"tool_runner/rerun?id="+e,show_params:"datasets/"+e+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+e+"&metadata_name="};return n.each(t,function(e,i){t[i]=Galaxy.root+e}),this.urls=t,t},_downloadQueryParameters:function(){return"?to_ext="+this.get("file_ext")},_setUpListeners:function(){this.on("change:state",function(e,t){this.log(this+" has changed state:",e,t),this.inReadyState()&&this.trigger("state:ready",e,t,this.previous("state"))}),this.on("change:id change:file_ext",function(e){this._generateUrls()})},toJSON:function(){var t=e.Model.prototype.toJSON.call(this);return n.extend(t,{urls:this.urls})},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},inReadyState:function(){var e=n.contains(l.default.READY_STATES,this.get("state"));return this.isDeletedOrPurged()||e},hasDetails:function(){return!this.get("accessible")||this.has("annotation")},hasData:function(){return this.get("file_size")>0},fetch:function(t){var i=this;return e.Model.prototype.fetch.call(this,t).always(function(){i._generateUrls()})},parse:function(t,i){var n=e.Model.prototype.parse.call(this,t,i);return n.create_time&&(n.create_time=new Date(n.create_time)),n.update_time&&(n.update_time=new Date(n.update_time)),n},save:function(t,i){return i=i||{},i.wait=!!n.isUndefined(i.wait)||i.wait,e.Model.prototype.save.call(this,t,i)},delete:function(e){return 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t.matches(e)})},toString:function(){return["DatasetAssociationCollection(",this.length,")"].join("")}});t.default={DatasetAssociation:f,DatasetAssociationCollection:p}}).call(t,i(2),i(1),i(0))},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),i(5)),o=(n(a),i(3)),l=(n(o),1e3);try{l=localStorage.getItem("collectionFuzzyCountDefault")||l}catch(e){}var r={defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",hidden:function(){return!this.get("visible")},isVisible:function(e,t){var i=!0;return e||!this.get("deleted")&&!this.get("purged")||(i=!1),t||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var e=this.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 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loading tool info...";a.find(".toolFormBody").append(c);var d=e("");"subworkflow"!==t&&d.append(e("").addClass("fa-icon-button fa fa-files-o").click(function(e){l.clone()})),d.append(e("").addClass("fa-icon-button fa fa-times").click(function(e){l.destroy()})),a.appendTo("#canvas-container");var u=e("#canvas-container").position(),h=e("#canvas-container").parent(),f=a.width(),p=a.height();return a.css({left:-u.left+h.width()/2-f/2,top:-u.top+h.height()/2-p/2}),d.prependTo(a.find(".toolFormTitle")),f+=d.width()+10,a.css("width",f),a.bind("dragstart",function(){r.workflow.activate_node(l)}).bind("dragend",function(){r.workflow.node_changed(this),r.workflow.fit_canvas_to_nodes(),r.canvas_manager.draw_overview()}).bind("dragclickonly",function(){r.workflow.activate_node(l)}).bind("drag",function(t,n){var i=e(this).offsetParent().offset(),r=n.offsetX-i.left,a=n.offsetY-i.top;e(this).css({left:r,top:a}),e(this).find(".terminal").each(function(){this.terminal.redraw()})}),l}})}).call(t,n(0),n(2),n(1))},301:function(e,t,n){"use strict";(function(e){function i(e,t){this.app=e,this.canvas_container=t,this.id_counter=0,this.nodes={},this.name=null,this.has_changes=!1,this.active_form_has_changes=!1,this.workflowOutputLabels={}}Object.defineProperty(t,"__esModule",{value:!0});var r=n(125),a=function(e){return e&&e.__esModule?e:{default:e}}(r),o=n(7),s=function(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}(o);e.extend(i.prototype,{canLabelOutputWith:function(e){return!e||!(e in this.workflowOutputLabels)},registerOutputLabel:function(e){e&&(this.workflowOutputLabels[e]=!0)},unregisterOutputLabel:function(e){e&&delete this.workflowOutputLabels[e]},updateOutputLabel:function(e,t){e&&this.unregisterOutputLabel(e),this.canLabelOutputWith(t)||s.warning("Workflow contains duplicate workflow output labels "+t+". This must be fixed before it can be saved."),t&&this.registerOutputLabel(t)},attemptUpdateOutputLabel:function(e,t,n){return!!this.canLabelOutputWith(n)&&(e.labelWorkflowOutput(t,n),e.nodeView.redrawWorkflowOutputs(),!0)},create_node:function(e,t,n){var i=this.app.prebuildNode(e,t,n);return this.add_node(i),this.fit_canvas_to_nodes(),this.app.canvas_manager.draw_overview(),this.activate_node(i),i},add_node:function(e){e.id=this.id_counter,e.element.attr("id","wf-node-step-"+e.id),this.id_counter++,this.nodes[e.id]=e,this.has_changes=!0,e.workflow=this},remove_node:function(e){this.active_node==e&&this.clear_active_node(),delete this.nodes[e.id],this.has_changes=!0},remove_all:function(){var t=this;e.each(this.nodes,function(e,n){n.destroy(),t.remove_node(n)})},rectify_workflow_outputs:function(){var t=!1,n=!1;if(e.each(this.nodes,function(i,r){r.workflow_outputs&&r.workflow_outputs.length>0&&(t=!0),e.each(r.post_job_actions,function(e,t){"HideDatasetAction"===t.action_type&&(n=!0)})}),!1!==t||!1!==n){var i=this;e.each(this.nodes,function(n,r){if("tool"===r.type){var a=!1;null===r.post_job_actions&&(r.post_job_actions={},a=!0);var o=[];e.each(r.post_job_actions,function(e,t){"HideDatasetAction"==t.action_type&&o.push(e)}),o.length>0&&e.each(o,function(e,t){a=!0,delete r.post_job_actions[t]}),t&&e.each(r.output_terminals,function(e,t){if(!0==!r.isWorkflowOutput(t.name)){a=!0;var n={action_type:"HideDatasetAction",output_name:t.name,action_arguments:{}};r.post_job_actions["HideDatasetAction"+t.name]=null,r.post_job_actions["HideDatasetAction"+t.name]=n}}),i.active_node==r&&!0===a&&i.reload_active_node()}})}},to_simple:function(){var t={};return e.each(this.nodes,function(n,i){var r={};e.each(i.input_terminals,function(t,n){r[n.name]=null;var i=[];e.each(n.connectors,function(e,t){if(t.handle1){var a={id:t.handle1.node.id,output_name:t.handle1.name},o=n.attributes.input.input_subworkflow_step_id;void 0!==o&&(a.input_subworkflow_step_id=o),i[e]=a,r[n.name]=i}})});var a={};i.post_job_actions&&e.each(i.post_job_actions,function(e,t){var n={action_type:t.action_type,output_name:t.output_name,action_arguments:t.action_arguments};a[t.action_type+t.output_name]=null,a[t.action_type+t.output_name]=n}),i.workflow_outputs||(i.workflow_outputs=[]);var o={id:i.id,type:i.type,content_id:i.content_id,tool_version:i.config_form.version,tool_state:i.tool_state,errors:i.errors,input_connections:r,position:e(i.element).position(),annotation:i.annotation,post_job_actions:i.post_job_actions,uuid:i.uuid,label:i.label,workflow_outputs:i.workflow_outputs};t[i.id]=o}),{steps:t}},from_simple:function(t,n){var i=void 0===n||n,r=this,o=0;i?r.name=t.name:o=Object.keys(r.nodes).length;var s=o,l=!1;e.each(t.steps,function(t,n){var a=r.app.prebuildNode(n.type,n.name,n.content_id);i||(n.uuid=null,e.each(n.workflow_outputs,function(e,t){t.uuid=null})),a.init_field_data(n),n.position&&a.element.css({top:n.position.top,left:n.position.left}),a.id=parseInt(n.id)+o,r.nodes[a.id]=a,s=Math.max(s,parseInt(t)+o),l||(a.workflow_outputs.length>0?l=!0:e.each(a.post_job_actions||[],function(e,t){"HideDatasetAction"===t.action_type&&(l=!0)}))}),r.id_counter=s+1,e.each(t.steps,function(t,n){var i=r.nodes[parseInt(t)+o];e.each(n.input_connections,function(t,n){n&&(e.isArray(n)||(n=[n]),e.each(n,function(e,n){var s=r.nodes[parseInt(n.id)+o],l=new a.default;l.connect(s.output_terminals[n.output_name],i.input_terminals[t]),l.redraw()}))}),l&&e.each(i.output_terminals,function(t,n){if(void 0===i.post_job_actions["HideDatasetAction"+n.name]){i.addWorkflowOutput(n.name);e(i.element).find(".callout."+n.name).find("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png"),r.has_changes=!0}})})},check_changes_in_active_form:function(){this.active_form_has_changes&&(this.has_changes=!0,e("#right-content").find("form").submit(),this.active_form_has_changes=!1)},reload_active_node:function(){if(this.active_node){var e=this.active_node;this.clear_active_node(),this.activate_node(e)}},clear_active_node:function(){this.active_node&&(this.active_node.make_inactive(),this.active_node=null),document.activeElement.blur(),this.app.showAttributes()},activate_node:function(e){this.active_node!=e&&(this.check_changes_in_active_form(),this.clear_active_node(),this.app.showForm(e.config_form,e),e.make_active(),this.active_node=e)},node_changed:function(e,t){this.has_changes=!0,this.active_node==e&&t&&(this.check_changes_in_active_form(),this.app.showForm(e.config_form,e)),this.app.showWorkflowParameters()},layout:function(){this.check_changes_in_active_form(),this.has_changes=!0;var t={},n={};e.each(this.nodes,function(e,i){void 0===t[e]&&(t[e]=0),void 0===n[e]&&(n[e]=[])}),e.each(this.nodes,function(i,r){e.each(r.input_terminals,function(i,a){e.each(a.connectors,function(e,i){var a=i.handle1.node;t[r.id]+=1,n[a.id].push(r.id)})})});for(var i=[];;){var r=[];for(var a in t)0===t[a]&&r.push(a);if(0===r.length)break;i.push(r);for(var o in r){var s=r[o];delete t[s];for(var l in n[s])t[n[s][l]]-=1}}if(!t.length){var c=this.nodes,d=80;e.each(i,function(t,n){n.sort(function(t,n){return e(c[t].element).position().top-e(c[n].element).position().top});var i=0,r=30;e.each(n,function(t,n){var a=c[n],o=e(a.element);e(o).css({top:r,left:d}),i=Math.max(i,e(o).width()),r+=e(o).height()+30}),d+=i+80}),e.each(c,function(e,t){t.redraw()})}},bounds_for_all_nodes:function(){var t,n=1/0,i=-1/0,r=1/0,a=-1/0;return e.each(this.nodes,function(o,s){var l=e(s.element);t=l.position(),n=Math.min(n,t.left),i=Math.max(i,t.left+l.width()),r=Math.min(r,t.top),a=Math.max(a,t.top+l.width())}),{xmin:n,xmax:i,ymin:r,ymax:a}},fit_canvas_to_nodes:function(){function t(e,t){return Math.ceil(e/t)*t}function n(e,t){if(e3*t){return-(e-(Math.ceil(e%t/t)+1)*t)}return 0}var i=this.bounds_for_all_nodes(),r=this.canvas_container.position(),a=this.canvas_container.parent(),o=n(i.xmin,100),s=n(i.ymin,100);o=Math.max(o,r.left),s=Math.max(s,r.top);var l=r.left-o,c=r.top-s,d=t(i.xmax+100,100)+o,u=t(i.ymax+100,100)+s;d=Math.max(d,-l+a.width()),u=Math.max(u,-c+a.height()),this.canvas_container.css({left:l,top:c,width:d,height:u}),this.canvas_container.children().each(function(){var t=e(this).position();e(this).css("left",t.left+o),e(this).css("top",t.top+s)})}}),t.default=i}).call(t,n(0))},302:function(e,t,n){"use strict";(function(e){function n(e,t,n){this.app=e,this.cv=t,this.cc=this.cv.find("#canvas-container"),this.overview=n,this.oc=n.find("#overview-canvas"),this.ov=n.find("#overview-viewport"),this.init_drag(),this.init_copy_paste()}function i(e){this.panel=e}Object.defineProperty(t,"__esModule",{value:!0}),e.extend(n.prototype,{init_drag:function(){var t=this,n=function(e,n){e=Math.min(e,t.cv.width()/2),e=Math.max(e,-t.cc.width()+t.cv.width()/2),n=Math.min(n,t.cv.height()/2),n=Math.max(n,-t.cc.height()+t.cv.height()/2),t.cc.css({left:e,top:n}),t.cv.css({"background-position-x":e,"background-position-y":n}),t.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new i(this)});var r,a;this.cv.bind("click",function(){document.activeElement.blur()}).bind("dragstart",function(){var n=e(this).offset(),i=t.cc.position();a=i.top-n.top,r=i.left-n.left}).bind("drag",function(e,t){n(t.offsetX+r,t.offsetY+a)}).bind("dragend",function(){t.app.workflow.fit_canvas_to_nodes(),t.draw_overview()}),this.overview.click(function(e){if(t.overview.hasClass("blockaclick"))t.overview.removeClass("blockaclick");else{var i=t.cc.width(),r=t.cc.height(),a=t.oc.width(),o=t.oc.height(),s=e.pageX-t.oc.offset().left-t.ov.width()/2,l=e.pageY-t.oc.offset().top-t.ov.height()/2;n(-s/a*i,-l/o*r),t.app.workflow.fit_canvas_to_nodes(),t.draw_overview()}}),this.ov.bind("drag",function(e,i){var r=t.cc.width(),a=t.cc.height(),o=t.oc.width(),s=t.oc.height(),l=i.offsetX-t.overview.offset().left,c=i.offsetY-t.overview.offset().top;n(-l/o*r,-c/s*a)}).bind("dragend",function(){t.overview.addClass("blockaclick"),t.app.workflow.fit_canvas_to_nodes(),t.draw_overview()}),e("#overview-border").bind("drag",function(n,i){var r=e(this).offsetParent(),a=r.offset(),o=Math.max(r.width()-(i.offsetX-a.left),r.height()-(i.offsetY-a.top));e(this).css({width:o,height:o}),t.draw_overview()}),e("#overview-border div").bind("drag",function(){})},init_copy_paste:function(){var e=this;document.addEventListener("copy",function(t){""===window.getSelection().toString()&&(e.app.workflow.active_node&&"subworkflow"!==e.app.workflow.active_node.type&&t.clipboardData.setData("application/json",JSON.stringify({nodeId:e.app.workflow.active_node.id})),t.preventDefault())}),document.addEventListener("paste",function(t){if(document.activeElement&&"textarea"!==document.activeElement.type&&"text"!==document.activeElement.type){var n;try{n=JSON.parse(t.clipboardData.getData("application/json")).nodeId}catch(e){}n&&e.app.workflow.nodes.hasOwnProperty(n)&&e.app.workflow.nodes[n].clone(),t.preventDefault()}})},update_viewport_overlay:function(){var e=this.cc,t=this.cv,n=this.oc,i=this.ov,r=e.width(),a=e.height(),o=n.width(),s=n.height(),l=e.position();i.css({left:-l.left/r*o,top:-l.top/a*s,width:t.width()/r*o-2,height:t.height()/a*s-2})},draw_overview:function(){var t,n,i,r,a=e("#overview-canvas"),o=a.parent().parent().width(),s=a.get(0).getContext("2d"),l=e("#canvas-container").width(),c=e("#canvas-container").height(),d=this.cv.width(),u=this.cv.height();l0&&(s.fillStyle="#E8A92D",s.strokeStyle="#E8A92D"),s.fillRect(d,u,h,f),s.strokeRect(d,u,h,f)}),this.update_viewport_overlay()}}),e.extend(i.prototype,{test:function(t,n){var i=this;clearTimeout(this.timeout);var r=t.pageX,a=t.pageY,o=e(this.panel),s=o.position(),l=o.width(),c=o.height(),d=o.parent(),u=d.width(),h=d.height(),f=d.offset(),p=f.left,_=f.top,g=p+d.width(),m=_+d.height(),v=-(l-u/2),y=-(c-h/2),b=u/2,w=h/2,x=!1,k=0;r-5g?s.left>v&&(k=Math.min(23,s.left-v),o.css("left",s.left-k),x=!0):a-5<_?s.topm&&s.top>y&&(k=Math.min(23,s.top-v),o.css("top",s.top-k+"px"),x=!0),x&&(n(),this.timeout=setTimeout(function(){i.test(t,n)},50))},stop:function(){clearTimeout(this.timeout)}}),t.default=n}).call(t,n(0))},303: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(4),s=a(o),l=n(304),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))},308: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(4),h=r(u),f=n(11),p=r(f),_=n(46),g=r(_),m=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 g.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:m,Tool:v}}).call(t,n(2),n(0))},309: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(310),u=r(d),h=n(28),f=a(h),p=n(4),_=a(p),g=n(38),m=a(g),v=n(42),y=a(v);n(41);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.$el[0]).append("svg").attr("width",t).attr("height",n).attr("pointer-events","all").append("svg:g").call(u.behavior.zoom().on("zoom",function(){var t=u.event.scale;s.attr("transform","translate("+u.event.translate+") scale("+t+")"),e.scale!==t&&(e.zoom_drag_timeout&&clearTimeout(e.zoom_drag_timeout),e.zoom_drag_timeout=setTimeout(function(){},400))})).attr("transform","translate("+t/2+","+n/2+")").append("svg:g").attr("class","tracks");this.circular_views=i.map(function(t,n){var i=new S({el:s.append("g")[0],track:t,radius_bounds:o[n],genome:e.genome,total_gap:a});return i.render(),i}),this.chords_views=r.map(function(t){var n=new T({el:s.append("g")[0],track:t,radius_bounds:o[0],genome:e.genome,total_gap:a});return n.render(),n});var l=this.circular_views[this.circular_views.length-1].radius_bounds[1],c=[l,l+this.label_arc_height];this.label_track_view=new M({el:s.append("g")[0],track:new x,radius_bounds:c,genome:e.genome,total_gap:a}),this.label_track_view.render()},add_track:function(e){var t=this.model.get("config").get_value("total_gap");if("DiagonalHeatmapTrack"===e.get("track_type")){var n=this.circular_views[0].radius_bounds,i=new T({el:u.select("g.tracks").append("g")[0],track:e,radius_bounds:n,genome:this.genome,total_gap:t});i.render(),this.chords_views.push(i)}else{var r=this.get_tracks_bounds();c.each(this.circular_views,function(e,t){e.update_radius_bounds(r[t])}),c.each(this.chords_views,function(e){e.update_radius_bounds(r[0])});var a=this.circular_views.length,o=new S({el:u.select("g.tracks").append("g")[0],track:e,radius_bounds:r[a],genome:this.genome,total_gap:t});o.render(),this.circular_views.push(o)}},remove_track:function(e,t,n){var i=this.circular_views[n.index];this.circular_views.splice(n.index,1),i.$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])})}}),j=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 this.parent_elt.selectAll("path.chrom-data").filter(function(e,t){return r.is_visible(this)}).each(function(t,r){var a,o=u.select(this),s=o.attr("chrom"),l=n.genome.get_chrom_region(s),d=n.track.get("data_manager");d.can_get_more_detailed_data(l)&&(a=n.track.get("data_manager").get_more_detailed_data(l,"Coverage",0,e),i.when(a).then(function(e){o.remove(),n._update_data_bounds();var t=c.find(n.chroms_layout,function(e){return e.data.chrom===s}),i=n.get_fill_color();n._render_chrom_data(n.parent_elt,t,e).style("stroke",i).style("fill",i)}))}),n}},_transition_chrom_data:function(){var e=this.track,t=this.chroms_layout,n=this.parent_elt.selectAll("g>path.chrom-data");if(n[0].length>0){var r=this;i.when(e.get("data_manager").get_genome_wide_data(this.genome)).then(function(i){var a=c.reject(c.map(i,function(e,n){var i=null,a=r._get_path_function(t[n],e);return a&&(i=a(e.data)),i}),function(e){return 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;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})}}),M=j.extend({initialize:function(e){j.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(M.prototype,w);var C=j.extend({initialize:function(e){j.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 m.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 e._data_bounds_ticks_fn()(t)}));this.parent_elt.selectAll("g.tick").data(i).transition().attr("transform",function(e){return"rotate("+(180*e.angle/Math.PI-90)+")translate("+e.radius+",0)"})}},_data_bounds_ticks_fn:function(){var e=this;return visibleChroms=0,function(t){return[{radius:e.radius_bounds[0],angle:t.startAngle,label:e.formatNum(e.data_bounds[0])},{radius:e.radius_bounds[1],angle:t.startAngle,label:e.formatNum(e.data_bounds[1])}]}},get_data_bounds:function(e){}});c.extend(C.prototype,w);var S=C.extend({get_data_bounds:function(e){var t=c.flatten(c.map(e,function(e){return e?c.map(e.data,function(e){return parseInt(e[1],10)||0}):0}));return[c.min(t),this._quantile(t,.98)||c.max(t)]}}),T=j.extend({render:function(){var e=this;i.when(e.track.get("data_manager").data_is_ready()).then(function(){i.when(e.track.get("data_manager").get_genome_wide_data(e.genome)).then(function(t){var n=[],i=e.genome.get_chroms_info();c.each(t,function(t,r){var a=i[r].chrom,o=c.map(t.data,function(t){var n=e._get_region_angle(a,t[1]),i=e._get_region_angle(t[3],t[4]);return{source:{startAngle:n,endAngle:n+.01},target:{startAngle:i,endAngle:i+.01}}});n=n.concat(o)}),e.parent_elt.append("g").attr("class","chord").selectAll("path").data(n).enter().append("path").style("fill",e.get_fill_color()).attr("d",u.svg.chord().radius(e.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(e){this.radius_bounds=e,this.parent_elt.selectAll("path").transition().attr("d",u.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(e,t){var n=c.find(this.chroms_layout,function(t){return t.data.chrom===e});return n.endAngle-(n.endAngle-n.startAngle)*(n.data.len-t)/n.data.len}}),O=e.View.extend({initialize:function(){_.default.cssLoadFile("static/style/circster.css");var e=new f.default.Genome(galaxy_config.app.genome),t=new 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h.default.FolderListView({id:e}),Galaxy.libraries.folderToolbarView.showImportModal({source:t}))}),e.history.start({pushState:!1})}});t.default={GalaxyApp:S}}).call(t,n(2),n(0))},312:function(e,t,n){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var i=function(e,t){return function(n,i){return n.get("type")===i.get("type")?n.has(e)||i.has(e)?n.has(e)?i.has(e)?n.get(e).toLowerCase()>i.get(e).toLowerCase()?"asc"===t?1:-1:i.get(e).toLowerCase()>n.get(e).toLowerCase()?"asc"===t?-1:1:0:-1:1:0:"folder"===n.get("type")?-1:1}},r=function(e,t){return function(n,i){return n.get(e).toLowerCase()>i.get(e).toLowerCase()?"asc"===t?1:-1:i.get(e).toLowerCase()>n.get(e).toLowerCase()?"asc"===t?-1:1:0}};t.default={generateFolderComparator:i,generateLibraryComparator:r}},313: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(13),c=a(l),d=n(314),u=a(d),h=e.View.extend({el:"#folder_items_element",progress:0,progressStep:1,folderContainer:null,current_sort_order:"asc",current_sort_key:"name",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .folder_row":"selectClickedRow","click .sort-folder-name":"sortColumnClicked","click .sort-folder-file_ext":"sortColumnClicked","click .sort-folder-description":"sortColumnClicked","click .sort-folder-state":"sortColumnClicked"},collection:null,defaults:{include_deleted:!1,page_count:null,show_page:null},initialize:function(e){this.options=i.defaults(this.options||{},this.defaults,e),this.modal=null,this.rowViews={},this.collection=new c.default.Folder,this.listenTo(this.collection,"add",this.renderOne),this.listenTo(this.collection,"remove",this.removeOne),this.listenTo(this.collection,"sort",this.rePaint),this.listenTo(this.collection,"reset",this.rePaint),this.fetchFolder()},fetchFolder:function(e){var e=e||{};this.options.include_deleted=e.include_deleted;var t=this;this.folderContainer=new c.default.FolderContainer({id:this.options.id}),this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents",this.options.include_deleted&&(this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"),this.folderContainer.fetch({success:function(e){t.folder_container=e,t.render()},error:function(e,t){void 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))},314: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(13),c=a(l),d=n(126),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))},315: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(13),l=r(s),c=n(316),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.$el.html(t({length:0,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options)),i("#center [data-toggle]").tooltip(),i("#center").css("overflow","auto")},fetchDeleted:function(){if(this.options.all_fetched)this.render();else{var e=this;this.collection.url=this.collection.urlRoot+"?deleted=true",this.collection.fetch({remove:!1,success:function(){e.options.all_fetched=!0,e.render()},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occurred.")}})}},renderRows:function(e){for(var t=0;t',"<% if(length === 0) { %>","<% if(search_term.length > 0) { %>","',"",'
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o=i(3),l=a(o),r=i(5),d=(a(r),i(49)),c=a(d),u=i(256),h=a(u),f=i(89),p=a(f),m=i(90),g=a(m),_=i(26),v=a(_),w=i(12),y=a(w),b=i(6),x=a(b),$=i(257),C=a($);i(91),t.default=e.View.extend({upload_size:0,collection:new c.default.Collection,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ui_button=e.ui_button,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.$uploadbox=this.$(".upload-box"),this.$uploadtable=this.$(".upload-table"),this.btnLocal=new x.default.Button({id:"btn-local",title:(0,l.default)("Choose local file"),onclick:function(){t.uploadbox.select()},icon:"fa fa-laptop"}),this.btnFtp=new x.default.Button({id:"btn-ftp",title:(0,l.default)("Choose FTP file"),onclick:function(){t._eventFtp()},icon:"fa fa-folder-open-o"}),this.btnCreate=new x.default.Button({id:"btn-new",title:"Paste/Fetch data",onclick:function(){t._eventCreate()},icon:"fa fa-edit"}),this.btnStart=new x.default.Button({id:"btn-start",title:(0,l.default)("Start"),onclick:function(){t._eventStart()}}),this.btnStop=new x.default.Button({id:"btn-stop",title:(0,l.default)("Pause"),onclick:function(){t._eventStop()}}),this.btnReset=new x.default.Button({id:"btn-reset",title:(0,l.default)("Reset"),onclick:function(){t._eventReset()}}),this.btnClose=new x.default.Button({id:"btn-close",title:(0,l.default)("Close"),onclick:function(){t.app.modal.hide()}}),n.each([this.btnLocal,this.btnFtp,this.btnCreate,this.btnStop,this.btnReset,this.btnStart,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.uploadbox=this.$uploadbox.uploadbox({url:this.app.options.nginx_upload_path,announce:function(e,i){t._eventAnnounce(e,i)},initialize:function(e){return t.app.toData([t.collection.get(e)],t.history_id)},progress:function(e,i){t._eventProgress(e,i)},success:function(e,i){t._eventSuccess(e,i)},error:function(e,i){t._eventError(e,i)},complete:function(){t._eventComplete()},ondragover:function(){t.$uploadbox.addClass("highlight")},ondragleave:function(){t.$uploadbox.removeClass("highlight")}}),this.ftp=new v.default.View({title:(0,l.default)("FTP files"),container:this.btnFtp.$el}),this.select_extension=new y.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-extension"),data:n.filter(this.list_extensions,function(e){return!e.composite_files}),value:this.options.default_extension,onchange:function(e){t._changeExtension(e)}}),this.$(".upload-footer-extension-info").on("click",function(e){new g.default({$el:s(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),list:t.list_extensions,placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new 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 file..."),this.uploadbox.stop())},_eventReset:function(){if(0==this.counter.running){this.collection.reset(),this.counter.reset(),this.uploadbox.reset(),this.select_extension.value(this.options.default_extension),this.select_genome.value(this.options.default_genome),this.ui_button.model.set("percentage",0),this.render()}},_changeExtension:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("extension")!=i.options.default_extension&&t||n.set("extension",e)})},_changeGenome:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("genome")!=i.options.default_genome&&t||n.set("genome",e)})},_uploadFtp:function(){var 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(88)),h=a(u),f=i(26),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 g.default.View({css:"upload-genome",data:i.app.list_genomes,container:this.$(".upload-genome"),value:s,onchange:function(e){i.model.set("genome",e)}}),this.select_extension=new g.default.View({css:"upload-extension",data:i.app.list_extensions,container:this.$(".upload-extension"),value:a,onchange:function(e){i.model.set("extension",e)}}),this.model.set({genome:s,extension:a}),this.$symbol.on("click",function(){i._removeRow()}),this.$(".upload-extension-info").on("click",function(e){i.app.showExtensionInfo({$el:n(e.target),title:i.select_extension.text(),extension:i.select_extension.value()})}).on("mousedown",function(e){e.preventDefault()}),this.$settings.on("click",function(e){i._showSettings()}).on("mousedown",function(e){e.preventDefault()}),this.$text_content.on("change input",function(e){i.model.set({url_paste:n(e.target).val(),file_size:n(e.target).val().length})}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:genome",function(){i._refreshGenome()}),this.listenTo(this.model,"change:extension",function(){i._refreshExtension()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()})},render:function(){this._refreshType(),this._refreshPercentage(),this._refreshStatus(),this._refreshInfo(),this._refreshGenome(),this._refreshExtension(),this._refreshFileSize()},remove:function(){this.select_genome.remove(),this.select_extension.remove(),e.View.prototype.remove.apply(this)},_refreshType:function(){var e=this.model.attributes;this.$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.$percentage.html(100!=e?e+"%":"Adding to 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'+this.options.content+" "}}),v=e.View.extend({initialize:function(){this.setElement(""),this.render()},render:function(){var e=this;s.getJSON(Galaxy.root+"workflow/upload_import_workflow",function(t){e.$el.empty().append(e._mainTemplate(t))})},_mainTemplate:function(e){return"
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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.extend(this.options,e),this.fetchExtAndGenomes(),this.options.id&&this.fetchDataset()},fetchDataset:function(e){this.options=i.extend(this.options,e),this.model=new h.default.Item({id:this.options.id});var t=this;this.model.fetch({success:function(){t.options.show_permissions?t.showPermissions():t.options.show_version?t.fetchVersion():t.render()},error:function(e,t){void 0!==t.responseJSON?d.default.error(t.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}}):d.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),r(".tooltip").remove();var t=this.templateDataset();this.$el.html(t({item:this.model})),r(".peek").html(this.model.get("peek")),r("#center [data-toggle]").tooltip()},fetchVersion:function(e){this.options=i.extend(this.options,e);var t=this;this.options.ldda_id?(this.ldda=new h.default.Ldda({id:this.options.ldda_id}),this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id,this.ldda.fetch({success:function(){t.renderVersion()},error:function(e,t){void 0!==t.responseJSON?d.default.error(t.responseJSON.err_msg):d.default.error("An error occurred.")}})):(this.render(),d.default.error("Library dataset version requested but no id provided."))},renderVersion:function(){r(".tooltip").remove();var e=this.templateVersion();this.$el.html(e({item:this.model,ldda:this.ldda})),r(".peek").html(this.ldda.get("peek"))},enableModification:function(){r(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model})),this.renderSelectBoxes({genome_build:this.model.get("genome_build"),file_ext:this.model.get("file_ext")}),r(".peek").html(this.model.get("peek")),r("#center [data-toggle]").tooltip()},downloadDataset:function(){var e=Galaxy.root+"api/libraries/datasets/download/uncompressed",t={ld_ids:this.id};this.processDownload(e,t)},processDownload:function(e,t,n){if(e&&t){t="string"==typeof t?t:r.param(t);var i="";r.each(t.split("&"),function(){var e=this.split("=");i+=''}),r('").appendTo("body").submit().remove(),d.default.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var t=e.templateBulkImportInModal();e.modal=Galaxy.modal,e.modal.show({closing_events:!0,title:(0,l.default)("Import into History"),body:t({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(e){var t=this;this.histories=new h.default.GalaxyHistories,this.histories.fetch({success:function(n){0===n.length?d.default.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location=Galaxy.root}}):e(t)},error:function(e,t){void 0!==t.responseJSON?d.default.error(t.responseJSON.err_msg):d.default.error("An error occurred.")}})},importCurrentIntoHistory:function(){this.modal.disableButton("Import");var e=this.modal.$("input[name=history_name]").val(),t=this;if(""!==e)r.post(Galaxy.root+"api/histories",{name:e}).done(function(e){t.processImportToHistory(e.id)}).fail(function(e,t,n){d.default.error("An error occurred.")}).always(function(){t.modal.enableButton("Import")});else{var n=r(this.modal.$el).find("select[name=dataset_import_single] option:selected").val();this.processImportToHistory(n),this.modal.enableButton("Import")}},processImportToHistory:function(e){var t=new h.default.HistoryItem;t.url=t.urlRoot+e+"/contents",a.getJSON(Galaxy.root+"history/set_as_current?id="+e),t.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide(),d.default.success("Dataset imported. 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Please try again.")}})},showPermissions:function(e){var t=this.templateDatasetPermissions(),n=this;this.options=i.extend(this.options,e),r(".tooltip").remove(),void 0!==this.options.fetched_permissions&&(0===this.options.fetched_permissions.access_dataset_roles.length?this.model.set({is_unrestricted:!0}):this.model.set({is_unrestricted:!1})),this.$el.html(t({item:this.model,is_admin:Galaxy.config.is_admin_user})),r.get(Galaxy.root+"api/libraries/datasets/"+n.id+"/permissions?scope=current").done(function(e){n.prepareSelectBoxes({fetched_permissions:e,is_admin:Galaxy.config.is_admin_user})}).fail(function(){d.default.error("An error occurred while attempting to fetch dataset permissions.")}),r("#center [data-toggle]").tooltip(),r("#center").css("overflow","auto")},_serializeRoles:function(e){for(var t=[],n=0;n0))return void d.default.warning("Library dataset name has to be at least 1 character long.");n.set("name",i),t=!0}var r=this.$el.find(".input_dataset_misc_info").val();void 0!==r&&r!==n.get("misc_info")&&(n.set("misc_info",r),t=!0);var a=this.select_genome.$el.select2("data").id;void 0!==a&&a!==n.get("genome_build")&&(n.set("genome_build",a),t=!0);var o=this.select_extension.$el.select2("data").id;void 0!==o&&o!==n.get("file_ext")&&(n.set("file_ext",o),t=!0);var s=this;t?n.save(null,{patch:!0,success:function(e){s.render(),d.default.success("Changes to library dataset saved.")},error:function(e,t){void 0!==t.responseJSON?d.default.error(t.responseJSON.err_msg):d.default.error("An error occured while attempting to update the library dataset.")}}):(s.render(),d.default.info("Nothing has changed."))},copyToClipboard:function(t){t.preventDefault();var n=e.history.location.href;-1!==n.lastIndexOf("/permissions")&&(n=n.substr(0,n.lastIndexOf("/permissions"))),window.prompt("Copy to clipboard: Ctrl+C, Enter",n)},makeDatasetPrivate:function(){var e=this;r.post(Galaxy.root+"api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(t){e.model.set({is_unrestricted:!1}),e.showPermissions({fetched_permissions:t}),d.default.success("The dataset is now private to you.")}).fail(function(){d.default.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;r.post(Galaxy.root+"api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(t){e.model.set({is_unrestricted:!0}),e.showPermissions({fetched_permissions:t}),d.default.success("Access to this dataset is now unrestricted.")}).fail(function(){d.default.error("An error occurred while attempting to make dataset unrestricted.")})},_extractIds:function(e){for(var t=[],n=e.length-1;n>=0;n--)t.push(e[n].id);return t},savePermissions:function(e){var t=this,n=this._extractIds(this.accessSelectObject.$el.select2("data")),i=this._extractIds(this.manageSelectObject.$el.select2("data")),a=this._extractIds(this.modifySelectObject.$el.select2("data"));r.post(Galaxy.root+"api/libraries/datasets/"+t.id+"/permissions?action=set_permissions",{"access_ids[]":n,"manage_ids[]":i,"modify_ids[]":a}).done(function(e){t.showPermissions({fetched_permissions:e}),d.default.success("Permissions saved.")}).fail(function(){d.default.error("An error occurred while attempting to set dataset permissions.")})},fetchExtAndGenomes:function(){var e=this;0==this.list_genomes.length&&p.default.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(t){for(var n in t)e.list_extensions.push({id:t[n].extension,text:t[n].extension,description:t[n].description,description_url:t[n].description_url});e.list_extensions.sort(function(e,t){return e.id>t.id?1:e.idt.id?1:e.id',' "].join(""))},templateVersion:function(){return i.template([' 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e=this;e.expanded=!1,this.$details().slideUp(e.fxSpeed,function(){e.trigger("collapsed",e)})}})),u=d.extend(l.default.mixin(l.default.SelectableViewMixin,l.default.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){d.prototype.initialize.call(this,e),l.default.SelectableViewMixin.initialize.call(this,e),l.default.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(e){e?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var e=d.prototype._buildNewRender.call(this);return e.children(".warnings").replaceWith(this._renderWarnings()),e.children(".title-bar").replaceWith(this._renderTitleBar()),e.children(".primary-actions").append(this._renderPrimaryActions()),e.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),e},_swapNewRender:function(e){return d.prototype._swapNewRender.call(this,e),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var e=this,t=i(''),n=e.model.toJSON();return r.each(e.templates.warnings,function(r){t.append(i(r(n,e)))}),t},_renderTitleBar:function(){return i(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return i(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(e){e.stopPropagation(),e.altKey?(this.toggleSelect(e),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(e){return!e||"keydown"!==e.type||32!==e.keyCode&&13!==e.keyCode||(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){return"ListItemView("+(this.model?""+this.model:"(no model)")+")"}}));u.prototype.templates=function(){return{el:l.default.wrapTemplate(['
'),n.join(" ")},tagsToCSV:function(){var e=this,t=this.model.get("tags");return!i.isArray(t)||i.isEmpty(t)?"":t.map(function(t){return i.escape(e._nameToHash(t))}).sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){var e=this;return i.map(Galaxy.user.get("tags_used"),e._nameToHash)},_setUpBehaviors:function(){var e=this;this.$input().on("change",function(t){t.val=i.map(t.val,e._hashToName),e.model.save({tags:t.val}),t.added&&e._addNewTagToTagsUsed(""+t.added.text)})},_addNewTagToTagsUsed:function(e){var t=Galaxy.user.get("tags_used");i.contains(t,e)||(t.push(e),t.sort(),Galaxy.user.set("tags_used",t))},remove:function(){this.$input.off(),this.stopListening(this.model),e.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",""+this.model,")"].join("")}});t.default={TagsEditor:c}}).call(t,n(2),n(1))},,,,,,function(e,t,n){"use strict";(function(e){function i(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=n(28),a=i(r),o=n(51),s=i(o),l=n(3),c=(i(l),s.default.HistoryContentMixin),d=a.default.DatasetCollection,u=d.extend(c).extend({defaults:e.extend(e.clone(d.prototype.defaults),{history_content_type:"dataset_collection",model_class:"HistoryDatasetCollectionAssociation"}),save:function(e,t){return this.isNew()&&(t=t||{},t.url=this.urlRoot+this.get("history_id")+"/contents",e=e||{},e.type="dataset_collection"),d.prototype.save.call(this,e,t)},toString:function(){return"History"+d.prototype.toString.call(this)}});t.default={HistoryDatasetCollection:u}}).call(t,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(50),s=a(o),l=n(4),c=a(l),d=n(3),u=(a(d),{defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(t){return e.extend(t,t.object,{element_id:t.id}),delete t.object,t},constructor:function(e,t){e=this._mergeObject(e),this.idAttribute="element_id",i.Model.apply(this,arguments)},parse:function(e,t){var n=e;return n=this._mergeObject(n)}}),h=i.Model.extend(c.default.LoggableMixin).extend(u).extend({_logNamespace:"collections"}),f=i.Collection.extend(c.default.LoggableMixin).extend({_logNamespace:"collections",model:h,toString:function(){return["DatasetCollectionElementCollection(",this.length,")"].join("")}}),p=s.default.DatasetAssociation.extend(c.default.mixin(u,{url:function(){return this.has("history_id")?Galaxy.root+"api/histories/"+this.get("history_id")+"/contents/"+this.get("id"):(console.warn("no endpoint for non-hdas within a collection yet"),Galaxy.root+"api/datasets")},defaults:e.extend({},s.default.DatasetAssociation.prototype.defaults,u.defaults),_downloadQueryParameters:function(){var e=this.get("file_ext"),t=this.get("element_identifier");return"?to_ext="+e+"&hdca_id="+this.get("parent_hdca_id")+"&element_identifier="+t},constructor:function(e,t){this.debug("\t DatasetDCE.constructor:",e,t),u.constructor.call(this,e,t)},hasDetails:function(){return this.elements&&this.elements.length},toString:function(){this.get("element_identifier");return"DatasetDCE({objStr})"}})),g=f.extend({model:p,toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),m=i.Model.extend(c.default.LoggableMixin).extend(c.default.SearchableModelMixin).extend({_logNamespace:"collections",defaults:{collection_type:null,deleted:!1},collectionClass:function(){return this.attributes.collection_type.indexOf(":")>0?v:g},initialize:function(e,t){this.debug(this+"(DatasetCollection).initialize:",e,t,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){var t=this.collectionClass();this.debug(this+"._createElementsModel",t,this.get("elements"),this.elements);var n=this.get("elements")||[];this.unset("elements",{silent:!0});var i=this;return e.each(n,function(t,n){e.extend(t,{parent_hdca_id:i.get("id")})}),this.elements=new t(n),this.elements},toJSON:function(){var e=i.Model.prototype.toJSON.call(this);return this.elements&&(e.elements=this.elements.toJSON()),e},inReadyState:function(){var e=this.get("populated");return this.isDeletedOrPurged()||e},hasDetails:function(){return 0!==this.elements.length},getVisibleContents:function(e){return this.elements},parse:function(e,t){var n=i.Model.prototype.parse.call(this,e,t);return n.create_time&&(n.create_time=new Date(n.create_time)),n.update_time&&(n.update_time=new Date(n.update_time)),n},delete:function(e){return this.get("deleted")?r.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},e)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name","tags"],toString:function(){return"DatasetCollection("+[this.get("id"),this.get("name")||this.get("element_identifier")].join(",")+")"}}),_=m.extend(c.default.mixin(u,{constructor:function(e,t){this.debug("\t NestedDCDCE.constructor:",e,t),u.constructor.call(this,e,t)},toString:function(){return["NestedDCDCE(",this.object?""+this.object:this.get("element_identifier"),")"].join("")}})),v=f.extend({model:_,toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}});t.default={DatasetCollection:m}}).call(t,n(1),n(2),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(16),l=o(s),c=n(30),d=(o(c),n(56)),u=o(d),h=n(5),f=o(h),p=n(4),g=o(p),m=n(3),_=o(m),v=e.Model.extend(g.default.LoggableMixin).extend(g.default.mixin(g.default.SearchableModelMixin,{_logNamespace:"history",UPDATE_DELAY:4e3,defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",deleted:!1,contents_active:{},contents_states:{}},urlRoot:Galaxy.root+"api/histories",contentsClass:l.default.HistoryContents,searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},initialize:function(e,t){t=t||{},this.logger=t.logger||null,this.log(this+".initialize:",e,t),this.contents=new this.contentsClass([],{history:this,historyId:this.get("id"),order:t.order}),this._setUpListeners(),this._setUpCollectionListeners(),this.updateTimeoutId=null},_setUpListeners:function(){return this.on({error:function(e,t,n,i,r){this.clearUpdateTimeout()},"change:id":function(e,t){this.contents&&(this.contents.historyId=t)}})},_setUpCollectionListeners:function(){return this.contents?this.listenTo(this.contents,{error:function(){this.trigger.apply(this,i.makeArray(arguments))}}):this},contentsShown:function(){var e=this.get("contents_active"),t=e.active||0;return t+=this.contents.includeDeleted?e.deleted:0,t+=this.contents.includeHidden?e.hidden:0},nice_size:function(){var e=this.get("size");return e?f.default.bytesToString(e,!0,2):(0,_.default)("(empty)")},toJSON:function(){return r.extend(e.Model.prototype.toJSON.call(this),{nice_size:this.nice_size()})},get:function(t){return"nice_size"===t?this.nice_size():e.Model.prototype.get.apply(this,arguments)},ownedByCurrUser:function(){return!(!Galaxy||!Galaxy.user)&&(!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.get("user_id"))},numOfUnfinishedJobs:function(){var e=this.get("non_ready_jobs");return e?e.length:0},numOfUnfinishedShownContents:function(){return this.contents.runningAndActive().length||0},_fetchContentRelatedAttributes:function(){var e=["size","non_ready_jobs","contents_active","hid_counter"];return this.fetch({data:a.param({keys:e.join(",")})})},refresh:function(e){var t=this;e=e||{};var n=this.lastUpdateTime;return this.contents.allFetched=!1,(0!==this.contents.currentPage?function(){return t.contents.fetchPage(t.contents.currentPage)}:function(){return t.contents.fetchUpdated(n)})().done(function(n,i,r){var a;try{a=new Date(r.getResponseHeader("Date"))}catch(e){}t.lastUpdateTime=a||new Date,t.checkForUpdates(e)})},checkForUpdates:function(e){var t=this;e=e||{};var n=this.UPDATE_DELAY;if(this.id){var i=function(){t.clearUpdateTimeout(),t.updateTimeoutId=setTimeout(function(){t.refresh(e)},n)};this.numOfUnfinishedShownContents()>0?i():this._fetchContentRelatedAttributes().done(function(e){t.numOfUnfinishedJobs()>0?i():t.trigger("ready")})}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},stopPolling:function(){this.clearUpdateTimeout(),this.contents&&this.contents.stopPolling()},parse:function(t,n){var i=e.Model.prototype.parse.call(this,t,n);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},fetchWithContents:function(e,t){e=e||{};var n=this;return e.view="dev-detailed",this.fetch(e).then(function(e){return n.contents.history=n,n.contents.setHistoryId(e.id),n.fetchContents(t)})},fetchContents:function(e){e=e||{};var t=this;return t.lastUpdateTime=new Date,t.contents.fetchCurrentPage(e)},_delete:function(e){return this.get("deleted")?i.when():this.save({deleted:!0},e)},purge:function(e){return this.get("purged")?i.when():this.save({deleted:!0,purged:!0},e)},undelete:function(e){return this.get("deleted")?this.save({deleted:!1},e):i.when()},copy:function(e,t,n){if(e=void 0===e||e,!this.id)throw new Error("You must set the history ID before copying it.");var r={history_id:this.id};e&&(r.current=!0),t&&(r.name=t),n||(r.all_datasets=!1),r.view="dev-detailed";var a=this,o=i.post(this.urlRoot,r);return e?o.then(function(e){return new v(e).setAsCurrent().done(function(){a.trigger("copied",a,e)})}):o.done(function(e){a.trigger("copied",a,e)})},setAsCurrent:function(){var e=this,t=i.getJSON(Galaxy.root+"history/set_as_current?id="+this.id);return t.done(function(){e.trigger("set-as-current",e)}),t},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}})),y=u.default.InfinitelyScrollingCollection,b=y.extend(g.default.LoggableMixin).extend({_logNamespace:"history",model:v,order:"update_time",limitOnFirstFetch:10,limitPerFetch:10,initialize:function(e,t){t=t||{},this.log("HistoryCollection.initialize",e,t),y.prototype.initialize.call(this,e,t),this.includeDeleted=t.includeDeleted||!1,this.currentHistoryId=t.currentHistoryId,this.setUpListeners()},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot},setUpListeners:function(){return this.on({"change:deleted":function(e){this.debug("change:deleted",this.includeDeleted,e.get("deleted")),!this.includeDeleted&&e.get("deleted")&&this.remove(e)},copied:function(e,t){this.setCurrent(new v(t,[]))},"set-as-current":function(e){var t=this.currentHistoryId;this.trigger("no-longer-current",t),this.currentHistoryId=e.id}})},_buildFetchData:function(e){return r.extend(y.prototype._buildFetchData.call(this,e),{view:"dev-detailed"})},_buildFetchFilters:function(e){var t=y.prototype._buildFetchFilters.call(this,e)||{},n={};return this.includeDeleted?n.deleted=null:(n.deleted=!1,n.purged=!1),r.defaults(t,n)},fetchFirst:function(e){var t=this,n=a.when();return this.currentHistoryId&&(n=y.prototype.fetchFirst.call(t,{silent:!0,limit:1,filters:{purged:"",deleted:"","encoded_id-in":this.currentHistoryId}})),n.then(function(){return e=e||{},e.offset=0,t.fetchMore(e)})},comparators:r.extend(r.clone(y.prototype.comparators),{name:g.default.buildComparator("name",{ascending:!0}),"name-dsc":g.default.buildComparator("name",{ascending:!1}),size:g.default.buildComparator("size",{ascending:!1}),"size-asc":g.default.buildComparator("size",{ascending:!0})}),sort:function(e){e=e||{};var t=e.silent,n=this.remove(this.get(this.currentHistoryId));return y.prototype.sort.call(this,r.defaults({silent:!0},e)),this.unshift(n,{silent:!0}),t||this.trigger("sort",this,e),this},create:function(e,t,n,r){var a=this;return i.getJSON(Galaxy.root+"history/create_new_current").done(function(e){a.setCurrent(new v(e,[],n||{}))})},setCurrent:function(e,t){return t=t||{},this.unshift(e,t),this.currentHistoryId=e.get("id"),t.silent||this.trigger("new-current",e,this),this},toString:function(){return"HistoryCollection("+this.length+",current:"+this.currentHistoryId+")"}});t.default={History:v,HistoryCollection:b}}).call(t,n(2),n(0),n(1),n(0))},function(e,t,n){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var i=n(4),r=function(e){return e&&e.__esModule?e:{default:e}}(i),a=r.default.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:!1,show_hidden:!1},addExpanded:function(e){var t=this.get("expandedIds");t[e.id]=e.get("id"),this.save("expandedIds",t)},removeExpanded:function(e){var t=this.get("expandedIds");delete t[e.id],this.save("expandedIds",t)},isExpanded:function(t){return e.result(this.get("expandedIds"),t,!1)},allExpanded:function(){return e.values(this.get("expandedIds"))},clearExpanded:function(){this.set("expandedIds",{})},includeDeleted:function(t){return e.isUndefined(t)||this.set("show_deleted",t),this.get("show_deleted")},includeHidden:function(t){return e.isUndefined(t)||this.set("show_hidden",t),this.get("show_hidden")},toString:function(){return"HistoryPrefs("+this.id+")"}},{storageKeyPrefix:"history:",historyStorageKey:function(e){if(!e)throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+e);return a.storageKeyPrefix+e},get:function(e){return new a({id:a.historyStorageKey(e)})},clearAll:function(e){for(var t in sessionStorage)0===t.indexOf(a.storageKeyPrefix)&&sessionStorage.removeItem(t)}});t.default={HistoryPrefs:a}}).call(t,n(1))},function(e,t,n){"use strict";(function(e){function n(e,t){if(!e)throw new ReferenceError("this hasn't been initialised - super() hasn't been called");return!t||"object"!=typeof t&&"function"!=typeof t?e:t}function i(e,t){if("function"!=typeof t&&null!==t)throw new TypeError("Super expression must either be null or a function, not "+typeof t);e.prototype=Object.create(t&&t.prototype,{constructor:{value:e,enumerable:!1,writable:!0,configurable:!0}}),t&&(Object.setPrototypeOf?Object.setPrototypeOf(e,t):e.__proto__=t)}function r(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}Object.defineProperty(t,"__esModule",{value:!0});var a=function e(t,n,i){null===t&&(t=Function.prototype);var r=Object.getOwnPropertyDescriptor(t,n);if(void 0===r){var a=Object.getPrototypeOf(t);return null===a?void 0:e(a,n,i)}if("value"in r)return r.value;var o=r.get;if(void 0!==o)return o.call(i)},o=function(){function e(e,t){for(var n=0;n .title-bar .subtitle").replaceWith(this._renderSubtitle())})},_renderSubtitle:function(){return i(this.templates.subtitle(this.model.toJSON(),this))},_getFoldoutPanelOptions:function(){var t=p.prototype._getFoldoutPanelOptions.call(this);return e.extend(t,{linkTarget:this.linkTarget,hasUser:this.hasUser})},$selector:function(){return this.$("> .selector")},toString:function(){return"DCListItemView("+(this.model?""+this.model:"(no model)")+")"}});m.prototype.templates=function(){var t=e.extend({},p.prototype.templates.warnings,{error:u.default.wrapTemplate(["<% if( model.error ){ %>",'","<% } %>"]),purged:u.default.wrapTemplate(["<% if( model.purged ){ %>",'","<% } %>"]),deleted:u.default.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'","<% } %>"])}),n=u.default.wrapTemplate(['"],"collection"),i=u.default.wrapTemplate([' .clear-selected").show():this.$(".collection-elements-controls > .clear-selected").hide()},_renderList:function(e,t){var n=this,r=a(""),o=n.$list();i.each(this.elementViews,function(e){e.destroy(),n.removeElementView(e)}),n.workingElements.forEach(function(e){var t=n._createElementView(e);r.append(t.$el)}),n._renderClearSelected(),o.empty().append(r.children()),i.invoke(n.elementViews,"render"),o.height()>o.css("max-height")?o.css("border-width","1px 0px 1px 0px"):o.css("border-width","0px")},_createElementView:function(e){var t=new this.elementViewClass({element:e,selected:i.has(this.selectedIds,e.id)});return this.elementViews.push(t),this._listenToElementView(t),t},_listenToElementView:function(e){var t=this;t.listenTo(e,{select:function(e){var n=e.source.element;e.selected?t.selectedIds[n.id]=!0:delete t.selectedIds[n.id],t.trigger("elements:select",e)},discard:function(e){t.trigger("elements:discard",e)}})},addElementView:function(e){},removeElementView:function(e){delete this.selectedIds[e.element.id],this._renderClearSelected(),this.elementViews=i.without(this.elementViews,e),this.stopListening(e)},_renderNoElementsLeft:function(){this._disableNameAndCreate(!0),this.$(".collection-elements").append(this.templates.noElementsLeft())},_elementToJSON:function(e){return e},createList:function(e){if(!this.workingElements.length){var t=(0,b.default)("No valid elements for final list")+". ";return t+=''+(0,b.default)("Cancel")+" ",t+=(0,b.default)("or"),t+=' '+(0,b.default)("start over")+".",void this._showAlert(t)}var n=this,i=this.workingElements.map(function(e){return n._elementToJSON(e)});return n.blocking=!0,n.creationFn(i,e,n.hideOriginals).always(function(){n.blocking=!1}).fail(function(e,t,i){n.trigger("error",{xhr:e,status:t,message:(0,b.default)("An error occurred while creating this collection")})}).done(function(e,t,i){n.trigger("collection:created",e,t,i),n.metric("collection:created",e),"function"==typeof n.oncreate&&n.oncreate.call(this,e,t,i)})},_setUpBehaviors:function(){return this.on("error",this._errorHandler),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this.on("elements:select",function(e){this._renderClearSelected()}),this.on("elements:discard",function(e){var t=e.source.element;this.removeElementView(e.source),this.workingElements=i.without(this.workingElements,t),this.workingElements.length||this._renderNoElementsLeft()}),this},_errorHandler:function(e){this.error(e);var t=this,n=e.message||(0,b.default)("An error occurred");if(e.xhr){var i=e.xhr,r=e.message;0===i.readyState&&0===i.status?n+=": "+(0,b.default)("Galaxy could not be reached and may be updating.")+(0,b.default)(" Try again in a few minutes."):i.responseJSON?n+=":
=0&&ae&&a-o','',(0,b.default)("More help"),"",'"," ",'
","',e.html," "].join("");return r(t).click(function(t){return t.preventDefault(),e.func(t)})});return i.find("ul").append(a),t.replaceWith(i),i},multiselectActions:function(){return[]},$scrollContainer:function(e){return(e||this.$el).parent().parent()},$controls:function(e){return(e||this.$el).find("> .controls")},$list:function(e){return(e||this.$el).find("> .list-items")},$messages:function(e){return(e||this.$el).find("> .controls .messages")},$emptyMessage:function(e){return(e||this.$el).find("> .empty-message")},renderItems:function(e){e=e||this.$el;var t=this;t.log(this+".renderItems",e);var n=t.$list(e);t.freeViews();var i=t._filterCollection();return t.views=i.map(function(e){return t._createItemView(e)}),n.empty(),t.views.length&&t._attachItems(e),t._renderEmptyMessage(e).toggle(!t.views.length),t.trigger("views:ready",t.views),t.views},_filterCollection:function(){var e=this;return e.collection.filter(i.bind(e._filterItem,e))},_filterItem:function(e){var t=this;return i.every(t.filters.map(function(t){return t.call(e)}))&&(!t.searchFor||e.matchesAll(t.searchFor))},_createItemView:function(e){var t=this._getItemViewClass(e),n=i.extend(this._getItemViewOptions(e),{model:e}),r=new t(n);return this._setUpItemViewListeners(r),r},_destroyItemView:function(e){this.stopListening(e),this.views=i.without(this.views,e)},_destroyItemViews:function(e){var t=this;return t.views.forEach(function(e){t.stopListening(e)}),t.views=[],t},freeViews:function(){return this._destroyItemViews()},_getItemViewClass:function(e){return this.viewClass},_getItemViewOptions:function(e){return{fxSpeed:this.fxSpeed,expanded:!1,selectable:this.selecting,selected:i.contains(this.selected,e.id),draggable:this.dragItems}},_setUpItemViewListeners:function(e){var t=this;return this.listenTo(e,"all",function(){var e=Array.prototype.slice.call(arguments,0);e[0]="view:"+e[0],t.trigger.apply(t,e)}),this.listenTo(e,"draggable:dragstart",function(e,t){var n={},i=this.getSelectedModels();n=i.length?i.toJSON():[t.model.toJSON()],e.dataTransfer.setData("text",JSON.stringify(n))},this),t},_attachItems:function(e){var t=this;return this.$list(e).append(this.views.map(function(e){return t._renderItemView$el(e)})),this},_renderItemView$el:function(e){return e.render(0).$el},_renderEmptyMessage:function(e){this.debug("_renderEmptyMessage",e,this.searchFor);var t=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(e).text(t)},expandAll:function(){i.each(this.views,function(e){e.expand()})},collapseAll:function(){i.each(this.views,function(e){e.collapse()})},addItemView:function(e,t,n){var i=this,a=i._filterCollection().indexOf(e);if(-1!==a){var o=i._createItemView(e);return r(o).queue("fx",[function(e){i.$emptyMessage().is(":visible")?i.$emptyMessage().fadeOut(i.fxSpeed,e):e()},function(e){i._attachView(o,a),e()}]),o}},_attachView:function(e,t,n){n=!!i.isUndefined(n)||n,t=t||0;var r=this;return r.views.splice(t,0,e),r._insertIntoListAt(t,r._renderItemView$el(e).hide()),r.trigger("view:attached",e),n?e.$el.slideDown(r.fxSpeed,function(){r.trigger("view:attached:rendered")}):(e.$el.show(),r.trigger("view:attached:rendered")),e},_insertIntoListAt:function(e,t){var n=this.$list();return 0===e?n.prepend(t):n.children().eq(e-1).after(t),t},removeItemView:function(e,t,n){var a=this,o=i.find(a.views,function(t){return t.model===e});if(o)return a.views=i.without(a.views,o),a.trigger("view:removed",o),r({}).queue("fx",[function(e){o.$el.fadeOut(a.fxSpeed,e)},function(e){o.remove(),a.trigger("view:removed:rendered"),a.views.length?e():a._renderEmptyMessage().fadeIn(a.fxSpeed,e)}]),o},viewFromModelId:function(e){return i.find(this.views,function(t){return t.model.id===e})},viewFromModel:function(e){return e?this.viewFromModelId(e.id):void 0},viewsWhereModel:function(e){return this.views.filter(function(t){return i.isMatch(t.model.attributes,e)})},viewRange:function(e,t){if(e===t)return 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o=i(3),l=a(o),r=i(4),d=(a(r),i(30)),c=a(d),u=i(244),h=a(u),f=i(56),p=a(f),m=i(57),g=a(m),_=i(16),v=a(_),y=i(10),w=a(y),b=i(6),x=a(b),C=i(245),$=a(C);i(58),t.default=e.View.extend({upload_size:0,collection:new c.default.Collection,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ui_button=e.ui_button,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.$uploadbox=this.$(".upload-box"),this.$uploadtable=this.$(".upload-table"),this.btnLocal=new x.default.Button({id:"btn-local",title:(0,l.default)("Choose local file"),onclick:function(){t.uploadbox.select()},icon:"fa fa-laptop"}),this.btnFtp=new x.default.Button({id:"btn-ftp",title:(0,l.default)("Choose FTP file"),onclick:function(){t._eventFtp()},icon:"fa fa-folder-open-o"}),this.btnCreate=new x.default.Button({id:"btn-new",title:"Paste/Fetch data",onclick:function(){t._eventCreate()},icon:"fa fa-edit"}),this.btnStart=new x.default.Button({id:"btn-start",title:(0,l.default)("Start"),onclick:function(){t._eventStart()}}),this.btnStop=new x.default.Button({id:"btn-stop",title:(0,l.default)("Pause"),onclick:function(){t._eventStop()}}),this.btnReset=new x.default.Button({id:"btn-reset",title:(0,l.default)("Reset"),onclick:function(){t._eventReset()}}),this.btnClose=new x.default.Button({id:"btn-close",title:(0,l.default)("Close"),onclick:function(){t.app.modal.hide()}}),n.each([this.btnLocal,this.btnFtp,this.btnCreate,this.btnStop,this.btnReset,this.btnStart,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.uploadbox=this.$uploadbox.uploadbox({url:this.app.options.nginx_upload_path,announce:function(e,i){t._eventAnnounce(e,i)},initialize:function(e){return t.app.toData([t.collection.get(e)],t.history_id)},progress:function(e,i){t._eventProgress(e,i)},success:function(e,i){t._eventSuccess(e,i)},error:function(e,i){t._eventError(e,i)},complete:function(){t._eventComplete()},ondragover:function(){t.$uploadbox.addClass("highlight")},ondragleave:function(){t.$uploadbox.removeClass("highlight")}}),this.ftp=new v.default.View({title:(0,l.default)("FTP files"),container:this.btnFtp.$el}),this.select_extension=new w.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-extension"),data:n.filter(this.list_extensions,function(e){return!e.composite_files}),value:this.options.default_extension,onchange:function(e){t._changeExtension(e)}}),this.$(".upload-footer-extension-info").on("click",function(e){new g.default({$el:s(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),list:t.list_extensions,placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new w.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 $.default({$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.$el),i.render(),i}}),this.collection.on("remove",function(e){t._eventRemove(e)}),this.render()},render:function(){var e="";e=0==this.counter.announce?this.uploadbox.compatible()?" ":"Browser does not support Drag & Drop. Try Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.":0==this.counter.running?"You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed.":"Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining.",this.$(".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 file..."),this.uploadbox.stop())},_eventReset:function(){if(0==this.counter.running){this.collection.reset(),this.counter.reset(),this.uploadbox.reset(),this.select_extension.value(this.options.default_extension),this.select_genome.value(this.options.default_genome),this.ui_button.model.set("percentage",0),this.render()}},_changeExtension:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("extension")!=i.options.default_extension&&t||n.set("extension",e)})},_changeGenome:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("genome")!=i.options.default_genome&&t||n.set("genome",e)})},_uploadFtp:function(){var 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(4),d=a(r),c=i(30),u=(a(c),i(55)),h=a(u),f=i(16),p=a(f),m=i(10),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 g.default.View({css:"upload-genome",data:i.app.list_genomes,container:this.$(".upload-genome"),value:s,onchange:function(e){i.model.set("genome",e)}}),this.select_extension=new g.default.View({css:"upload-extension",data:i.app.list_extensions,container:this.$(".upload-extension"),value:a,onchange:function(e){i.model.set("extension",e)}}),this.model.set({genome:s,extension:a}),this.$symbol.on("click",function(){i._removeRow()}),this.$(".upload-extension-info").on("click",function(e){i.app.showExtensionInfo({$el:n(e.target),title:i.select_extension.text(),extension:i.select_extension.value()})}).on("mousedown",function(e){e.preventDefault()}),this.$settings.on("click",function(e){i._showSettings()}).on("mousedown",function(e){e.preventDefault()}),this.$text_content.on("change input",function(e){i.model.set({url_paste:n(e.target).val(),file_size:n(e.target).val().length})}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:genome",function(){i._refreshGenome()}),this.listenTo(this.model,"change:extension",function(){i._refreshExtension()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()})},render:function(){this._refreshType(),this._refreshPercentage(),this._refreshStatus(),this._refreshInfo(),this._refreshGenome(),this._refreshExtension(),this._refreshFileSize()},remove:function(){this.select_genome.remove(),this.select_extension.remove(),e.View.prototype.remove.apply(this)},_refreshType:function(){var e=this.model.attributes;this.$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.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$symbol.removeClass().addClass("upload-symbol").addClass(this.status_classes[e]),this.model.set("enabled","init"==e);var t=this.model.get("enabled");this.$text_content.attr("disabled",!t),t?(this.select_genome.enable(),this.select_extension.enable()):(this.select_genome.disable(),this.select_extension.disable()),"success"==e&&(this.$el.addClass("success"),this.$percentage.html("100%")),"error"==e&&(this.$el.addClass("danger"),this.$info_progress.hide())},_refreshFileSize:function(){this.$size.html(d.default.bytesToString(this.model.get("file_size")))},_removeRow:function(){-1!==["init","success","error"].indexOf(this.model.get("status"))&&this.app.collection.remove(this.model)},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new h.default(this).$el),this.settings.show())},_template:function(e){return'
","=c?l.push(e.createPair.call(this,{listA:n,indexA:a,listB:s,indexB:o.index})):a+=1,!n.length||!s.length)return l}return this.debug("paired:",JSON.stringify(l,null," ")),this.debug("autopair _strategy ---------------------------"),l}}function r(e,t){var i=e.toJSON();return b(i,{historyId:e.historyId,defaultHideSourceItems:t})}Object.defineProperty(t,"__esModule",{value:!0});var d=i(263),c=o(d),u=i(109),h=o(u),f=i(108),p=o(f),m=i(5),g=o(m),_=i(3),v=o(_);i(110);var y=e.View.extend(g.default.LoggableMixin).extend({_logNamespace:"collections",tagName:"li",className:"dataset paired",initialize:function(e){this.pair=e.pair||{}},template:n.template(['<%- pair.forward.name %>','','<%- pair.name %>',"",'<%- pair.reverse.name %>'].join("")),render:function(){this.dragStartHandler=n.bind(this._dragstart,this),this.dragEndHandler=n.bind(this._dragend,this);var e=this.$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.$el.parent().trigger(e)},toString:function(){return"PairView("+this.pair.name+")"}}),w=e.View.extend(g.default.LoggableMixin).extend(p.default.CollectionCreatorMixin).extend({_logNamespace:"collections",className:"list-of-pairs-collection-creator collection-creator flex-row-container",initialize:function(e){this.metric("PairedCollectionCreator.initialize",e),e=n.defaults(e,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:!0,strategy:"lcs",matchPercentage:.9,twoPassAutopairing:!0}),this.initialList=e.datasets,this.historyId=e.historyId,this.filters=this.commonFilters[e.filters]||this.commonFilters[this.DEFAULT_FILTERS],n.isArray(e.filters)&&(this.filters=e.filters),this.automaticallyPair=e.automaticallyPair,this.strategy=this.strategies[e.strategy]||this.strategies[this.DEFAULT_STRATEGY],n.isFunction(e.strategy)&&(this.strategy=e.strategy),this.matchPercentage=e.matchPercentage,this.twoPassAutopairing=e.twoPassAutopairing,this.removeExtensions=!0,this.oncancel=e.oncancel,this.oncreate=e.oncreate,this.autoscrollDist=e.autoscrollDist||24,this.unpairedPanelHidden=!1,this.pairedPanelHidden=!1,this.$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.$(".collection-name").val()),element_identifiers:t.paired.map(function(e){return t._pairToJSON(e)})};return t.blocking=!0,s.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(a)}).always(function(){t.blocking=!1}).fail(function(e,i,n){t._ajaxErrHandler(e,i,n)}).done(function(e,i,n){t.trigger("collection:created",e,i,n),t.metric("collection:created",e),"function"==typeof t.oncreate&&t.oncreate.call(this,e,i,n)})},_ajaxErrHandler:function(e,t,i){this.error(e,t,i);var n=this,s=(0,v.default)("An error occurred while creating this collection");e&&(0===e.readyState&&0===e.status?s+=": "+(0,v.default)("Galaxy could not be reached and may be updating.")+(0,v.default)(" Try again in a few minutes."):e.responseJSON?s+="
=0&&ae&&s-o",e.name)},toString:function(){return"PairedCollectionCreator"},templates:n.extend({},p.default.CollectionCreatorMixin._creatorTemplates,{header:n.template(['
").addClass("ui-panel-table"));var a=h.default.get("message"),o=h.default.get("status");a&&o&&e.$preferences.prepend(new c.default.Message({message:a,status:o}).$el),t.use_remote_user||(e._addLink("information"),e._addLink("password")),t.enable_communication_server&&e._addLink("communication"),e._addLink("custom_builds"),e._addLink("permissions"),e._addLink("api_key"),t.has_user_tool_filters&&e._addLink("toolbox_filters"),t.enable_openid&&!t.use_remote_user&&e._addLink("openids"),Galaxy.session_csrf_token&&e._addLink("logout"),e.$preferences.append(e._templateFooter(i)),e.$el.empty().append(e.$preferences)})},_addLink:function(e){var t=this.model.get(e),i=n(this._templateLink(t)),s=i.find("a");t.onclick?s.on("click",function(){t.onclick()}):s.attr("href",Galaxy.root+"user/"+e),this.$table.append(i)},_templateLink:function(e){return''+e.title+'
');s.each(i.shared_by_others,function(t,i){var n=Galaxy.root+e.item+"/display_by_username_and_slug?username="+t.username+"&slug="+t.slug;a.append(''+s.escape(t.title)+" "+s.escape(t.username)+" '+(this.model.get("owner")===Galaxy.user.attributes.username?"You":this.model.get("owner"))+" "+this.model.get("number_of_steps")+" "+(this.model.get("published")?"Yes":"No")+" "+i+" "},renderTagEditor:function(){var e=new d.default.TagsEditor({model:this.model,el:s.find("."+this.model.id+".tags-display"),workflow_mode:!0});e.toggle(!0),e.render()},_templateActions:function(){return this.model.get("owner")===Galaxy.user.attributes.username?'':''}}),_=e.View.extend({title:(0,m.default)("Workflows"),initialize:function(){this.setElement(""),n.bindAll(this,"adjustActiondropdown"),this.collection=new u.default.WorkflowCollection,this.collection.fetch().done(this.render()),this.collection.bind("add",this.appendItem),this.collection.on("sync",this.render,this)},events:{dragleave:"unhighlightDropZone",drop:"drop",dragover:function(e){s(".hidden_description_layer").addClass("dragover"),s(".menubutton").addClass("background-none"),e.preventDefault()}},unhighlightDropZone:function(){s(".hidden_description_layer").removeClass("dragover"),s(".menubutton").removeClass("background-none")},drop:function(e){this.unhighlightDropZone(),e.preventDefault();for(var t,i=e.dataTransfer.files,n=this,s=0;t=i[s];s++)n.readWorkflowFiles(t)},readWorkflowFiles:function(e){var t=this,i=new FileReader;i.onload=function(n){var s;try{s=JSON.parse(i.result)}catch(t){l.error("Could not read file '"+e.name+"'. Verify it is a valid Galaxy workflow"),s=null}s&&t.collection.create(s,{at:0,wait:!0,success:function(){l.success("Successfully imported workflow '"+s.name+"'")},error:function(e,t,i){l.error(i.errorThrown)}})},i.readAsText(e,"utf-8")},_showArgErrors:n.once(function(){var e=f.default.get("message");"error"===f.default.get("status")?l.error(n.escape(e||"Unknown Error, please report this to an administrator.")):e&&l.info(n.escape(e))}),render:function(){var e=this._templateHeader(),t=this._templateActionButtons(),i=this._templateWorkflowTable();this.$el.html(e+t+i);var s=this;n(this.collection.models).each(function(e){s.appendItem(e),s.confirmDelete(e)},this);return this.searchWorkflow(this.$(".search-wf"),this.$(".workflow-search tr"),3),this.adjustActiondropdown(),this._showArgErrors(),this},appendItem:function(e){var t=new g({model:e,collection:this.collection});s(".workflow-search").append(t.render().el),t.renderTagEditor()},confirmDelete:function(e){this.$(".link-confirm-shared-"+e.id).click(function(){return window.confirm("Are you sure you want to remove the shared workflow '"+e.attributes.name+"'?")})},searchWorkflow:function(e,t,i){e.on("keyup",function(){var e=s(this).val();if(e.length>=i){var n=new RegExp(e,"i");t.hide(),t.filter(function(){return n.test(s(this).text())}).show()}else t.show()})},adjustActiondropdown:function(){s(this.el).on("show.bs.dropdown",function(){s(this.el).css("overflow","inherit")}),s(this.el).on("hide.bs.dropdown",function(){s(this.el).css("overflow","auto")})},_templateNoWorkflow:function(){return'
'},_templateHeader:function(){return'\n \n
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\n '+(e.escape(t.name)||e.escape(t.element_identifier))+'
\n \n '+n+'\n
\n \n
\n \n \n \n \n \n
\n ';t.name&&t.help?(s+="Tool help for "+t.name+"
",s+=t.help):s+="Tool help is unavailable for this dataset.
",s+="
",i.$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=y.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(y.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)")+")"}});w.prototype.templates=function(){var t=e.extend({},y.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+="
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","<% } %>"],"visualizations");return e.extend({},y.prototype.templates,{warnings:t,visualizations:i})}(),t.default={DatasetListItemEdit:w}}).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(5),o=s(a),l=i(3),r=s(l);i(21);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";(function(e){function t(e){return e&&e.__esModule?e:{default:e}}var n=i(0),s=t(n),a=i(24),o=t(a),l=i(54),r=t(l),d=i(240),c=t(d),u=i(250),h=t(u),f=i(27),p=t(f),m=i(87),g=t(m),_=i(69),v=t(_),y=i(264),w=t(y),b=i(265),x=t(b),C=i(81),$=t(C),k=i(20),S=t(k),T=i(266),P=t(T),E=i(267),D=t(E),A=i(269),M=t(A),I=i(274),L=t(I),O=i(111),N=t(O),j=i(15),G=t(j),V=i(4),H=t(V),z=i(6),U=t(z),F=i(275),R=t(F),B=i(276),W=t(B),J=i(92),q=t(J),Y=i(32),Q=t(Y),K=s.default;window.app=function(t,i){window.Galaxy=new o.default.GalaxyApp(t,i),Galaxy.debug("analysis 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n=r.default.extend({routes:{"(/)":"home","(/)root*":"home","(/)tours(/)(:tour_id)":"show_tours","(/)user(/)":"show_user","(/)user(/)(:form_id)":"show_user_form","(/)openids(/)list":"show_openids","(/)pages(/)create(/)":"show_pages_create","(/)pages(/)edit(/)":"show_pages_edit","(/)pages(/)(:action_id)":"show_pages","(/)visualizations(/)edit(/)":"show_visualizations_edit","(/)visualizations/(:action_id)":"show_visualizations","(/)workflows/import_workflow":"show_import_workflow","(/)workflows/run(/)":"show_run","(/)workflows(/)list":"show_workflows","(/)workflows/list_published(/)":"show_workflows_published","(/)workflows/create(/)":"show_workflows_create","(/)histories(/)citations(/)":"show_history_citations","(/)histories(/)rename(/)":"show_histories_rename","(/)histories(/)import(/)":"show_histories_import","(/)histories(/)permissions(/)":"show_histories_permissions","(/)histories(/)(:action_id)":"show_histories","(/)datasets(/)list(/)":"show_datasets","(/)custom_builds":"show_custom_builds","(/)datasets/edit":"show_dataset_edit_attributes","(/)datasets/error":"show_dataset_error"},require_login:["show_user","show_user_form","show_workflows"],authenticate:function(e,t){return Galaxy.user&&Galaxy.user.id||-1==this.require_login.indexOf(t)},show_tours:function(e){e?$.default.giveTourById(e):this.page.display(new $.default.ToursView)},show_user:function(){this.page.display(new w.default.View)},show_user_form:function(e){var t=new w.default.Model({user_id:Galaxy.params.id});this.page.display(new v.default.View(t.get(e)))},show_visualizations:function(e){this.page.display(new P.default.View({action_id:e,plural:"Visualizations",item:"visualization"}))},show_visualizations_edit:function(){this.page.display(new v.default.View({url:"visualization/edit?id="+G.default.get("id"),redirect:"visualizations/list"}))},show_workflows_published:function(){this.page.display(new S.default({url_base:Galaxy.root+"workflow/list_published"}))},show_histories:function(e){this.page.display(new L.default.View({action_id:e}))},show_history_citations:function(){var e=Q.default.extend(q.default),t=document.createElement("div");this.page.display(t),new e({propsData:{id:G.default.get("id"),source:"histories"}}).$mount(t)},show_histories_rename:function(){this.page.display(new v.default.View({url:"history/rename?id="+G.default.get("id"),redirect:"histories/list"}))},show_histories_import:function(){var e=Q.default.extend(M.default),t=document.createElement("div");this.page.display(t),(new e).$mount(t)},show_histories_permissions:function(){this.page.display(new v.default.View({url:"history/permissions?id="+G.default.get("id"),redirect:"histories/list"}))},show_openids:function(){this.page.display(new S.default({url_base:Galaxy.root+"user/openids_list"}))},show_datasets:function(){this.page.display(new S.default({url_base:Galaxy.root+"dataset/list"}))},show_pages:function(e){this.page.display(new P.default.View({action_id:e,plural:"Pages",item:"page"}))},show_pages_create:function(){this.page.display(new v.default.View({url:"page/create",redirect:"pages/list"}))},show_pages_edit:function(){this.page.display(new 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R.default.View)},home:function(e){e.tool_id||e.job_id?"upload1"===e.tool_id?(this.page.toolPanel.upload.show(),this._loadCenterIframe("welcome")):this._loadToolForm(e):e.workflow_id?this._loadWorkflow():e.m_c?this._loadCenterIframe(e.m_c+"/"+e.m_a):this._loadCenterIframe("welcome")},_loadToolForm:function(e){e.id=decodeURIComponent(e.tool_id),this.page.display(new g.default.View(e))},_loadCenterIframe:function(e,t){t=t||Galaxy.root,e=t+e,this.page.$("#galaxy_main").prop("src",e)},_loadWorkflow:function(){var e=this;H.default.get({url:Galaxy.root+"api/workflows/"+H.default.getQueryString("id")+"/download?style=run",success:function(t){e.page.display(new N.default.View(t))},error:function(t){var i=t.err_msg||"Error occurred while loading the resource.",n={message:i,status:"danger",persistent:!0};e.page.display(new U.default.Message(n))}})}});K(function(){Galaxy.page=new p.default.View(e.extend(t,{Left:c.default,Right:h.default,Router:n}))})}}).call(t,i(1))},function(e,t,i){"use 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e=this;this.tool_panel.get("layout").size()>0&&(this.$el.prepend(this.tool_panel_view.$el),this.tool_panel_view.render()),e.$("#internal-workflows").append(e._templateAllWorkflow({title:(0,c.default)("All workflows"),href:"workflows/list"})),n.each(this.stored_workflow_menu_entries,function(t){e.$("#internal-workflows").append(e._templateWorkflowLink({title:t.stored_workflow.name,href:"workflows/run?id="+t.encoded_stored_workflow_id}))})},_templateTool:function(e){return['','',e.title,"","
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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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this.get("name")&&(e='"'+this.get("name")+'",'+e),"Dataset("+e+")"}})),p=e.Collection.extend(d.default.LoggableMixin).extend({_logNamespace:"dataset",model:f,urlRoot:Galaxy.root+"api/datasets",url:function(){return this.urlRoot},ids:function(){return this.map(function(e){return e.get("id")})},notReady:function(){return this.filter(function(e){return!e.inReadyState()})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},ajaxQueue:function(e,t){var i=s.Deferred(),n=this.length,a=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(s,l){return function(){var r=e.call(s,t);r.done(function(e){i.notify({curr:l,total:n,response:e,model:s})}),r.always(function(e){a.push(e),o.length?o.shift()():i.resolve(a)})}}).value();return o.shift()(),i},matches:function(e){return this.filter(function(t){return t.matches(e)})},toString:function(){return["DatasetAssociationCollection(",this.length,")"].join("")}});t.default={DatasetAssociation:f,DatasetAssociationCollection:p}}).call(t,i(2),i(1),i(0))},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),i(4)),o=(n(a),i(3)),l=(n(o),1e3);try{l=localStorage.getItem("collectionFuzzyCountDefault")||l}catch(e){}var r={defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",hidden:function(){return!this.get("visible")},isVisible:function(e,t){var i=!0;return e||!this.get("deleted")&&!this.get("purged")||(i=!1),t||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var e=this.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+"$1"+a).split(a),r=new Date(n).getTime(),d=r?new Date(s).getTime():null;if(d){if(r
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";this.modal.$(".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 > 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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'
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'},i=x.default.wrapTemplate(['','
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",'',"','",'","
",'","\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(21),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(31),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(94),m=a(p),g=i(21),_=a(g),v=i(61),w=a(v),y=i(35),b=a(y),x=i(97),$=a(x),C=i(98),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,O=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"):"")+")"}});O.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:O}}).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 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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%
'+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
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Here is a snippet from an example multi-fasta file:
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| Title | Owner |
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'+(0,m.default)("Your workflows")+"
Import Galaxy workflow
Click the link above to visit myExperiment and browse for Galaxy workflows.
Dataset Error
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"),e.$el.append("Tool execution generated the following messages:
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Report This Error"),e.$el.append("
Usually the local Galaxy administrators regularly review errors that occur on the server. However, if you would like to provide additional information (such as what you were trying to do when the error occurred) and a contact e-mail address, we will be better able to investigate your problem and get back to you.
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diff --git a/static/scripts/bundled/extended.bundled.js b/static/scripts/bundled/extended.bundled.js
index a7814fb4092..6e656187e43 100644
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| Message | ','<%= _.escape(item.get("message")) %> | ',"
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"],"collection");return r.extend({},u.prototype.templates,{details:e})}(),t.default={ExpandableView:d,ListItemView:u,FoldoutListItemView:h}}).call(t,n(2),n(0),n(1),n(0))},function(e,t,n){"use strict";(function(e,i){function r(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=n(4),o=r(a),s=n(3),l=r(s),c=e.View.extend(o.default.LoggableMixin).extend(o.default.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",select_width:"100%",events:{},initialize:function(e){this.show_editor=!1,!1===e.usePrompt?this.label="":this.label='",this.workflow_mode=e.workflow_mode||!1,this.workflow_mode&&(this.events.click="showEditor",this.events.keydown="keydownHandler"),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.workflow_mode?this.$el.html(this._workflowTemplate()):this.$el.html(this._defaultTemplate()),this.$input().select2({placeholder:"Add tags",width:this.workflow_mode?this.width:this.select_width,tags:function(){return e._getTagsUsed()}}),this._setUpBehaviors(),this},_hashToName:function(e){return e.startsWith("#")?"name:"+e.slice(1):e},_nameToHash:function(e){return e.startsWith("name:")&&(e="#"+e.slice(5)),e},_defaultTemplate:function(){return[this.label,this._renderEditor()].join("")},_workflowTemplate:function(){return[this.show_editor?this._renderEditor():this._renderTags()].join(" ")},keydownHandler:function(e){switch(e.which){case 27:this.hideEditor()}},showEditor:function(){this.show_editor=!0,this.render()},hideEditor:function(){this.show_editor=!1,this.render()},_renderEditor:function(){return''},_renderTags:function(){var e=this.model.get("tags"),t=Galaxy.root+"static/images/fugue/tag--plus.png",n=[];return i.each(e,function(e){e=0==e.indexOf("name:")?e.slice(5):e;var t=''+e+"";n.push(t)}),0===n.length&&n.push("','<% var countText = collection.element_count? ( collection.element_count + " " ) : ""; %>','<% if( collection.collection_type === "list" ){ %>',(0,f.default)("a list of <%- countText %>datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',(0,f.default)("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',(0,f.default)("a list of <%- countText %>dataset pairs"),'<% } else if( collection.collection_type === "list:list" ){ %>',(0,f.default)("a list of <%- countText %>dataset lists"),"<% } %>","
"],"collection");return e.extend({},p.prototype.templates,{warnings:t,titleBar:n,subtitle:i})}();var _=g.extend({className:g.prototype.className+" dataset-collection-element",initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log("DCEListItemView.initialize:",e),g.prototype.initialize.call(this,e)},toString:function(){return"DCEListItemView("+(this.model?""+this.model:"(no model)")+")"}});_.prototype.templates=function(){var t=u.default.wrapTemplate(['"],"element");return e.extend({},g.prototype.templates,{titleBar:t})}();var v=c.default.DatasetListItemView.extend({className:c.default.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log("DatasetDCEListItemView.initialize:",e),c.default.DatasetListItemView.prototype.initialize.call(this,e)},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):r.when()},toString:function(){return"DatasetDCEListItemView("+(this.model?""+this.model:"(no model)")+")"}});v.prototype.templates=function(){var t=u.default.wrapTemplate(['"],"element");return e.extend({},c.default.DatasetListItemView.prototype.templates,{titleBar:t})}();var y=m.extend({className:m.prototype.className+" dataset-collection-element",_swapNewRender:function(e){m.prototype._swapNewRender.call(this,e);var t=this.model.get("state")||"ok";return this.$el.addClass("state-"+t),this.$el},toString:function(){return"NestedDCDCEListItemView("+(this.model?""+this.model:"(no model)")+")"}});t.default={DCListItemView:m,DCEListItemView:_,DatasetDCEListItemView:v,NestedDCDCEListItemView:y}}).call(t,n(1),n(0),n(0))},function(e,t,n){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var i=e.Model.extend({defaults:{url:"https://toolshed.g2.bx.psu.edu/",name:"Galaxy Main Tool 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p=e.View.extend(u.default.LoggableMixin).extend({_logNamespace:"list",viewClass:s.default.ListItemView,collectionClass:e.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:(0,f.default)("This list is empty"),noneFoundMsg:(0,f.default)("No matching items found"),searchPlaceholder:(0,f.default)("search"),initialize:function(e,t){e=e||{},e.logger&&(this.logger=e.logger),this.log(this+".initialize:",e),this.fxSpeed=i.has(e,"fxSpeed")?e.fxSpeed:this.fxSpeed,this.filters=[],this.searchFor=e.searchFor||"",this.selecting=void 0===e.selecting||e.selecting,this.selected=e.selected||[],this.lastSelected=null,this.dragItems=e.dragItems||!1,this.viewClass=e.viewClass||this.viewClass,this.views=[],this.collection=e.collection||this._createDefaultCollection(),this.filters=e.filters||[],this.$scrollContainer=e.$scrollContainer||this.$scrollContainer,this.title=e.title||"",this.subtitle=e.subtitle||"",this._setUpListeners()},_setUpListeners:function(){return 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t=e.which;27===t&&(this.value=s),27!==t&&13!==t&&37!==t&&38!==t&&39!==t&&40!==t&&32!==t||e.stopImmediatePropagation(),27!==t&&13!==t||(e.preventDefault(),this.blur())},click:function(e){e.stopImmediatePropagation()},mousedown:function(e){e.stopImmediatePropagation()},keyup:function(e){c.width(Math.min(l.text("pW"+this.value).width(),r))},keypress:function(e){if(13===e.which)return!1}}),d={fontFamily:a.css("fontFamily")||"",fontSize:a.css("fontSize")||"",fontWeight:a.css("fontWeight")||"",fontStyle:a.css("fontStyle")||"",fontStretch:a.css("fontStretch")||"",fontVariant:a.css("fontVariant")||"",letterSpacing:a.css("letterSpacing")||"",wordSpacing:a.css("wordSpacing")||""};o.attr("class",a.attr("class")).append(a.contents().clone()).append(c),a.replaceWith(o),l.css(d),c.css(d).width(Math.min(l.text("pW"+c[0].value).width(),r))[0].select()},set_theme:function(t,n){if(!t)return!1;if(!0===n){var 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i&&(a+="h&&(l=h-(d+20)),c+u+20>f&&(c=f-(u+20)),n.element.css({left:l,top:c}).show().find("a:eq(0)").focus().parent().addClass("vakata-context-hover"),n.is_visible=!0,e.vakata.context._trigger("show"))},hide:function(){n.is_visible&&(n.element.hide().find("ul").hide().end().find(":focus").blur(),n.is_visible=!1,e.vakata.context._trigger("hide"))}},e(function(){t="rtl"===e("body").css("direction");var i=!1;n.element=e(" ').hide().appendTo("body");e(document).bind("dnd_start.vakata",function(e,n){t=!1}).bind("dnd_move.vakata",function(a,o){if(i&&clearTimeout(i),o&&o.data&&o.data.jstree&&(!o.event.target.id||"jstree-marker"!==o.event.target.id)){var s,l,c,d,u,h,f,p,g,m,_,v,y,b,w=e.jstree.reference(o.event.target),x=!1,k=!1,M=!1;if(w&&w._data&&w._data.dnd)if(r.attr("class","jstree-"+w.get_theme()+(w.settings.core.themes.responsive?" jstree-dnd-responsive":"")),o.helper.children().attr("class","jstree-"+w.get_theme()+(w.settings.core.themes.responsive?" 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// the check will work anyway, as when moving the node will be loaded first and checked again
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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.$el.parent().trigger(e)},toString:function(){return"PairView("+this.pair.name+")"}}),b=e.View.extend(m.default.LoggableMixin).extend(p.default.CollectionCreatorMixin).extend({_logNamespace:"collections",className:"list-of-pairs-collection-creator collection-creator flex-row-container",initialize:function(e){this.metric("PairedCollectionCreator.initialize",e),e=i.defaults(e,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:!0,strategy:"lcs",matchPercentage:.9,twoPassAutopairing:!0}),this.initialList=e.datasets,this.historyId=e.historyId,this.filters=this.commonFilters[e.filters]||this.commonFilters[this.DEFAULT_FILTERS],i.isArray(e.filters)&&(this.filters=e.filters),this.automaticallyPair=e.automaticallyPair,this.strategy=this.strategies[e.strategy]||this.strategies[this.DEFAULT_STRATEGY],i.isFunction(e.strategy)&&(this.strategy=e.strategy),this.matchPercentage=e.matchPercentage,this.twoPassAutopairing=e.twoPassAutopairing,this.removeExtensions=!0,this.oncancel=e.oncancel,this.oncreate=e.oncreate,this.autoscrollDist=e.autoscrollDist||24,this.unpairedPanelHidden=!1,this.pairedPanelHidden=!1,this.$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=i.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)}),n=[[],[]];return this.unpaired.forEach(function(i){t.forEach(function(t,r){e(i,t)&&n[r].push(i)})}),n},_addToUnpaired:function(e){var t=this;this.unpaired.splice(function n(i,r){if(i===r)return i;var a=Math.floor((r-i)/2)+i,o=(0,h.default)(e.name,t.unpaired[a].name);if(o<0)return n(i,a);if(o>0)return n(a+1,r);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(),n=[];return this.twoPassAutopairing&&(n=this.autopairSimple({listA:t[0],listB:t[1]}),t=this._splitByFilters()),e=e||this.strategy,t=this._splitByFilters(),n=n.concat(this[e].call(this,{listA:t[0],listB:t[1]}))},autopairSimple:s({scoreThreshold:function(){return.6},match:function(e){return e=e||{},e.matchTo===e.possible?{index:e.index,score:1}:e.bestMatch}}),autopairLevenshtein:s({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var t=(0,d.default)(e.matchTo,e.possible),n=1-t/Math.max(e.matchTo.length,e.possible.length);return n>e.bestMatch.score?{index:e.index,score:n}:e.bestMatch}}),autopairLCS:s({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var t=this._naiveStartingAndEndingLCS(e.matchTo,e.possible).length,n=t/Math.max(e.matchTo.length,e.possible.length);return n>e.bestMatch.score?{index:e.index,score:n}:e.bestMatch}}),_naiveStartingAndEndingLCS:function(e,t){for(var n="",i="",r=0,a=0;r=0&&a>=0&&e[r]===t[a];)i=[e[r],i].join(""),r-=1,a-=1;return n+i},_pair:function(e,t,n){n=n||{},this.debug("_pair:",e,t);var r=this._createPair(e,t,n.name);return this.paired.push(r),this.unpaired=i.without(this.unpaired,e,t),n.silent||this.trigger("pair:new",r),r},_createPair:function(e,t,n){if(!e||!t||e===t)throw new Error("Bad pairing: "+[JSON.stringify(e),JSON.stringify(t)]);return n=n||this._guessNameForPair(e,t),{forward:e,name:n,reverse:t}},_guessNameForPair:function(e,t,n){n=void 0!==n?n:this.removeExtensions;var i=e.name,r=t.name,a=this._naiveStartingAndEndingLCS(i.replace(new RegExp(this.filters[0]),""),r.replace(new RegExp(this.filters[1]),""));if(n){var o=a.lastIndexOf(".");if(o>0){var s=a.slice(o,a.length);a=a.replace(s,""),i=i.replace(s,""),r=r.replace(s,"")}}return a||i+" & "+r},_unpair:function(e,t){if(t=t||{},!e)throw new Error("Bad pair: "+JSON.stringify(e));return this.paired=i.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,n=Galaxy.root+"api/histories/"+this.historyId+"/contents/dataset_collections",a={type:"dataset_collection",collection_type:"list:paired",hide_source_items:t.hideOriginals||!1,name:i.escape(e||t.$(".collection-name").val()),element_identifiers:t.paired.map(function(e){return t._pairToJSON(e)})};return t.blocking=!0,r.ajax(n,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(a)}).always(function(){t.blocking=!1}).fail(function(e,n,i){t._ajaxErrHandler(e,n,i)}).done(function(e,n,i){t.trigger("collection:created",e,n,i),t.metric("collection:created",e),"function"==typeof t.oncreate&&t.oncreate.call(this,e,n,i)})},_ajaxErrHandler:function(e,t,n){this.error(e,t,n);var i=this,r=(0,v.default)("An error occurred while creating this collection");e&&(0===e.readyState&&0===e.status?r+=": "+(0,v.default)("Galaxy could not be reached and may be updating.")+(0,v.default)(" Try again in a few minutes."):e.responseJSON?r+="
=0&&ae&&r-o",e.name)},toString:function(){return"PairedCollectionCreator"},templates:i.extend({},p.default.CollectionCreatorMixin._creatorTemplates,{header:i.template(['1||v.length>1)&&(x=1,k=3),b.draw_outlined_curve(r,a,o,s,h,x,k,_[w%_.length],v[w%v.length])}}},draw_outlined_curve:function(e,t,n,i,r,a,o,s,l){var s=s||0,l=l||0,c=this.canvas.getContext("2d");c.lineCap="round",c.strokeStyle=this.outer_color,c.lineWidth=o,c.beginPath(),c.moveTo(e,t+s),c.bezierCurveTo(e+r,t+s,n-r,i+l,n,i+l),c.stroke(),c.strokeStyle=this.inner_color,c.lineWidth=a,c.beginPath(),c.moveTo(e,t+s),c.bezierCurveTo(e+r,t+s,n-r,i+l,n,i+l),c.stroke()}}),t.default=n}).call(t,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(7),d=o(c),u=n(18),h=o(u),f=n(5),p=o(f),g=n(12),m=o(g),_=e.View.extend({el:"#center",model:null,options:{},defaults:{edit_mode:!1},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .copy-link-to-clipboard":"copyToClipboard","click .make-private":"makeDatasetPrivate","click .remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"saveModifications"},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.extend(this.options,e),this.fetchExtAndGenomes(),this.options.id&&this.fetchDataset()},fetchDataset:function(e){this.options=i.extend(this.options,e),this.model=new h.default.Item({id:this.options.id});var t=this;this.model.fetch({success:function(){t.options.show_permissions?t.showPermissions():t.options.show_version?t.fetchVersion():t.render()},error:function(e,t){void 0!==t.responseJSON?d.default.error(t.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}}):d.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),r(".tooltip").remove();var t=this.templateDataset();this.$el.html(t({item:this.model})),r(".peek").html(this.model.get("peek")),r("#center [data-toggle]").tooltip()},fetchVersion:function(e){this.options=i.extend(this.options,e);var t=this;this.options.ldda_id?(this.ldda=new h.default.Ldda({id:this.options.ldda_id}),this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id,this.ldda.fetch({success:function(){t.renderVersion()},error:function(e,t){void 0!==t.responseJSON?d.default.error(t.responseJSON.err_msg):d.default.error("An error occurred.")}})):(this.render(),d.default.error("Library dataset version requested but no id provided."))},renderVersion:function(){r(".tooltip").remove();var e=this.templateVersion();this.$el.html(e({item:this.model,ldda:this.ldda})),r(".peek").html(this.ldda.get("peek"))},enableModification:function(){r(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model})),this.renderSelectBoxes({genome_build:this.model.get("genome_build"),file_ext:this.model.get("file_ext")}),r(".peek").html(this.model.get("peek")),r("#center [data-toggle]").tooltip()},downloadDataset:function(){var e=Galaxy.root+"api/libraries/datasets/download/uncompressed",t={ld_ids:this.id};this.processDownload(e,t)},processDownload:function(e,t,n){if(e&&t){t="string"==typeof t?t:r.param(t);var i="";r.each(t.split("&"),function(){var e=this.split("=");i+=''}),r('").appendTo("body").submit().remove(),d.default.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var t=e.templateBulkImportInModal();e.modal=Galaxy.modal,e.modal.show({closing_events:!0,title:(0,l.default)("Import into History"),body:t({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(e){var t=this;this.histories=new h.default.GalaxyHistories,this.histories.fetch({success:function(n){0===n.length?d.default.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location=Galaxy.root}}):e(t)},error:function(e,t){void 0!==t.responseJSON?d.default.error(t.responseJSON.err_msg):d.default.error("An error occurred.")}})},importCurrentIntoHistory:function(){this.modal.disableButton("Import");var e=this.modal.$("input[name=history_name]").val(),t=this;if(""!==e)r.post(Galaxy.root+"api/histories",{name:e}).done(function(e){t.processImportToHistory(e.id)}).fail(function(e,t,n){d.default.error("An error occurred.")}).always(function(){t.modal.enableButton("Import")});else{var n=r(this.modal.$el).find("select[name=dataset_import_single] option:selected").val();this.processImportToHistory(n),this.modal.enableButton("Import")}},processImportToHistory:function(e){var t=new h.default.HistoryItem;t.url=t.urlRoot+e+"/contents",a.getJSON(Galaxy.root+"history/set_as_current?id="+e),t.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide(),d.default.success("Dataset imported. Click this to start analyzing it.","",{onclick:function(){window.location=Galaxy.root}})},error:function(e,t){void 0!==t.responseJSON?d.default.error("Dataset not imported. "+t.responseJSON.err_msg):d.default.error("An error occured. Dataset not imported. Please try again.")}})},showPermissions:function(e){var t=this.templateDatasetPermissions(),n=this;this.options=i.extend(this.options,e),r(".tooltip").remove(),void 0!==this.options.fetched_permissions&&(0===this.options.fetched_permissions.access_dataset_roles.length?this.model.set({is_unrestricted:!0}):this.model.set({is_unrestricted:!1})),this.$el.html(t({item:this.model,is_admin:Galaxy.config.is_admin_user})),r.get(Galaxy.root+"api/libraries/datasets/"+n.id+"/permissions?scope=current").done(function(e){n.prepareSelectBoxes({fetched_permissions:e,is_admin:Galaxy.config.is_admin_user})}).fail(function(){d.default.error("An error occurred while attempting to fetch dataset permissions.")}),r("#center [data-toggle]").tooltip(),r("#center").css("overflow","auto")},_serializeRoles:function(e){for(var t=[],n=0;n0))return void d.default.warning("Library dataset name has to be at least 1 character long.");n.set("name",i),t=!0}var r=this.$el.find(".input_dataset_misc_info").val();void 0!==r&&r!==n.get("misc_info")&&(n.set("misc_info",r),t=!0);var a=this.select_genome.$el.select2("data").id;void 0!==a&&a!==n.get("genome_build")&&(n.set("genome_build",a),t=!0);var o=this.select_extension.$el.select2("data").id;void 0!==o&&o!==n.get("file_ext")&&(n.set("file_ext",o),t=!0);var s=this;t?n.save(null,{patch:!0,success:function(e){s.render(),d.default.success("Changes to library dataset saved.")},error:function(e,t){void 0!==t.responseJSON?d.default.error(t.responseJSON.err_msg):d.default.error("An error occured while attempting to update the library dataset.")}}):(s.render(),d.default.info("Nothing has changed."))},copyToClipboard:function(t){t.preventDefault();var n=e.history.location.href;-1!==n.lastIndexOf("/permissions")&&(n=n.substr(0,n.lastIndexOf("/permissions"))),window.prompt("Copy to clipboard: Ctrl+C, Enter",n)},makeDatasetPrivate:function(){var e=this;r.post(Galaxy.root+"api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(t){e.model.set({is_unrestricted:!1}),e.showPermissions({fetched_permissions:t}),d.default.success("The dataset is now private to you.")}).fail(function(){d.default.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;r.post(Galaxy.root+"api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(t){e.model.set({is_unrestricted:!0}),e.showPermissions({fetched_permissions:t}),d.default.success("Access to this dataset is now unrestricted.")}).fail(function(){d.default.error("An error occurred while attempting to make dataset unrestricted.")})},_extractIds:function(e){for(var t=[],n=e.length-1;n>=0;n--)t.push(e[n].id);return t},savePermissions:function(e){var t=this,n=this._extractIds(this.accessSelectObject.$el.select2("data")),i=this._extractIds(this.manageSelectObject.$el.select2("data")),a=this._extractIds(this.modifySelectObject.$el.select2("data"));r.post(Galaxy.root+"api/libraries/datasets/"+t.id+"/permissions?action=set_permissions",{"access_ids[]":n,"manage_ids[]":i,"modify_ids[]":a}).done(function(e){t.showPermissions({fetched_permissions:e}),d.default.success("Permissions saved.")}).fail(function(){d.default.error("An error occurred while attempting to set dataset permissions.")})},fetchExtAndGenomes:function(){var e=this;0==this.list_genomes.length&&p.default.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(t){for(var n in t)e.list_extensions.push({id:t[n].extension,text:t[n].extension,description:t[n].description,description_url:t[n].description_url});e.list_extensions.sort(function(e,t){return e.id>t.id?1:e.idt.id?1:e.id','
"].join(""))},templateVersion:function(){return i.template(['\n Loading job data for '+n+'...\n '}return i},toString:function(){return"HDCAListItemView("+(this.model?""+this.model:"(no model)")+")"}});m.prototype.templates=function(){var t=e.extend({},g.prototype.templates.warnings,{hidden:function(e){e.visible||(0,p.default)("This collection has been hidden")}}),n=function(t){return'\n \n "};return e.extend({},g.prototype.templates,{warnings:t,titleBar:n})}(),t.default={HDCAListItemView:m}}).call(t,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(8),s=a(o),l=n(4),c=a(l),d=n(3),u=a(d),h=c.default.SearchableModelMixin,f=e.Model.extend(c.default.LoggableMixin).extend(c.default.mixin(h,{_logNamespace:"dataset",defaults:{state:s.default.NEW,deleted:!1,purged:!1,name:"(unnamed dataset)",accessible:!0,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(e,t){this.debug(this+"(Dataset).initialize",e,t),
+//!! this state is not in trans.app.model.Dataset.states - set it here -
+this.get("accessible")||this.set("state",s.default.NOT_VIEWABLE),this.urls=this._generateUrls(),this._setUpListeners()},_generateUrls:function(){var e=this.get("id");if(!e)return{};var t={purge:"datasets/"+e+"/purge_async",display:"datasets/"+e+"/display/?preview=True",edit:"datasets/edit?dataset_id="+e,download:"datasets/"+e+"/display"+this._downloadQueryParameters(),report_error:"dataset/errors?id="+e,rerun:"tool_runner/rerun?id="+e,show_params:"datasets/"+e+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+e+"&metadata_name="};return i.each(t,function(e,n){t[n]=Galaxy.root+e}),this.urls=t,t},_downloadQueryParameters:function(){return"?to_ext="+this.get("file_ext")},_setUpListeners:function(){this.on("change:state",function(e,t){this.log(this+" has changed state:",e,t),this.inReadyState()&&this.trigger("state:ready",e,t,this.previous("state"))}),this.on("change:id change:file_ext",function(e){this._generateUrls()})},toJSON:function(){var t=e.Model.prototype.toJSON.call(this);return i.extend(t,{urls:this.urls})},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},inReadyState:function(){var e=i.contains(s.default.READY_STATES,this.get("state"));return this.isDeletedOrPurged()||e},hasDetails:function(){return!this.get("accessible")||this.has("annotation")},hasData:function(){return this.get("file_size")>0},fetch:function(t){var n=this;return e.Model.prototype.fetch.call(this,t).always(function(){n._generateUrls()})},parse:function(t,n){var i=e.Model.prototype.parse.call(this,t,n);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},save:function(t,n){return n=n||{},n.wait=!!i.isUndefined(n.wait)||n.wait,e.Model.prototype.save.call(this,t,n)},delete:function(e){return this.get("deleted")?r.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},e)},purge:function(e){if(this.get("purged"))return r.when();e=e||{},e.url=this.urls.purge;var t=this,n=r.ajax(e);return n.done(function(e,n,i){t.set({deleted:!0,purged:!0})}),n.fail(function(n,i,r){var a=(0,u.default)("Unable to purge dataset");n.responseJSON&&n.responseJSON.error?a=n.responseJSON.error:-1!==n.responseText.indexOf("Removal of datasets by users is not allowed in this Galaxy instance")&&(a="Removal of datasets by users is not allowed in this Galaxy instance"),n.responseText=a,t.trigger("error",t,n,e,(0,u.default)(a),{error:a})}),n},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var e=this.get("id")||"";return this.get("name")&&(e='"'+this.get("name")+'",'+e),"Dataset("+e+")"}})),p=e.Collection.extend(c.default.LoggableMixin).extend({_logNamespace:"dataset",model:f,urlRoot:Galaxy.root+"api/datasets",url:function(){return this.urlRoot},ids:function(){return this.map(function(e){return e.get("id")})},notReady:function(){return this.filter(function(e){return!e.inReadyState()})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},ajaxQueue:function(e,t){var n=r.Deferred(),i=this.length,a=[];if(!i)return n.resolve([]),n;var o=this.chain().reverse().map(function(r,s){return function(){var l=e.call(r,t);l.done(function(e){n.notify({curr:s,total:i,response:e,model:r})}),l.always(function(e){a.push(e),o.length?o.shift()():n.resolve(a)})}}).value();return o.shift()(),n},matches:function(e){return this.filter(function(t){return 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l.default.NestedDCDCEListItemEdit.extend({foldoutPanelClass:m})},initialize:function(e){g.prototype.initialize.call(this,e)},_setUpBehaviors:function(e){if(e=e||this.$el,g.prototype._setUpBehaviors.call(this,e),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()){this.tagsEditorShown=!0;var t=this;e.find("> .controls .name").attr("title",(0,p.default)("Click to rename collection")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(e){var n=t.model.get("name");e&&e!==n?(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(n)}}),this.tagsEditor=new u.default.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},usePrompt:!1}),this.tagsEditor.toggle(!0)}},toString:function(){return"CollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}});t.default={CollectionViewEdit:m}},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(32),o=r(a),s=n(60),l=r(s),c=n(4),d=(r(c),n(3)),u=(r(d),o.default.DCListItemView),h=u.extend({initialize:function(e){u.prototype.initialize.call(this,e)},toString:function(){return"DCListItemEdit("+(this.model?""+this.model:"(no model)")+")"}}),f=o.default.DCEListItemView,p=f.extend({initialize:function(e){f.prototype.initialize.call(this,e)},toString:function(){return"DCEListItemEdit("+(this.model?""+this.model:"(no model)")+")"}}),g=l.default.DatasetListItemEdit.extend({initialize:function(e){l.default.DatasetListItemEdit.prototype.initialize.call(this,e)},_fetchModelDetails:function(){var t=this;return t.model.inReadyState()&&!t.model.hasDetails()?t.model.fetch({silent:!0}):e.when()},_renderDeleteButton:function(){return null},toString:function(){return"DatasetDCEListItemEdit("+(this.model?""+this.model:"(no model)")+")"}});g.prototype.templates=function(){return i.extend({},l.default.DatasetListItemEdit.prototype.templates,{titleBar:o.default.DatasetDCEListItemView.prototype.templates.titleBar})}();var m=o.default.NestedDCDCEListItemView.extend({toString:function(){return"NestedDCDCEListItemEdit("+(this.model?""+this.model:"(no model)")+")"}});t.default={DCListItemEdit:h,DCEListItemEdit:p,DatasetDCEListItemEdit:g,NestedDCDCEListItemEdit:m}}).call(t,n(0),n(1))},function(e,t,n){"use strict";(function(e,i,r){function a(e){return e&&e.__esModule?e:{default:e}}function o(e,t){var n=e.toJSON();return v(n,{defaultHideSourceItems:t,creationFn:function(t,n,i){return t=[{name:"forward",src:"hda",id:t[0].id},{name:"reverse",src:"hda",id:t[1].id}],e.createHDCA(t,"paired",n,i)}})}Object.defineProperty(t,"__esModule",{value:!0});var s=n(35),l=a(s),c=n(27),d=a(c),u=n(4),h=a(u),f=n(3),p=a(f),g=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:i.template(['<%- identifier %>','<%- element.name %>'].join("")),destroy:function(){this.off(),this.$el.remove()},toString:function(){return"DatasetCollectionElementView()"}}),m=l.default.ListCollectionCreator,_=m.extend({elementViewClass:g,collectionClass:d.default.HistoryDatasetCollection,className:"pair-collection-creator collection-creator flex-row-container",_mangleDuplicateNames:function(){},render:function(e,t){return 2===this.workingElements.length?m.prototype.render.call(this,e,t):this._renderInvalid(e,t)},_renderList:function(e,t){var n=this,a=r(""),o=n.$list();i.each(this.elementViews,function(e){e.destroy(),n.removeElementView(e)}),a.append(n._createForwardElementView().$el),a.append(n._createReverseElementView().$el),o.empty().append(a.children()),i.invoke(n.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 n=new this.elementViewClass(i.extend(t,{element:e}));return this.elementViews.push(n),n},swap:function(){this.workingElements=[this.workingElements[1],this.workingElements[0]],this._renderList()},events:i.extend(i.clone(m.prototype.events),{"click .swap":"swap"}),templates:i.extend(i.clone(m.prototype.templates),{middle:i.template(['",''+this.progressive+"...
";this.modal.$(".modal-body").empty().append(e).css({"margin-top":"8px"})},dialog:function(t,n,a){function o(){var e=t.$("#copy-modal-title").val();if(!e)return void t.$(".invalid-title").show();var i="copy-all"===t.$('input[name="copy-what"]:checked').val();t.$("button").prop("disabled",!0),s._showAjaxIndicator(),n.copy(!0,e,i).done(function(e){l.resolve(e)}).fail(function(t,r,a){var o={name:e,copyAllDatasets:i};c.default.ajaxErrorModal(n,t,o,s.errorMessage),l.rejectWith(l,arguments)}).done(function(){g&&t.hide()})}a=a||{};var s=this,l=i.Deferred(),d=a.nameFn||this.defaultName,h=d({name:n.get("name")}),f=a.allDatasets?"copy-all":"copy-non-deleted",p=!!e.isUndefined(a.allowAll)||a.allowAll,g=!!e.isUndefined(a.autoClose)||a.autoClose;this.modal=t;var m=a.closing_callback;return t.show(e.extend(a,{title:this.title({name:n.get("name")}),body:r(s._template({name:h,isAnon:Galaxy.user.isAnonymous(),allowAll:p,copyWhat:f,activeLabel:this.activeLabel,allLabel:this.allLabel,anonWarning:this.anonWarning})),buttons:e.object([[(0,u.default)("Cancel"),function(){t.hide()}],[this.submitLabel,o]]),height:"auto",closing_events:!0,closing_callback:function(e){e&&l.reject({cancelled:!0}),m&&m(e)}})),t.$("#copy-modal-title").focus().select(),t.$("#copy-modal-title").on("keydown",function(e){13===e.keyCode&&(e.preventDefault(),o())}),l}},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 n=window.parent.Galaxy.modal||new s.default.View({});return t.useImport?f.dialog(n,e,t):h.dialog(n,e,t)};t.default=p}).call(t,n(1),n(0),n(0))},function(e,t,n){"use strict";(function(e){function i(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}Object.defineProperty(t,"__esModule",{value:!0});var r=n(1),a=i(r),o=n(2),s=i(o),l=n(4),c=function(e){return e&&e.__esModule?e:{default:e}}(l),d=s.Collection.extend({initialize:function(e,t){s.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),s.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 n=this._buildFetchFilters(e);return Galaxy.debug("filters:",n),a.isEmpty(n)||a.extend(e.data,this._fetchFiltersToAjaxData(n)),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,n){void 0!==e&&""!==e&&(!0===e&&(e="True"),!1===e&&(e="False"),null===e&&(e="None"),t.q.push(n),t.qv.push(e))}),t},reset:function(e,t){return this.allFetched=!1,s.Collection.prototype.reset.call(this,e,t)},order:null,comparators:{update_time:c.default.buildComparator("update_time",{ascending:!1}),"update_time-asc":c.default.buildComparator("update_time",{ascending:!0}),create_time:c.default.buildComparator("create_time",{ascending:!1}),"create_time-asc":c.default.buildComparator("create_time",{ascending:!0})},setOrder:function(e,t){t=t||{};var n=this,i=n.comparators[e];if(a.isUndefined(i))throw new Error("unknown order: "+e);if(i!==n.comparator)return n.order=e,n.comparator=i,t.silent||n.trigger("changed-order",t),n}}),u=d.extend({limitPerPage:500,initialize:function(e,t){d.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 n=this;return e=n.constrainPageNum(e),n.currentPage=e,t=a.defaults(t||{},n.getPageLimitOffset(e)),n.trigger("fetching-more"),n.fetch(t).always(function(){n.trigger("fetching-more-done")})},fetchCurrentPage:function(e){return this.fetchPage(this.currentPage,e)},fetchPrevPage:function(e){return this.fetchPage(this.currentPage-1,e)},fetchNextPage:function(e){return this.fetchPage(this.currentPage+1,e)}}),h=d.extend({limitOnFirstFetch:null,limitPerFetch:100,initialize:function(e,t){d.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,d.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 n=this;if(Galaxy.debug("fetchMore, options.reset:",t.reset),!t.reset&&n.allFetched)return e.when();t.reset?t.offset=0:void 0===t.offset&&(t.offset=n.lastFetched);var i=t.limit=t.limit||n.limitPerFetch||null;return Galaxy.debug("fetchMore, limit:",i,"offset:",t.offset),n.trigger("fetching-more"),n.fetch(t).always(function(){n.trigger("fetching-more-done")}).done(function(e){var t=a.isArray(e)?e.length:0;n.lastFetched+=t,Galaxy.debug("fetchMore, lastFetched:",n.lastFetched),(!i||t'):this.$list().find(".contents-loading-indicator").remove()},renderItems:function(e){e=e||this.$el;var t=this.$list(e);i(".tooltip").remove(),t.empty(),this.views=[];var n=this._filterCollection();return n.length?(this._renderPagination(e),this.views=this._renderSomeItems(n,t)):e.find("> .controls .list-pagination").empty(),this._renderEmptyMessage(e).toggle(!n.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 n=this,i=[];return t.append(e.map(function(e){var t=n._createItemView(e);return i.push(t),n._renderItemView$el(t)})),i},_filterItem:function(e){var t=this.model.contents;return(t.includeHidden||!e.hidden())&&(t.includeDeleted||!e.isDeletedOrPurged())&&C.prototype._filterItem.call(this,e)},_getItemViewClass:function(e){var t=e.get("history_content_type");switch(t){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+t)},_getItemViewOptions:function(t){var n=C.prototype._getItemViewOptions.call(this,t);return e.extend(n,{linkTarget:this.linkTarget,expanded:this.model.contents.storage.isExpanded(t.id),hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(e){var t=this;return C.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{expanded:function(e){t.model.contents.storage.addExpanded(e.model)},collapsed:function(e){t.model.contents.storage.removeExpanded(e.model)}})},collapseAll:function(){this.model.contents.storage.clearExpanded(),C.prototype.collapseAll.call(this)},getSelectedModels:function(){var e=C.prototype.getSelectedModels.call(this);return e.historyId=this.collection.historyId,e},events:e.extend(e.clone(C.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click > 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t=this;if(this.log("onFirstSearch",e),this.model.contents.haveSearchDetails())return void this.searchItems(e);this.$("> .controls .search-input").searchInput("toggle-loading"),this.searchFor=e;this.model.contents.progressivelyFetchDetails({silent:!0}).progress(function(e,n,i){t.renderItems(),t.trigger("search:loading-progress",n,i)}).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,n,i){if(!n||0!==n.status||0!==n.readyState){if(this.error(t,n,i),e.isString(t)&&e.isString(n)){var r=t,a=n;return v.default.errorModal(r,a,i)}return n&&502===n.status?v.default.badGatewayErrorModal():v.default.ajaxErrorModal(t,n,i)}},clearMessages:function(t){return(e.isUndefined(t)?this.$messages().children('[class$="message"]'):i(t.currentTarget)).fadeOut(this.fxSpeed,function(){i(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
'},n=x.default.wrapTemplate(['','
"],"history"),i=x.default.wrapTemplate(['','",''],"pages");return e.extend(e.clone(C.prototype.templates),{el:t,controls:n,pagination:i})}(),t.default={HistoryView:S}}).call(t,n(1),n(0))},function(e,t,n){"use strict";(function(e){function n(t){return 0==t.indexOf("name:")?''+e.escape(t.slice(5))+"":""}function i(t){return'"}Object.defineProperty(t,"__esModule",{value:!0}),t.default={nametagTemplate:i}}).call(t,n(1))},function(e,t,n){"use strict";(function(e){function i(e){return e&&e.__esModule?e:{default:e}}function r(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"),n="a "+r(e);if(t){var i;1==t?i="with 1 item":t&&(i="with "+t+" items"),n=n+" "+(0,f.default)(i)}return n}Object.defineProperty(t,"__esModule",{value:!0});var o=n(38),s=i(o),l=n(28),c=(i(l),n(32)),d=i(c),u=n(4),h=(i(u),n(3)),f=i(h),p=s.default.ModelListPanel,g=p.extend({_logNamespace:"collections",className:p.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:d.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 d.default.NestedDCDCEListItemView.extend({foldoutPanelClass:g})},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var n=this;this.handleWarning(e),n.log("_queueNewRender:",e,t),n._swapNewRender(e),n.trigger("rendered",n)},handleWarning:function(e){var t=this.views.length,n=this.model.get("element_count");if(n&&n!==t){var i=(0,f.default)("displaying only "+t+" of "+n+" 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 n=p.prototype._getItemViewOptions.call(this,t);return e.extend(n,{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"):"")+")"}});g.prototype.templates=function(){var t=function(t,n){var i=a(n.model);return'\n ','
",'','<%- history.name %>
',"<%- history.nice_size %>
','','",'','','','',"
",'','
",'',"','",'","
",'","\n \n
'};return e.extend(e.clone(p.prototype.templates),{controls:t})}(),t.default={collectionTypeDescription:r,collectionDescription:a,CollectionView:g}}).call(t,n(1))},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(8),o=r(a),s=n(17),l=r(s),c=n(21),d=r(c),u=n(61),h=r(u),f=n(10),p=r(f),g=n(4),m=r(g),_=n(3),v=r(_),y=l.default.DatasetListItemView,b=y.extend({initialize:function(e){y.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=y.prototype._renderPrimaryActions.call(this);return this.model.get("state")===o.default.NOT_VIEWABLE?e:y.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 n=this.model.get("purged"),i=this.model.get("deleted"),r={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 i||n?(r.disabled=!0,n?r.title=(0,v.default)("Cannot edit attributes of datasets removed from disk"):i&&(r.title=(0,v.default)("Undelete dataset to edit attributes"))):e.contains([o.default.UPLOAD,o.default.NEW],this.model.get("state"))&&(r.disabled=!0,r.title=(0,v.default)("This dataset is not yet editable")),(0,p.default)(r)},_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.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},_renderDetails:function(){var t=y.prototype._renderDetails.call(this),n=this.model.get("state");return!this.model.isDeletedOrPurged()&&e.contains([o.default.OK,o.default.FAILED_METADATA],n)&&(this._renderTags(t),this._renderAnnotation(t),this._makeDbkeyEditLink(t)),this._setUpBehaviors(t),t},_renderToolHelpButton:function(){var e=this.model.attributes.dataset_id,t=this.model.attributes.creating_job,n=this,r=function(t){var r='\n
\n '+(e.escape(t.name)||e.escape(t.element_identifier))+'
\n \n '+i+'\n
\n \n
\n \n \n \n \n \n
\n ';t.name&&t.help?(r+="Tool help for "+t.name+"
",r+=t.help):r+="Tool help is unavailable for this dataset.
",r+="
",n.$el.find(".details").append(i.parseHTML(r))},a=function(e){i.ajax({url:Galaxy.root+"api/tools/"+e.tool_id+"/build"}).done(function(e){r(e)}).fail(function(){r({})})};return null===Galaxy.user.id?null:(0,p.default)({title:(0,v.default)("Tool Help"),classes:"icon-btn",href:"#",faIcon:"fa-question",onclick:function(){n.$el.find(".toolhelp").length>0?n.$el.find(".toolhelp").toggle():i.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=y.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 n=i(this.templates.visualizations(t,this));return n.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(n.find(".visualization-link").addBack(".visualization-link")),n},_addScratchBookFn:function(e){e.click(function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:(0,v.default)("Visualization"),url:i(this).attr("href")}),e.preventDefault(),e.stopPropagation())})},_renderTags:function(e){if(this.hasUser){var t=this;this.tagsEditor=new d.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=i('?').attr("href",this.model.urls.edit).attr("target","_top");e.find(".dbkey .value").replaceWith(t)}},events:e.extend(e.clone(y.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)")+")"}});b.prototype.templates=function(){var t=e.extend({},y.prototype.templates.warnings,{failed_metadata:m.default.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','","<% } %>"],"dataset"),deleted:m.default.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'","<% } %>"],"dataset")}),n=m.default.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'",r+=t.help):r+="Tool help is unavailable for this dataset.
",r+="
','','',"",'","
","<% } %>"],"visualizations");return e.extend({},y.prototype.templates,{warnings:t,visualizations:n})}(),t.default={DatasetListItemEdit:b}}).call(t,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(4),o=r(a),s=n(3),l=r(s);n(15);var c=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.$annotation().text(e.model.previous("annotation"))})}}),this},_template:function(){var e=this.model.get("annotation");return['",'',i.escape(e),"
"].join("")},$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:c}}).call(t,n(2),n(1))},,,,,,,,,function(e,t,n){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var i=n(2),r=function(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}(i),a=n(31),o=function(e){return e&&e.__esModule?e:{default:e}}(a),s=["new","queued","running"],l=["error","deleted"],c=r.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(l)},states:function(){return this.get("states")||{}},anyWithState:function(e){return(this.states()[e]||0)>0},anyWithStates:function(e){var t=this.states();for(var n in e)if((t[e[n]]||0)>0)return!0;return!1},numWithStates:function(e){var t=this.states(),n=0;for(var i in e)n+=t[e[i]]||0;return n},numInError:function(){return this.numWithStates(l)},running:function(){return this.anyWithState("running")},terminal:function(){return!this.new()&&!this.anyWithStates(s)},jobCount:function(){var e=this.states(),t=0;for(var n in e)t+=e[n];return t},toString:function(){return"JobStatesSummary(id="+this.get("id")+")"}}),d=r.Collection.extend({model:c,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(","),n=e.map(function(e){return e.get("model")}).join(",");return Galaxy.root+"api/histories/"+this.historyId+"/jobs_summary?ids="+t+"&types="+n},monitor:function(){var e=this;if(this.clearUpdateTimeout(),this.active){var t=function(){e.updateTimeoutId=setTimeout(function(){e.monitor()},2e3)},n=this.models.filter(function(e){return!e.terminal()});if(n.length,!1){var i=n.map(function(e){return function(){return e.fetch()}});return new o.default.AjaxQueue(i).done(t)}n.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:c,JobStatesSummaryCollection:d,FETCH_STATE_ON_ADD:!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(57),s=a(o),l=n(16),c=(a(l),n(8)),d=(a(c),n(37)),u=a(d),h=n(72),f=a(h),p=n(94),g=a(p),m=n(21),_=a(m),v=n(61),y=a(v),b=n(35),w=a(b),x=n(97),k=a(x),M=n(98),C=a(M),S=n(10),T=a(S),E=n(47),j=(a(E),n(4)),A=a(j),L=n(3),N=a(L);n(15);var I=s.default.HistoryView,D=I.extend({HDAViewClass:f.default.HDAListItemEdit,HDCAViewClass:g.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.$("> .controls .deleted-count").html(""+(0,N.default)("loading...")+"")},"fetching-hidden":function(e){this.$("> .controls .hidden-count").html(""+(0,N.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 n=this.templates.counts(this.model.toJSON(),this);return t.find("> .controls .subtitle").html(n)},_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)},$activator:(0,T.default)({title:(0,N.default)("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".controls .actions"))})},_renderAnnotation:function(e){var t=this;this.annotationEditor=new y.default.AnnotationEditor({model:this.model,el:e.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDAAnnotationEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDAAnnotationEditors(!1,t.fxSpeed)},$activator:(0,T.default)({title:(0,N.default)("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".controls .actions"))})},_setUpBehaviors:function(e){if(e=e||this.$el,I.prototype._setUpBehaviors.call(this,e),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.model.get("user_id")){var t=this;e.find("> .controls .name").attr("title",(0,N.default)("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(e){var n=t.model.get("name");e&&e!==n?(t.$el.find("> .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(n)}})}},multiselectActions:function(){var e=this,t=[{html:(0,N.default)("Hide datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.hide;e.getSelectedModels().ajaxQueue(t)}},{html:(0,N.default)("Unhide datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.unhide;e.getSelectedModels().ajaxQueue(t)}},{html:(0,N.default)("Delete datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.delete;e.getSelectedModels().ajaxQueue(t)}},{html:(0,N.default)("Undelete datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.undelete;e.getSelectedModels().ajaxQueue(t)}}];return e.purgeAllowed&&t.push({html:(0,N.default)("Permanently delete datasets"),func:function(){if(confirm((0,N.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,N.default)("Build Dataset List"),func:function(){e.buildCollection("list")}},{html:(0,N.default)("Build Dataset Pair"),func:function(){e.buildCollection("paired")}},{html:(0,N.default)("Build List of Dataset Pairs"),func:function(){e.buildCollection("list:paired")}}]},buildCollection:function(e,t,n){var i,r=this,t=t||r.getSelectedModels(),n=n||!1;"list"==e?i=w.default.createListCollection:"paired"==e?i=k.default.createPairCollection:"list:paired"==e?i=C.default.createListOfPairsCollection:console.warn("Unknown collectionType encountered "+e),i(t,n).done(function(){r.model.refresh()})},_getItemViewOptions:function(e){var t=I.prototype._getItemViewOptions.call(this,e);return i.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){i.each(this.views,function(n){n.tagsEditor&&n.tagsEditor.toggle(e,t)})},toggleHDAAnnotationEditors:function(e,t){i.each(this.views,function(n){n.annotationEditor&&n.annotationEditor.toggle(e,t)})},events:i.extend(i.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 n=e+t;return this.$("> .controls .subtitle").html(["",(0,N.default)("Searching "),n,"/",this.model.contentsShown(),""].join(""))},_renderSearchFindings:function(t){t=t instanceof e?t:this.$el;var n=this.templates.found(this.model.toJSON(),this);return t.find("> .controls .subtitle").html(n),this},dropTargetOn:function(){if(this.dropTarget)return this;this.dropTarget=!0;var e={dragenter:i.bind(this.dragenter,this),dragover:i.bind(this.dragover,this),dragleave:i.bind(this.dragleave,this),drop:i.bind(this.drop,this)},t=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),t]);for(var n in e)e.hasOwnProperty(n)&&t.on(n,e[n]);return this},_renderDropTarget:function(){return this.$(".history-drop-target").remove(),r("").addClass("history-drop-target")},_renderDropTargetHelp:function(){return this.$(".history-drop-target-help").remove(),r("").addClass("history-drop-target-help").text((0,N.default)("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget)return this;this.dropTarget=!1;var e=this.$(".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,n=e.originalEvent.dataTransfer,i=n.getData("text");n.dropEffect="move";try{i=JSON.parse(i)}catch(e){t.warn("error parsing JSON from drop:",i)}return t.trigger("droptarget:drop",e,i,t),!1},dataDropped:function(t){var n=this;return i.isObject(t)&&"HistoryDatasetAssociation"===t.model_class&&t.id?0!==n.contents.currentPage?n.contents.fetchPage(0).then(function(){return n.model.contents.copy(t.id)}):n.model.contents.copy(t.id):e.when()},toString:function(){return"HistoryViewEdit("+(this.model?this.model.get("name"):"")+")"}});D.prototype.templates=function(){var e=A.default.wrapTemplate(["<% var shown = Math.max( view.views.length, history.contents_active.active ) %>","<% if( shown ){ %>",'',"<%- shown %> ",(0,N.default)("shown"),"","<% } %>","<% if( history.contents_active.deleted ){ %>",'',"<% if( view.model.contents.includeDeleted ){ %>",'',(0,N.default)("hide deleted"),"","<% } else { %>","<%- history.contents_active.deleted %> ",'',(0,N.default)("deleted"),"","<% } %>","","<% } %>","<% if( history.contents_active.hidden ){ %>",'',"<% if( view.model.contents.includeHidden ){ %>",'',(0,N.default)("hide hidden"),"","<% } else { %>","<%- history.contents_active.hidden %> ",'',(0,N.default)("hidden"),"","<% } 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",'",'<%= title %>
','',"| Workflows | ','Tool IDs | ','Shed | ','Name | ','Owner | ','Actions | ',"||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
','
| ",'','
| ",'<%= workflow.get("shed") %> | ','<%= workflow.get("repository") %> | ','<%= workflow.get("owner") %> | ','','
| ","").addClass("settings").appendTo(this.$el),r=i("").addClass("track-info").hide().appendTo(n);r.append(i("").css("font-weight","bold").text("Track Settings")),e.get("inputs").each(function(e){r.append(e.get("label")+": "+t[e.get("name")]+" | ").addClass("tile").html(i(" |
").addClass("tiles");i("#right").append(a.append(this.track_collection_container)),t.model.get("tracks").each(function(e){t.add_track(e)});var o=i(this.helpText).addClass("help"),l=M.default.create_icon_buttons_menu([{title:(0,s.default)("Close"),icon_class:"cross-circle",on_click:function(){i(".tooltip").remove(),o.remove()}}]);o.prepend(l.$el.css("float","right")),i("#center").append(o),this.tool_param_tree_view.render(),i("#center").append(this.tool_param_tree_view.$el),this.handle_node_clicks();var d=M.default.create_icon_buttons_menu([{icon_class:"chevron-expand",title:"Set display mode"},{icon_class:"cross-circle",title:(0,s.default)("Close"),on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tooltip_config:{placement:"bottom"}}),u=["Squish","Pack"],h={};c.each(u,function(e){h[e]=function(){t.model.set("default_mode",e),t.model.get("tracks").each(function(t){t.set("mode",e)})}}),make_popupmenu(d.$el.find(".chevron-expand"),h),d.$el.attr("style","float: right"),i("#right .unified-panel-header-inner").append(d.$el)},get_base_color:function(e){return this.config.get_value(e.toLowerCase()+"_color")||this.config.get_value("n_color")},run_tool_on_dataset:function(e){var t=this.model.get("tool"),n=t.get("name"),r=this.model.get("dataset");t.set_input_values(e.get("values")),i.when(t.rerun(r)).then(function(e){}),show_modal("Running "+n+" on complete dataset",n+" is running on dataset '"+r.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(e){var t=this,n=this.model.get("parameter_tree");t.model.add_track(e);var i=new A({model:e,canvas_manager:t.canvas_manager});return i.on("run_on_dataset",t.run_tool_on_dataset,t),t.track_collection_container.append(i.$el),i.$el.hover(function(){var i=n.get_leaf(e.get("settings").get("values")),r=c.pluck(n.get_connected_nodes(i),"id");u.select(t.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(e){return void 0!==c.find(r,function(t){return t===e.id})}).style("fill","#f00")},function(){u.select(t.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")}),e},handle_node_clicks:function(){var e=this,t=this.model.get("parameter_tree"),n=this.model.get("regions");u.select(this.tool_param_tree_view.$el[0]).selectAll("g.node").on("click",function(r,a){var o=e.model.get("tool"),s=e.model.get("dataset"),l=t.get_node_settings(r),d=i.Deferred();l.length>=10?show_modal("Whoa there cowboy!","You clicked on a node to try "+e.model.get("tool").get("name")+" with "+l.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal(),d.resolve(!1)}}):d.resolve(!0),i.when(d).then(function(t){if(t){var r=c.map(l,function(t){var i=new T({settings:t,regions:n,mode:e.model.get("default_mode")});return e.add_track(i),i});c.each(r,function(t,r){setTimeout(function(){o.set_input_values(t.get("settings").get("values")),i.when(o.rerun(s,n)).then(function(n){var i=n.first(),r=i.get("track_config");r.dataset=i,r.tool=null,r.prefs=e.config.to_key_value_dict();var a=m.default.object_from_template(r,e,null);a.init_for_tool_data(),t.set("track",a)})},1e4*r)})}})})}});t.default={SweepsterVisualization:j,SweepsterVisualizationView:D}}).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}}Object.defineProperty(t,"__esModule",{value:!0});var a=n(5),o=(r(a),n(7)),s=r(o),l=n(4),c=r(l),d=n(18),u=(r(d),n(317)),h=r(u),f=n(319),p=r(f),g=n(321),m=r(g),_=n(322),v=r(_),y=n(138),b=r(y),w=n(323),x=r(w),k=n(324),M=r(k),C=e.Router.extend({initialize:function(){this.routesHit=0,e.history.on("route",function(){this.routesHit++},this),this.bind("route",this.trackPageview)},routes:{"":"libraries","page/:show_page":"libraries_page","library/:library_id/permissions":"library_permissions","folders/:folder_id/permissions":"folder_permissions","folders/:id":"folder_content","folders/:id/page/:show_page":"folder_page","folders/:folder_id/datasets/:dataset_id":"dataset_detail","folders/:folder_id/datasets/:dataset_id/permissions":"dataset_permissions","folders/:folder_id/datasets/:dataset_id/versions/:ldda_id":"dataset_version","folders/:folder_id/download/:format":"download","folders/:folder_id/import/:source":"import_datasets"},back:function(){this.routesHit>1?window.history.back():this.navigate("#",{trigger:!0,replace:!0})},trackPageview:function(){var t=e.history.getFragment();/^\//.test(t)||""==t||(t="/"+t),"undefined"!=typeof ga&&ga("send","pageview",Galaxy.root+"library/list"+t)}}),S=c.default.SessionStorageModel.extend({defaults:{with_deleted:!1,without_restricted:!1,sort_order:"asc",sort_by:"name",library_page_size:20,folder_page_size:15}}),T=e.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,libraryView:null,folderToolbarView:null,folderListView:null,datasetView:null,initialize:function(){window.Galaxy.config.ga_code&&(!function(e,t,n,i,r,a,o){e.GoogleAnalyticsObject=r,e[r]=e[r]||function(){(e[r].q=e[r].q||[]).push(arguments)},e[r].l=1*new Date,a=t.createElement(n),o=t.getElementsByTagName(n)[0],a.async=1,a.src="//www.google-analytics.com/analytics.js",o.parentNode.insertBefore(a,o)}(window,document,"script",0,"ga"),ga("create",window.Galaxy.config.ga_code,"auto"),ga("send","pageview")),Galaxy.libraries=this,this.preferences=new S({id:"global-lib-prefs"}),this.library_router=new C,this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView&&Galaxy.libraries.libraryToolbarView.$el.unbind("click"),Galaxy.libraries.libraryToolbarView=new m.default.LibraryToolbarView,Galaxy.libraries.libraryListView=new p.default.LibraryListView}),this.library_router.on("route:libraries_page",function(e){null===Galaxy.libraries.libraryToolbarView?(Galaxy.libraries.libraryToolbarView=new m.default.LibraryToolbarView,Galaxy.libraries.libraryListView=new p.default.LibraryListView({show_page:e})):Galaxy.libraries.libraryListView.render({show_page:e})}),this.library_router.on("route:folder_content",function(e){Galaxy.libraries.folderToolbarView&&Galaxy.libraries.folderToolbarView.$el.unbind("click"),Galaxy.libraries.folderToolbarView=new v.default.FolderToolbarView({id:e}),Galaxy.libraries.folderListView=new h.default.FolderListView({id:e})}),this.library_router.on("route:folder_page",function(e,t){null===Galaxy.libraries.folderToolbarView?(Galaxy.libraries.folderToolbarView=new v.default.FolderToolbarView({id:e}),Galaxy.libraries.folderListView=new h.default.FolderListView({id:e,show_page:t})):Galaxy.libraries.folderListView.render({id:e,show_page:parseInt(t)})}),this.library_router.on("route:download",function(e,t){0===i("#folder_list_body").find(":checked").length?(s.default.info("You must select at least one dataset to download"),Galaxy.libraries.library_router.navigate("folders/"+e,{trigger:!0,replace:!0})):(Galaxy.libraries.folderToolbarView.download(e,t),Galaxy.libraries.library_router.navigate("folders/"+e,{trigger:!1,replace:!0}))}),this.library_router.on("route:dataset_detail",function(e,t){Galaxy.libraries.datasetView&&Galaxy.libraries.datasetView.$el.unbind("click"),Galaxy.libraries.datasetView=new b.default.LibraryDatasetView({id:t,show_version:!1,show_permissions:!1})}),this.library_router.on("route:dataset_version",function(e,t,n){Galaxy.libraries.datasetView&&Galaxy.libraries.datasetView.$el.unbind("click"),Galaxy.libraries.datasetView=new b.default.LibraryDatasetView({id:t,ldda_id:n,show_version:!0})}),this.library_router.on("route:dataset_permissions",function(e,t){Galaxy.libraries.datasetView&&Galaxy.libraries.datasetView.$el.unbind("click"),Galaxy.libraries.datasetView=new b.default.LibraryDatasetView({id:t,show_permissions:!0})}),this.library_router.on("route:library_permissions",function(e){Galaxy.libraries.libraryView&&Galaxy.libraries.libraryView.$el.unbind("click"),Galaxy.libraries.libraryView=new x.default.LibraryView({id:e,show_permissions:!0})}),this.library_router.on("route:folder_permissions",function(e){Galaxy.libraries.folderView&&Galaxy.libraries.folderView.$el.unbind("click"),Galaxy.libraries.folderView=new M.default.FolderView({id:e,show_permissions:!0})}),this.library_router.on("route:import_datasets",function(e,t){Galaxy.libraries.folderToolbarView&&Galaxy.libraries.folderListView?Galaxy.libraries.folderToolbarView.showImportModal({source:t}):(Galaxy.libraries.folderToolbarView=new v.default.FolderToolbarView({id:e}),Galaxy.libraries.folderListView=new h.default.FolderListView({id:e}),Galaxy.libraries.folderToolbarView.showImportModal({source:t}))}),e.history.start({pushState:!1})}});t.default={GalaxyApp:T}}).call(t,n(2),n(0))},function(e,t,n){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var i=function(e,t){return function(n,i){return n.get("type")===i.get("type")?n.has(e)||i.has(e)?n.has(e)?i.has(e)?n.get(e).toLowerCase()>i.get(e).toLowerCase()?"asc"===t?1:-1:i.get(e).toLowerCase()>n.get(e).toLowerCase()?"asc"===t?-1:1:0:-1:1:0:"folder"===n.get("type")?-1:1}},r=function(e,t){return function(n,i){return 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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. 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",'"].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 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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. 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| synopsis | ",'<%- library.get("synopsis") %> | ',"
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','
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','',"| 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","
",{Insert:function(){var t=e(s._options.rowsSelector).val(),n=e(s._options.colsSelector).val();if(t>0&&n>0){var i=s._doc.createElement(u.TABLE),r=null,a=e(s._options.captionSelector).val();i.createCaption().innerHTML=a;for(var o=0;o
",logoHtml:"WYMeditor",iframeHtml:"",editorStyles:[],toolsHtml:""+WYMeditor.TOOLS+"
"+WYMeditor.CONTAINERS+WYMeditor.CLASSES+"
"+WYMeditor.HTML+WYMeditor.IFRAME+WYMeditor.STATUS+"
"+WYMeditor.LOGO+"
{Tools}
- "+WYMeditor.TOOLS_ITEMS+"
{Containers}
- "+WYMeditor.CONTAINERS_ITEMS+"
{Classes}
- "+WYMeditor.CLASSES_ITEMS+"