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','
",'",'<%= title %>
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|---|---|---|---|---|
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','',"| Workflows | ','Tool IDs | ','Shed | ','Name | ','Owner | ','Actions | ',"||||||
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| ",'','
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+>>>>>>> 854854cdf6... Rebuild client.
diff --git a/static/scripts/bundled/analysis.bundled.js b/static/scripts/bundled/analysis.bundled.js
index 5c227d32ac2..12f8e7e26c5 100644
--- a/static/scripts/bundled/analysis.bundled.js
+++ b/static/scripts/bundled/analysis.bundled.js
@@ -1,3 +1,3 @@
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l=i(5),r=o(l),d=i(3),c=(o(d),e.View.extend(r.default.LoggableMixin).extend({_logNamespace:"list",initialize:function(e){this.expanded=e.expanded||!1,this.log("\t expanded:",this.expanded),this.fxSpeed=void 0!==e.fxSpeed?e.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(e){var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){var e=n(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(e).replaceWith(this._renderDetails().show()),e},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;0===t?(i._swapNewRender(e),i.trigger("rendered",i)):n(i).queue("fx",[function(e){i.$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",s.isFunction(this.className)?this.className():this.className).append(e.children())},_setUpBehaviors:function(e){e=e||this.$el,e.find("[title]").tooltip({placement:"bottom"})},$details:function(e){return e=e||this.$el,e.find("> .details")},_renderDetails:function(){var e=n(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(e),e},toggleExpanded:function(e){return e=void 0===e?!this.expanded:e,e?this.expand():this.collapse(),this},expand:function(){var e=this;return e._fetchModelDetails().always(function(){e._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?a.when():this.model.fetch()},_expand:function(){var e=this,t=e._renderDetails();e.$details().replaceWith(t),e.expanded=!0,e.$details().slideDown(e.fxSpeed,function(){e.trigger("expanded",e)})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var e=this;e.expanded=!1,this.$details().slideUp(e.fxSpeed,function(){e.trigger("collapsed",e)})}})),u=c.extend(r.default.mixin(r.default.SelectableViewMixin,r.default.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){c.prototype.initialize.call(this,e),r.default.SelectableViewMixin.initialize.call(this,e),r.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=c.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 c.prototype._swapNewRender.call(this,e),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var e=this,t=n(''),i=e.model.toJSON();return s.each(e.templates.warnings,function(s){t.append(n(s(i,e)))}),t},_renderTitleBar:function(){return n(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return n(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(e){e.stopPropagation(),e.altKey?(this.toggleSelect(e),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(e){return!e||"keydown"!==e.type||32!==e.keyCode&&13!==e.keyCode||(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){return"ListItemView("+(this.model?""+this.model:"(no model)")+")"}}));u.prototype.templates=function(){return{el:r.default.wrapTemplate(['','","
","','','
"]),warnings:{},titleBar:r.default.wrapTemplate(['"],"element"),subtitle:r.default.wrapTemplate(['']),details:r.default.wrapTemplate([''])}}();var h=u.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(e){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=e.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=e.foldoutPanelClass||this.foldoutPanelClass,u.prototype.initialize.call(this,e),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return n();var e=u.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,e)},_createFoldoutPanel:function(){var e=this.model,t=this._getFoldoutPanelClass(e),i=this._getFoldoutPanelOptions(e);return new t(s.extend(i,{model:e}))},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(e,t){return t=t||this.$("> .details"),this.foldout=e.render(0),e.$("> .controls").hide(),t.append(e.$el)},expand:function(){var e=this;return e._fetchModelDetails().always(function(){"foldout"===e.foldoutStyle?e._expand():"drilldown"===e.foldoutStyle&&e._expandByDrilldown()})},_expandByDrilldown:function(){var e=this;e.listenTo(e.foldout,"close",function(){e.trigger("collapsed:drilldown",e,e.foldout)}),e.trigger("expanded:drilldown",e,e.foldout)}});h.prototype.templates=function(){var e=r.default.wrapTemplate(['','',"
",'','','',"',"
"],"collection");return s.extend({},u.prototype.templates,{details:e})}(),t.default={ExpandableView:c,ListItemView:u,FoldoutListItemView:h}}).call(t,i(2),i(0),i(1),i(0))},function(e,t,i){"use strict";(function(e,n,s,a){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var l=i(65),r=o(l),d=i(16),c=o(d),u=i(21),h=o(u),f=i(5),p=o(f),m=i(3),g=o(m),_=r.default.ListItemView,v=_.extend({_logNamespace:"dataset",className:_.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log(this+".initialize:",e),_.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_setUpListeners:function(){_.prototype._setUpListeners.call(this);var t=this;return t.listenTo(t.model,{change:function(i){t.model.changedAttributes().state&&t.model.inReadyState()&&t.expanded&&!t.model.hasDetails()?t.model.fetch({silent:!0}).done(function(){t.render()}):e.has(i.changed,"tags")&&1===e.keys(i.changed).length?t.$(".nametags").html(t._renderNametags()):t.render()}})},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):n.when()},remove:function(e,t){var i=this;e=e||this.fxSpeed,this.$el.fadeOut(e,function(){s.View.prototype.remove.call(i),t&&t.call(i)})},_swapNewRender:function(e){return _.prototype._swapNewRender.call(this,e),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var e=this.model.get("state");if(e===c.default.NOT_VIEWABLE||e===c.default.DISCARDED||!this.model.get("accessible"))return null;var t={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))t.disabled=!0,t.title=(0,g.default)("Cannot display datasets removed from disk");else if(e===c.default.UPLOAD)t.disabled=!0,t.title=(0,g.default)("This dataset must finish uploading before it can be viewed");else if(e===c.default.NEW)t.disabled=!0,t.title=(0,g.default)("This dataset is not yet viewable");else{t.title=(0,g.default)("View data"),t.href=this.model.urls.display;var i=this;t.onclick=function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.addDataset(i.model.get("id")),e.preventDefault())}}return t.faIcon="fa-eye",(0,h.default)(t)},_renderDetails:function(){if(this.model.get("state")===c.default.NOT_VIEWABLE)return a(this.templates.noAccess(this.model.toJSON(),this));var e=_.prototype._renderDetails.call(this);return e.find(".actions .left").empty().append(this._renderSecondaryActions()),e.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),e.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(e),e},_renderSummary:function(){var e=this.model.toJSON(),t=this.templates.summaries[e.state];return(t=t||this.templates.summaries.unknown)(e,this)},_renderDetailMessages:function(){var t=this,i=a(''),n=t.model.toJSON();return e.each(t.templates.detailMessages,function(e){i.append(a(e(n,t)))}),i},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case c.default.NOT_VIEWABLE:return[];case c.default.OK:case c.default.FAILED_METADATA:case c.default.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return(0,h.default)({title:(0,g.default)("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle",onclick:function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:(0,g.default)("Dataset details"),url:this.href}),e.preventDefault(),e.stopPropagation())}})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:e.isEmpty(this.model.get("meta_files"))?a(['','',""].join("")):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var t=this.model.urls;return a(['"].join("\n"))},_renderNametags:function(){return e.template(["<% _.each(_.sortBy(_.uniq(tags), function(x) { return x }), function(tag){ %>",'<% if (tag.indexOf("name:") == 0){ %>','<%- tag.slice(5) %>',"<% } %>","<% }); %>"].join(""))({tags:this.model.get("tags")})},events:e.extend(e.clone(_.prototype.events),{"click .display-btn":function(e){this.trigger("display",this,e)},"click .params-btn":function(e){this.trigger("params",this,e)},"click .download-btn":function(e){this.trigger("download",this,e)}}),toString:function(){return"DatasetListItemView("+(this.model?""+this.model:"(no model)")+")"}});v.prototype.templates=function(){var t=e.extend({},_.prototype.templates.warnings,{failed_metadata:p.default.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','","<% } %>"]),error:p.default.wrapTemplate(["<% if( model.error ){ %>",'","<% } %>"]),purged:p.default.wrapTemplate(["<% if( model.purged ){ %>",'","<% } %>"]),deleted:p.default.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'","<% } %>"])}),i=p.default.wrapTemplate(['','','
"],"dataset"),n=p.default.wrapTemplate(['','','',"
","<% if( !dataset.deleted && !dataset.purged ){ %>",'','','',"<% if( dataset.peek ){ %>",'<%= dataset.peek %>',"<% } %>","<% } %>","
','
"],"dataset"),s={};s[c.default.OK]=s[c.default.FAILED_METADATA]=p.default.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'',(0,g.default)("You do not have permission to view this dataset"),"
","','<%- dataset.misc_blurb %>',"
","<% } %>","<% if( dataset.file_ext ){ %>",'','",'<%- dataset.file_ext %>',"
","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'','",'',"<%- dataset.metadata_dbkey %>","","
","<% } %>","<% if( dataset.misc_info ){ %>",'','<%- dataset.misc_info %>',"
","<% } %>"],"dataset"),s[c.default.NEW]=p.default.wrapTemplate(["",(0,g.default)("This is a new dataset and not all of its data are available yet"),"
"],"dataset"),s[c.default.NOT_VIEWABLE]=p.default.wrapTemplate(["",(0,g.default)("You do not have permission to view this dataset"),"
"],"dataset"),s[c.default.DISCARDED]=p.default.wrapTemplate(["",(0,g.default)("The job creating this dataset was cancelled before completion"),"
"],"dataset"),s[c.default.QUEUED]=p.default.wrapTemplate(["",(0,g.default)("This job is waiting to run"),"
"],"dataset"),s[c.default.RUNNING]=p.default.wrapTemplate(["",(0,g.default)("This job is currently running"),"
"],"dataset"),s[c.default.UPLOAD]=p.default.wrapTemplate(["",(0,g.default)("This dataset is currently uploading"),"
"],"dataset"),s[c.default.SETTING_METADATA]=p.default.wrapTemplate(["",(0,g.default)("Metadata is being auto-detected"),"
"],"dataset"),s[c.default.PAUSED]=p.default.wrapTemplate(["",(0,g.default)('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"
"],"dataset"),s[c.default.ERROR]=p.default.wrapTemplate(["<% if( !dataset.purged ){ %>","<%- dataset.misc_blurb %>
","<% } %>",'',(0,g.default)("An error occurred with this dataset"),":",'<%- dataset.misc_info %>
'],"dataset"),s[c.default.EMPTY]=p.default.wrapTemplate(["",(0,g.default)("No data"),": <%- dataset.misc_blurb %>
"],"dataset"),s.unknown=p.default.wrapTemplate(['Error: unknown dataset state: "<%- dataset.state %>"
'],"dataset");var a={resubmitted:p.default.wrapTemplate(["<% if( model.resubmitted ){ %>",'","<% } %>"])},o=p.default.wrapTemplate(["<% _.each( apps, function( app ){ %>",'','<%- app.label %> ','',"<% _.each( app.links, function( link ){ %>",'',"<% print( _l( link.text ) ); %>"," ","<% }); %>","","
","<% }); %>"],"apps");return e.extend({},_.prototype.templates,{warnings:t,details:i,noAccess:n,summaries:s,detailMessages:a,displayApplications:o})}(),t.default={DatasetListItemView:v}}).call(t,i(1),i(0),i(2),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(65),l=a(o),r=i(66),d=a(r),c=i(5),u=a(c),h=i(3),f=a(h),p=l.default.FoldoutListItemView,m=l.default.ListItemView,g=p.extend({className:p.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},initialize:function(e){this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,p.prototype.initialize.call(this,e)},_setUpListeners:function(){p.prototype._setUpListeners.call(this),this.listenTo(this.model,"change",function(t,i){e.has(t.changed,"deleted")?this.render():e.has(t.changed,"element_count")&&this.$("> .title-bar .subtitle").replaceWith(this._renderSubtitle())})},_renderSubtitle:function(){return n(this.templates.subtitle(this.model.toJSON(),this))},_getFoldoutPanelOptions:function(){var t=p.prototype._getFoldoutPanelOptions.call(this);return e.extend(t,{linkTarget:this.linkTarget,hasUser:this.hasUser})},$selector:function(){return this.$("> .selector")},toString:function(){return"DCListItemView("+(this.model?""+this.model:"(no model)")+")"}});g.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 ){ %>",'","<% } %>"])}),i=u.default.wrapTemplate(['"],"collection"),n=u.default.wrapTemplate(['','<% 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:i,subtitle:n})}();var _=m.extend({className:m.prototype.className+" dataset-collection-element",initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log("DCEListItemView.initialize:",e),m.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({},m.prototype.templates,{titleBar:t})}();var v=d.default.DatasetListItemView.extend({className:d.default.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log("DatasetDCEListItemView.initialize:",e),d.default.DatasetListItemView.prototype.initialize.call(this,e)},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):s.when()},toString:function(){return"DatasetDCEListItemView("+(this.model?""+this.model:"(no model)")+")"}});v.prototype.templates=function(){var t=u.default.wrapTemplate(['"],"element");return e.extend({},d.default.DatasetListItemView.prototype.templates,{titleBar:t})}();var y=g.extend({className:g.prototype.className+" dataset-collection-element",_swapNewRender:function(e){g.prototype._swapNewRender.call(this,e);var t=this.model.get("state")||"ok";return this.$el.addClass("state-"+t),this.$el},toString:function(){return"NestedDCDCEListItemView("+(this.model?""+this.model:"(no model)")+")"}});t.default={DCListItemView:g,DCEListItemView:_,DatasetDCEListItemView:v,NestedDCDCEListItemView:y}}).call(t,i(1),i(0),i(0))},function(e,t,i){"use strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(11),o=s(a),l=i(6),r=s(l),d=e.View.extend({initialize:function(t){this.model=new e.Model(t),this.url=this.model.get("url"),this.redirect=this.model.get("redirect"),this.setElement(""),this.render()},render:function(){var e=this;n.ajax({url:Galaxy.root+this.url,type:"GET"}).done(function(t){var i=n.extend({},e.model.attributes,t),s=new o.default({title:i.title,message:i.message,status:i.status||"warning",icon:i.icon,initial_errors:!0,errors:i.errors,inputs:i.inputs,buttons:{submit:new r.default.Button({tooltip:i.submit_tooltip,title:i.submit_title||"Save",icon:i.submit_icon||"fa-save",cls:"btn btn-primary ui-clear-float",onclick:function(){e._submit(s)}})}});e.$el.empty().append(s.$el)}).fail(function(t){e.$el.empty().append(new r.default.Message({message:"Failed to load resource "+e.url+".",status:"danger",persistent:!0}).$el)})},_submit:function(e){var t=this;n.ajax({url:Galaxy.root+t.url,data:JSON.stringify(e.data.create()),type:"PUT",contentType:"application/json"}).done(function(i){var s={};i.id?s.id=i.id:s={message:i.message,status:"success",persistent:!1},t.redirect?window.location=Galaxy.root+t.redirect+"?"+n.param(s):(e.data.matchModel(i,function(t,i){e.field_list[i].value(t.value)}),t._showMessage(e,success_message))}).fail(function(i){t._showMessage(e,{message:i.responseJSON.err_msg,status:"danger",persistent:!1})})},_showMessage:function(e,t){e.$el.parents().filter(function(){return-1!=["auto","scroll"].indexOf(n(this).css("overflow"))}).first().animate({scrollTop:0},500),e.message.update(t)}});t.default={View:d}}).call(t,i(2),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(16),l=a(o),r=i(5),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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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(16),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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",'","\n Creating jobs...\n ';if(s.errored()){return"a "+i+" with "+s.numInError()+" / "+o+" jobs in error"}if(s.terminal())return n;var l=s.states().running||0,r=s.states().ok||0,c=r/(1*o),u=l/(1*o),h=1-c-u;return'\n " 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:n}}).call(t,i(1),i(0),i(2))},305:function(e,t,i){"use strict";(function(e,s,a){function r(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(42),n=r(o),l=i(156),d=r(l),c=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=s.defaults(this.options||{},e,this.defaults),this.render()},render:function(){var e=this.templateToolBar(),t=!1,i=!0;Galaxy.user&&(t=Galaxy.user.isAdmin(),i=Galaxy.user.isAnonymous()),this.$el.html(e({admin_user:t,anon_user:i})),t&&(this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted"),this.$el.find("#exclude_restricted_chk")[0].checked=Galaxy.libraries.preferences.get("without_restricted"))},renderPaginator:function(e){this.options=s.extend(this.options,e);var t=this.templatePaginator();this.$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:"Create New 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t=a(".library-search-input").val();this.options.search_term=t,Galaxy.libraries.libraryListView.searchLibraries(t)},templateToolBar:function(){return s.template(['t.id?1:e.id=0;h--){var _=l[h].trim();0!==_.length&&d.push(_)}this.initChainCallControl({length:d.length,action:"adding_datasets"}),this.chainCallImportingFolders({paths:d,preserve_dirs:e,link_data:t,space_to_tab:i,to_posix_lines:s,source:"admin_path",file_type:o,tag_using_filenames:r,dbkey:n})}else c.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.$el.find(".modal-body").html(t({history_name:e.history_name}));break;default:Galaxy.emit.error("Wrong action specified.","datalibs")}this.progress=0,this.progressStep=100/e.length,this.options.chain_call_control.total_number=e.length,this.options.chain_call_control.failed_number=0},importFromJstreePath:function(e,t){var i=a("#jstree_browser").jstree().get_selected(!0),r=s.filter(i,function(e){return 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e=this.modal.$el.find("#selected_history_content").find(":checked"),t=[],i=[],s=[];if(e.length<1)c.default.info("You must select some datasets first.");else{this.modal.disableButton("Add"),e.each(function(){var e=a(this).closest("li").data("id");if(e){var s=a(this).closest("li").data("name");t.push(e),i.push(s)}});for(var r=t.length-1;r>=0;r--){var o=t[r],n=new _.default.Item;n.url=Galaxy.root+"api/folders/"+this.options.id+"/contents","collection"===i[r]?n.set({from_hdca_id:o}):n.set({from_hda_id:o}),s.push(n)}this.initChainCallControl({length:s.length,action:"adding_datasets"}),this.chainCallAddingHdas(s)}},chainCallImportingIntoHistory:function(e,t){var i=this,s=e.pop();if(void 0===s)return 0===this.options.chain_call_control.failed_number?c.default.success("Selected datasets imported into history. 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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. "),_template:e.template(["<% if( isAnon ){ %>",'","<% } %>",""].join("")),_showAjaxIndicator:function(){var e='1?this.renderItems():1===i.added.length?this.addItemView(n.first(i.added),e,t):1===i.removed.length?this.removeItemView(n.first(i.removed),e,t):void 0}}),this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners"),this.on({"view:selected":function(e,t){if(t&&t.shiftKey&&this.lastSelected){var i=this.viewFromModelId(this.lastSelected);i&&this.selectRange(e,i)}else t&&t.altKey&&!this.selecting&&this.showSelectors();this.selected.push(e.model.id),this.lastSelected=e.model.id},"view:de-selected":function(e,t){this.selected=n.without(this.selected,e.model.id)}})},render:function(e){this.log(this+".render",e);var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var e=s(this.templates.el({},this));return this._renderControls(e),this._renderTitle(e),this._renderSubtitle(e),this._renderSearch(e),this.renderItems(e),e},_renderControls:function(e){this.debug(this+"(ListPanel)._renderControls");var t=s(this.templates.controls({},this));return e.find(".controls").replaceWith(t),t},_renderTitle:function(e){},_renderSubtitle:function(e){},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;i.log("_queueNewRender:",e,t),s(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",this.className).append(e.children()),this.selecting&&this.showSelectors(0),this},_setUpBehaviors:function(e){return e=e||this.$el,this.$controls(e).find("[title]").tooltip(),this._renderMultiselectActionMenu(e),this},_renderMultiselectActionMenu:function(e){e=e||this.$el;var t=e.find(".list-action-menu"),i=this.multiselectActions();if(!i.length)return t.empty();var n=s(['"].join("")),a=i.map(function(e){var t=['',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(["',"",'
",'"].join(""))}});t.default={FolderListView:_}}).call(t,i(1),i(2),i(0))},302:function(e,t,i){"use strict";(function(e,s,a){function r(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(42),n=r(o),l=i(156),d=r(l),c=i(225),h=r(c),_=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=s.defaults(e||{},this.defaults),this.render(this.options)},render:function(e){this.options=s.extend(this.options,e);var t=this.options.model,i=null;return"folder"===t.get("type")||"LibraryFolder"===t.get("model_class")?(this.options.type="folder",this.prepareButtons(t),i=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",i=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(i({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 h.default.LibraryDatasetView({id:this.id})},undeleteDataset:function(e){a(".tooltip").hide();var t=this,i=a(e.target).closest("tr").data("id"),s=Galaxy.libraries.folderListView.collection.get(i);s.url=s.urlRoot+s.id+"?undelete=true",s.destroy({success:function(e,s){Galaxy.libraries.folderListView.collection.remove(i);var a=new d.default.Item(s);Galaxy.libraries.folderListView.collection.add(a),Galaxy.libraries.folderListView.collection.sortFolder("name","asc"),n.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?n.default.error("Dataset was not undeleted. "+t.responseJSON.err_msg):n.default.error("An error occured! Dataset was not undeleted. Please try again.")}})},undeleteFolder:function(e){a(".tooltip").hide();var t=a(e.target).closest("tr").data("id"),i=Galaxy.libraries.folderListView.collection.get(t);i.url=i.urlRoot+i.id+"?undelete=true",i.destroy({success:function(e,i){Galaxy.libraries.folderListView.collection.remove(t);var s=new d.default.FolderAsModel(i);Galaxy.libraries.folderListView.collection.add(s),Galaxy.libraries.folderListView.collection.sortFolder("name","asc"),n.default.success("Folder undeleted.")},error:function(e,t){void 0!==t.responseJSON?n.default.error("Folder was not undeleted. "+t.responseJSON.err_msg):n.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,i=this.$el.find(".input_folder_name").val();if(void 0!==i&&i!==e.get("name")){if(!(i.length>2))return void n.default.warning("Folder name has to be at least 3 characters long.");e.set("name",i),t=!0}var s=this.$el.find(".input_folder_description").val();if(void 0!==s&&s!==e.get("description")&&(e.set("description",s),t=!0),t){var a=this;e.save(null,{patch:!0,success:function(e){a.options.edit_mode=!1,a.repaint(e),n.default.success("Changes to folder saved.")},error:function(e,t){void 0!==t.responseJSON?n.default.error(t.responseJSON.err_msg):n.default.error("An error occured while attempting to update the folder.")}})}else this.options.edit_mode=!1,this.repaint(e),n.default.info("Nothing has changed.")},repaint:function(){a(".tooltip").hide();var e=this.$el;this.render(),e.replaceWith(this.$el),this.$el.find("[data-toggle]").tooltip()},templateRowFolder:function(){return s.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 s.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 s.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 s.template(['',"",''," ","','<%- content_item.get("name") %>'," ","",'<%- content_item.get("description") %>'," ","","folder"," ","",'<%= _.escape(content_item.get("update_time")) %>'," ","",'','"," "," "].join(""))}});t.default={FolderRowView:_}}).call(t,i(1),i(2),i(0))},303:function(e,t,i){"use strict";(function(e,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var r=i(42),o=a(r),n=i(156),l=a(n),d=i(304),c=a(d),h=i(2),_=a(h),p=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=_.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=_.default.extend(this.options,e),this.setElement("#libraries_element");var t=this.templateLibraryList(),i=null,a=null,r=function(e){return!0===e.get("public")};if(s(".tooltip").hide(),void 0!==e&&(a=void 0!==e.models?e.models:null),null!==this.collection&&null===a)this.sortLibraries(),i=Galaxy.libraries.preferences.get("with_deleted")?this.collection.models:this.collection.where({deleted:!1}),Galaxy.libraries.preferences.get("without_restricted")&&(i=_.default.filter(i,r));else if(null!==a){if(Galaxy.libraries.preferences.get("with_deleted"))i=a;else{var o=function(e){return!1===e.get("deleted")};i=_.default.filter(a,o)}Galaxy.libraries.preferences.get("without_restricted")&&(i=_.default.filter(i,r))}else i=[];(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.options.total_libraries_count=i.length;var n=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&&nthis.options.total_libraries_count+Galaxy.libraries.preferences.get("library_page_size")&&(i=[]),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(i)):(this.$el.html(t({length:0,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options)),s("#center [data-toggle]").tooltip(),s("#center").css("overflow","auto")},fetchDeleted:function(){if(this.options.all_fetched)this.render();else{var e=this;this.collection.url=this.collection.urlRoot+"?deleted=true",this.collection.fetch({remove:!1,success:function(){e.options.all_fetched=!0,e.render()},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occurred.")}})}},renderRows:function(e){for(var t=0;t',"<% if(length === 0) { %>","<% if(search_term.length > 0) { %>","',"",'
","<% }%>","
"].join(""))}});t.default={LibraryListView:p}}).call(t,i(1),i(0))},304:function(e,t,i){"use strict";(function(e,s,a){Object.defineProperty(t,"__esModule",{value:!0});var r=i(42),o=function(e){return e&&e.__esModule?e:{default:e}}(r),n=e.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library"},edit_mode:!1,element_visibility_config:{upload_library_btn:!1,edit_library_btn:!1,permission_library_btn:!1,save_library_btn:!1,cancel_library_btn:!1,delete_library_btn:!1,undelete_library_btn:!1},initialize:function(e){this.render(e)},render:function(e){void 0===e&&(e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))),this.prepareButtons(e);var t=this.templateRow();return this.setElement(t({library:e,button_config:this.element_visibility_config,edit_mode:this.edit_mode})),this.$el.show(),this},repaint:function(e){s(".tooltip").hide();var t=this.$el;this.render(),t.replaceWith(this.$el),this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){var t=this.element_visibility_config;!1===this.edit_mode?(t.save_library_btn=!1,t.cancel_library_btn=!1,t.delete_library_btn=!1,!0===e.get("deleted")?(t.undelete_library_btn=!0,t.upload_library_btn=!1,t.edit_library_btn=!1,t.permission_library_btn=!1):!1===e.get("deleted")&&(t.save_library_btn=!1,t.cancel_library_btn=!1,t.undelete_library_btn=!1,!0===e.get("can_user_add")&&(t.upload_library_btn=!0),!0===e.get("can_user_modify")&&(t.edit_library_btn=!0),!0===e.get("can_user_manage")&&(t.permission_library_btn=!0))):!0===this.edit_mode&&(t.upload_library_btn=!1,t.edit_library_btn=!1,t.permission_library_btn=!1,t.save_library_btn=!0,t.cancel_library_btn=!0,t.delete_library_btn=!0,t.undelete_library_btn=!1),this.element_visibility_config=t},edit_button_clicked:function(){this.edit_mode=!0,this.repaint()},cancel_library_modification:function(){this.edit_mode=!1,this.repaint()},save_library_modification:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=!1,i=this.$el.find(".input_library_name").val();if(void 0!==i&&i!==e.get("name")){if(!(i.length>2))return void o.default.warning("Library name has to be at least 3 characters long.");e.set("name",i),t=!0}var s=this.$el.find(".input_library_description").val();void 0!==s&&s!==e.get("description")&&(e.set("description",s),t=!0);var a=this.$el.find(".input_library_synopsis").val();if(void 0!==a&&a!==e.get("synopsis")&&(e.set("synopsis",a),t=!0),t){var r=this;e.save(null,{patch:!0,success:function(e){r.edit_mode=!1,r.repaint(e),o.default.success("Changes to library saved.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured while attempting to update the library.")}})}else this.edit_mode=!1,this.repaint(e),o.default.info("Nothing has changed.")},delete_library:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=this;e.destroy({success:function(e){e.set("deleted",!0),Galaxy.libraries.libraryListView.collection.add(e),t.edit_mode=!1,!1===Galaxy.libraries.preferences.get("with_deleted")?(s(".tooltip").hide(),t.repaint(e),t.$el.remove()):!0===Galaxy.libraries.preferences.get("with_deleted")&&t.repaint(e),o.default.success("Library has been marked deleted.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured during deleting the library.")}})},undelete_library:function(){var e=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id")),t=this;e.url=e.urlRoot+e.id+"?undelete=true",e.destroy({success:function(e){e.set("deleted",!1),Galaxy.libraries.libraryListView.collection.add(e),t.edit_mode=!1,t.repaint(e),o.default.success("Library has been undeleted.")},error:function(e,t){void 0!==t.responseJSON?o.default.error(t.responseJSON.err_msg):o.default.error("An error occured while undeleting the library.")}})},templateRow:function(){return a.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){function n(e){return e&&e.__esModule?e:{default:e}}function s(e){var t=e.get("collection_type");return"list"==t?(0,f.default)("list"):"paired"==t?(0,f.default)("dataset pair"):"list:paired"==t?(0,f.default)("list of pairs"):(0,f.default)("nested list")}function a(e){var t=e.get("element_count"),i="a "+s(e);if(t){var n;1==t?n="with 1 item":t&&(n="with "+t+" items"),i=i+" "+(0,f.default)(n)}return i}Object.defineProperty(t,"__esModule",{value:!0});var o=i(117),l=n(o),r=i(60),d=(n(r),i(67)),c=n(d),u=i(5),h=(n(u),i(3)),f=n(h),p=l.default.ModelListPanel,m=p.extend({_logNamespace:"collections",className:p.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:c.default.DatasetDCEListItemView,modelCollectionKey:"elements",initialize:function(e){p.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,this.panelStack=[],this.parentName=e.parentName,this.foldoutStyle=e.foldoutStyle||"foldout",this.downloadUrl=Galaxy.root+"api/dataset_collections/"+this.model.attributes.id+"/download"},getNestedDCDCEViewClass:function(){return c.default.NestedDCDCEListItemView.extend({foldoutPanelClass:m})},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;this.handleWarning(e),i.log("_queueNewRender:",e,t),i._swapNewRender(e),i.trigger("rendered",i)},handleWarning:function(e){var t=this.views.length,i=this.model.get("element_count");if(i&&i!==t){var n=(0,f.default)("displaying only "+t+" of "+i+" items");e.find(".elements-warning").html('")}},_filterCollection:function(){return this.model.getVisibleContents()},_getItemViewClass:function(e){switch(e.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.getNestedDCDCEViewClass()}throw new TypeError("Unknown element type:",e.get("element_type"))},_getItemViewOptions:function(t){var i=p.prototype._getItemViewOptions.call(this,t);return e.extend(i,{linkTarget:this.linkTarget,hasUser:this.hasUser,foldoutStyle:this.foldoutStyle})},_setUpItemViewListeners:function(e){var t=this;return p.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}}),this},_expandDrilldownPanel:function(e){this.panelStack.push(e),this.$("> .controls").add(this.$list()).hide(),e.parentName=this.model.get("name"),this.$el.append(e.render().$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.render()},events:{"click .navigation .back":"close"},close:function(e){this.remove(),this.trigger("close")},toString:function(){return"CollectionView("+(this.model?this.model.get("name"):"")+")"}});m.prototype.templates=function(){var t=function(t,i){var n=a(i.model);return'\n i.text?1:e.text0){var n={file_count:e.length,dbkey:e[0].get("genome","?"),file_type:e[0].get("extension","auto")};for(var s in e){var a=e[s];if(a.set("status","running"),!(a.get("file_size")>0)){i.error_message="Upload content incomplete.",a.set("status","error"),a.set("info",i.error_message);break}var o="files_"+s+"|";switch(n[o+"type"]="upload_dataset",n[o+"space_to_tab"]=a.get("space_to_tab")&&"Yes"||null,n[o+"to_posix_lines"]=a.get("to_posix_lines")&&"Yes"||null,n[o+"dbkey"]=a.get("genome",null),n[o+"file_type"]=a.get("extension",null),a.get("file_mode")){case"new":n[o+"url_paste"]=a.get("url_paste");break;case"ftp":n[o+"ftp_files"]=a.get("file_path");break;case"local":i.files.push({name:o+"file_data",file:a.get("file_data")})}}i.payload.inputs=JSON.stringify(n)}return i}})}).call(t,i(2))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),a=function(e){return e&&e.__esModule?e:{default:e}}(s),o=e.View.extend({initialize:function(t){var i=this;this.model=t&&t.model||new e.Model({icon:"fa-upload",tooltip:(0,a.default)("Download from URL or upload files from disk"),label:"Load Data",percentage:0,status:"",onunload:function(){},onclick:function(){}}).set(t),this.setElement(this._template()),this.$progress=this.$(".progress-bar"),this.listenTo(this.model,"change",this.render,this),this.render(),n(window).on("beforeunload",function(){return i.model.get("onunload")()})},render:function(){var e=this.model.attributes;this.$el.off("click").on("click",function(t){e.onclick(t)}).tooltip({title:this.model.get("tooltip"),placement:"bottom"}),this.$progress.removeClass().addClass("progress-bar").addClass("progress-bar-notransition").addClass(""!=e.status&&"progress-bar-"+e.status).css({width:e.percentage+"%"})},_template:function(){return''}});t.default={View:o}}).call(t,i(2),i(0))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),l=a(o),r=i(4),d=(a(r),i(29)),c=a(d),u=i(244),h=a(u),f=i(55),p=a(f),m=i(56),g=a(m),_=i(15),v=a(_),y=i(10),w=a(y),b=i(6),x=a(b),C=i(245),$=a(C);i(57),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(29),u=(a(c),i(54)),h=a(u),f=i(15),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
'};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(16),o=s(a),l=i(66),r=s(l),d=i(39),c=s(d),u=i(124),h=s(u),f=i(21),p=s(f),m=i(5),g=s(m),_=i(3),v=s(_),y=r.default.DatasetListItemView,w=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 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=y.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=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+="
','','',"",'","
","<% } %>"],"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(20);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),"
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You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
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Drop files here
You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.
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r.default.NestedDCDCEListItemEdit.extend({foldoutPanelClass:g})},initialize:function(e){m.prototype.initialize.call(this,e)},_setUpBehaviors:function(e){if(e=e||this.$el,m.prototype._setUpBehaviors.call(this,e),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()){this.tagsEditorShown=!0;var t=this;e.find("> .controls .name").attr("title",(0,p.default)("Click to rename collection")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(e){var i=t.model.get("name");e&&e!==i?(t.$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)}}),this.tagsEditor=new 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o="files_"+s+"|";switch(n[o+"type"]="upload_dataset",n[o+"space_to_tab"]=a.get("space_to_tab")&&"Yes"||null,n[o+"to_posix_lines"]=a.get("to_posix_lines")&&"Yes"||null,n[o+"dbkey"]=a.get("genome",null),n[o+"file_type"]=a.get("extension",null),a.get("file_mode")){case"new":n[o+"url_paste"]=a.get("url_paste");break;case"ftp":n[o+"ftp_files"]=a.get("file_path");break;case"local":i.files.push({name:o+"file_data",file:a.get("file_data")})}}i.payload.inputs=JSON.stringify(n)}return i}})}).call(t,i(2))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),a=function(e){return e&&e.__esModule?e:{default:e}}(s),o=e.View.extend({initialize:function(t){var i=this;this.model=t&&t.model||new e.Model({icon:"fa-upload",tooltip:(0,a.default)("Download from URL or upload files from disk"),label:"Load 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o=i(3),l=a(o),r=i(4),d=(a(r),i(29)),c=a(d),u=i(244),h=a(u),f=i(55),p=a(f),m=i(56),g=a(m),_=i(15),v=a(_),y=i(10),w=a(y),b=i(6),x=a(b),C=i(245),$=a(C);i(57),t.default=e.View.extend({upload_size:0,collection:new c.default.Collection,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ui_button=e.ui_button,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.$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(29),u=(a(c),i(54)),h=a(u),f=i(15),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
'};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(16),o=s(a),l=i(66),r=s(l),d=i(39),c=s(d),u=i(124),h=s(u),f=i(21),p=s(f),m=i(5),g=s(m),_=i(3),v=s(_),y=r.default.DatasetListItemView,w=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 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=y.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=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+="
','','',"",'","
","<% } %>"],"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(20);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),"
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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","(/)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 $.default.ToursView)},show_user:function(){this.page.display(new w.default.View)},show_user_form:function(e){var t=new w.default.Model({user_id:Galaxy.params.id});this.page.display(new v.default.View(t.get(e)))},show_visualizations:function(e){this.page.display(new P.default.View({action_id:e,plural:"Visualizations",item:"visualization"}))},show_visualizations_edit:function(){this.page.display(new v.default.View({url:"visualization/edit?id="+G.default.get("id"),redirect:"visualizations/list"}))},show_workflows_published:function(){this.page.display(new S.default({url_base:Galaxy.root+"workflow/list_published",dict_format:!0}))},show_histories:function(e){this.page.display(new L.default.View({action_id:e}))},show_history_citations:function(){var e=Q.default.extend(q.default),t=document.createElement("div");this.page.display(t),new e({propsData:{id:G.default.get("id"),source:"histories"}}).$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).$mount(t)},show_histories_permissions:function(){this.page.display(new v.default.View({url:"history/permissions?id="+G.default.get("id"),redirect:"histories/list"}))},show_datasets:function(){this.page.display(new S.default({url_base:Galaxy.root+"dataset/list",dict_format:!0}))},show_pages:function(e){this.page.display(new P.default.View({action_id:e,plural:"Pages",item:"page"}))},show_pages_create:function(){this.page.display(new v.default.View({url:"page/create",redirect:"pages/list"}))},show_pages_edit:function(){this.page.display(new v.default.View({url:"page/edit?id="+G.default.get("id"),redirect:"pages/list"}))},show_workflows:function(){this.page.display(new D.default.View)},show_workflows_create:function(){this.page.display(new v.default.View({url:"workflow/create",redirect:"workflow/editor"}))},show_run:function(){this._loadWorkflow()},show_import_workflow:function(){this.page.display(new D.default.ImportWorkflowView)},show_custom_builds:function(){var e=this,t=this.page.historyPanel.historyView;if(!t||!t.model||!t.model.id)return void window.setTimeout(function(){e.show_custom_builds()},500);this.page.display(new x.default.View)},show_dataset_edit_attributes:function(){this.page.display(new W.default.View)},show_dataset_error:function(){this.page.display(new R.default.View)},home:function(e){e.tool_id||e.job_id?"upload1"===e.tool_id?(this.page.toolPanel.upload.show(),this._loadCenterIframe("welcome")):this._loadToolForm(e):e.workflow_id?this._loadWorkflow():e.m_c?this._loadCenterIframe(e.m_c+"/"+e.m_a):this._loadCenterIframe("welcome")},_loadToolForm:function(e){e.id=decodeURIComponent(e.tool_id),this.page.display(new g.default.View(e))},_loadCenterIframe:function(e,t){t=t||Galaxy.root,e=t+e,this.page.$("#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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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).
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diff --git a/static/scripts/bundled/library.bundled.js b/static/scripts/bundled/library.bundled.js
index f53862848c3..3782ba93a74 100644
--- a/static/scripts/bundled/library.bundled.js
+++ b/static/scripts/bundled/library.bundled.js
@@ -46,4 +46,8 @@ n=i,l=e("",{css:{position:"absolute",top:"-200px",left:s?"0px":"-1000px",
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*/
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| Size | ','<%= _.escape(item.get("file_size")) %> | ',"
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