From 24cfb6b52216ac9bfccf8eea02a7ff0344129e2f Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Mon, 8 Jan 2018 17:12:29 -0500 Subject: [PATCH] Client build. --- static/scripts/bundled/analysis.bundled.js | 4 ++-- static/scripts/mvc/dataset/dataset-error.js | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/static/scripts/bundled/analysis.bundled.js b/static/scripts/bundled/analysis.bundled.js index 2fb2a8e699c..e89b89fb6c0 100644 --- a/static/scripts/bundled/analysis.bundled.js +++ b/static/scripts/bundled/analysis.bundled.js @@ -1,3 +1,3 @@ -webpackJsonp([1],[,,,,,,,,function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var n={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};n.READY_STATES=[n.OK,n.EMPTY,n.PAUSED,n.FAILED_METADATA,n.NOT_VIEWABLE,n.DISCARDED,n.ERROR],n.NOT_READY_STATES=[n.UPLOAD,n.QUEUED,n.RUNNING,n.SETTING_METADATA,n.NEW],t.default=n},,function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var n=i(0),s=function(e){return e&&e.__esModule?e:{default:e}}(n),a=s.default,o=function(t){t=t||{},t.tooltipConfig=t.tooltipConfig||{placement:"bottom"},t.classes=["icon-btn"].concat(t.classes||[]),t.disabled&&t.classes.push("disabled");var i=['','',""].join(""),n=a(i).tooltip(t.tooltipConfig);return e.isFunction(t.onclick)&&n.click(t.onclick),n};t.default=o}).call(t,i(1))},,function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var s=i(5),a=function(e){return e&&e.__esModule?e:{default:e}}(s),o=e.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:!1,minimumInputLength:0,initialData:""},initialize:function(e){if(this.options=a.default.merge(e,this.optionsDefault),this.setElement(this._template(this.options)),!this.options.container)return void console.log("ui-select::initialize() : container not specified.");if(this.options.container.append(this.$el),this.select_data=this.options.data,this._refresh(),!this.options.multiple){this.options.value&&this._setValue(this.options.value);var t=this;this.options.onchange&&this.$el.on("change",function(){t.options.onchange(t.value())})}},value:function(e){var t=this._getValue();void 0!==e&&this._setValue(e);var i=this._getValue();return i!=t&&this.options.onchange&&this.options.onchange(i),i},text:function(){return this.$el.select2("data").text},disabled:function(){return!this.$el.select2("enable")},enable:function(){this.$el.select2("enable",!0)},disable:function(){this.$el.select2("enable",!1)},add:function(e){this.select_data.push({id:e.id,text:e.text}),this._refresh()},del:function(e){var t=this._getIndex(e);-1!=t&&(this.select_data.splice(t,1),this._refresh())},remove:function(){this.$el.select2("destroy")},update:function(e){this.select_data=[];for(var t in e.data)this.select_data.push(e.data[t]);this._refresh()},_refresh:function(){if(this.options.multiple){var e={multiple:this.options.multiple,containerCssClass:this.options.css,placeholder:this.options.placeholder,minimumInputLength:this.options.minimumInputLength,ajax:this.options.ajax,dropdownCssClass:this.options.dropdownCssClass,escapeMarkup:this.options.escapeMarkup,formatResult:this.options.formatResult,formatSelection:this.options.formatSelection,initSelection:this.options.initSelection,initialData:this.options.initialData};this.$el.select2(e)}else{var t=this._getValue(),e={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,dropdownAutoWidth:!0};this.$el.select2(e),this._setValue(t)}},_getIndex:function(e){n.findIndex(this.select_data,{id:e})},_getValue:function(){return this.$el.select2("val")},_setValue:function(e){-1==this._getIndex(e)&&this.select_data.length>0&&(e=this.select_data[0].id),this.$el.select2("val",e)},_template:function(e){return''}});t.default={View:o}}).call(t,i(2),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(56),l=a(o),r=i(37),d=a(r),c=i(20),u=a(c),h=i(31),f=a(h),p=i(70),m=a(p),g=i(4),_=a(g),v=i(32),w=a(v),y=500;try{y=localStorage.getItem("historyContentsLimitPerPageDefault")||y}catch(e){}var b=l.default.PaginatedCollection,x=b.extend(_.default.LoggableMixin).extend({_logNamespace:"history",limitPerPage:y,limitPerProgressiveFetch:y,order:"hid",urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(e,t){this.on({"sync add":this.trackJobStates}),t=t||{},b.prototype.initialize.call(this,e,t),this.history=t.history||null,this.setHistoryId(t.historyId||null),this.includeDeleted=t.includeDeleted||this.includeDeleted,this.includeHidden=t.includeHidden||this.includeHidden,this.model.prototype.idAttribute="type_id"},trackJobStates:function(){var e=this;this.each(function(t){if(!t.has("job_states_summary")&&"dataset_collection"===t.attributes.history_content_type){var i=t.attributes.job_source_type,n=t.attributes.job_source_id;if(i){e.jobStateSummariesCollection.add({id:n,model:i,history_id:e.history_id,collection_id:t.attributes.id});var s=e.jobStateSummariesCollection.get(n);t.jobStatesSummary=s}}})},model:function(e,t){return"dataset"===e.history_content_type?new d.default.HistoryDatasetAssociation(e,t):"dataset_collection"===e.history_content_type?new u.default.HistoryDatasetCollection(e,t):{validationError:"Unknown history_content_type: "+e.history_content_type}},stopPolling:function(){this.jobStateSummariesCollection&&(this.jobStateSummariesCollection.active=!1,this.jobStateSummariesCollection.clearUpdateTimeout())},setHistoryId:function(e){this.stopPolling(),this.historyId=e,e&&(this._setUpWebStorage(),this.jobStateSummariesCollection=new m.default.JobStatesSummaryCollection,this.jobStateSummariesCollection.historyId=e,this.jobStateSummariesCollection.monitor())},_setUpWebStorage:function(e){return this.storage=new f.default.HistoryPrefs({id:f.default.HistoryPrefs.historyStorageKey(this.historyId)}),this.trigger("new-storage",this.storage,this),this.on({"include-deleted":function(e){this.storage.includeDeleted(e)},"include-hidden":function(e){this.storage.includeHidden(e)}}),this.includeDeleted=this.storage.includeDeleted()||!1,this.includeHidden=this.storage.includeHidden()||!1,this},comparators:e.extend(e.clone(b.prototype.comparators),{name:_.default.buildComparator("name",{ascending:!0}),"name-dsc":_.default.buildComparator("name",{ascending:!1}),hid:_.default.buildComparator("hid",{ascending:!1}),"hid-asc":_.default.buildComparator("hid",{ascending:!0})}),running:function(){return this.filter(function(e){return!e.inReadyState()})},runningAndActive:function(){return this.filter(function(e){return!e.inReadyState()&&e.get("visible")&&!e.get("deleted")})},getByHid:function(e){return this.findWhere({hid:e})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},hidden:function(){return this.filter(function(e){return e.hidden()})},deleted:function(){return this.filter(function(e){return e.get("deleted")})},visibleAndUndeleted:function(){return this.filter(function(e){return e.get("visible")&&!e.get("deleted")})},setIncludeDeleted:function(t,i){if(e.isBoolean(t)&&t!==this.includeDeleted){if(this.includeDeleted=t,e.result(i,"silent"))return;this.trigger("include-deleted",t,this)}},setIncludeHidden:function(t,i){if(e.isBoolean(t)&&t!==this.includeHidden){if(this.includeHidden=t,i=i||{},e.result(i,"silent"))return;this.trigger("include-hidden",t,this)}},fetch:function(t){if(t=t||{},this.historyId&&!t.details){var i=f.default.HistoryPrefs.get(this.historyId).toJSON();e.isEmpty(i.expandedIds)||(t.details=e.values(i.expandedIds).join(","))}return b.prototype.fetch.call(this,t)},_buildFetchData:function(t){return e.extend(b.prototype._buildFetchData.call(this,t),{v:"dev"})},_fetchParams:b.prototype._fetchParams.concat(["v","details"]),_buildFetchFilters:function(t){var i=b.prototype._buildFetchFilters.call(this,t)||{},n={};return this.includeDeleted||(n.deleted=!1,n.purged=!1),this.includeHidden||(n.visible=!0),e.defaults(i,n)},getTotalItemCount:function(){return this.history.contentsShown()},fetchUpdated:function(e,t){return e&&(t=t||{filters:{}},t.remove=!1,t.filters={"update_time-ge":e.toISOString(),visible:""}),this.fetch(t)},fetchDeleted:function(t){var i=this;return t=t||{},t.filters=e.extend(t.filters,{deleted:!0,purged:void 0}),t.remove=!1,this.trigger("fetching-deleted",this),this.fetch(t).always(function(){i.trigger("fetching-deleted-done",i)})},fetchHidden:function(t){t=t||{};var i=this;return t.filters=e.extend(t.filters,{visible:!1}),t.remove=!1,i.trigger("fetching-hidden",i),i.fetch(t).always(function(){i.trigger("fetching-hidden-done",i)})},fetchAllDetails:function(t){t=t||{};var i={details:"all"};return t.data=e.extend(t.data||{},i),this.fetch(t)},_filterAndUpdate:function(e,t){var i=this,n=i.model.prototype.idAttribute,s=[t];return i.fetch({filters:e,remove:!1}).then(function(e){return e=e.reduce(function(e,t,s){var a=i.get(t[n]);return a?e.concat(a):e},[]),i.ajaxQueue("save",s,e)})},ajaxQueue:function(t,i,n){return n=n||this.models,new w.default.AjaxQueue(n.slice().reverse().map(function(n,s){var a=e.isString(t)?n[t]:t;return function(){return a.apply(n,i)}})).deferred},progressivelyFetchDetails:function(t){function i(n){n=n||0;var l=e.extend(e.clone(t),{view:"summary",keys:r,limit:o,offset:n,reset:0===n,remove:!1});e.defer(function(){a.fetch.call(a,l).fail(s.reject).done(function(e){s.notify(e,o,n),e.length!==o?(a.allFetched=!0,s.resolve(e,o,n)):i(n+o)})})}t=t||{};var s=n.Deferred(),a=this,o=t.limitPerCall||a.limitPerProgressiveFetch,l=d.default.HistoryDatasetAssociation.prototype.searchAttributes,r=l.join(",");return i(),s},isCopyable:function(t){var i=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return e.isObject(t)&&t.id&&e.contains(i,t.model_class)},copy:function(t){var i,s,a;e.isString(t)?(i=t,a="hda",s="dataset"):(i=t.id,a={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[t.model_class]||"hda",s="hdca"===a?"dataset_collection":"dataset");var o=this,l=n.ajax(this.url(),{method:"POST",contentType:"application/json",data:JSON.stringify({content:i,source:a,type:s})}).done(function(e){o.add([e],{parse:!0})}).fail(function(e,t,n){o.trigger("error",o,l,{},"Error copying contents",{type:s,id:i,source:a})});return l},createHDCA:function(e,t,i,n,s){return this.model({history_content_type:"dataset_collection",collection_type:t,history_id:this.historyId,name:i,hide_source_items:n||!1,element_identifiers:e}).save(s)},haveSearchDetails:function(){return this.allFetched&&this.all(function(t){return e.has(t.attributes,"annotation")})},matches:function(e){return this.filter(function(t){return t.matches(e)})},clone:function(){var e=s.Collection.prototype.clone.call(this);return e.historyId=this.historyId,e},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});t.default={HistoryContents:x}}).call(t,i(1),i(0),i(2))},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(21),r=o(l),d=i(8),c=o(d),u=i(10),h=o(u),f=i(4),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('\n \n \n '):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var t=this.model.urls;return a('\n
\n \n \n \n \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" ){ %>','
',(0,g.default)("An error occurred setting the metadata for this dataset"),"
","<% } %>"]),error:p.default.wrapTemplate(["<% if( model.error ){ %>",'
',(0,g.default)("There was an error getting the data for this dataset"),": <%- model.error %>","
","<% } %>"]),purged:p.default.wrapTemplate(["<% if( model.purged ){ %>",'
',(0,g.default)("This dataset has been deleted and removed from disk"),"
","<% } %>"]),deleted:p.default.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
',(0,g.default)("This dataset has been deleted"),"
","<% } %>"])}),i=p.default.wrapTemplate(['
','
','
','
','
',"
","<% if( !dataset.deleted && !dataset.purged ){ %>",'
','
','
',"<% if( dataset.peek ){ %>",'
<%= dataset.peek %>
',"<% } %>","<% } %>","
"],"dataset"),n=p.default.wrapTemplate(['
','
',(0,g.default)("You do not have permission to view this dataset"),"
","
"],"dataset"),s={};s[c.default.OK]=s[c.default.FAILED_METADATA]=p.default.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'
','<%- 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 ){ %>",'
',(0,g.default)("The job creating this dataset has been 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){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(29),a=n(s),o=i(51),l=n(o),r=i(3),d=(n(r),l.default.HistoryContentMixin),c=a.default.DatasetCollection,u=c.extend(d).extend({defaults:e.extend(e.clone(c.prototype.defaults),{history_content_type:"dataset_collection",model_class:"HistoryDatasetCollectionAssociation"}),save:function(e,t){return this.isNew()&&(t=t||{},t.url=this.urlRoot+this.get("history_id")+"/contents",e=e||{},e.type="dataset_collection"),c.prototype.save.call(this,e,t)},toString:function(){return"History"+c.prototype.toString.call(this)}});t.default={HistoryDatasetCollection:u}}).call(t,i(1))},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(4),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.name %>',"
",'
',"
"],"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.$el)},expand:function(){var e=this;return e._fetchModelDetails().always(function(){"foldout"===e.foldoutStyle?e._expand():"drilldown"===e.foldoutStyle&&e._expandByDrilldown()})},_expandByDrilldown:function(){var e=this;e.listenTo(e.foldout,"close",function(){e.trigger("collapsed:drilldown",e,e.foldout)}),e.trigger("expanded:drilldown",e,e.foldout)}});h.prototype.templates=function(){var e=r.default.wrapTemplate(['
',"
"],"collection");return s.extend({},u.prototype.templates,{details:e})}(),t.default={ExpandableView:c,ListItemView:u,FoldoutListItemView:h}}).call(t,i(2),i(0),i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(4),o=s(a),l=i(3),r=s(l),d=e.View.extend(o.default.LoggableMixin).extend(o.default.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",select_width:"100%",events:{},initialize:function(e){this.show_editor=!1,!1===e.usePrompt?this.label="":this.label='",this.workflow_mode=e.workflow_mode||!1,this.workflow_mode&&(this.events.click="showEditor",this.events.keydown="keydownHandler"),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.workflow_mode?this.$el.html(this._workflowTemplate()):this.$el.html(this._defaultTemplate()),this.$input().select2({placeholder:"Add tags",width:this.workflow_mode?this.width:this.select_width,tags:function(){return e._getTagsUsed()}}),this._setUpBehaviors(),this},_hashToName:function(e){return e.startsWith("#")?"name:"+e.slice(1):e},_nameToHash:function(e){return e.startsWith("name:")&&(e="#"+e.slice(5)),e},_defaultTemplate:function(){return[this.label,this._renderEditor()].join("")},_workflowTemplate:function(){return[this.show_editor?this._renderEditor():this._renderTags()].join(" ")},keydownHandler:function(e){switch(e.which){case 27:this.hideEditor()}},showEditor:function(){this.show_editor=!0,this.render()},hideEditor:function(){this.show_editor=!1,this.render()},_renderEditor:function(){return''},_renderTags:function(){var e=this.model.get("tags"),t=Galaxy.root+"static/images/fugue/tag--plus.png",i=[];return n.each(e,function(e){e=0==e.indexOf("name:")?e.slice(5):e;var t=''+e+"";i.push(t)}),0===i.length&&i.push("'),i.join(" ")},tagsToCSV:function(){var e=this,t=this.model.get("tags");return!n.isArray(t)||n.isEmpty(t)?"":t.map(function(t){return n.escape(e._nameToHash(t))}).sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){var e=this;return n.map(Galaxy.user.get("tags_used"),e._nameToHash)},_setUpBehaviors:function(){var e=this;this.$input().on("change",function(t){t.val=n.map(t.val,e._hashToName),e.model.save({tags:t.val}),t.added&&e._addNewTagToTagsUsed(""+t.added.text)})},_addNewTagToTagsUsed:function(e){var t=Galaxy.user.get("tags_used");n.contains(t,e)||(t.push(e),t.sort(),Galaxy.user.set("tags_used",t))},remove:function(){this.$input.off(),this.stopListening(this.model),e.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",""+this.model,")"].join("")}});t.default={TagsEditor:d}}).call(t,i(2),i(1))},,,,,function(e,t,i){"use strict";(function(e,n,s){Object.defineProperty(t,"__esModule",{value:!0});var a=i(5),o=function(e){return e&&e.__esModule?e:{default:e}}(a),l=e.View.extend({optionsDefault:{with_close:!0,title:null,placement:"top",container:"body",body:null},initialize:function(e){this.setElement(this._template()),this.uid=o.default.uid(),this.options=n.defaults(e||{},this.optionsDefault),this.options.container.parent().append(this.el),this.$title=this.$(".popover-title-label"),this.$close=this.$(".popover-close"),this.$body=this.$(".popover-content"),this.options.body&&this.append(this.options.body);var t=this;s("body").on("mousedown."+this.uid,function(e){t.visible&&!s(t.options.container).is(e.target)&&!s(t.el).is(e.target)&&0===s(t.el).has(e.target).length&&t.hide()})},render:function(){this.$title.html(this.options.title),this.$el.removeClass().addClass("ui-popover popover fade in").addClass(this.options.placement),this.$el.css(this._get_placement(this.options.placement));var e=this;this.options.with_close?this.$close.on("click",function(){e.hide()}).show():this.$close.off().hide()},title:function(e){void 0!==e&&(this.options.title=e,this.$title.html(e))},show:function(){this.render(),this.$el.show(),this.visible=!0},hide:function(){this.$el.hide(),this.visible=!1},append:function(e){this.$body.append(e)},empty:function(){this.$body.empty()},remove:function(){s("body").off("mousedown."+this.uid),this.$el.remove()},_get_placement:function(e){var t,i,n=this._get_width(this.$el),s=this.$el.height(),a=this.options.container,o=this._get_width(a),l=this._get_height(a),r=a.position();if(t=i=0,-1!=["top","bottom"].indexOf(e))switch(i=r.left-n+(o+n)/2,e){case"top":t=r.top-s-5;break;case"bottom":t=r.top+l+5}else switch(t=r.top-s+(l+s)/2,e){case"right":i=r.left+o}return{top:t,left:i}},_get_width:function(e){return e.width()+parseInt(e.css("padding-left"))+parseInt(e.css("margin-left"))+parseInt(e.css("padding-right"))+parseInt(e.css("margin-right"))},_get_height:function(e){return e.height()+parseInt(e.css("padding-top"))+parseInt(e.css("padding-bottom"))},_template:function(e){return'
'}});t.default={View:l}}).call(t,i(2),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}}function l(e,t){var i=e.toJSON();return C(i,{defaultHideSourceItems:t,creationFn:function(t,i,n){return t=t.map(function(e){return{id:e.id,name:e.name,src:"dataset"===e.history_content_type?"hda":"hdca"}}),e.createHDCA(t,"list",i,n)}})}Object.defineProperty(t,"__esModule",{value:!0});var r=i(20),d=o(r),c=i(8),u=o(c),h=i(4),f=o(h),p=i(52),m=o(p),g=i(9),_=o(g),v=i(53),w=(o(v),i(3)),y=o(w);i(54);var b=e.View.extend(f.default.LoggableMixin).extend({_logNamespace:"collections",tagName:"li",className:"collection-element",initialize:function(e){this.element=e.element||{},this.selected=e.selected||!1},render:function(){this.dragStartHandler=n.bind(this._dragstart,this),this.dragEndHandler=n.bind(this._dragend,this);var e=this.$el.attr("data-element-id",this.element.id).attr("draggable",!0).html(this.template({element:this.element})).get(0);return e.addEventListener("dragstart",this.dragStartHandler,!1),e.addEventListener("dragend",this.dragEndHandler,!1),this.selected&&this.$el.addClass("selected"),this},template:n.template(['',"<%- element.name %>","",'"].join("")),select:function(e){this.$el.toggleClass("selected",e),this.trigger("select",{source:this,selected:this.$el.hasClass("selected")})},discard:function(){var e=this,t=this.$el.parent().width();this.$el.animate({"margin-right":t},"fast",function(){e.trigger("discard",{source:e}),e.destroy()})},destroy:function(){this.off(),this.$el.remove()},events:{click:"_click","click .name":"_clickName","click .discard":"_clickDiscard",dragover:"_sendToParent",drop:"_sendToParent"},_click:function(e){e.stopPropagation(),this.select(e)},_clickName:function(e){e.stopPropagation(),e.preventDefault();var t=([(0,y.default)("Enter a new name for the element"),":\n(",(0,y.default)("Note that changing the name here will not rename the dataset"),")"].join(""),prompt((0,y.default)("Enter a new name for the element")+":",this.element.name));t&&(this.element.name=t,this.render())},_clickDiscard:function(e){e.stopPropagation(),this.discard()},_dragstart:function(e){e.originalEvent&&(e=e.originalEvent),e.dataTransfer.effectAllowed="move",e.dataTransfer.setData("text/plain",JSON.stringify(this.element)),this.$el.addClass("dragging"),this.$el.parent().trigger("collection-element.dragstart",[this])},_dragend:function(e){this.$el.removeClass("dragging"),this.$el.parent().trigger("collection-element.dragend",[this])},_sendToParent:function(e){this.$el.parent().trigger(e)},toString:function(){return"DatasetCollectionElementView()"}}),x=e.View.extend(f.default.LoggableMixin).extend(m.default.CollectionCreatorMixin).extend({_logNamespace:"collections",elementViewClass:b,collectionClass:d.default.HistoryDatasetCollection,className:"list-collection-creator collection-creator flex-row-container",minElements:1,defaultAttributes:{creationFn:function(){throw new TypeError("no creation fn for creator")},oncreate:function(){},oncancel:function(){},autoscrollDist:24,highlightClr:"rgba( 64, 255, 255, 1.0 )"},footerSettings:{".hide-originals":"hideOriginals"},initialize:function(e){this.metric("ListCollectionCreator.initialize",e);var t=this;n.each(this.defaultAttributes,function(i,n){i=e[n]||i,t[n]=i}),t.initialElements=e.elements||[],this._setUpCommonSettings(e),this._instanceSetUp(),this._elementsSetUp(),this._setUpBehaviors()},_instanceSetUp:function(){this.selectedIds={},this.$dragging=null,this.blocking=!1},_elementsSetUp:function(){this.invalidElements=[],this.workingElements=[],this.elementViews=[],this.workingElements=this.initialElements.slice(0),this._ensureElementIds(),this._validateElements(),this._mangleDuplicateNames(),this._sortElements()},_ensureElementIds:function(){return this.workingElements.forEach(function(e){e.hasOwnProperty("id")||(e.id=n.uniqueId())}),this.workingElements},_validateElements:function(){var e=this;return e.invalidElements=[],this.workingElements=this.workingElements.filter(function(t){var i=e._isElementInvalid(t);return i&&e.invalidElements.push({element:t,text:i}),!i}),this.workingElements},_isElementInvalid:function(e){return"dataset_collection"===e.history_content_type?(0,y.default)("is a collection, this is not allowed"):e.state===u.default.OK||n.contains(u.default.NOT_READY_STATES,e.state)?e.deleted||e.purged?(0,y.default)("has been deleted or purged"):null:(0,y.default)("has errored, is paused, or is not accessible")},_mangleDuplicateNames:function(){var e=1,t={};this.workingElements.forEach(function(i){for(var n=i.name;t.hasOwnProperty(n);)if(n=i.name+" ("+e+")",(e+=1)>=900)throw new Error("Safety hit in while loop - thats impressive");i.name=n,t[i.name]=!0})},_sortElements:function(e){},render:function(e,t){return this.workingElements.length .clear-selected").show():this.$(".collection-elements-controls > .clear-selected").hide()},_renderList:function(e,t){var i=this,s=a("
"),o=i.$list();n.each(this.elementViews,function(e){e.destroy(),i.removeElementView(e)}),i.workingElements.forEach(function(e){var t=i._createElementView(e);s.append(t.$el)}),i._renderClearSelected(),o.empty().append(s.children()),n.invoke(i.elementViews,"render"),o.height()>o.css("max-height")?o.css("border-width","1px 0px 1px 0px"):o.css("border-width","0px")},_createElementView:function(e){var t=new this.elementViewClass({element:e,selected:n.has(this.selectedIds,e.id)});return this.elementViews.push(t),this._listenToElementView(t),t},_listenToElementView:function(e){var t=this;t.listenTo(e,{select:function(e){var i=e.source.element;e.selected?t.selectedIds[i.id]=!0:delete t.selectedIds[i.id],t.trigger("elements:select",e)},discard:function(e){t.trigger("elements:discard",e)}})},addElementView:function(e){},removeElementView:function(e){delete this.selectedIds[e.element.id],this._renderClearSelected(),this.elementViews=n.without(this.elementViews,e),this.stopListening(e)},_renderNoElementsLeft:function(){this._disableNameAndCreate(!0),this.$(".collection-elements").append(this.templates.noElementsLeft())},_elementToJSON:function(e){return e},createList:function(e){if(!this.workingElements.length){var t=(0,y.default)("No valid elements for final list")+". ";return t+=''+(0,y.default)("Cancel")+" ",t+=(0,y.default)("or"),t+=' '+(0,y.default)("start over")+".",void this._showAlert(t)}var i=this,n=this.workingElements.map(function(e){return i._elementToJSON(e)});return i.blocking=!0,i.creationFn(n,e,i.hideOriginals).always(function(){i.blocking=!1}).fail(function(e,t,n){i.trigger("error",{xhr:e,status:t,message:(0,y.default)("An error occurred while creating this collection")})}).done(function(e,t,n){i.trigger("collection:created",e,t,n),i.metric("collection:created",e),"function"==typeof i.oncreate&&i.oncreate.call(this,e,t,n)})},_setUpBehaviors:function(){return this.on("error",this._errorHandler),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this.on("elements:select",function(e){this._renderClearSelected()}),this.on("elements:discard",function(e){var t=e.source.element;this.removeElementView(e.source),this.workingElements=n.without(this.workingElements,t),this.workingElements.length||this._renderNoElementsLeft()}),this},_errorHandler:function(e){this.error(e);var t=this,i=e.message||(0,y.default)("An error occurred");if(e.xhr){var n=e.xhr,s=e.message;0===n.readyState&&0===n.status?i+=": "+(0,y.default)("Galaxy could not be reached and may be updating.")+(0,y.default)(" Try again in a few minutes."):n.responseJSON?i+=":
"+JSON.stringify(n.responseJSON)+"
":i+=": "+s}t._showAlert(i,"alert-danger")},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .main-help":"_toggleHelp","click .header .alert button":"_hideAlert","click .reset":"reset","click .clear-selected":"clearSelectedElements","click .collection-elements":"clearSelectedElements","dragover .collection-elements":"_dragoverElements","drop .collection-elements":"_dropElements","collection-element.dragstart .collection-elements":"_elementDragstart","collection-element.dragend .collection-elements":"_elementDragend","change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","change .hide-originals":"_changeHideOriginals","click .cancel-create":"_cancelCreate","click .create-collection":"_clickCreate"},reset:function(){this._instanceSetUp(),this._elementsSetUp(),this.render()},clearSelectedElements:function(e){this.$(".collection-elements .collection-element").removeClass("selected"),this.$(".collection-elements-controls > .clear-selected").hide()},_dragoverElements:function(e){e.preventDefault();var t=this.$list();this._checkForAutoscroll(t,e.originalEvent.clientY);var i=this._getNearestElement(e.originalEvent.clientY);this.$(".element-drop-placeholder").remove();var n=s('
');i.length?i.before(n):t.append(n)},_checkForAutoscroll:function(e,t){var i=e.offset(),n=e.scrollTop(),s=t-i.top,a=i.top+e.outerHeight()-t;s>=0&&s=0&&ae&&a-o','',(0,y.default)("More help"),"",'
','',(0,y.default)("Less"),"","
","
",'
','','',"
"].join("")),middle:n.template(['
','',(0,y.default)("Start over"),"",'',(0,y.default)("Clear selected"),"","
",'
',"
"].join("")),footer:n.template(['
','
','","
",'
','','
',(0,y.default)("Name"),":
","
","
",'
','
','",'
','",'","
","
",'
','","
","
"].join("")),helpContent:n.template(["

",(0,y.default)(["Collections of datasets are permanent, ordered lists of datasets that can be passed to tools and ","workflows in order to have analyses done on each member of the entire group. This interface allows ","you to create a collection and re-order the final collection."].join("")),"

","
    ","
  • ",(0,y.default)(["Rename elements in the list by clicking on ",'the existing name.'].join("")),"
    • ","
  • ",(0,y.default)(["Discard elements from the final created list by clicking on the ",'"Discard" button.'].join("")),"
    • ","
  • ",(0,y.default)(["Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ",'them and you can then move those selected by dragging the ',"entire group. Deselect them by clicking them again or by clicking the ",'the "Clear selected" link.'].join("")),"
    • ","
  • ",(0,y.default)(['Click the "Start over" link to begin again as if you had just opened ',"the interface."].join("")),"
    • ","
  • ",(0,y.default)(['Click the "Cancel" button to exit the interface.'].join("")),"
    • ","

","

",(0,y.default)(['Once your collection is complete, enter a name and ','click "Create list".'].join("")),"

"].join("")),invalidElements:n.template([(0,y.default)("The following selections could not be included due to problems:"),"
    <% _.each( problems, function( problem ){ %>","
  • <%- problem.element.name %>: <%- problem.text %>
    • ","<% }); %>
"].join("")),noElementsLeft:n.template(['
  • ',(0,y.default)("No elements left! "),(0,y.default)("Would you like to "),'',(0,y.default)("start over"),"?","
    • "].join("")),invalidInitial:n.template(['
    ','
    ','',"<% if( _.size( problems ) ){ %>",(0,y.default)("The following selections could not be included due to problems"),":","
      <% _.each( problems, function( problem ){ %>","
    • <%- problem.element.name %>: <%- problem.text %>
      • ","<% }); %>
    ","<% } else if( _.size( elements ) < 1 ){ %>",(0,y.default)("No datasets were selected"),".","<% } %>","
    ",(0,y.default)("At least one element is needed for the collection"),". ",(0,y.default)("You may need to "),'',(0,y.default)("cancel")," ",(0,y.default)("and reselect new elements"),".","    ","
    ","
    ",'
    ','
    ','
    ','","
    ","
    ","
    "].join(""))}),toString:function(){return"ListCollectionCreator"}}),$=function(e,t,i){var s,o=a.Deferred(),l=Galaxy.modal||new _.default.View;return t=n.defaults(t||{},{elements:e,oncancel:function(){l.hide(),o.reject("cancelled")},oncreate:function(e,t){l.hide(),o.resolve(t)}}),s=new i(t),l.show({title:t.title||(0,y.default)("Create a collection"),body:s.$el,width:"80%",height:"100%",closing_events:!0}),s.render(),window._collectionCreator=s,o},C=function(e,t){return t=t||{},t.title=(0,y.default)("Create a collection from a list of datasets"),$(e,t,x)};t.default={DatasetCollectionElementView:b,ListCollectionCreator:x,collectionCreatorModal:$,listCollectionCreatorModal:C,createListCollection:l}}).call(t,i(2),i(1),i(0),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(50),l=a(o),r=i(4),d=a(r),c=i(3),u=(a(c),{defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(t){return e.extend(t,t.object,{element_id:t.id}),delete t.object,t},constructor:function(e,t){e=this._mergeObject(e),this.idAttribute="element_id",n.Model.apply(this,arguments)},parse:function(e,t){var i=e;return i=this._mergeObject(i)}}),h=n.Model.extend(d.default.LoggableMixin).extend(u).extend({_logNamespace:"collections"}),f=n.Collection.extend(d.default.LoggableMixin).extend({_logNamespace:"collections",model:h,toString:function(){return["DatasetCollectionElementCollection(",this.length,")"].join("")}}),p=l.default.DatasetAssociation.extend(d.default.mixin(u,{url:function(){return this.has("history_id")?Galaxy.root+"api/histories/"+this.get("history_id")+"/contents/"+this.get("id"):(console.warn("no endpoint for non-hdas within a collection yet"),Galaxy.root+"api/datasets")},defaults:e.extend({},l.default.DatasetAssociation.prototype.defaults,u.defaults),_downloadQueryParameters:function(){var e=this.get("file_ext"),t=this.get("element_identifier");return"?to_ext="+e+"&hdca_id="+this.get("parent_hdca_id")+"&element_identifier="+t},constructor:function(e,t){this.debug("\t DatasetDCE.constructor:",e,t),u.constructor.call(this,e,t)},hasDetails:function(){return this.elements&&this.elements.length},toString:function(){this.get("element_identifier");return"DatasetDCE({objStr})"}})),m=f.extend({model:p,toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),g=n.Model.extend(d.default.LoggableMixin).extend(d.default.SearchableModelMixin).extend({_logNamespace:"collections",defaults:{collection_type:null,deleted:!1},collectionClass:function(){return this.attributes.collection_type.indexOf(":")>0?v:m},initialize:function(e,t){this.debug(this+"(DatasetCollection).initialize:",e,t,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){var t=this.collectionClass();this.debug(this+"._createElementsModel",t,this.get("elements"),this.elements);var i=this.get("elements")||[];this.unset("elements",{silent:!0});var n=this;return e.each(i,function(t,i){e.extend(t,{parent_hdca_id:n.get("id")})}),this.elements=new t(i),this.elements},toJSON:function(){var e=n.Model.prototype.toJSON.call(this);return this.elements&&(e.elements=this.elements.toJSON()),e},inReadyState:function(){var e=this.get("populated");return this.isDeletedOrPurged()||e},hasDetails:function(){return 0!==this.elements.length},getVisibleContents:function(e){return this.elements},parse:function(e,t){var i=n.Model.prototype.parse.call(this,e,t);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},delete:function(e){return this.get("deleted")?s.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?s.when():this.save({deleted:!1},e)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name","tags"],toString:function(){return"DatasetCollection("+[this.get("id"),this.get("name")||this.get("element_identifier")].join(",")+")"}}),_=g.extend(d.default.mixin(u,{constructor:function(e,t){this.debug("\t NestedDCDCE.constructor:",e,t),u.constructor.call(this,e,t)},toString:function(){return["NestedDCDCE(",this.object?""+this.object:this.get("element_identifier"),")"].join("")}})),v=f.extend({model:_,toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}});t.default={DatasetCollection:g}}).call(t,i(1),i(2),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(16),r=o(l),d=i(31),c=(o(d),i(56)),u=o(c),h=i(5),f=o(h),p=i(4),m=o(p),g=i(3),_=o(g),v=e.Model.extend(m.default.LoggableMixin).extend(m.default.mixin(m.default.SearchableModelMixin,{_logNamespace:"history",UPDATE_DELAY:4e3,defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",deleted:!1,contents_active:{},contents_states:{}},urlRoot:Galaxy.root+"api/histories",contentsClass:r.default.HistoryContents,searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},initialize:function(e,t){t=t||{},this.logger=t.logger||null,this.log(this+".initialize:",e,t),this.contents=new this.contentsClass([],{history:this,historyId:this.get("id"),order:t.order}),this._setUpListeners(),this._setUpCollectionListeners(),this.updateTimeoutId=null},_setUpListeners:function(){return this.on({error:function(e,t,i,n,s){this.clearUpdateTimeout()},"change:id":function(e,t){this.contents&&(this.contents.historyId=t)}})},_setUpCollectionListeners:function(){return this.contents?this.listenTo(this.contents,{error:function(){this.trigger.apply(this,n.makeArray(arguments))}}):this},contentsShown:function(){var e=this.get("contents_active"),t=e.active||0;return t+=this.contents.includeDeleted?e.deleted:0,t+=this.contents.includeHidden?e.hidden:0},nice_size:function(){var e=this.get("size");return e?f.default.bytesToString(e,!0,2):(0,_.default)("(empty)")},toJSON:function(){return s.extend(e.Model.prototype.toJSON.call(this),{nice_size:this.nice_size()})},get:function(t){return"nice_size"===t?this.nice_size():e.Model.prototype.get.apply(this,arguments)},ownedByCurrUser:function(){return!(!Galaxy||!Galaxy.user)&&(!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.get("user_id"))},numOfUnfinishedJobs:function(){var e=this.get("non_ready_jobs");return e?e.length:0},numOfUnfinishedShownContents:function(){return this.contents.runningAndActive().length||0},_fetchContentRelatedAttributes:function(){var e=["size","non_ready_jobs","contents_active","hid_counter"];return this.fetch({data:a.param({keys:e.join(",")})})},refresh:function(e){var t=this;e=e||{};var i=this.lastUpdateTime;return this.contents.allFetched=!1,(0!==this.contents.currentPage?function(){return t.contents.fetchPage(t.contents.currentPage)}:function(){return t.contents.fetchUpdated(i)})().done(function(i,n,s){var a;try{a=new Date(s.getResponseHeader("Date"))}catch(e){}t.lastUpdateTime=a||new Date,t.checkForUpdates(e)})},checkForUpdates:function(e){var t=this;e=e||{};var i=this.UPDATE_DELAY;if(this.id){var n=function(){t.clearUpdateTimeout(),t.updateTimeoutId=setTimeout(function(){t.refresh(e)},i)};this.numOfUnfinishedShownContents()>0?n():this._fetchContentRelatedAttributes().done(function(e){t.numOfUnfinishedJobs()>0?n():t.trigger("ready")})}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},stopPolling:function(){this.clearUpdateTimeout(),this.contents&&this.contents.stopPolling()},parse:function(t,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},fetchWithContents:function(e,t){e=e||{};var i=this;return e.view="dev-detailed",this.fetch(e).then(function(e){return i.contents.history=i,i.contents.setHistoryId(e.id),i.fetchContents(t)})},fetchContents:function(e){e=e||{};var t=this;return t.lastUpdateTime=new Date,t.contents.fetchCurrentPage(e)},_delete:function(e){return this.get("deleted")?n.when():this.save({deleted:!0},e)},purge:function(e){return this.get("purged")?n.when():this.save({deleted:!0,purged:!0},e)},undelete:function(e){return this.get("deleted")?this.save({deleted:!1},e):n.when()},copy:function(e,t,i){if(e=void 0===e||e,!this.id)throw new Error("You must set the history ID before copying it.");var s={history_id:this.id};e&&(s.current=!0),t&&(s.name=t),i||(s.all_datasets=!1),s.view="dev-detailed";var a=this,o=n.post(this.urlRoot,s);return e?o.then(function(e){return new v(e).setAsCurrent().done(function(){a.trigger("copied",a,e)})}):o.done(function(e){a.trigger("copied",a,e)})},setAsCurrent:function(){var e=this,t=n.getJSON(Galaxy.root+"history/set_as_current?id="+this.id);return t.done(function(){e.trigger("set-as-current",e)}),t},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}})),w=u.default.InfinitelyScrollingCollection,y=w.extend(m.default.LoggableMixin).extend({_logNamespace:"history",model:v,order:"update_time",limitOnFirstFetch:10,limitPerFetch:10,initialize:function(e,t){t=t||{},this.log("HistoryCollection.initialize",e,t),w.prototype.initialize.call(this,e,t),this.includeDeleted=t.includeDeleted||!1,this.currentHistoryId=t.currentHistoryId,this.setUpListeners()},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot},setUpListeners:function(){return this.on({"change:deleted":function(e){this.debug("change:deleted",this.includeDeleted,e.get("deleted")),!this.includeDeleted&&e.get("deleted")&&this.remove(e)},copied:function(e,t){this.setCurrent(new v(t,[]))},"set-as-current":function(e){var t=this.currentHistoryId;this.trigger("no-longer-current",t),this.currentHistoryId=e.id}})},_buildFetchData:function(e){return s.extend(w.prototype._buildFetchData.call(this,e),{view:"dev-detailed"})},_buildFetchFilters:function(e){var t=w.prototype._buildFetchFilters.call(this,e)||{},i={};return this.includeDeleted?i.deleted=null:(i.deleted=!1,i.purged=!1),s.defaults(t,i)},fetchFirst:function(e){var t=this,i=a.when();return this.currentHistoryId&&(i=w.prototype.fetchFirst.call(t,{silent:!0,limit:1,filters:{purged:"",deleted:"","encoded_id-in":this.currentHistoryId}})),i.then(function(){return e=e||{},e.offset=0,t.fetchMore(e)})},comparators:s.extend(s.clone(w.prototype.comparators),{name:m.default.buildComparator("name",{ascending:!0}),"name-dsc":m.default.buildComparator("name",{ascending:!1}),size:m.default.buildComparator("size",{ascending:!1}),"size-asc":m.default.buildComparator("size",{ascending:!0})}),sort:function(e){e=e||{};var t=e.silent,i=this.remove(this.get(this.currentHistoryId));return w.prototype.sort.call(this,s.defaults({silent:!0},e)),this.unshift(i,{silent:!0}),t||this.trigger("sort",this,e),this},create:function(e,t,i,s){var a=this;return n.getJSON(Galaxy.root+"history/create_new_current").done(function(e){a.setCurrent(new v(e,[],i||{}))})},setCurrent:function(e,t){return t=t||{},this.unshift(e,t),this.currentHistoryId=e.get("id"),t.silent||this.trigger("new-current",e,this),this},toString:function(){return"HistoryCollection("+this.length+",current:"+this.currentHistoryId+")"}});t.default={History:v,HistoryCollection:y}}).call(t,i(2),i(0),i(1),i(0))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var n=i(4),s=function(e){return e&&e.__esModule?e:{default:e}}(n),a=s.default.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:!1,show_hidden:!1},addExpanded:function(e){var t=this.get("expandedIds");t[e.id]=e.get("id"),this.save("expandedIds",t)},removeExpanded:function(e){var t=this.get("expandedIds");delete t[e.id],this.save("expandedIds",t)},isExpanded:function(t){return e.result(this.get("expandedIds"),t,!1)},allExpanded:function(){return e.values(this.get("expandedIds"))},clearExpanded:function(){this.set("expandedIds",{})},includeDeleted:function(t){return e.isUndefined(t)||this.set("show_deleted",t),this.get("show_deleted")},includeHidden:function(t){return e.isUndefined(t)||this.set("show_hidden",t),this.get("show_hidden")},toString:function(){return"HistoryPrefs("+this.id+")"}},{storageKeyPrefix:"history:",historyStorageKey:function(e){if(!e)throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+e);return a.storageKeyPrefix+e},get:function(e){return new a({id:a.historyStorageKey(e)})},clearAll:function(e){for(var t in sessionStorage)0===t.indexOf(a.storageKeyPrefix)&&sessionStorage.removeItem(t)}});t.default={HistoryPrefs:a}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function i(e,t){if(!e)throw new ReferenceError("this hasn't been initialised - super() hasn't been called");return!t||"object"!=typeof t&&"function"!=typeof t?e:t}function n(e,t){if("function"!=typeof t&&null!==t)throw new TypeError("Super expression must either be null or a function, not "+typeof t);e.prototype=Object.create(t&&t.prototype,{constructor:{value:e,enumerable:!1,writable:!0,configurable:!0}}),t&&(Object.setPrototypeOf?Object.setPrototypeOf(e,t):e.__proto__=t)}function s(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}Object.defineProperty(t,"__esModule",{value:!0});var a=function e(t,i,n){null===t&&(t=Function.prototype);var s=Object.getOwnPropertyDescriptor(t,i);if(void 0===s){var a=Object.getPrototypeOf(t);return null===a?void 0:e(a,i,n)}if("value"in s)return s.value;var o=s.get;if(void 0!==o)return o.call(n)},o=function(){function e(e,t){for(var i=0;i .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 ){ %>",'
    ',(0,f.default)("There was an error getting the data for this collection"),": <%- model.error %>","
    ","<% } %>"]),purged:u.default.wrapTemplate(["<% if( model.purged ){ %>",'
    ',(0,f.default)("This collection has been deleted and removed from disk"),"
    ","<% } %>"]),deleted:u.default.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
    ',(0,f.default)("This collection has been deleted"),"
    ","<% } %>"])}),i=u.default.wrapTemplate(['
    ','
    ','<%- collection.element_identifier || collection.name %>',"
    ",'
    ',"
    "],"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.element_identifier %>',"
    ",'
    ',"
    "],"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.element_identifier %>',"
    ","
    "],"element");return e.extend({},d.default.DatasetListItemView.prototype.templates,{titleBar:t})}();var w=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:w}}).call(t,i(1),i(0),i(0))},,,function(e,t,i){"use strict";(function(e,n){function s(t,i,n){return Galaxy.modal.show({title:i,body:t,closing_events:!0,buttons:{Ok:function(){Galaxy.modal.hide()}}}),Galaxy.modal.$el.addClass("error-modal"),n&&(Galaxy.modal.$(".error-details").add(Galaxy.modal.$('button:contains("Details")')).remove(),e("
    ").addClass("error-details").hide().appendTo(Galaxy.modal.$(".modal-content")).append([e("

    ").text(p),e("

    ").text(JSON.stringify(n,null,"  "))]),e('").appendTo(Galaxy.modal.$(".buttons")).click(function(){Galaxy.modal.$(".error-details").toggle()})),Galaxy.modal}function a(e,t,i){if(e){if(e=(0,u.default)(e),t=(0,u.default)(t)||(0,u.default)("Error:"),window.Galaxy&&Galaxy.modal)return s(e,t,i);alert(t+"\n\n"+e),console.log("error details:",JSON.stringify(i))}}function o(){return a((0,u.default)("You appear to be offline. Please check your connection and try again."),(0,u.default)("Offline?"))}function l(){return a((0,u.default)("Galaxy is currently unreachable. Please try again in a few minutes.")+" "+h,(0,u.default)("Cannot connect to Galaxy"))}function r(e,t,i,n,s){return n=n||f,n+=" "+h,s=s||(0,u.default)("An error occurred"),a(n,s,d(e,t,i))}function d(e,t,i){return{raven:n.result(window.Raven,"lastEventId"),userAgent:navigator.userAgent,onLine:navigator.onLine,version:n.result(Galaxy.config,"version_major"),xhr:n.omit(t,n.functions(t)),options:n.omit(i,"xhr"),url:n.result(Galaxy.lastAjax,"url"),data:n.result(Galaxy.lastAjax,"data"),model:n.result(e,"toJSON",""+e),user:n.omit(n.result(Galaxy.user,"toJSON"),"email")}}Object.defineProperty(t,"__esModule",{value:!0});var c=i(3),u=function(e){return e&&e.__esModule?e:{default:e}}(c),h=(0,u.default)("Please contact a Galaxy administrator if the problem persists."),f=(0,u.default)("An error occurred while updating information with the server."),p=(0,u.default)("The following information can assist the developers in finding the source of the error:");t.default={errorModal:a,offlineErrorModal:o,badGatewayErrorModal:l,ajaxErrorModal:r}}).call(t,i(0),i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(50),a=n(s),o=i(51),l=n(o),r=i(4),d=n(r),c=i(3),u=(n(c),a.default.DatasetAssociation),h=l.default.HistoryContentMixin,f=u.extend(d.default.mixin(h,{defaults:e.extend({},u.prototype.defaults,h.defaults,{history_content_type:"dataset",model_class:"HistoryDatasetAssociation"})}));t.default={HistoryDatasetAssociation:f}}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(21),l=a(o),r=i(95),d=a(r),c=i(4),u=a(c),h=i(3),f=a(h);i(39);var p=e.View.extend(u.default.LoggableMixin).extend({_logNamespace:"list",viewClass:l.default.ListItemView,collectionClass:e.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:(0,f.default)("This list is empty"),noneFoundMsg:(0,f.default)("No matching items found"),searchPlaceholder:(0,f.default)("search"),initialize:function(e,t){e=e||{},e.logger&&(this.logger=e.logger),this.log(this+".initialize:",e),this.fxSpeed=n.has(e,"fxSpeed")?e.fxSpeed:this.fxSpeed,this.filters=[],this.searchFor=e.searchFor||"",this.selecting=void 0===e.selecting||e.selecting,this.selected=e.selected||[],this.lastSelected=null,this.dragItems=e.dragItems||!1,this.viewClass=e.viewClass||this.viewClass,this.views=[],this.collection=e.collection||this._createDefaultCollection(),this.filters=e.filters||[],this.$scrollContainer=e.$scrollContainer||this.$scrollContainer,this.title=e.title||"",this.subtitle=e.subtitle||"",this._setUpListeners()},_setUpListeners:function(){return this.off(),this.on({error:function(e,t,i,n,s){console.error(e,t,i,n,s)},loading:function(){this._showLoadingIndicator("loading...",40)},"loading-done":function(){this._hideLoadingIndicator(40)}}),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this._setUpCollectionListeners(),this._setUpViewListeners(),this},_createDefaultCollection:function(){return new this.collectionClass([])},_setUpCollectionListeners:function(){return this.log(this+"._setUpCollectionListeners",this.collection),this.stopListening(this.collection),this.listenTo(this.collection,{error:function(e,t,i,n,s){this.trigger("error",e,t,i,n,s)},update:function(e,t){var i=t.changes;return t.renderAll||i.added.length+i.removed.length>1?this.renderItems():1===i.added.length?this.addItemView(n.first(i.added),e,t):1===i.removed.length?this.removeItemView(n.first(i.removed),e,t):void 0}}),this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners"),this.on({"view:selected":function(e,t){if(t&&t.shiftKey&&this.lastSelected){var i=this.viewFromModelId(this.lastSelected);i&&this.selectRange(e,i)}else t&&t.altKey&&!this.selecting&&this.showSelectors();this.selected.push(e.model.id),this.lastSelected=e.model.id},"view:de-selected":function(e,t){this.selected=n.without(this.selected,e.model.id)}})},render:function(e){this.log(this+".render",e);var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var e=s(this.templates.el({},this));return this._renderControls(e),this._renderTitle(e),this._renderSubtitle(e),this._renderSearch(e),this.renderItems(e),e},_renderControls:function(e){this.debug(this+"(ListPanel)._renderControls");var t=s(this.templates.controls({},this));return e.find(".controls").replaceWith(t),t},_renderTitle:function(e){},_renderSubtitle:function(e){},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;i.log("_queueNewRender:",e,t),s(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",this.className).append(e.children()),this.selecting&&this.showSelectors(0),this},_setUpBehaviors:function(e){return e=e||this.$el,this.$controls(e).find("[title]").tooltip(),this._renderMultiselectActionMenu(e),this},_renderMultiselectActionMenu:function(e){e=e||this.$el;var t=e.find(".list-action-menu"),i=this.multiselectActions();if(!i.length)return t.empty();var n=s(['
    ','",'","
    "].join("")),a=i.map(function(e){var t=['
  • ',e.html,"
    • "].join("");return s(t).click(function(t){return t.preventDefault(),e.func(t)})});return n.find("ul").append(a),t.replaceWith(n),n},multiselectActions:function(){return[]},$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(["
    ",'
    ','
    ','
    ',"
    "]),controls:u.default.wrapTemplate(['
    ','
    ','
    <%- view.title %>
    ',"
    ",'
    <%- view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
    "])}}();var m=p.extend({modelCollectionKey:"contents",initialize:function(e){p.prototype.initialize.call(this,e),this.selecting=void 0!==e.selecting&&e.selecting,this.setModel(this.model,e)},setModel:function(e,t){if(t=t||{},this.debug(this+".setModel:",e,t),this.freeModel(),this.freeViews(),e){var i=this.model?this.model.get("id"):null;this.model=e,this.logger&&(this.model.logger=this.logger),this._setUpModelListeners(),this.stopListening(this.collection),this.collection=this.model[this.modelCollectionKey]||t.collection||this._createDefaultCollection(),this._setUpCollectionListeners(),i&&e.get("id")!==i&&this.trigger("new-model",this)}return this},freeModel:function(){return this.model&&this.stopListening(this.model),this},_setUpModelListeners:function(){return this.log(this+"._setUpModelListeners",this.model),this.listenTo(this.model,"error",function(){var e=Array.prototype.slice.call(arguments,0);e.unshift("error"),this.trigger.apply(this,e)},this),this.logger&&this.listenTo(this.model,"all",function(e){this.info(this+"(model)",e,arguments)}),this},_renderControls:function(e){this.debug(this+"(ModelListPanel)._renderControls");var t=this.model?this.model.toJSON():{},i=s(this.templates.controls(t,this));return e.find(".controls").replaceWith(i),i},toString:function(){return"ModelListPanel("+this.model+")"}});m.prototype.templates=function(){var e=u.default.wrapTemplate(['
    ','
    ','
    <%- model.name %>
    ',"
    ",'
    <%- view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
    "]);return n.extend(n.clone(p.prototype.templates),{controls:e})}(),t.default={ListPanel:p,ModelListPanel:m}}).call(t,i(2),i(1),i(0))},function(e,t,i){"use strict";function n(e,t){function i(e){o(this).parent().children("input").val("").trigger("searchInput.clear").blur(),t.onclear()}function n(e,n){if(!n)return i();o(this).trigger("search.search",n),"function"==typeof t.onfirstsearch&&u?(u=!1,t.onfirstsearch(n)):t.onsearch(n)}function s(){return['"].join("")}var r=27,d=13,c=o(e),u=!0,h={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onfirstsearch:null,onsearch:function(e){},minSearchLen:0,escWillClear:!0,oninit:function(){}};return"string"===a.default.type(t)?("toggle-loading"===t&&function(){c.find(".search-loading").toggle(),c.find(".search-clear").toggle()}(),c):("object"===a.default.type(t)&&(t=a.default.extend(!0,{},h,t)),c.addClass("search-input").prepend([function(){return o(s()).focus(function(e){o(this).select()}).keyup(function(e){if(e.preventDefault(),e.stopPropagation(),e.which===r&&t.escWillClear)i.call(this,e);else{var s=o(this).val();(e.which===d||t.minSearchLen&&s.length>=t.minSearchLen)&&n.call(this,e,s)}}).val(t.initialVal)}(),function(){return o([''].join("")).tooltip({placement:"bottom"}).click(function(e){i.call(this,e)})}(),function(){return o([''].join("")).hide().tooltip({placement:"bottom"})}()]))}var s=i(0),a=function(e){return e&&e.__esModule?e:{default:e}}(s),o=a.default,l=window._l||function(e){return e};a.default.fn.extend({searchInput:function(e){return this.each(function(){return n(this,e)})}})},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(17),a=n(s),o=i(4),l=n(o),r=i(58),d=n(r),c=i(3),u=n(c),h=a.default.DatasetListItemView,f=h.extend({className:h.prototype.className+" history-content",initialize:function(e,t){h.prototype.initialize.call(this,e,t)},toString:function(){return"HDAListItemView("+(this.model?""+this.model:"(no model)")+")"}});f.prototype.templates=function(){var t=function(t){return'\n        
    \n            \n            
    \n                '+t.hid+'\n                '+e.escape(t.name)+"\n            
    \n            
    \n            "+d.default.nametagTemplate(t)+"\n        
    \n    "},i=e.extend({},h.prototype.templates.warnings,{hidden:l.default.wrapTemplate(["<% if( !dataset.visible ){ %>",'
    ',(0,u.default)("This dataset has been hidden"),"
    ","<% } %>"],"dataset")});return e.extend({},h.prototype.templates,{titleBar:t,warnings:i})}(),t.default={HDAListItemView:f}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(8),a=n(s),o=i(33),l=n(o),r=i(59),d=n(r),c=i(4),u=(n(c),i(58)),h=n(u),f=i(3),p=n(f),m=l.default.DCListItemView,g=m.extend({className:m.prototype.className+" history-content",_setUpListeners:function(){var e=this;m.prototype._setUpListeners.call(this);var t=function(t,i){e.render()};this.model.jobStatesSummary&&this.listenTo(this.model.jobStatesSummary,"change",t),this.listenTo(this.model,{"change:tags change:visible change:state":t})},_getFoldoutPanelClass:function(){return d.default.CollectionView},_swapNewRender:function(e){m.prototype._swapNewRender.call(this,e);var t,i=this.model.jobStatesSummary;t=i?i.new()?"loading":i.errored()?"error":i.terminal()?"ok":i.running()?"running":"queued":this.model.get("job_source_id")?"loading":this.model.get("populated_state")?a.default.OK:a.default.RUNNING,this.$el.addClass("state-"+t);var n=this.stateDescription();return this.$(".state-description").html(n),this.$el},stateDescription:function(){var e=this.model,t=(e.get("element_count"),e.get("job_source_type")),i=(this.model.get("collection_type"),d.default.collectionTypeDescription(e)),n=d.default.collectionDescription(e),s=e.jobStatesSummary;if(t&&"Job"!=t){if(s&&s.hasDetails()){var a=s.new(),o=a?null:s.jobCount();if(a)return'\n                        
    \n                            Creating jobs...\n                            
    \n                        
    ';if(s.errored()){return"a "+i+" with "+s.numInError()+" / "+o+" jobs in error"}if(s.terminal())return n;var l=s.states().running||0,r=s.states().ok||0,c=r/(1*o),u=l/(1*o),h=1-c-u;return'\n                        
    \n                            '+(o&&o>1?o+" jobs":"a job")+" generating a "+i+'\n                            
    \n                            
    \n                            
    \n                        
    '}return'\n                    
    \n                        Loading job data for '+i+'...\n                        
    \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            \n            
    \n                '+t.hid+'\n                '+e.escape(t.name)+'\n            
    \n            
    \n            
    \n            '+h.default.nametagTemplate(t)+"\n        
    \n    "};return e.extend({},m.prototype.templates,{warnings:t,titleBar:i})}(),t.default={HDCAListItemView:g}}).call(t,i(1))},,function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(67),l=a(o),r=i(42),d=a(r),c=i(9),u=a(c),h=i(5),f=a(h),p=e.View.extend({el:"body",className:"full-content",_panelids:["left","right"],initialize:function(t){var i=this;this.config=n.defaults(t.config||{},{message_box_visible:!1,message_box_content:"",message_box_class:"info",show_inactivity_warning:!1,inactivity_box_content:""}),Galaxy.modal=this.modal=new u.default.View,Galaxy.display=this.display=function(e){e.title?(f.default.setWindowTitle(e.title),e.allow_title_display=!1):(f.default.setWindowTitle(),e.allow_title_display=!0),i.center.display(e)},Galaxy.router=this.router=t.Router&&new t.Router(i,t),this.masthead=new l.default.View(this.config),this.center=new d.default.CenterPanel,this.$el.attr("scroll","no"),this.$el.html(this._template()),this.$("#masthead").replaceWith(this.masthead.$el),this.$("#center").append(this.center.$el),this.$el.append(this.masthead.frame.$el),this.$el.append(this.modal.$el),this.$messagebox=this.$("#messagebox"),this.$inactivebox=this.$("#inactivebox"),this.panels={},n.each(this._panelids,function(e){var n=e.charAt(0).toUpperCase()+e.slice(1),s=t[n];if(s){var a=new s(i,t);i[a.toString()]=a,i.panels[e]=new d.default.SidePanel({id:e,el:i.$("#"+e),view:a})}}),this.render(),this.router&&e.history.start({root:Galaxy.root,pushState:!0})},render:function(){return s(".select2-hidden-accessible").remove(),this.masthead.render(),this.renderMessageBox(),this.renderInactivityBox(),this.renderPanels(),this._checkCommunicationServerOnline(),this},renderMessageBox:function(){if(this.config.message_box_visible){var e=this.config.message_box_content||"",t=this.config.message_box_class||"info";this.$el.addClass("has-message-box"),this.$messagebox.attr("class","panel-"+t+"-message").html(e).toggle(!!e).show()}else this.$el.removeClass("has-message-box"),this.$messagebox.hide();return this},renderInactivityBox:function(){if(this.config.show_inactivity_warning){var e=this.config.inactivity_box_content||"",t=s("").attr("href",Galaxy.root+"user/resend_verification").text("Resend verification");this.$el.addClass("has-inactivity-box"),this.$inactivebox.html(e+" ").append(t).toggle(!!e).show()}else this.$el.removeClass("has-inactivity-box"),this.$inactivebox.hide();return this},renderPanels:function(){var e=this;return n.each(this._panelids,function(t){var i=e.panels[t];i?i.render():(e.$("#center").css(t,0),e.$("#"+t).hide())}),this},_template:function(){return['
    ','
    ','
    ','
    ','
    ','
    ','
    ','",'
    '].join("")},toString:function(){return"PageLayoutView"},_checkCommunicationServerOnline:function(){var e=window.Galaxy.config.communication_server_host,t=window.Galaxy.config.communication_server_port,i=window.Galaxy.user.attributes.preferences,n=s("#show-chat-online");i&&-1!=["1","true"].indexOf(i.communication_server)?s.ajax({url:e+":"+t}).success(function(e){null!==window.Galaxy.user.id&&"hidden"===n.css("visibility")&&n.css("visibility","visible")}).error(function(e){n.css("visibility","hidden")}):n.css("visibility","hidden")}});t.default={View:p}}).call(t,i(2),i(1),i(0))},,,,,,function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var i=e.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_name:"",file_mode:"",file_size:0,file_type:null,file_path:"",file_data:null,percentage:0,space_to_tab:!1,to_posix_lines:!0,enabled:!0},reset:function(e){this.clear().set(this.defaults).set(e)}}),n=e.Collection.extend({model:i});t.default={Model:i,Collection:n}}).call(t,i(2))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(8),l=a(o),r=i(4),d=a(r),c=i(3),u=a(c),h=d.default.SearchableModelMixin,f=e.Model.extend(d.default.LoggableMixin).extend(d.default.mixin(h,{_logNamespace:"dataset",defaults:{state:l.default.NEW,deleted:!1,purged:!1,name:"(unnamed dataset)",accessible:!0,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(e,t){this.debug(this+"(Dataset).initialize",e,t),
+webpackJsonp([1],[,,,,,,,,function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var n={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};n.READY_STATES=[n.OK,n.EMPTY,n.PAUSED,n.FAILED_METADATA,n.NOT_VIEWABLE,n.DISCARDED,n.ERROR],n.NOT_READY_STATES=[n.UPLOAD,n.QUEUED,n.RUNNING,n.SETTING_METADATA,n.NEW],t.default=n},,function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var n=i(0),s=function(e){return e&&e.__esModule?e:{default:e}}(n),a=s.default,o=function(t){t=t||{},t.tooltipConfig=t.tooltipConfig||{placement:"bottom"},t.classes=["icon-btn"].concat(t.classes||[]),t.disabled&&t.classes.push("disabled");var i=['','',""].join(""),n=a(i).tooltip(t.tooltipConfig);return e.isFunction(t.onclick)&&n.click(t.onclick),n};t.default=o}).call(t,i(1))},,function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var s=i(5),a=function(e){return e&&e.__esModule?e:{default:e}}(s),o=e.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null,multiple:!1,minimumInputLength:0,initialData:""},initialize:function(e){if(this.options=a.default.merge(e,this.optionsDefault),this.setElement(this._template(this.options)),!this.options.container)return void console.log("ui-select::initialize() : container not specified.");if(this.options.container.append(this.$el),this.select_data=this.options.data,this._refresh(),!this.options.multiple){this.options.value&&this._setValue(this.options.value);var t=this;this.options.onchange&&this.$el.on("change",function(){t.options.onchange(t.value())})}},value:function(e){var t=this._getValue();void 0!==e&&this._setValue(e);var i=this._getValue();return i!=t&&this.options.onchange&&this.options.onchange(i),i},text:function(){return this.$el.select2("data").text},disabled:function(){return!this.$el.select2("enable")},enable:function(){this.$el.select2("enable",!0)},disable:function(){this.$el.select2("enable",!1)},add:function(e){this.select_data.push({id:e.id,text:e.text}),this._refresh()},del:function(e){var t=this._getIndex(e);-1!=t&&(this.select_data.splice(t,1),this._refresh())},remove:function(){this.$el.select2("destroy")},update:function(e){this.select_data=[];for(var t in e.data)this.select_data.push(e.data[t]);this._refresh()},_refresh:function(){if(this.options.multiple){var e={multiple:this.options.multiple,containerCssClass:this.options.css,placeholder:this.options.placeholder,minimumInputLength:this.options.minimumInputLength,ajax:this.options.ajax,dropdownCssClass:this.options.dropdownCssClass,escapeMarkup:this.options.escapeMarkup,formatResult:this.options.formatResult,formatSelection:this.options.formatSelection,initSelection:this.options.initSelection,initialData:this.options.initialData};this.$el.select2(e)}else{var t=this._getValue(),e={data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder,dropdownAutoWidth:!0};this.$el.select2(e),this._setValue(t)}},_getIndex:function(e){n.findIndex(this.select_data,{id:e})},_getValue:function(){return this.$el.select2("val")},_setValue:function(e){-1==this._getIndex(e)&&this.select_data.length>0&&(e=this.select_data[0].id),this.$el.select2("val",e)},_template:function(e){return''}});t.default={View:o}}).call(t,i(2),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(56),l=a(o),r=i(37),d=a(r),c=i(20),u=a(c),h=i(31),f=a(h),p=i(70),m=a(p),g=i(4),_=a(g),v=i(32),w=a(v),y=500;try{y=localStorage.getItem("historyContentsLimitPerPageDefault")||y}catch(e){}var b=l.default.PaginatedCollection,x=b.extend(_.default.LoggableMixin).extend({_logNamespace:"history",limitPerPage:y,limitPerProgressiveFetch:y,order:"hid",urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(e,t){this.on({"sync add":this.trackJobStates}),t=t||{},b.prototype.initialize.call(this,e,t),this.history=t.history||null,this.setHistoryId(t.historyId||null),this.includeDeleted=t.includeDeleted||this.includeDeleted,this.includeHidden=t.includeHidden||this.includeHidden,this.model.prototype.idAttribute="type_id"},trackJobStates:function(){var e=this;this.each(function(t){if(!t.has("job_states_summary")&&"dataset_collection"===t.attributes.history_content_type){var i=t.attributes.job_source_type,n=t.attributes.job_source_id;if(i){e.jobStateSummariesCollection.add({id:n,model:i,history_id:e.history_id,collection_id:t.attributes.id});var s=e.jobStateSummariesCollection.get(n);t.jobStatesSummary=s}}})},model:function(e,t){return"dataset"===e.history_content_type?new d.default.HistoryDatasetAssociation(e,t):"dataset_collection"===e.history_content_type?new u.default.HistoryDatasetCollection(e,t):{validationError:"Unknown history_content_type: "+e.history_content_type}},stopPolling:function(){this.jobStateSummariesCollection&&(this.jobStateSummariesCollection.active=!1,this.jobStateSummariesCollection.clearUpdateTimeout())},setHistoryId:function(e){this.stopPolling(),this.historyId=e,e&&(this._setUpWebStorage(),this.jobStateSummariesCollection=new m.default.JobStatesSummaryCollection,this.jobStateSummariesCollection.historyId=e,this.jobStateSummariesCollection.monitor())},_setUpWebStorage:function(e){return this.storage=new f.default.HistoryPrefs({id:f.default.HistoryPrefs.historyStorageKey(this.historyId)}),this.trigger("new-storage",this.storage,this),this.on({"include-deleted":function(e){this.storage.includeDeleted(e)},"include-hidden":function(e){this.storage.includeHidden(e)}}),this.includeDeleted=this.storage.includeDeleted()||!1,this.includeHidden=this.storage.includeHidden()||!1,this},comparators:e.extend(e.clone(b.prototype.comparators),{name:_.default.buildComparator("name",{ascending:!0}),"name-dsc":_.default.buildComparator("name",{ascending:!1}),hid:_.default.buildComparator("hid",{ascending:!1}),"hid-asc":_.default.buildComparator("hid",{ascending:!0})}),running:function(){return this.filter(function(e){return!e.inReadyState()})},runningAndActive:function(){return this.filter(function(e){return!e.inReadyState()&&e.get("visible")&&!e.get("deleted")})},getByHid:function(e){return this.findWhere({hid:e})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},hidden:function(){return this.filter(function(e){return e.hidden()})},deleted:function(){return this.filter(function(e){return e.get("deleted")})},visibleAndUndeleted:function(){return this.filter(function(e){return e.get("visible")&&!e.get("deleted")})},setIncludeDeleted:function(t,i){if(e.isBoolean(t)&&t!==this.includeDeleted){if(this.includeDeleted=t,e.result(i,"silent"))return;this.trigger("include-deleted",t,this)}},setIncludeHidden:function(t,i){if(e.isBoolean(t)&&t!==this.includeHidden){if(this.includeHidden=t,i=i||{},e.result(i,"silent"))return;this.trigger("include-hidden",t,this)}},fetch:function(t){if(t=t||{},this.historyId&&!t.details){var i=f.default.HistoryPrefs.get(this.historyId).toJSON();e.isEmpty(i.expandedIds)||(t.details=e.values(i.expandedIds).join(","))}return b.prototype.fetch.call(this,t)},_buildFetchData:function(t){return e.extend(b.prototype._buildFetchData.call(this,t),{v:"dev"})},_fetchParams:b.prototype._fetchParams.concat(["v","details"]),_buildFetchFilters:function(t){var i=b.prototype._buildFetchFilters.call(this,t)||{},n={};return this.includeDeleted||(n.deleted=!1,n.purged=!1),this.includeHidden||(n.visible=!0),e.defaults(i,n)},getTotalItemCount:function(){return this.history.contentsShown()},fetchUpdated:function(e,t){return e&&(t=t||{filters:{}},t.remove=!1,t.filters={"update_time-ge":e.toISOString(),visible:""}),this.fetch(t)},fetchDeleted:function(t){var i=this;return t=t||{},t.filters=e.extend(t.filters,{deleted:!0,purged:void 0}),t.remove=!1,this.trigger("fetching-deleted",this),this.fetch(t).always(function(){i.trigger("fetching-deleted-done",i)})},fetchHidden:function(t){t=t||{};var i=this;return t.filters=e.extend(t.filters,{visible:!1}),t.remove=!1,i.trigger("fetching-hidden",i),i.fetch(t).always(function(){i.trigger("fetching-hidden-done",i)})},fetchAllDetails:function(t){t=t||{};var i={details:"all"};return t.data=e.extend(t.data||{},i),this.fetch(t)},_filterAndUpdate:function(e,t){var i=this,n=i.model.prototype.idAttribute,s=[t];return i.fetch({filters:e,remove:!1}).then(function(e){return e=e.reduce(function(e,t,s){var a=i.get(t[n]);return a?e.concat(a):e},[]),i.ajaxQueue("save",s,e)})},ajaxQueue:function(t,i,n){return n=n||this.models,new w.default.AjaxQueue(n.slice().reverse().map(function(n,s){var a=e.isString(t)?n[t]:t;return function(){return a.apply(n,i)}})).deferred},progressivelyFetchDetails:function(t){function i(n){n=n||0;var l=e.extend(e.clone(t),{view:"summary",keys:r,limit:o,offset:n,reset:0===n,remove:!1});e.defer(function(){a.fetch.call(a,l).fail(s.reject).done(function(e){s.notify(e,o,n),e.length!==o?(a.allFetched=!0,s.resolve(e,o,n)):i(n+o)})})}t=t||{};var s=n.Deferred(),a=this,o=t.limitPerCall||a.limitPerProgressiveFetch,l=d.default.HistoryDatasetAssociation.prototype.searchAttributes,r=l.join(",");return i(),s},isCopyable:function(t){var i=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return e.isObject(t)&&t.id&&e.contains(i,t.model_class)},copy:function(t){var i,s,a;e.isString(t)?(i=t,a="hda",s="dataset"):(i=t.id,a={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[t.model_class]||"hda",s="hdca"===a?"dataset_collection":"dataset");var o=this,l=n.ajax(this.url(),{method:"POST",contentType:"application/json",data:JSON.stringify({content:i,source:a,type:s})}).done(function(e){o.add([e],{parse:!0})}).fail(function(e,t,n){o.trigger("error",o,l,{},"Error copying contents",{type:s,id:i,source:a})});return l},createHDCA:function(e,t,i,n,s){return this.model({history_content_type:"dataset_collection",collection_type:t,history_id:this.historyId,name:i,hide_source_items:n||!1,element_identifiers:e}).save(s)},haveSearchDetails:function(){return this.allFetched&&this.all(function(t){return e.has(t.attributes,"annotation")})},matches:function(e){return this.filter(function(t){return t.matches(e)})},clone:function(){var e=s.Collection.prototype.clone.call(this);return e.historyId=this.historyId,e},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});t.default={HistoryContents:x}}).call(t,i(1),i(0),i(2))},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(21),r=o(l),d=i(8),c=o(d),u=i(10),h=o(u),f=i(4),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('\n                    \n                    \n                '):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var t=this.model.urls;return a('\n                
    \n                    \n                        \n                    \n                    \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" ){ %>','
    ',(0,g.default)("An error occurred setting the metadata for this dataset"),"
    ","<% } %>"]),error:p.default.wrapTemplate(["<% if( model.error ){ %>",'
    ',(0,g.default)("There was an error getting the data for this dataset"),": <%- model.error %>","
    ","<% } %>"]),purged:p.default.wrapTemplate(["<% if( model.purged ){ %>",'
    ',(0,g.default)("This dataset has been deleted and removed from disk"),"
    ","<% } %>"]),deleted:p.default.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
    ',(0,g.default)("This dataset has been deleted"),"
    ","<% } %>"])}),i=p.default.wrapTemplate(['
    ','
    ','
    ','
    ','
    ',"
    ","<% if( !dataset.deleted && !dataset.purged ){ %>",'
    ','
    ','
    ',"<% if( dataset.peek ){ %>",'
    <%= dataset.peek %>
    ',"<% } %>","<% } %>","
    "],"dataset"),n=p.default.wrapTemplate(['
    ','
    ',(0,g.default)("You do not have permission to view this dataset"),"
    ","
    "],"dataset"),s={};s[c.default.OK]=s[c.default.FAILED_METADATA]=p.default.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'
    ','<%- 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 ){ %>",'
    ',(0,g.default)("The job creating this dataset has been 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){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(29),a=n(s),o=i(51),l=n(o),r=i(3),d=(n(r),l.default.HistoryContentMixin),c=a.default.DatasetCollection,u=c.extend(d).extend({defaults:e.extend(e.clone(c.prototype.defaults),{history_content_type:"dataset_collection",model_class:"HistoryDatasetCollectionAssociation"}),save:function(e,t){return this.isNew()&&(t=t||{},t.url=this.urlRoot+this.get("history_id")+"/contents",e=e||{},e.type="dataset_collection"),c.prototype.save.call(this,e,t)},toString:function(){return"History"+c.prototype.toString.call(this)}});t.default={HistoryDatasetCollection:u}}).call(t,i(1))},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(4),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.name %>',"
    ",'
    ',"
    "],"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){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(4),o=s(a),l=i(3),r=s(l),d=e.View.extend(o.default.LoggableMixin).extend(o.default.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",select_width:"100%",events:{},initialize:function(e){this.show_editor=!1,!1===e.usePrompt?this.label="":this.label='",this.workflow_mode=e.workflow_mode||!1,this.workflow_mode&&(this.events.click="showEditor",this.events.keydown="keydownHandler"),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.workflow_mode?this.$el.html(this._workflowTemplate()):this.$el.html(this._defaultTemplate()),this.$input().select2({placeholder:"Add tags",width:this.workflow_mode?this.width:this.select_width,tags:function(){return e._getTagsUsed()}}),this._setUpBehaviors(),this},_hashToName:function(e){return e.startsWith("#")?"name:"+e.slice(1):e},_nameToHash:function(e){return e.startsWith("name:")&&(e="#"+e.slice(5)),e},_defaultTemplate:function(){return[this.label,this._renderEditor()].join("")},_workflowTemplate:function(){return[this.show_editor?this._renderEditor():this._renderTags()].join(" ")},keydownHandler:function(e){switch(e.which){case 27:this.hideEditor()}},showEditor:function(){this.show_editor=!0,this.render()},hideEditor:function(){this.show_editor=!1,this.render()},_renderEditor:function(){return''},_renderTags:function(){var e=this.model.get("tags"),t=Galaxy.root+"static/images/fugue/tag--plus.png",i=[];return n.each(e,function(e){e=0==e.indexOf("name:")?e.slice(5):e;var t=''+e+"";i.push(t)}),0===i.length&&i.push("'),i.join(" ")},tagsToCSV:function(){var e=this,t=this.model.get("tags");return!n.isArray(t)||n.isEmpty(t)?"":t.map(function(t){return n.escape(e._nameToHash(t))}).sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){var e=this;return n.map(Galaxy.user.get("tags_used"),e._nameToHash)},_setUpBehaviors:function(){var e=this;this.$input().on("change",function(t){t.val=n.map(t.val,e._hashToName),e.model.save({tags:t.val}),t.added&&e._addNewTagToTagsUsed(""+t.added.text)})},_addNewTagToTagsUsed:function(e){var t=Galaxy.user.get("tags_used");n.contains(t,e)||(t.push(e),t.sort(),Galaxy.user.set("tags_used",t))},remove:function(){this.$input.off(),this.stopListening(this.model),e.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",""+this.model,")"].join("")}});t.default={TagsEditor:d}}).call(t,i(2),i(1))},,,,,function(e,t,i){"use strict";(function(e,n,s){Object.defineProperty(t,"__esModule",{value:!0});var a=i(5),o=function(e){return e&&e.__esModule?e:{default:e}}(a),l=e.View.extend({optionsDefault:{with_close:!0,title:null,placement:"top",container:"body",body:null},initialize:function(e){this.setElement(this._template()),this.uid=o.default.uid(),this.options=n.defaults(e||{},this.optionsDefault),this.options.container.parent().append(this.el),this.$title=this.$(".popover-title-label"),this.$close=this.$(".popover-close"),this.$body=this.$(".popover-content"),this.options.body&&this.append(this.options.body);var t=this;s("body").on("mousedown."+this.uid,function(e){t.visible&&!s(t.options.container).is(e.target)&&!s(t.el).is(e.target)&&0===s(t.el).has(e.target).length&&t.hide()})},render:function(){this.$title.html(this.options.title),this.$el.removeClass().addClass("ui-popover popover fade in").addClass(this.options.placement),this.$el.css(this._get_placement(this.options.placement));var e=this;this.options.with_close?this.$close.on("click",function(){e.hide()}).show():this.$close.off().hide()},title:function(e){void 0!==e&&(this.options.title=e,this.$title.html(e))},show:function(){this.render(),this.$el.show(),this.visible=!0},hide:function(){this.$el.hide(),this.visible=!1},append:function(e){this.$body.append(e)},empty:function(){this.$body.empty()},remove:function(){s("body").off("mousedown."+this.uid),this.$el.remove()},_get_placement:function(e){var t,i,n=this._get_width(this.$el),s=this.$el.height(),a=this.options.container,o=this._get_width(a),l=this._get_height(a),r=a.position();if(t=i=0,-1!=["top","bottom"].indexOf(e))switch(i=r.left-n+(o+n)/2,e){case"top":t=r.top-s-5;break;case"bottom":t=r.top+l+5}else switch(t=r.top-s+(l+s)/2,e){case"right":i=r.left+o}return{top:t,left:i}},_get_width:function(e){return e.width()+parseInt(e.css("padding-left"))+parseInt(e.css("margin-left"))+parseInt(e.css("padding-right"))+parseInt(e.css("margin-right"))},_get_height:function(e){return e.height()+parseInt(e.css("padding-top"))+parseInt(e.css("padding-bottom"))},_template:function(e){return'
    '}});t.default={View:l}}).call(t,i(2),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}}function l(e,t){var i=e.toJSON();return $(i,{defaultHideSourceItems:t,creationFn:function(t,i,n){return t=t.map(function(e){return{id:e.id,name:e.name,src:"dataset"===e.history_content_type?"hda":"hdca"}}),e.createHDCA(t,"list",i,n)}})}Object.defineProperty(t,"__esModule",{value:!0});var r=i(20),d=o(r),c=i(8),u=o(c),h=i(4),f=o(h),p=i(52),m=o(p),g=i(9),_=o(g),v=i(53),w=(o(v),i(3)),y=o(w);i(54);var b=e.View.extend(f.default.LoggableMixin).extend({_logNamespace:"collections",tagName:"li",className:"collection-element",initialize:function(e){this.element=e.element||{},this.selected=e.selected||!1},render:function(){this.dragStartHandler=n.bind(this._dragstart,this),this.dragEndHandler=n.bind(this._dragend,this);var e=this.$el.attr("data-element-id",this.element.id).attr("draggable",!0).html(this.template({element:this.element})).get(0);return e.addEventListener("dragstart",this.dragStartHandler,!1),e.addEventListener("dragend",this.dragEndHandler,!1),this.selected&&this.$el.addClass("selected"),this},template:n.template(['',"<%- element.name %>","",'"].join("")),select:function(e){this.$el.toggleClass("selected",e),this.trigger("select",{source:this,selected:this.$el.hasClass("selected")})},discard:function(){var e=this,t=this.$el.parent().width();this.$el.animate({"margin-right":t},"fast",function(){e.trigger("discard",{source:e}),e.destroy()})},destroy:function(){this.off(),this.$el.remove()},events:{click:"_click","click .name":"_clickName","click .discard":"_clickDiscard",dragover:"_sendToParent",drop:"_sendToParent"},_click:function(e){e.stopPropagation(),this.select(e)},_clickName:function(e){e.stopPropagation(),e.preventDefault();var t=([(0,y.default)("Enter a new name for the element"),":\n(",(0,y.default)("Note that changing the name here will not rename the dataset"),")"].join(""),prompt((0,y.default)("Enter a new name for the element")+":",this.element.name));t&&(this.element.name=t,this.render())},_clickDiscard:function(e){e.stopPropagation(),this.discard()},_dragstart:function(e){e.originalEvent&&(e=e.originalEvent),e.dataTransfer.effectAllowed="move",e.dataTransfer.setData("text/plain",JSON.stringify(this.element)),this.$el.addClass("dragging"),this.$el.parent().trigger("collection-element.dragstart",[this])},_dragend:function(e){this.$el.removeClass("dragging"),this.$el.parent().trigger("collection-element.dragend",[this])},_sendToParent:function(e){this.$el.parent().trigger(e)},toString:function(){return"DatasetCollectionElementView()"}}),x=e.View.extend(f.default.LoggableMixin).extend(m.default.CollectionCreatorMixin).extend({_logNamespace:"collections",elementViewClass:b,collectionClass:d.default.HistoryDatasetCollection,className:"list-collection-creator collection-creator flex-row-container",minElements:1,defaultAttributes:{creationFn:function(){throw new TypeError("no creation fn for creator")},oncreate:function(){},oncancel:function(){},autoscrollDist:24,highlightClr:"rgba( 64, 255, 255, 1.0 )"},footerSettings:{".hide-originals":"hideOriginals"},initialize:function(e){this.metric("ListCollectionCreator.initialize",e);var t=this;n.each(this.defaultAttributes,function(i,n){i=e[n]||i,t[n]=i}),t.initialElements=e.elements||[],this._setUpCommonSettings(e),this._instanceSetUp(),this._elementsSetUp(),this._setUpBehaviors()},_instanceSetUp:function(){this.selectedIds={},this.$dragging=null,this.blocking=!1},_elementsSetUp:function(){this.invalidElements=[],this.workingElements=[],this.elementViews=[],this.workingElements=this.initialElements.slice(0),this._ensureElementIds(),this._validateElements(),this._mangleDuplicateNames(),this._sortElements()},_ensureElementIds:function(){return this.workingElements.forEach(function(e){e.hasOwnProperty("id")||(e.id=n.uniqueId())}),this.workingElements},_validateElements:function(){var e=this;return e.invalidElements=[],this.workingElements=this.workingElements.filter(function(t){var i=e._isElementInvalid(t);return i&&e.invalidElements.push({element:t,text:i}),!i}),this.workingElements},_isElementInvalid:function(e){return"dataset_collection"===e.history_content_type?(0,y.default)("is a collection, this is not allowed"):e.state===u.default.OK||n.contains(u.default.NOT_READY_STATES,e.state)?e.deleted||e.purged?(0,y.default)("has been deleted or purged"):null:(0,y.default)("has errored, is paused, or is not accessible")},_mangleDuplicateNames:function(){var e=1,t={};this.workingElements.forEach(function(i){for(var n=i.name;t.hasOwnProperty(n);)if(n=i.name+" ("+e+")",(e+=1)>=900)throw new Error("Safety hit in while loop - thats impressive");i.name=n,t[i.name]=!0})},_sortElements:function(e){},render:function(e,t){return this.workingElements.length .clear-selected").show():this.$(".collection-elements-controls > .clear-selected").hide()},_renderList:function(e,t){var i=this,s=a("
    "),o=i.$list();n.each(this.elementViews,function(e){e.destroy(),i.removeElementView(e)}),i.workingElements.forEach(function(e){var t=i._createElementView(e);s.append(t.$el)}),i._renderClearSelected(),o.empty().append(s.children()),n.invoke(i.elementViews,"render"),o.height()>o.css("max-height")?o.css("border-width","1px 0px 1px 0px"):o.css("border-width","0px")},_createElementView:function(e){var t=new this.elementViewClass({element:e,selected:n.has(this.selectedIds,e.id)});return this.elementViews.push(t),this._listenToElementView(t),t},_listenToElementView:function(e){var t=this;t.listenTo(e,{select:function(e){var i=e.source.element;e.selected?t.selectedIds[i.id]=!0:delete t.selectedIds[i.id],t.trigger("elements:select",e)},discard:function(e){t.trigger("elements:discard",e)}})},addElementView:function(e){},removeElementView:function(e){delete this.selectedIds[e.element.id],this._renderClearSelected(),this.elementViews=n.without(this.elementViews,e),this.stopListening(e)},_renderNoElementsLeft:function(){this._disableNameAndCreate(!0),this.$(".collection-elements").append(this.templates.noElementsLeft())},_elementToJSON:function(e){return e},createList:function(e){if(!this.workingElements.length){var t=(0,y.default)("No valid elements for final list")+". ";return t+=''+(0,y.default)("Cancel")+" ",t+=(0,y.default)("or"),t+=' '+(0,y.default)("start over")+".",void this._showAlert(t)}var i=this,n=this.workingElements.map(function(e){return i._elementToJSON(e)});return i.blocking=!0,i.creationFn(n,e,i.hideOriginals).always(function(){i.blocking=!1}).fail(function(e,t,n){i.trigger("error",{xhr:e,status:t,message:(0,y.default)("An error occurred while creating this collection")})}).done(function(e,t,n){i.trigger("collection:created",e,t,n),i.metric("collection:created",e),"function"==typeof i.oncreate&&i.oncreate.call(this,e,t,n)})},_setUpBehaviors:function(){return this.on("error",this._errorHandler),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this.on("elements:select",function(e){this._renderClearSelected()}),this.on("elements:discard",function(e){var t=e.source.element;this.removeElementView(e.source),this.workingElements=n.without(this.workingElements,t),this.workingElements.length||this._renderNoElementsLeft()}),this},_errorHandler:function(e){this.error(e);var t=this,i=e.message||(0,y.default)("An error occurred");if(e.xhr){var n=e.xhr,s=e.message;0===n.readyState&&0===n.status?i+=": "+(0,y.default)("Galaxy could not be reached and may be updating.")+(0,y.default)(" Try again in a few minutes."):n.responseJSON?i+=":
    "+JSON.stringify(n.responseJSON)+"
    ":i+=": "+s}t._showAlert(i,"alert-danger")},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .main-help":"_toggleHelp","click .header .alert button":"_hideAlert","click .reset":"reset","click .clear-selected":"clearSelectedElements","click .collection-elements":"clearSelectedElements","dragover .collection-elements":"_dragoverElements","drop .collection-elements":"_dropElements","collection-element.dragstart .collection-elements":"_elementDragstart","collection-element.dragend   .collection-elements":"_elementDragend","change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","change .hide-originals":"_changeHideOriginals","click .cancel-create":"_cancelCreate","click .create-collection":"_clickCreate"},reset:function(){this._instanceSetUp(),this._elementsSetUp(),this.render()},clearSelectedElements:function(e){this.$(".collection-elements .collection-element").removeClass("selected"),this.$(".collection-elements-controls > .clear-selected").hide()},_dragoverElements:function(e){e.preventDefault();var t=this.$list();this._checkForAutoscroll(t,e.originalEvent.clientY);var i=this._getNearestElement(e.originalEvent.clientY);this.$(".element-drop-placeholder").remove();var n=s('
    ');i.length?i.before(n):t.append(n)},_checkForAutoscroll:function(e,t){var i=e.offset(),n=e.scrollTop(),s=t-i.top,a=i.top+e.outerHeight()-t;s>=0&&s=0&&ae&&a-o','',(0,y.default)("More help"),"",'
    ','',(0,y.default)("Less"),"","
    ","
    ",'
    ','','',"
    "].join("")),middle:n.template(['
    ','',(0,y.default)("Start over"),"",'',(0,y.default)("Clear selected"),"","
    ",'
    ',"
    "].join("")),footer:n.template(['
    ','
    ','","
    ",'
    ','','
    ',(0,y.default)("Name"),":
    ","
    ","
    ",'
    ','
    ','",'
    ','",'","
    ","
    ",'
    ','","
    ","
    "].join("")),helpContent:n.template(["
    ",(0,y.default)(["Collections of datasets are permanent, ordered lists of datasets that can be passed to tools and ","workflows in order to have analyses done on each member of the entire group. This interface allows ","you to create a collection and re-order the final collection."].join("")),"
    ","
      ","
    • ",(0,y.default)(["Rename elements in the list by clicking on ",'the existing name.'].join("")),"
      • ","
    • ",(0,y.default)(["Discard elements from the final created list by clicking on the ",'"Discard" button.'].join("")),"
      • ","
    • ",(0,y.default)(["Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ",'them and you can then move those selected by dragging the ',"entire group. Deselect them by clicking them again or by clicking the ",'the "Clear selected" link.'].join("")),"
      • ","
    • ",(0,y.default)(['Click the "Start over" link to begin again as if you had just opened ',"the interface."].join("")),"
      • ","
    • ",(0,y.default)(['Click the "Cancel" button to exit the interface.'].join("")),"
      • ","

    ","
    ",(0,y.default)(['Once your collection is complete, enter a name and ','click "Create list".'].join("")),"
    "].join("")),invalidElements:n.template([(0,y.default)("The following selections could not be included due to problems:"),"
      <% _.each( problems, function( problem ){ %>","
    • <%- problem.element.name %>: <%- problem.text %>
      • ","<% }); %>
    "].join("")),noElementsLeft:n.template(['
  • ',(0,y.default)("No elements left! "),(0,y.default)("Would you like to "),'',(0,y.default)("start over"),"?","
    • "].join("")),invalidInitial:n.template(['
    ','
    ','',"<% if( _.size( problems ) ){ %>",(0,y.default)("The following selections could not be included due to problems"),":","
      <% _.each( problems, function( problem ){ %>","
    • <%- problem.element.name %>: <%- problem.text %>
      • ","<% }); %>
    ","<% } else if( _.size( elements ) < 1 ){ %>",(0,y.default)("No datasets were selected"),".","<% } %>","
    ",(0,y.default)("At least one element is needed for the collection"),". ",(0,y.default)("You may need to "),'',(0,y.default)("cancel")," ",(0,y.default)("and reselect new elements"),".","    ","
    ","
    ",'
    ','
    ','
    ','","
    ","
    ","
    "].join(""))}),toString:function(){return"ListCollectionCreator"}}),C=function(e,t,i){var s,o=a.Deferred(),l=Galaxy.modal||new _.default.View;return t=n.defaults(t||{},{elements:e,oncancel:function(){l.hide(),o.reject("cancelled")},oncreate:function(e,t){l.hide(),o.resolve(t)}}),s=new i(t),l.show({title:t.title||(0,y.default)("Create a collection"),body:s.$el,width:"80%",height:"100%",closing_events:!0}),s.render(),window._collectionCreator=s,o},$=function(e,t){return t=t||{},t.title=(0,y.default)("Create a collection from a list of datasets"),C(e,t,x)};t.default={DatasetCollectionElementView:b,ListCollectionCreator:x,collectionCreatorModal:C,listCollectionCreatorModal:$,createListCollection:l}}).call(t,i(2),i(1),i(0),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(50),l=a(o),r=i(4),d=a(r),c=i(3),u=(a(c),{defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(t){return e.extend(t,t.object,{element_id:t.id}),delete t.object,t},constructor:function(e,t){e=this._mergeObject(e),this.idAttribute="element_id",n.Model.apply(this,arguments)},parse:function(e,t){var i=e;return i=this._mergeObject(i)}}),h=n.Model.extend(d.default.LoggableMixin).extend(u).extend({_logNamespace:"collections"}),f=n.Collection.extend(d.default.LoggableMixin).extend({_logNamespace:"collections",model:h,toString:function(){return["DatasetCollectionElementCollection(",this.length,")"].join("")}}),p=l.default.DatasetAssociation.extend(d.default.mixin(u,{url:function(){return this.has("history_id")?Galaxy.root+"api/histories/"+this.get("history_id")+"/contents/"+this.get("id"):(console.warn("no endpoint for non-hdas within a collection yet"),Galaxy.root+"api/datasets")},defaults:e.extend({},l.default.DatasetAssociation.prototype.defaults,u.defaults),_downloadQueryParameters:function(){var e=this.get("file_ext"),t=this.get("element_identifier");return"?to_ext="+e+"&hdca_id="+this.get("parent_hdca_id")+"&element_identifier="+t},constructor:function(e,t){this.debug("\t DatasetDCE.constructor:",e,t),u.constructor.call(this,e,t)},hasDetails:function(){return this.elements&&this.elements.length},toString:function(){this.get("element_identifier");return"DatasetDCE({objStr})"}})),m=f.extend({model:p,toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),g=n.Model.extend(d.default.LoggableMixin).extend(d.default.SearchableModelMixin).extend({_logNamespace:"collections",defaults:{collection_type:null,deleted:!1},collectionClass:function(){return this.attributes.collection_type.indexOf(":")>0?v:m},initialize:function(e,t){this.debug(this+"(DatasetCollection).initialize:",e,t,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){var t=this.collectionClass();this.debug(this+"._createElementsModel",t,this.get("elements"),this.elements);var i=this.get("elements")||[];this.unset("elements",{silent:!0});var n=this;return e.each(i,function(t,i){e.extend(t,{parent_hdca_id:n.get("id")})}),this.elements=new t(i),this.elements},toJSON:function(){var e=n.Model.prototype.toJSON.call(this);return this.elements&&(e.elements=this.elements.toJSON()),e},inReadyState:function(){var e=this.get("populated");return this.isDeletedOrPurged()||e},hasDetails:function(){return 0!==this.elements.length},getVisibleContents:function(e){return this.elements},parse:function(e,t){var i=n.Model.prototype.parse.call(this,e,t);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},delete:function(e){return this.get("deleted")?s.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?s.when():this.save({deleted:!1},e)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name","tags"],toString:function(){return"DatasetCollection("+[this.get("id"),this.get("name")||this.get("element_identifier")].join(",")+")"}}),_=g.extend(d.default.mixin(u,{constructor:function(e,t){this.debug("\t NestedDCDCE.constructor:",e,t),u.constructor.call(this,e,t)},toString:function(){return["NestedDCDCE(",this.object?""+this.object:this.get("element_identifier"),")"].join("")}})),v=f.extend({model:_,toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}});t.default={DatasetCollection:g}}).call(t,i(1),i(2),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(16),r=o(l),d=i(31),c=(o(d),i(56)),u=o(c),h=i(5),f=o(h),p=i(4),m=o(p),g=i(3),_=o(g),v=e.Model.extend(m.default.LoggableMixin).extend(m.default.mixin(m.default.SearchableModelMixin,{_logNamespace:"history",UPDATE_DELAY:4e3,defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",deleted:!1,contents_active:{},contents_states:{}},urlRoot:Galaxy.root+"api/histories",contentsClass:r.default.HistoryContents,searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},initialize:function(e,t){t=t||{},this.logger=t.logger||null,this.log(this+".initialize:",e,t),this.contents=new this.contentsClass([],{history:this,historyId:this.get("id"),order:t.order}),this._setUpListeners(),this._setUpCollectionListeners(),this.updateTimeoutId=null},_setUpListeners:function(){return this.on({error:function(e,t,i,n,s){this.clearUpdateTimeout()},"change:id":function(e,t){this.contents&&(this.contents.historyId=t)}})},_setUpCollectionListeners:function(){return this.contents?this.listenTo(this.contents,{error:function(){this.trigger.apply(this,n.makeArray(arguments))}}):this},contentsShown:function(){var e=this.get("contents_active"),t=e.active||0;return t+=this.contents.includeDeleted?e.deleted:0,t+=this.contents.includeHidden?e.hidden:0},nice_size:function(){var e=this.get("size");return e?f.default.bytesToString(e,!0,2):(0,_.default)("(empty)")},toJSON:function(){return s.extend(e.Model.prototype.toJSON.call(this),{nice_size:this.nice_size()})},get:function(t){return"nice_size"===t?this.nice_size():e.Model.prototype.get.apply(this,arguments)},ownedByCurrUser:function(){return!(!Galaxy||!Galaxy.user)&&(!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.get("user_id"))},numOfUnfinishedJobs:function(){var e=this.get("non_ready_jobs");return e?e.length:0},numOfUnfinishedShownContents:function(){return this.contents.runningAndActive().length||0},_fetchContentRelatedAttributes:function(){var e=["size","non_ready_jobs","contents_active","hid_counter"];return this.fetch({data:a.param({keys:e.join(",")})})},refresh:function(e){var t=this;e=e||{};var i=this.lastUpdateTime;return this.contents.allFetched=!1,(0!==this.contents.currentPage?function(){return t.contents.fetchPage(t.contents.currentPage)}:function(){return t.contents.fetchUpdated(i)})().done(function(i,n,s){var a;try{a=new Date(s.getResponseHeader("Date"))}catch(e){}t.lastUpdateTime=a||new Date,t.checkForUpdates(e)})},checkForUpdates:function(e){var t=this;e=e||{};var i=this.UPDATE_DELAY;if(this.id){var n=function(){t.clearUpdateTimeout(),t.updateTimeoutId=setTimeout(function(){t.refresh(e)},i)};this.numOfUnfinishedShownContents()>0?n():this._fetchContentRelatedAttributes().done(function(e){t.numOfUnfinishedJobs()>0?n():t.trigger("ready")})}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},stopPolling:function(){this.clearUpdateTimeout(),this.contents&&this.contents.stopPolling()},parse:function(t,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},fetchWithContents:function(e,t){e=e||{};var i=this;return e.view="dev-detailed",this.fetch(e).then(function(e){return i.contents.history=i,i.contents.setHistoryId(e.id),i.fetchContents(t)})},fetchContents:function(e){e=e||{};var t=this;return t.lastUpdateTime=new Date,t.contents.fetchCurrentPage(e)},_delete:function(e){return this.get("deleted")?n.when():this.save({deleted:!0},e)},purge:function(e){return this.get("purged")?n.when():this.save({deleted:!0,purged:!0},e)},undelete:function(e){return this.get("deleted")?this.save({deleted:!1},e):n.when()},copy:function(e,t,i){if(e=void 0===e||e,!this.id)throw new Error("You must set the history ID before copying it.");var s={history_id:this.id};e&&(s.current=!0),t&&(s.name=t),i||(s.all_datasets=!1),s.view="dev-detailed";var a=this,o=n.post(this.urlRoot,s);return e?o.then(function(e){return new v(e).setAsCurrent().done(function(){a.trigger("copied",a,e)})}):o.done(function(e){a.trigger("copied",a,e)})},setAsCurrent:function(){var e=this,t=n.getJSON(Galaxy.root+"history/set_as_current?id="+this.id);return t.done(function(){e.trigger("set-as-current",e)}),t},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}})),w=u.default.InfinitelyScrollingCollection,y=w.extend(m.default.LoggableMixin).extend({_logNamespace:"history",model:v,order:"update_time",limitOnFirstFetch:10,limitPerFetch:10,initialize:function(e,t){t=t||{},this.log("HistoryCollection.initialize",e,t),w.prototype.initialize.call(this,e,t),this.includeDeleted=t.includeDeleted||!1,this.currentHistoryId=t.currentHistoryId,this.setUpListeners()},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot},setUpListeners:function(){return this.on({"change:deleted":function(e){this.debug("change:deleted",this.includeDeleted,e.get("deleted")),!this.includeDeleted&&e.get("deleted")&&this.remove(e)},copied:function(e,t){this.setCurrent(new v(t,[]))},"set-as-current":function(e){var t=this.currentHistoryId;this.trigger("no-longer-current",t),this.currentHistoryId=e.id}})},_buildFetchData:function(e){return s.extend(w.prototype._buildFetchData.call(this,e),{view:"dev-detailed"})},_buildFetchFilters:function(e){var t=w.prototype._buildFetchFilters.call(this,e)||{},i={};return this.includeDeleted?i.deleted=null:(i.deleted=!1,i.purged=!1),s.defaults(t,i)},fetchFirst:function(e){var t=this,i=a.when();return this.currentHistoryId&&(i=w.prototype.fetchFirst.call(t,{silent:!0,limit:1,filters:{purged:"",deleted:"","encoded_id-in":this.currentHistoryId}})),i.then(function(){return e=e||{},e.offset=0,t.fetchMore(e)})},comparators:s.extend(s.clone(w.prototype.comparators),{name:m.default.buildComparator("name",{ascending:!0}),"name-dsc":m.default.buildComparator("name",{ascending:!1}),size:m.default.buildComparator("size",{ascending:!1}),"size-asc":m.default.buildComparator("size",{ascending:!0})}),sort:function(e){e=e||{};var t=e.silent,i=this.remove(this.get(this.currentHistoryId));return w.prototype.sort.call(this,s.defaults({silent:!0},e)),this.unshift(i,{silent:!0}),t||this.trigger("sort",this,e),this},create:function(e,t,i,s){var a=this;return n.getJSON(Galaxy.root+"history/create_new_current").done(function(e){a.setCurrent(new v(e,[],i||{}))})},setCurrent:function(e,t){return t=t||{},this.unshift(e,t),this.currentHistoryId=e.get("id"),t.silent||this.trigger("new-current",e,this),this},toString:function(){return"HistoryCollection("+this.length+",current:"+this.currentHistoryId+")"}});t.default={History:v,HistoryCollection:y}}).call(t,i(2),i(0),i(1),i(0))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var n=i(4),s=function(e){return e&&e.__esModule?e:{default:e}}(n),a=s.default.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:!1,show_hidden:!1},addExpanded:function(e){var t=this.get("expandedIds");t[e.id]=e.get("id"),this.save("expandedIds",t)},removeExpanded:function(e){var t=this.get("expandedIds");delete t[e.id],this.save("expandedIds",t)},isExpanded:function(t){return e.result(this.get("expandedIds"),t,!1)},allExpanded:function(){return e.values(this.get("expandedIds"))},clearExpanded:function(){this.set("expandedIds",{})},includeDeleted:function(t){return e.isUndefined(t)||this.set("show_deleted",t),this.get("show_deleted")},includeHidden:function(t){return e.isUndefined(t)||this.set("show_hidden",t),this.get("show_hidden")},toString:function(){return"HistoryPrefs("+this.id+")"}},{storageKeyPrefix:"history:",historyStorageKey:function(e){if(!e)throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+e);return a.storageKeyPrefix+e},get:function(e){return new a({id:a.historyStorageKey(e)})},clearAll:function(e){for(var t in sessionStorage)0===t.indexOf(a.storageKeyPrefix)&&sessionStorage.removeItem(t)}});t.default={HistoryPrefs:a}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function i(e,t){if(!e)throw new ReferenceError("this hasn't been initialised - super() hasn't been called");return!t||"object"!=typeof t&&"function"!=typeof t?e:t}function n(e,t){if("function"!=typeof t&&null!==t)throw new TypeError("Super expression must either be null or a function, not "+typeof t);e.prototype=Object.create(t&&t.prototype,{constructor:{value:e,enumerable:!1,writable:!0,configurable:!0}}),t&&(Object.setPrototypeOf?Object.setPrototypeOf(e,t):e.__proto__=t)}function s(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}Object.defineProperty(t,"__esModule",{value:!0});var a=function e(t,i,n){null===t&&(t=Function.prototype);var s=Object.getOwnPropertyDescriptor(t,i);if(void 0===s){var a=Object.getPrototypeOf(t);return null===a?void 0:e(a,i,n)}if("value"in s)return s.value;var o=s.get;if(void 0!==o)return o.call(n)},o=function(){function e(e,t){for(var i=0;i .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 ){ %>",'
    ',(0,f.default)("There was an error getting the data for this collection"),": <%- model.error %>","
    ","<% } %>"]),purged:u.default.wrapTemplate(["<% if( model.purged ){ %>",'
    ',(0,f.default)("This collection has been deleted and removed from disk"),"
    ","<% } %>"]),deleted:u.default.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
    ',(0,f.default)("This collection has been deleted"),"
    ","<% } %>"])}),i=u.default.wrapTemplate(['
    ','
    ','<%- collection.element_identifier || collection.name %>',"
    ",'
    ',"
    "],"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.element_identifier %>',"
    ",'
    ',"
    "],"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.element_identifier %>',"
    ","
    "],"element");return e.extend({},d.default.DatasetListItemView.prototype.templates,{titleBar:t})}();var w=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.$el},toString:function(){return"NestedDCDCEListItemView("+(this.model?""+this.model:"(no model)")+")"}});t.default={DCListItemView:g,DCEListItemView:_,DatasetDCEListItemView:v,NestedDCDCEListItemView:w}}).call(t,i(1),i(0),i(0))},,,function(e,t,i){"use strict";(function(e,n){function s(t,i,n){return Galaxy.modal.show({title:i,body:t,closing_events:!0,buttons:{Ok:function(){Galaxy.modal.hide()}}}),Galaxy.modal.$el.addClass("error-modal"),n&&(Galaxy.modal.$(".error-details").add(Galaxy.modal.$('button:contains("Details")')).remove(),e("
    ").addClass("error-details").hide().appendTo(Galaxy.modal.$(".modal-content")).append([e("
    ").text(p),e("
    ").text(JSON.stringify(n,null,"  "))]),e('").appendTo(Galaxy.modal.$(".buttons")).click(function(){Galaxy.modal.$(".error-details").toggle()})),Galaxy.modal}function a(e,t,i){if(e){if(e=(0,u.default)(e),t=(0,u.default)(t)||(0,u.default)("Error:"),window.Galaxy&&Galaxy.modal)return s(e,t,i);alert(t+"\n\n"+e),console.log("error details:",JSON.stringify(i))}}function o(){return a((0,u.default)("You appear to be offline. Please check your connection and try again."),(0,u.default)("Offline?"))}function l(){return a((0,u.default)("Galaxy is currently unreachable. Please try again in a few minutes.")+" "+h,(0,u.default)("Cannot connect to Galaxy"))}function r(e,t,i,n,s){return n=n||f,n+=" "+h,s=s||(0,u.default)("An error occurred"),a(n,s,d(e,t,i))}function d(e,t,i){return{raven:n.result(window.Raven,"lastEventId"),userAgent:navigator.userAgent,onLine:navigator.onLine,version:n.result(Galaxy.config,"version_major"),xhr:n.omit(t,n.functions(t)),options:n.omit(i,"xhr"),url:n.result(Galaxy.lastAjax,"url"),data:n.result(Galaxy.lastAjax,"data"),model:n.result(e,"toJSON",""+e),user:n.omit(n.result(Galaxy.user,"toJSON"),"email")}}Object.defineProperty(t,"__esModule",{value:!0});var c=i(3),u=function(e){return e&&e.__esModule?e:{default:e}}(c),h=(0,u.default)("Please contact a Galaxy administrator if the problem persists."),f=(0,u.default)("An error occurred while updating information with the server."),p=(0,u.default)("The following information can assist the developers in finding the source of the error:");t.default={errorModal:a,offlineErrorModal:o,badGatewayErrorModal:l,ajaxErrorModal:r}}).call(t,i(0),i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(50),a=n(s),o=i(51),l=n(o),r=i(4),d=n(r),c=i(3),u=(n(c),a.default.DatasetAssociation),h=l.default.HistoryContentMixin,f=u.extend(d.default.mixin(h,{defaults:e.extend({},u.prototype.defaults,h.defaults,{history_content_type:"dataset",model_class:"HistoryDatasetAssociation"})}));t.default={HistoryDatasetAssociation:f}}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(21),l=a(o),r=i(95),d=a(r),c=i(4),u=a(c),h=i(3),f=a(h);i(39);var p=e.View.extend(u.default.LoggableMixin).extend({_logNamespace:"list",viewClass:l.default.ListItemView,collectionClass:e.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:(0,f.default)("This list is empty"),noneFoundMsg:(0,f.default)("No matching items found"),searchPlaceholder:(0,f.default)("search"),initialize:function(e,t){e=e||{},e.logger&&(this.logger=e.logger),this.log(this+".initialize:",e),this.fxSpeed=n.has(e,"fxSpeed")?e.fxSpeed:this.fxSpeed,this.filters=[],this.searchFor=e.searchFor||"",this.selecting=void 0===e.selecting||e.selecting,this.selected=e.selected||[],this.lastSelected=null,this.dragItems=e.dragItems||!1,this.viewClass=e.viewClass||this.viewClass,this.views=[],this.collection=e.collection||this._createDefaultCollection(),this.filters=e.filters||[],this.$scrollContainer=e.$scrollContainer||this.$scrollContainer,this.title=e.title||"",this.subtitle=e.subtitle||"",this._setUpListeners()},_setUpListeners:function(){return this.off(),this.on({error:function(e,t,i,n,s){console.error(e,t,i,n,s)},loading:function(){this._showLoadingIndicator("loading...",40)},"loading-done":function(){this._hideLoadingIndicator(40)}}),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this._setUpCollectionListeners(),this._setUpViewListeners(),this},_createDefaultCollection:function(){return new this.collectionClass([])},_setUpCollectionListeners:function(){return this.log(this+"._setUpCollectionListeners",this.collection),this.stopListening(this.collection),this.listenTo(this.collection,{error:function(e,t,i,n,s){this.trigger("error",e,t,i,n,s)},update:function(e,t){var i=t.changes;return t.renderAll||i.added.length+i.removed.length>1?this.renderItems():1===i.added.length?this.addItemView(n.first(i.added),e,t):1===i.removed.length?this.removeItemView(n.first(i.removed),e,t):void 0}}),this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners"),this.on({"view:selected":function(e,t){if(t&&t.shiftKey&&this.lastSelected){var i=this.viewFromModelId(this.lastSelected);i&&this.selectRange(e,i)}else t&&t.altKey&&!this.selecting&&this.showSelectors();this.selected.push(e.model.id),this.lastSelected=e.model.id},"view:de-selected":function(e,t){this.selected=n.without(this.selected,e.model.id)}})},render:function(e){this.log(this+".render",e);var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var e=s(this.templates.el({},this));return this._renderControls(e),this._renderTitle(e),this._renderSubtitle(e),this._renderSearch(e),this.renderItems(e),e},_renderControls:function(e){this.debug(this+"(ListPanel)._renderControls");var t=s(this.templates.controls({},this));return e.find(".controls").replaceWith(t),t},_renderTitle:function(e){},_renderSubtitle:function(e){},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;i.log("_queueNewRender:",e,t),s(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",this.className).append(e.children()),this.selecting&&this.showSelectors(0),this},_setUpBehaviors:function(e){return e=e||this.$el,this.$controls(e).find("[title]").tooltip(),this._renderMultiselectActionMenu(e),this},_renderMultiselectActionMenu:function(e){e=e||this.$el;var t=e.find(".list-action-menu"),i=this.multiselectActions();if(!i.length)return t.empty();var n=s(['
    ','",'","
    "].join("")),a=i.map(function(e){var t=['
  • ',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(["
    ",'
    ','
    ','
    ',"
    "]),controls:u.default.wrapTemplate(['
    ','
    ','
    <%- view.title %>
    ',"
    ",'
    <%- view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
    "])}}();var m=p.extend({modelCollectionKey:"contents",initialize:function(e){p.prototype.initialize.call(this,e),this.selecting=void 0!==e.selecting&&e.selecting,this.setModel(this.model,e)},setModel:function(e,t){if(t=t||{},this.debug(this+".setModel:",e,t),this.freeModel(),this.freeViews(),e){var i=this.model?this.model.get("id"):null;this.model=e,this.logger&&(this.model.logger=this.logger),this._setUpModelListeners(),this.stopListening(this.collection),this.collection=this.model[this.modelCollectionKey]||t.collection||this._createDefaultCollection(),this._setUpCollectionListeners(),i&&e.get("id")!==i&&this.trigger("new-model",this)}return this},freeModel:function(){return this.model&&this.stopListening(this.model),this},_setUpModelListeners:function(){return this.log(this+"._setUpModelListeners",this.model),this.listenTo(this.model,"error",function(){var e=Array.prototype.slice.call(arguments,0);e.unshift("error"),this.trigger.apply(this,e)},this),this.logger&&this.listenTo(this.model,"all",function(e){this.info(this+"(model)",e,arguments)}),this},_renderControls:function(e){this.debug(this+"(ModelListPanel)._renderControls");var t=this.model?this.model.toJSON():{},i=s(this.templates.controls(t,this));return e.find(".controls").replaceWith(i),i},toString:function(){return"ModelListPanel("+this.model+")"}});m.prototype.templates=function(){var e=u.default.wrapTemplate(['
    ','
    ','
    <%- model.name %>
    ',"
    ",'
    <%- view.subtitle %>
    ','
    ','
    ','
    ','
    ',"
    ",'
    ','
    ','",'","
    ",'
    ',"
    ","
    ","
    "]);return n.extend(n.clone(p.prototype.templates),{controls:e})}(),t.default={ListPanel:p,ModelListPanel:m}}).call(t,i(2),i(1),i(0))},function(e,t,i){"use strict";function n(e,t){function i(e){o(this).parent().children("input").val("").trigger("searchInput.clear").blur(),t.onclear()}function n(e,n){if(!n)return i();o(this).trigger("search.search",n),"function"==typeof t.onfirstsearch&&u?(u=!1,t.onfirstsearch(n)):t.onsearch(n)}function s(){return['"].join("")}var r=27,d=13,c=o(e),u=!0,h={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onfirstsearch:null,onsearch:function(e){},minSearchLen:0,escWillClear:!0,oninit:function(){}};return"string"===a.default.type(t)?("toggle-loading"===t&&function(){c.find(".search-loading").toggle(),c.find(".search-clear").toggle()}(),c):("object"===a.default.type(t)&&(t=a.default.extend(!0,{},h,t)),c.addClass("search-input").prepend([function(){return o(s()).focus(function(e){o(this).select()}).keyup(function(e){if(e.preventDefault(),e.stopPropagation(),e.which===r&&t.escWillClear)i.call(this,e);else{var s=o(this).val();(e.which===d||t.minSearchLen&&s.length>=t.minSearchLen)&&n.call(this,e,s)}}).val(t.initialVal)}(),function(){return o([''].join("")).tooltip({placement:"bottom"}).click(function(e){i.call(this,e)})}(),function(){return o([''].join("")).hide().tooltip({placement:"bottom"})}()]))}var s=i(0),a=function(e){return e&&e.__esModule?e:{default:e}}(s),o=a.default,l=window._l||function(e){return e};a.default.fn.extend({searchInput:function(e){return this.each(function(){return n(this,e)})}})},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(17),a=n(s),o=i(4),l=n(o),r=i(58),d=n(r),c=i(3),u=n(c),h=a.default.DatasetListItemView,f=h.extend({className:h.prototype.className+" history-content",initialize:function(e,t){h.prototype.initialize.call(this,e,t)},toString:function(){return"HDAListItemView("+(this.model?""+this.model:"(no model)")+")"}});f.prototype.templates=function(){var t=function(t){return'\n        
    \n            \n            
    \n                '+t.hid+'\n                '+e.escape(t.name)+"\n            
    \n            
    \n            "+d.default.nametagTemplate(t)+"\n        
    \n    "},i=e.extend({},h.prototype.templates.warnings,{hidden:l.default.wrapTemplate(["<% if( !dataset.visible ){ %>",'
    ',(0,u.default)("This dataset has been hidden"),"
    ","<% } %>"],"dataset")});return e.extend({},h.prototype.templates,{titleBar:t,warnings:i})}(),t.default={HDAListItemView:f}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(8),a=n(s),o=i(33),l=n(o),r=i(59),d=n(r),c=i(4),u=(n(c),i(58)),h=n(u),f=i(3),p=n(f),m=l.default.DCListItemView,g=m.extend({className:m.prototype.className+" history-content",_setUpListeners:function(){var e=this;m.prototype._setUpListeners.call(this);var t=function(t,i){e.render()};this.model.jobStatesSummary&&this.listenTo(this.model.jobStatesSummary,"change",t),this.listenTo(this.model,{"change:tags change:visible change:state":t})},_getFoldoutPanelClass:function(){return d.default.CollectionView},_swapNewRender:function(e){m.prototype._swapNewRender.call(this,e);var t,i=this.model.jobStatesSummary;t=i?i.new()?"loading":i.errored()?"error":i.terminal()?"ok":i.running()?"running":"queued":this.model.get("job_source_id")?"loading":this.model.get("populated_state")?a.default.OK:a.default.RUNNING,this.$el.addClass("state-"+t);var n=this.stateDescription();return this.$(".state-description").html(n),this.$el},stateDescription:function(){var e=this.model,t=(e.get("element_count"),e.get("job_source_type")),i=(this.model.get("collection_type"),d.default.collectionTypeDescription(e)),n=d.default.collectionDescription(e),s=e.jobStatesSummary;if(t&&"Job"!=t){if(s&&s.hasDetails()){var a=s.new(),o=a?null:s.jobCount();if(a)return'\n                        
    \n                            Creating jobs...\n                            
    \n                        
    ';if(s.errored()){return"a "+i+" with "+s.numInError()+" / "+o+" jobs in error"}if(s.terminal())return n;var l=s.states().running||0,r=s.states().ok||0,c=r/(1*o),u=l/(1*o),h=1-c-u;return'\n                        
    \n                            '+(o&&o>1?o+" jobs":"a job")+" generating a "+i+'\n                            
    \n                            
    \n                            
    \n                        
    '}return'\n                    
    \n                        Loading job data for '+i+'...\n                        
    \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            \n            
    \n                '+t.hid+'\n                '+e.escape(t.name)+'\n            
    \n            
    \n            
    \n            '+h.default.nametagTemplate(t)+"\n        
    \n    "};return e.extend({},m.prototype.templates,{warnings:t,titleBar:i})}(),t.default={HDCAListItemView:g}}).call(t,i(1))},,function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(67),l=a(o),r=i(42),d=a(r),c=i(9),u=a(c),h=i(5),f=a(h),p=e.View.extend({el:"body",className:"full-content",_panelids:["left","right"],initialize:function(t){var i=this;this.config=n.defaults(t.config||{},{message_box_visible:!1,message_box_content:"",message_box_class:"info",show_inactivity_warning:!1,inactivity_box_content:""}),Galaxy.modal=this.modal=new u.default.View,Galaxy.display=this.display=function(e){e.title?(f.default.setWindowTitle(e.title),e.allow_title_display=!1):(f.default.setWindowTitle(),e.allow_title_display=!0),i.center.display(e)},Galaxy.router=this.router=t.Router&&new t.Router(i,t),this.masthead=new l.default.View(this.config),this.center=new d.default.CenterPanel,this.$el.attr("scroll","no"),this.$el.html(this._template()),this.$("#masthead").replaceWith(this.masthead.$el),this.$("#center").append(this.center.$el),this.$el.append(this.masthead.frame.$el),this.$el.append(this.modal.$el),this.$messagebox=this.$("#messagebox"),this.$inactivebox=this.$("#inactivebox"),this.panels={},n.each(this._panelids,function(e){var n=e.charAt(0).toUpperCase()+e.slice(1),s=t[n];if(s){var a=new s(i,t);i[a.toString()]=a,i.panels[e]=new d.default.SidePanel({id:e,el:i.$("#"+e),view:a})}}),this.render(),this.router&&e.history.start({root:Galaxy.root,pushState:!0})},render:function(){return s(".select2-hidden-accessible").remove(),this.masthead.render(),this.renderMessageBox(),this.renderInactivityBox(),this.renderPanels(),this._checkCommunicationServerOnline(),this},renderMessageBox:function(){if(this.config.message_box_visible){var e=this.config.message_box_content||"",t=this.config.message_box_class||"info";this.$el.addClass("has-message-box"),this.$messagebox.attr("class","panel-"+t+"-message").html(e).toggle(!!e).show()}else this.$el.removeClass("has-message-box"),this.$messagebox.hide();return this},renderInactivityBox:function(){if(this.config.show_inactivity_warning){var e=this.config.inactivity_box_content||"",t=s("").attr("href",Galaxy.root+"user/resend_verification").text("Resend verification");this.$el.addClass("has-inactivity-box"),this.$inactivebox.html(e+" ").append(t).toggle(!!e).show()}else this.$el.removeClass("has-inactivity-box"),this.$inactivebox.hide();return this},renderPanels:function(){var e=this;return n.each(this._panelids,function(t){var i=e.panels[t];i?i.render():(e.$("#center").css(t,0),e.$("#"+t).hide())}),this},_template:function(){return['
    ','
    ','
    ','
    ','
    ','
    ','
    ','",'
    '].join("")},toString:function(){return"PageLayoutView"},_checkCommunicationServerOnline:function(){var e=window.Galaxy.config.communication_server_host,t=window.Galaxy.config.communication_server_port,i=window.Galaxy.user.attributes.preferences,n=s("#show-chat-online");i&&-1!=["1","true"].indexOf(i.communication_server)?s.ajax({url:e+":"+t}).success(function(e){null!==window.Galaxy.user.id&&"hidden"===n.css("visibility")&&n.css("visibility","visible")}).error(function(e){n.css("visibility","hidden")}):n.css("visibility","hidden")}});t.default={View:p}}).call(t,i(2),i(1),i(0))},,,,,,function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var i=e.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",status:"init",info:null,file_name:"",file_mode:"",file_size:0,file_type:null,file_path:"",file_data:null,percentage:0,space_to_tab:!1,to_posix_lines:!0,enabled:!0},reset:function(e){this.clear().set(this.defaults).set(e)}}),n=e.Collection.extend({model:i});t.default={Model:i,Collection:n}}).call(t,i(2))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(8),l=a(o),r=i(4),d=a(r),c=i(3),u=a(c),h=d.default.SearchableModelMixin,f=e.Model.extend(d.default.LoggableMixin).extend(d.default.mixin(h,{_logNamespace:"dataset",defaults:{state:l.default.NEW,deleted:!1,purged:!1,name:"(unnamed dataset)",accessible:!0,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(e,t){this.debug(this+"(Dataset).initialize",e,t),
 //!! this state is not in trans.app.model.Dataset.states - set it here -
-this.get("accessible")||this.set("state",l.default.NOT_VIEWABLE),this.urls=this._generateUrls(),this._setUpListeners()},_generateUrls:function(){var e=this.get("id");if(!e)return{};var t={purge:"datasets/"+e+"/purge_async",display:"datasets/"+e+"/display/?preview=True",edit:"datasets/edit?dataset_id="+e,download:"datasets/"+e+"/display"+this._downloadQueryParameters(),report_error:"dataset/errors?id="+e,rerun:"tool_runner/rerun?id="+e,show_params:"datasets/"+e+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+e+"&metadata_name="};return n.each(t,function(e,i){t[i]=Galaxy.root+e}),this.urls=t,t},_downloadQueryParameters:function(){return"?to_ext="+this.get("file_ext")},_setUpListeners:function(){this.on("change:state",function(e,t){this.log(this+" has changed state:",e,t),this.inReadyState()&&this.trigger("state:ready",e,t,this.previous("state"))}),this.on("change:id change:file_ext",function(e){this._generateUrls()})},toJSON:function(){var t=e.Model.prototype.toJSON.call(this);return n.extend(t,{urls:this.urls})},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},inReadyState:function(){var e=n.contains(l.default.READY_STATES,this.get("state"));return this.isDeletedOrPurged()||e},hasDetails:function(){return!this.get("accessible")||this.has("annotation")},hasData:function(){return this.get("file_size")>0},fetch:function(t){var i=this;return e.Model.prototype.fetch.call(this,t).always(function(){i._generateUrls()})},parse:function(t,i){var n=e.Model.prototype.parse.call(this,t,i);return n.create_time&&(n.create_time=new Date(n.create_time)),n.update_time&&(n.update_time=new Date(n.update_time)),n},save:function(t,i){return i=i||{},i.wait=!!n.isUndefined(i.wait)||i.wait,e.Model.prototype.save.call(this,t,i)},delete:function(e){return this.get("deleted")?s.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?s.when():this.save({deleted:!1},e)},purge:function(e){if(this.get("purged"))return s.when();e=e||{},e.url=this.urls.purge;var t=this,i=s.ajax(e);return i.done(function(e,i,n){t.set({deleted:!0,purged:!0})}),i.fail(function(i,n,s){var a=(0,u.default)("Unable to purge dataset");i.responseJSON&&i.responseJSON.error?a=i.responseJSON.error:-1!==i.responseText.indexOf("Removal of datasets by users is not allowed in this Galaxy instance")&&(a="Removal of datasets by users is not allowed in this Galaxy instance"),i.responseText=a,t.trigger("error",t,i,e,(0,u.default)(a),{error:a})}),i},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var e=this.get("id")||"";return this.get("name")&&(e='"'+this.get("name")+'",'+e),"Dataset("+e+")"}})),p=e.Collection.extend(d.default.LoggableMixin).extend({_logNamespace:"dataset",model:f,urlRoot:Galaxy.root+"api/datasets",url:function(){return this.urlRoot},ids:function(){return this.map(function(e){return e.get("id")})},notReady:function(){return this.filter(function(e){return!e.inReadyState()})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},ajaxQueue:function(e,t){var i=s.Deferred(),n=this.length,a=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(s,l){return function(){var r=e.call(s,t);r.done(function(e){i.notify({curr:l,total:n,response:e,model:s})}),r.always(function(e){a.push(e),o.length?o.shift()():i.resolve(a)})}}).value();return o.shift()(),i},matches:function(e){return this.filter(function(t){return t.matches(e)})},toString:function(){return["DatasetAssociationCollection(",this.length,")"].join("")}});t.default={DatasetAssociation:f,DatasetAssociationCollection:p}}).call(t,i(2),i(1),i(0))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(8),a=(n(s),i(4)),o=(n(a),i(3)),l=(n(o),1e3);try{l=localStorage.getItem("collectionFuzzyCountDefault")||l}catch(e){}var r={defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",hidden:function(){return!this.get("visible")},isVisible:function(e,t){var i=!0;return e||!this.get("deleted")&&!this.get("purged")||(i=!1),t||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var e=this.get("history_content_type"),t=this.get("history_id"),i=this.get("id"),n=""+this.urlRoot+t+"/contents/"+e+"s/"+i;return"dataset_collection"==e&&(n=n+"?view=element-reference&fuzzy_count="+l),n},hide:function(t){return this.get("visible")?this.save({visible:!1},t):e.when()},unhide:function(t){return this.get("visible")?e.when():this.save({visible:!0},t)},toString:function(){return[this.get("type_id"),this.get("hid"),this.get("name")].join(":")}};t.default={HistoryContentMixin:r}}).call(t,i(0))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var i={_validationWarning:function(e,t){"name"===e&&(e=this.$(".collection-name").add(this.$(".collection-name-prompt")),this.$(".collection-name").focus().select()),t?(e=e||this.$(".validation-warning"),e.removeClass("validation-warning")):e.addClass("validation-warning")},_changeHideOriginals:function(e){this.hideOriginals=this.$(".hide-originals").prop("checked")},_changeName:function(e){this._validationWarning("name",!!this._getName())},_nameCheckForEnter:function(e){13!==e.keyCode||this.blocking||this._clickCreate()},_getName:function(){return e.escape(this.$(".collection-name").val())},_clickMoreHelp:function(e){e.stopPropagation(),this.$(".main-help").addClass("expanded"),this.$(".more-help").hide()},_clickLessHelp:function(e){e.stopPropagation(),this.$(".main-help").removeClass("expanded"),this.$(".more-help").show()},_toggleHelp:function(e){e.stopPropagation(),this.$(".main-help").toggleClass("expanded"),this.$(".more-help").toggle()},_showAlert:function(e,t){t=t||"alert-danger",this.$(".main-help").hide(),this.$(".header .alert").attr("class","alert alert-dismissable").addClass(t).show().find(".alert-message").html(e)},_hideAlert:function(e){this.$(".main-help").show(),this.$(".header .alert").hide()},_cancelCreate:function(e){"function"==typeof this.oncancel&&this.oncancel.call(this)},_clickCreate:function(e){var t=this._getName();t?this.blocking||this.createList(t):this._validationWarning("name")},_setUpCommonSettings:function(e){this.hideOriginals=e.defaultHideSourceItems||!1},_renderFooter:function(t,i){var n=this,s=this.$(".footer").empty().html(this.templates.footer());return e.each(this.footerSettings,function(e,t){n.$(t).prop("checked",n[e])}),"function"==typeof this.oncancel&&this.$(".cancel-create.btn").show(),s},_creatorTemplates:{main:e.template(['
    ','
    ','
    '].join(""))}};t.default={CollectionCreatorMixin:i}}).call(t,i(1))},function(e,t,i){"use strict";function n(e,t){var i=/(-?[0-9\.]+)/g,n=e.toString().toLowerCase()||"",s=t.toString().toLowerCase()||"",a=String.fromCharCode(0),o=n.replace(i,a+"$1"+a).split(a),l=s.replace(i,a+"$1"+a).split(a),r=new Date(n).getTime(),d=r?new Date(s).getTime():null;if(d){if(rd)return 1}for(var c,u,h=0,f=Math.max(o.length,l.length);hu)return 1}return 0}Object.defineProperty(t,"__esModule",{value:!0}),t.default=n},function(e,t,i){"use strict";var n=i(0),s=function(e){return e&&e.__esModule?e:{default:e}}(n),a=s.default;s.default.fn.extend({hoverhighlight:function(e,t){return e=e||"body",this.length?(a(this).each(function(){var i=a(this),n=i.data("target");n&&i.mouseover(function(i){a(n,e).css({background:t})}).mouseout(function(e){a(n).css({background:""})})}),this):this}})},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(9),l=a(o),r=i(36),d=a(r),c=i(3),u=a(c),h={defaultName:e.template("Copy of '<%- name %>'"),title:e.template((0,u.default)("Copying history")+' "<%- name %>"'),submitLabel:(0,u.default)("Copy"),errorMessage:(0,u.default)("History could not be copied."),progressive:(0,u.default)("Copying history"),activeLabel:(0,u.default)("Copy only the active, non-deleted datasets"),allLabel:(0,u.default)("Copy all datasets including deleted ones"),anonWarning:(0,u.default)("As an anonymous user, unless you login or register, you will lose your current history ")+(0,u.default)("after copying this history. "),_template:e.template(["<% if( isAnon ){ %>",'
    ',"<%- anonWarning %>",(0,u.default)("You can"),' ',(0,u.default)("login here")," ",(0,u.default)("or")," ",' ',(0,u.default)("register here"),".","
    ","<% } %>","
    ",'
    ",'','","<% if( allowAll ){ %>","
    ","
    ",(0,u.default)("Choose which datasets from the original history to include:"),"
    ",'/>','',"
    ",'/>','',"<% } %>","
    "].join("")),_showAjaxIndicator:function(){var e='
     '+this.progressive+"...
    ";this.modal.$(".modal-body").empty().append(e).css({"margin-top":"8px"})},dialog:function(t,i,a){function o(){var e=t.$("#copy-modal-title").val();if(!e)return void t.$(".invalid-title").show();var n="copy-all"===t.$('input[name="copy-what"]:checked').val();t.$("button").prop("disabled",!0),l._showAjaxIndicator(),i.copy(!0,e,n).done(function(e){r.resolve(e)}).fail(function(t,s,a){var o={name:e,copyAllDatasets:n};d.default.ajaxErrorModal(i,t,o,l.errorMessage),r.rejectWith(r,arguments)}).done(function(){m&&t.hide()})}a=a||{};var l=this,r=n.Deferred(),c=a.nameFn||this.defaultName,h=c({name:i.get("name")}),f=a.allDatasets?"copy-all":"copy-non-deleted",p=!!e.isUndefined(a.allowAll)||a.allowAll,m=!!e.isUndefined(a.autoClose)||a.autoClose;this.modal=t;var g=a.closing_callback;return t.show(e.extend(a,{title:this.title({name:i.get("name")}),body:s(l._template({name:h,isAnon:Galaxy.user.isAnonymous(),allowAll:p,copyWhat:f,activeLabel:this.activeLabel,allLabel:this.allLabel,anonWarning:this.anonWarning})),buttons:e.object([[(0,u.default)("Cancel"),function(){t.hide()}],[this.submitLabel,o]]),height:"auto",closing_events:!0,closing_callback:function(e){e&&r.reject({cancelled:!0}),g&&g(e)}})),t.$("#copy-modal-title").focus().select(),t.$("#copy-modal-title").on("keydown",function(e){13===e.keyCode&&(e.preventDefault(),o())}),r}},f=e.extend({},h,{defaultName:e.template("imported: <%- name %>"),title:e.template((0,u.default)("Importing history")+' "<%- name %>"'),submitLabel:(0,u.default)("Import"),errorMessage:(0,u.default)("History could not be imported."),progressive:(0,u.default)("Importing history"),activeLabel:(0,u.default)("Import only the active, non-deleted datasets"),allLabel:(0,u.default)("Import all datasets including deleted ones"),anonWarning:(0,u.default)("As an anonymous user, unless you login or register, you will lose your current history ")+(0,u.default)("after importing this history. ")}),p=function(e,t){t=t||{};var i=window.parent.Galaxy.modal||new l.default.View({});return t.useImport?f.dialog(i,e,t):h.dialog(i,e,t)};t.default=p}).call(t,i(1),i(0),i(0))},function(e,t,i){"use strict";(function(e){function n(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}Object.defineProperty(t,"__esModule",{value:!0});var s=i(1),a=n(s),o=i(2),l=n(o),r=i(4),d=function(e){return e&&e.__esModule?e:{default:e}}(r),c=l.Collection.extend({initialize:function(e,t){l.Collection.prototype.initialize.call(this,e,t),this.setOrder(t.order||this.order,{silent:!0})},_setUpListeners:function(){return this.on({"changed-order":this.sort})},fetch:function(e){return e=this._buildFetchOptions(e),Galaxy.debug("fetch options:",e),l.Collection.prototype.fetch.call(this,e)},_buildFetchOptions:function(e){e=a.clone(e)||{};var t=this;e.traditional=!0,e.data=e.data||t._buildFetchData(e),Galaxy.debug("data:",e.data);var i=this._buildFetchFilters(e);return Galaxy.debug("filters:",i),a.isEmpty(i)||a.extend(e.data,this._fetchFiltersToAjaxData(i)),Galaxy.debug("data:",e.data),e},_buildFetchData:function(e){var t={};return this.order&&(t.order=this.order),a.defaults(a.pick(e,this._fetchParams),t)},_fetchParams:["order","limit","offset","view","keys"],_buildFetchFilters:function(e){return a.clone(e.filters||{})},_fetchFiltersToAjaxData:function(e){var t={q:[],qv:[]};return a.each(e,function(e,i){void 0!==e&&""!==e&&(!0===e&&(e="True"),!1===e&&(e="False"),null===e&&(e="None"),t.q.push(i),t.qv.push(e))}),t},reset:function(e,t){return this.allFetched=!1,l.Collection.prototype.reset.call(this,e,t)},order:null,comparators:{update_time:d.default.buildComparator("update_time",{ascending:!1}),"update_time-asc":d.default.buildComparator("update_time",{ascending:!0}),create_time:d.default.buildComparator("create_time",{ascending:!1}),"create_time-asc":d.default.buildComparator("create_time",{ascending:!0})},setOrder:function(e,t){t=t||{};var i=this,n=i.comparators[e];if(a.isUndefined(n))throw new Error("unknown order: "+e);if(n!==i.comparator)return i.order=e,i.comparator=n,t.silent||i.trigger("changed-order",t),i}}),u=c.extend({limitPerPage:500,initialize:function(e,t){c.prototype.initialize.call(this,e,t),this.currentPage=t.currentPage||0},getTotalItemCount:function(){return this.length},shouldPaginate:function(){return this.getTotalItemCount()>=this.limitPerPage},getLastPage:function(){return Math.floor(this.getTotalItemCount()/this.limitPerPage)},getPageCount:function(){return this.getLastPage()+1},getPageLimitOffset:function(e){return e=this.constrainPageNum(e),{limit:this.limitPerPage,offset:e*this.limitPerPage}},constrainPageNum:function(e){return Math.max(0,Math.min(e,this.getLastPage()))},fetchPage:function(e,t){var i=this;return e=i.constrainPageNum(e),i.currentPage=e,t=a.defaults(t||{},i.getPageLimitOffset(e)),i.trigger("fetching-more"),i.fetch(t).always(function(){i.trigger("fetching-more-done")})},fetchCurrentPage:function(e){return this.fetchPage(this.currentPage,e)},fetchPrevPage:function(e){return this.fetchPage(this.currentPage-1,e)},fetchNextPage:function(e){return this.fetchPage(this.currentPage+1,e)}}),h=c.extend({limitOnFirstFetch:null,limitPerFetch:100,initialize:function(e,t){c.prototype.initialize.call(this,e,t),this.limitOnFirstFetch=t.limitOnFirstFetch||this.limitOnFirstFetch,this.limitPerFetch=t.limitPerFetch||this.limitPerFetch,this.allFetched=!1,this.lastFetched=t.lastFetched||0},_buildFetchOptions:function(e){return e.remove=e.remove||!1,c.prototype._buildFetchOptions.call(this,e)},fetchFirst:function(e){return Galaxy.debug("ControlledFetchCollection.fetchFirst:",e),e=e?a.clone(e):{},this.allFetched=!1,this.lastFetched=0,this.fetchMore(a.defaults(e,{reset:!0,limit:this.limitOnFirstFetch}))},fetchMore:function(t){Galaxy.debug("ControlledFetchCollection.fetchMore:",t),t=a.clone(t||{});var i=this;if(Galaxy.debug("fetchMore, options.reset:",t.reset),!t.reset&&i.allFetched)return e.when();t.reset?t.offset=0:void 0===t.offset&&(t.offset=i.lastFetched);var n=t.limit=t.limit||i.limitPerFetch||null;return Galaxy.debug("fetchMore, limit:",n,"offset:",t.offset),i.trigger("fetching-more"),i.fetch(t).always(function(){i.trigger("fetching-more-done")}).done(function(e){var t=a.isArray(e)?e.length:0;i.lastFetched+=t,Galaxy.debug("fetchMore, lastFetched:",i.lastFetched),(!n||t');this.$el.html(a.text(t).slideDown(e.isUndefined(i)?this.fxSpeed:i))},_hideLoadingIndicator:function(t){this.$(".loading-indicator").slideUp(e.isUndefined(t)?this.fxSpeed+200:t,function(){n(this).remove()})},_buildNewRender:function(){var e=k.prototype._buildNewRender.call(this);return this._renderSelectButton(e),e},_renderSelectButton:function(e){if(e=e||this.$el,!this.multiselectActions().length)return null;if(!this.views.length)return this.hideSelectors(),e.find(".controls .actions .show-selectors-btn").remove(),null;var t=e.find(".controls .actions .show-selectors-btn");return t.length?t:(0,y.default)({title:(0,C.default)("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"}).prependTo(e.find(".controls .actions"))},_renderEmptyMessage:function(e){var t=this.$emptyMessage(e);return this.model.get("contents_active").active<=0?t.empty().append(this.emptyMsg).show():this.searchFor&&this.model.contents.haveSearchDetails()&&!this.views.length?t.empty().append(this.noneFoundMsg).show():(t.hide(),n())},$scrollContainer:function(e){return this.$list(e)},_toggleContentsLoadingIndicator:function(e){e?this.$list().html('
    '):this.$list().find(".contents-loading-indicator").remove()},renderItems:function(e){e=e||this.$el;var t=this.$list(e);n(".tooltip").remove(),t.empty(),this.views=[];var i=this._filterCollection();return i.length?(this._renderPagination(e),this.views=this._renderSomeItems(i,t)):e.find("> .controls .list-pagination").empty(),this._renderEmptyMessage(e).toggle(!i.length),this.trigger("views:ready",this.views),this.views},_renderPagination:function(e){var t=e.find("> .controls .list-pagination");return this.searchFor||!this.model.contents.shouldPaginate()?t.empty():(t.html(this.templates.pagination({current:this.model.contents.currentPage+1,last:this.model.contents.getLastPage()+1},this)),t.find("select.pages").tooltip(),t)},_renderSomeItems:function(e,t){var i=this,n=[];return t.append(e.map(function(e){var t=i._createItemView(e);return n.push(t),i._renderItemView$el(t)})),n},_filterItem:function(e){var t=this.model.contents;return(t.includeHidden||!e.hidden())&&(t.includeDeleted||!e.isDeletedOrPurged())&&k.prototype._filterItem.call(this,e)},_getItemViewClass:function(e){var t=e.get("history_content_type");switch(t){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+t)},_getItemViewOptions:function(t){var i=k.prototype._getItemViewOptions.call(this,t);return e.extend(i,{linkTarget:this.linkTarget,expanded:this.model.contents.storage.isExpanded(t.id),hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(e){var t=this;return k.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{expanded:function(e){t.model.contents.storage.addExpanded(e.model)},collapsed:function(e){t.model.contents.storage.removeExpanded(e.model)}})},collapseAll:function(){this.model.contents.storage.clearExpanded(),k.prototype.collapseAll.call(this)},getSelectedModels:function(){var e=k.prototype.getSelectedModels.call(this);return e.historyId=this.collection.historyId,e},events:e.extend(e.clone(k.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click > .controls .prev":"_clickPrevPage","click > .controls .next":"_clickNextPage","change > .controls .pages":"_changePageSelect","click .messages [class$=message]":"clearMessages"}),_clickPrevPage:function(e){this.model.stopPolling(),this.model.contents.fetchPrevPage()},_clickNextPage:function(e){this.model.stopPolling(),this.model.contents.fetchNextPage()},_changePageSelect:function(e){this.model.stopPolling();var t=n(e.currentTarget).val();this.model.contents.fetchPage(t)},toggleShowDeleted:function(e,t){e=void 0!==e?e:!this.model.contents.includeDeleted;var i=this.model.contents;return i.setIncludeDeleted(e,t),this.trigger("show-deleted",e),i.fetchCurrentPage({renderAll:!0}),e},toggleShowHidden:function(e,t,i){e=void 0!==e?e:!this.model.contents.includeHidden;var n=this.model.contents;return n.setIncludeHidden(e,i),this.trigger("show-hidden",e),n.fetchCurrentPage({renderAll:!0}),e},_firstSearch:function(e){var t=this;if(this.log("onFirstSearch",e),this.model.contents.haveSearchDetails())return void this.searchItems(e);this.$("> .controls .search-input").searchInput("toggle-loading"),this.searchFor=e;this.model.contents.progressivelyFetchDetails({silent:!0}).progress(function(e,i,n){t.renderItems(),t.trigger("search:loading-progress",i,n)}).always(function(){t.$el.find("> .controls .search-input").searchInput("toggle-loading")}).done(function(){t.searchItems(e,"force")})},clearSearch:function(e){var t=this;return this.searchFor?(this.searchFor="",this.trigger("search:clear",this),this.$("> .controls .search-query").val(""),this.model.contents.fetchCurrentPage({silent:!0}).done(function(){t.renderItems()}),this):this},errorHandler:function(t,i,n){if(!i||0!==i.status||0!==i.readyState){if(this.error(t,i,n),e.isString(t)&&e.isString(i)){var s=t,a=i;return v.default.errorModal(s,a,n)}return i&&502===i.status?v.default.badGatewayErrorModal():v.default.ajaxErrorModal(t,i,n)}},clearMessages:function(t){return(e.isUndefined(t)?this.$messages().children('[class$="message"]'):n(t.currentTarget)).fadeOut(this.fxSpeed,function(){n(this).remove()}),this},scrollToHid:function(t){return this.scrollToItem(e.first(this.viewsWhereModel({hid:t})))},ordinalIndicator:function(e){var t=""+e;switch(t.charAt(t.length-1)){case"1":return t+"st";case"2":return t+"nd";case"3":return t+"rd";default:return t+"th"}},toString:function(){return"HistoryView("+(this.model?this.model.get("name"):"")+")"}});S.prototype.templates=function(){var t=function(){return'
    \n            
    \n            
      \n            
      \',\n        
      '},i=x.default.wrapTemplate(['
      ','
      ','
      <%- history.name %>
      ',"
      ",'
      ','
      <%- history.nice_size %>
      ','
      ','
      ',"<% if( history.deleted && history.purged ){ %>",'
      ',(0,C.default)("This history has been purged and deleted"),"
      ","<% } else if( history.deleted ){ %>",'
      ',(0,C.default)("This history has been deleted"),"
      ","<% } else if( history.purged ){ %>",'
      ',(0,C.default)("This history has been purged"),"
      ","<% } %>","<% if( history.message ){ %>",'
      messagesmall">',"<%= history.message.text %>","
      ","<% } %>","
      ",'
      ','
      ','
      ','
      ',"
      ",'
      ','
      ','",'","
      ",'
      ',"
      ","
      ",'
      ',"
      "],"history"),n=x.default.wrapTemplate(['','",''],"pages");return e.extend(e.clone(k.prototype.templates),{el:t,controls:i,pagination:n})}(),t.default={HistoryView:S}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e){function i(t){return''+e.escape(t.slice(5))+""}function n(t){var n=e.filter(e.uniq(t.tags),function(e){return 0===e.indexOf("name:")}),s=e.sortBy(n).map(i);return'\n        
      \n            '+s.join("")+"\n        
      "}Object.defineProperty(t,"__esModule",{value:!0}),t.default={nametagTemplate:n}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}function s(e){var t=e.get("collection_type");return"list"==t?(0,f.default)("list"):"paired"==t?(0,f.default)("dataset pair"):"list:paired"==t?(0,f.default)("list of pairs"):(0,f.default)("nested list")}function a(e){var t=e.get("element_count"),i="a "+s(e);if(t){var n;1==t?n="with 1 item":t&&(n="with "+t+" items"),i=i+" "+(0,f.default)(n)}return i}Object.defineProperty(t,"__esModule",{value:!0});var o=i(38),l=n(o),r=i(29),d=(n(r),i(33)),c=n(d),u=i(4),h=(n(u),i(3)),f=n(h),p=l.default.ModelListPanel,m=p.extend({_logNamespace:"collections",className:p.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:c.default.DatasetDCEListItemView,modelCollectionKey:"elements",initialize:function(e){p.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,this.panelStack=[],this.parentName=e.parentName,this.foldoutStyle=e.foldoutStyle||"foldout",this.downloadUrl=Galaxy.root+"api/dataset_collections/"+this.model.attributes.id+"/download"},getNestedDCDCEViewClass:function(){return c.default.NestedDCDCEListItemView.extend({foldoutPanelClass:m})},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;this.handleWarning(e),i.log("_queueNewRender:",e,t),i._swapNewRender(e),i.trigger("rendered",i)},handleWarning:function(e){var t=this.views.length,i=this.model.get("element_count");if(i&&i!==t){var n=(0,f.default)("displaying only "+t+" of "+i+" items");e.find(".elements-warning").html('
      '+n+"
      ")}},_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        
      \n            
      \n            \n                \n                '+(0,f.default)("Back to ")+"\n                "+e.escape(i.parentName)+'\n            \n            
      \n            
      \n                
      '+(e.escape(t.name)||e.escape(t.element_identifier))+'
      \n                
      \n                    '+n+'\n                
      \n            
      \n            
      \n            
      \n            
      \n            
      \n                \n                   \n                \n            
      \n        
      '};return e.extend(e.clone(p.prototype.templates),{controls:t})}(),t.default={collectionTypeDescription:s,collectionDescription:a,CollectionView:m}}).call(t,i(1))},function(e,t,i){"use strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(8),o=s(a),l=i(17),r=s(l),d=i(22),c=s(d),u=i(61),h=s(u),f=i(10),p=s(f),m=i(4),g=s(m),_=i(3),v=s(_),w=r.default.DatasetListItemView,y=w.extend({initialize:function(e){w.prototype.initialize.call(this,e),this.hasUser=e.hasUser,this.purgeAllowed=e.purgeAllowed||!1,this.tagsEditorShown=e.tagsEditorShown||!1,this.annotationEditorShown=e.annotationEditorShown||!1},_renderPrimaryActions:function(){var e=w.prototype._renderPrimaryActions.call(this);return this.model.get("state")===o.default.NOT_VIEWABLE?e:w.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){var t=this;if(this.model.get("state")===o.default.DISCARDED||!this.model.get("accessible"))return null;var i=this.model.get("purged"),n=this.model.get("deleted"),s={title:(0,v.default)("Edit attributes"),href:Galaxy.root+"datasets/edit?dataset_id="+this.model.attributes.id,faIcon:"fa-pencil",classes:"edit-btn",onclick:function(e){Galaxy.router&&(e.preventDefault(),Galaxy.router.push("datasets/edit",{dataset_id:t.model.attributes.id}))}};return n||i?(s.disabled=!0,i?s.title=(0,v.default)("Cannot edit attributes of datasets removed from disk"):n&&(s.title=(0,v.default)("Undelete dataset to edit attributes"))):e.contains([o.default.UPLOAD,o.default.NEW],this.model.get("state"))&&(s.disabled=!0,s.title=(0,v.default)("This dataset is not yet editable")),(0,p.default)(s)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var e=this,t=this.model.isDeletedOrPurged();return(0,p.default)({title:t?(0,v.default)("Dataset is already deleted"):(0,v.default)("Delete"),disabled:t,faIcon:"fa-times",classes:"delete-btn",onclick:function(){e.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},_renderDetails:function(){var t=w.prototype._renderDetails.call(this),i=this.model.get("state");return!this.model.isDeletedOrPurged()&&e.contains([o.default.OK,o.default.FAILED_METADATA],i)&&(this._renderTags(t),this._renderAnnotation(t),this._makeDbkeyEditLink(t)),this._setUpBehaviors(t),t},_renderToolHelpButton:function(){var e=this.model.attributes.dataset_id,t=this.model.attributes.creating_job,i=this,s=function(t){var s='
      ';t.name&&t.help?(s+="Tool help for "+t.name+"
      ",s+=t.help):s+="Tool help is unavailable for this dataset.
      ",s+="
      ",i.$el.find(".details").append(n.parseHTML(s))},a=function(e){n.ajax({url:Galaxy.root+"api/tools/"+e.tool_id+"/build"}).done(function(e){s(e)}).fail(function(){s({})})};return null===Galaxy.user.id?null:(0,p.default)({title:(0,v.default)("Tool Help"),classes:"icon-btn",href:"#",faIcon:"fa-question",onclick:function(){i.$el.find(".toolhelp").length>0?i.$el.find(".toolhelp").toggle():n.ajax({url:Galaxy.root+"api/jobs/"+t}).done(function(e){a(e)}).fail(function(){console.log('Failed at recovering job information from the  Galaxy API for job id "'+t+'".')})}})},_renderSecondaryActions:function(){var e=w.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case o.default.UPLOAD:case o.default.NOT_VIEWABLE:return e;case o.default.ERROR:return e.unshift(this._renderErrButton()),e.concat([this._renderRerunButton(),this._renderToolHelpButton()]);case o.default.OK:case o.default.FAILED_METADATA:return e.concat([this._renderRerunButton(),this._renderVisualizationsButton(),this._renderToolHelpButton()])}return e.concat([this._renderRerunButton(),this._renderToolHelpButton()])},_renderErrButton:function(){var e=this;return(0,p.default)({title:(0,v.default)("View or report this error"),href:Galaxy.root+"datasets/error?dataset_id="+this.model.attributes.id,classes:"report-error-btn",faIcon:"fa-bug",onclick:function(t){Galaxy.router&&(t.preventDefault(),Galaxy.router.push("datasets/error",{dataset_id:e.model.attributes.id}))}})},_renderRerunButton:function(){var e=this.model.get("creating_job");if(this.model.get("rerunnable"))return(0,p.default)({title:(0,v.default)("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(t){Galaxy.router&&(t.preventDefault(),Galaxy.router.push("/",{job_id:e}))}})},_renderVisualizationsButton:function(){var t=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||e.isEmpty(t))return null;if(!e.isObject(t[0]))return this.warn("Visualizations have been switched off"),null;var i=n(this.templates.visualizations(t,this));return i.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(i.find(".visualization-link").addBack(".visualization-link")),i},_addScratchBookFn:function(e){e.click(function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:(0,v.default)("Visualization"),url:n(this).attr("href")}),e.preventDefault(),e.stopPropagation())})},_renderTags:function(e){if(this.hasUser){var t=this;this.tagsEditor=new c.default.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.tagsEditorShown=!0},onhide:function(){t.tagsEditorShown=!1},$activator:(0,p.default)({title:(0,v.default)("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(e){if(this.hasUser){var t=this;this.annotationEditor=new h.default.AnnotationEditor({model:this.model,el:e.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.annotationEditorShown=!0},onhide:function(){t.annotationEditorShown=!1},$activator:(0,p.default)({title:(0,v.default)("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(e){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var t=n('?').attr("href",this.model.urls.edit).attr("target","_top");e.find(".dbkey .value").replaceWith(t)}},events:e.extend(e.clone(w.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(e){this.trigger("edit",this,e)},"click .delete-btn":function(e){this.trigger("delete",this,e)},"click .rerun-btn":function(e){this.trigger("rerun",this,e)},"click .report-err-btn":function(e){this.trigger("report-err",this,e)},"click .visualization-btn":function(e){this.trigger("visualize",this,e)},"click .dbkey a":function(e){this.trigger("edit",this,e)}}),_clickUndeleteLink:function(e){return this.model.undelete(),!1},_clickPurgeLink:function(e){return confirm((0,v.default)("This will permanently remove the data in your dataset. Are you sure?"))&&this.model.purge(),!1},toString:function(){return"HDAEditView("+(this.model?""+this.model:"(no model)")+")"}});y.prototype.templates=function(){var t=e.extend({},w.prototype.templates.warnings,{failed_metadata:g.default.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','
      ',(0,v.default)("An error occurred setting the metadata for this dataset"),'
      ',(0,v.default)("Set it manually or retry auto-detection"),"","
      ","<% } %>"],"dataset"),deleted:g.default.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'
      ',(0,v.default)("This dataset has been deleted"),'
      ',(0,v.default)("Undelete it"),"","<% if( view.purgeAllowed ){ %>",'
      ',(0,v.default)("Permanently remove it from disk"),"","<% } %>","
      ","<% } %>"],"dataset")}),i=g.default.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'">','',"","<% } else { %>",'
      ','','',"",'","
      ","<% } %>"],"visualizations");return e.extend({},w.prototype.templates,{warnings:t,visualizations:i})}(),t.default={DatasetListItemEdit:y}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(4),o=s(a),l=i(3),r=s(l);i(15);var d=e.View.extend(o.default.LoggableMixin).extend(o.default.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(e){e=e||{},this.tooltipConfig=e.tooltipConfig||{placement:"bottom"},this.listenTo(this.model,"change:annotation",function(){this.render()}),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.$el.html(this._template()),this.$annotation().make_text_editable({use_textarea:!0,on_finish:function(t){e.$annotation().text(t),e.model.save({annotation:t},{silent:!0}).fail(function(){e.$annotation().text(e.model.previous("annotation"))})}}),this},_template:function(){var e=this.model.get("annotation");return['",'
      ',n.escape(e),"
      "].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off(),this.stopListening(this.model),e.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",""+this.model,")"].join("")}});t.default={AnnotationEditor:d}}).call(t,i(2),i(1))},,,,,,,,,function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0});var n=i(2),s=function(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}(n),a=i(32),o=function(e){return e&&e.__esModule?e:{default:e}}(a),l=["new","queued","running"],r=["error","deleted"],d=s.Model.extend({url:function(){return Galaxy.root+"api/histories/"+this.attributes.history_id+"/contents/dataset_collections/"+this.attributes.collection_id+"/jobs_summary"},hasDetails:function(){return this.has("populated_state")},new:function(){return!this.hasDetails()||"new"==this.get("populated_state")},errored:function(){return"error"===this.get("populated_state")||this.anyWithStates(r)},states:function(){return this.get("states")||{}},anyWithState:function(e){return(this.states()[e]||0)>0},anyWithStates:function(e){var t=this.states();for(var i in e)if((t[e[i]]||0)>0)return!0;return!1},numWithStates:function(e){var t=this.states(),i=0;for(var n in e)i+=t[e[n]]||0;return i},numInError:function(){return this.numWithStates(r)},running:function(){return this.anyWithState("running")},terminal:function(){return!this.new()&&!this.anyWithStates(l)},jobCount:function(){var e=this.states(),t=0;for(var i in e)t+=e[i];return t},toString:function(){return"JobStatesSummary(id="+this.get("id")+")"}}),c=s.Collection.extend({model:d,initialize:function(){this.updateTimeoutId=null,this.active=!0},url:function(){var e=this.models.filter(function(e){return!e.terminal()}),t=e.map(function(e){return e.get("id")}).join(","),i=e.map(function(e){return e.get("model")}).join(",");return Galaxy.root+"api/histories/"+this.historyId+"/jobs_summary?ids="+t+"&types="+i},monitor:function(){var e=this;if(this.clearUpdateTimeout(),this.active){var t=function(){e.updateTimeoutId=setTimeout(function(){e.monitor()},2e3)},i=this.models.filter(function(e){return!e.terminal()});if(i.length,!1){var n=i.map(function(e){return function(){return e.fetch()}});return new o.default.AjaxQueue(n).done(t)}i.length>0?this.fetch({remove:!1}).done(t):t()}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},toString:function(){return"JobStatesSummaryCollection()"}});t.default={JobStatesSummary:d,JobStatesSummaryCollection:c,FETCH_STATE_ON_ADD:!1}},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(57),l=a(o),r=i(16),d=(a(r),i(8)),c=(a(d),i(37)),u=a(c),h=i(72),f=a(h),p=i(96),m=a(p),g=i(22),_=a(g),v=i(61),w=a(v),y=i(28),b=a(y),x=i(73),$=a(x),C=i(74),k=a(C),S=i(10),T=a(S),P=i(47),D=(a(P),i(4)),E=a(D),A=i(3),M=a(A);i(15);var I=l.default.HistoryView,j=I.extend({HDAViewClass:f.default.HDAListItemEdit,HDCAViewClass:m.default.HDCAListItemEdit,initialize:function(e){e=e||{},I.prototype.initialize.call(this,e),this.tagsEditor=null,this.dragItems=!0,this.annotationEditor=null,this.purgeAllowed=e.purgeAllowed||!1,this.annotationEditorShown=e.annotationEditorShown||!1,this.tagsEditorShown=e.tagsEditorShown||!1},_setUpListeners:function(){return I.prototype._setUpListeners.call(this),this.on({"droptarget:drop":function(e,t){this.dataDropped(t),this.dropTargetOff()},"view:attached view:removed":function(){this._renderCounts()},"search:loading-progress":this._renderSearchProgress,"search:searching":this._renderSearchFindings})},_setUpModelListeners:function(){return I.prototype._setUpModelListeners.call(this),this.listenTo(this.model,"change:size",this.updateHistoryDiskSize),this},_setUpCollectionListeners:function(){return I.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"change:deleted":this._handleItemDeletedChange,"change:visible":this._handleItemVisibleChange,"change:purged":function(e){this.model.fetch()},"fetching-deleted":function(e){this.$("> .controls .deleted-count").html(""+(0,M.default)("loading...")+"")},"fetching-hidden":function(e){this.$("> .controls .hidden-count").html(""+(0,M.default)("loading...")+"")},"fetching-deleted-done fetching-hidden-done":this._renderCounts}),this},_buildNewRender:function(){var e=I.prototype._buildNewRender.call(this);return this.model?(Galaxy&&Galaxy.user&&Galaxy.user.id&&Galaxy.user.id===this.model.get("user_id")&&(this._renderTags(e),this._renderAnnotation(e)),e):e},updateHistoryDiskSize:function(){this.$(".history-size").text(this.model.get("nice_size"))},renderItems:function(e){var t=I.prototype.renderItems.call(this,e);return this.searchFor?this._renderSearchFindings(e):this._renderCounts(e),t},_renderCounts:function(t){t=t instanceof e?t:this.$el;var i=this.templates.counts(this.model.toJSON(),this);return t.find("> .controls .subtitle").html(i)},_renderTags:function(e){var t=this;this.tagsEditor=new _.default.TagsEditor({model:this.model,el:e.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDATagEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDATagEditors(!1,t.fxSpeed)},$activator:(0,T.default)({title:(0,M.default)("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".controls .actions"))})},_renderAnnotation:function(e){var t=this;this.annotationEditor=new w.default.AnnotationEditor({model:this.model,el:e.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDAAnnotationEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDAAnnotationEditors(!1,t.fxSpeed)},$activator:(0,T.default)({title:(0,M.default)("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".controls .actions"))})},_setUpBehaviors:function(e){if(e=e||this.$el,I.prototype._setUpBehaviors.call(this,e),this.model&&Galaxy.user&&!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.model.get("user_id")){var t=this;e.find("> .controls .name").attr("title",(0,M.default)("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(e){var i=t.model.get("name");e&&e!==i?(t.$el.find("> .controls .name").text(e),t.model.save({name:e}).fail(function(){t.$el.find("> .controls .name").text(t.model.previous("name"))})):t.$el.find("> .controls .name").text(i)}})}},multiselectActions:function(){var e=this,t=[{html:(0,M.default)("Hide datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.hide;e.getSelectedModels().ajaxQueue(t)}},{html:(0,M.default)("Unhide datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.unhide;e.getSelectedModels().ajaxQueue(t)}},{html:(0,M.default)("Delete datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.delete;e.getSelectedModels().ajaxQueue(t)}},{html:(0,M.default)("Undelete datasets"),func:function(){var t=u.default.HistoryDatasetAssociation.prototype.undelete;e.getSelectedModels().ajaxQueue(t)}}];return e.purgeAllowed&&t.push({html:(0,M.default)("Permanently delete datasets"),func:function(){if(confirm((0,M.default)("This will permanently remove the data in your datasets. Are you sure?"))){var t=u.default.HistoryDatasetAssociation.prototype.purge;e.getSelectedModels().ajaxQueue(t)}}}),t=t.concat(e._collectionActions())},_collectionActions:function(){var e=this;return[{html:(0,M.default)("Build Dataset List"),func:function(){e.buildCollection("list")}},{html:(0,M.default)("Build Dataset Pair"),func:function(){e.buildCollection("paired")}},{html:(0,M.default)("Build List of Dataset Pairs"),func:function(){e.buildCollection("list:paired")}}]},buildCollection:function(e,t,i){var n,s=this,t=t||s.getSelectedModels(),i=i||!1;"list"==e?n=b.default.createListCollection:"paired"==e?n=$.default.createPairCollection:"list:paired"==e?n=k.default.createListOfPairsCollection:console.warn("Unknown collectionType encountered "+e),n(t,i).done(function(){s.model.refresh()})},_getItemViewOptions:function(e){var t=I.prototype._getItemViewOptions.call(this,e);return n.extend(t,{purgeAllowed:this.purgeAllowed,tagsEditorShown:this.tagsEditor&&!this.tagsEditor.hidden,annotationEditorShown:this.annotationEditor&&!this.annotationEditor.hidden}),t},_handleItemDeletedChange:function(e){e.get("deleted")?this._handleItemDeletion(e):this._handleItemUndeletion(e),this._renderCounts()},_handleItemDeletion:function(e){var t=this.model.get("contents_active");t.deleted+=1,t.active-=1,this.model.contents.includeDeleted||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUndeletion:function(e){var t=this.model.get("contents_active");t.deleted-=1,this.model.contents.includeDeleted||(t.active-=1),this.model.set("contents_active",t)},_handleItemVisibleChange:function(e){e.hidden()?this._handleItemHidden(e):this._handleItemUnhidden(e),this._renderCounts()},_handleItemHidden:function(e){var t=this.model.get("contents_active");t.hidden+=1,t.active-=1,this.model.contents.includeHidden||this.removeItemView(e),this.model.set("contents_active",t)},_handleItemUnhidden:function(e){var t=this.model.get("contents_active");t.hidden-=1,this.model.contents.includeHidden||(t.active-=1),this.model.set("contents_active",t)},toggleHDATagEditors:function(e,t){n.each(this.views,function(i){i.tagsEditor&&i.tagsEditor.toggle(e,t)})},toggleHDAAnnotationEditors:function(e,t){n.each(this.views,function(i){i.annotationEditor&&i.annotationEditor.toggle(e,t)})},events:n.extend(n.clone(I.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(e){this.toggleShowDeleted()},"click .toggle-hidden-link":function(e){this.toggleShowHidden()}}),_renderSearchProgress:function(e,t){var i=e+t;return this.$("> .controls .subtitle").html(["",(0,M.default)("Searching "),i,"/",this.model.contentsShown(),""].join(""))},_renderSearchFindings:function(t){t=t instanceof e?t:this.$el;var i=this.templates.found(this.model.toJSON(),this);return t.find("> .controls .subtitle").html(i),this},dropTargetOn:function(){if(this.dropTarget)return this;this.dropTarget=!0;var e={dragenter:n.bind(this.dragenter,this),dragover:n.bind(this.dragover,this),dragleave:n.bind(this.dragleave,this),drop:n.bind(this.drop,this)},t=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),t]);for(var i in e)e.hasOwnProperty(i)&&t.on(i,e[i]);return this},_renderDropTarget:function(){return this.$(".history-drop-target").remove(),s("
      ").addClass("history-drop-target")},_renderDropTargetHelp:function(){return this.$(".history-drop-target-help").remove(),s("
      ").addClass("history-drop-target-help").text((0,M.default)("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget)return this;this.dropTarget=!1;var e=this.$(".history-drop-target").get(0);for(var t in this._dropHandlers)this._dropHandlers.hasOwnProperty(t)&&e.off(t,this._dropHandlers[t]);return this.$(".history-drop-target").remove(),this.$(".history-drop-target-help").remove(),this},dropTargetToggle:function(){return this.dropTarget?this.dropTargetOff():this.dropTargetOn(),this},dragenter:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","2px solid black")},dragover:function(e){e.preventDefault(),e.stopPropagation()},dragleave:function(e){e.preventDefault(),e.stopPropagation(),this.$(".history-drop-target").css("border","1px dashed black")},drop:function(e){e.preventDefault();var t=this,i=e.originalEvent.dataTransfer,n=i.getData("text");i.dropEffect="move";try{n=JSON.parse(n)}catch(e){t.warn("error parsing JSON from drop:",n)}return t.trigger("droptarget:drop",e,n,t),!1},dataDropped:function(t){var i=this;return n.isObject(t)&&"HistoryDatasetAssociation"===t.model_class&&t.id?0!==i.contents.currentPage?i.contents.fetchPage(0).then(function(){return i.model.contents.copy(t.id)}):i.model.contents.copy(t.id):e.when()},toString:function(){return"HistoryViewEdit("+(this.model?this.model.get("name"):"")+")"}});j.prototype.templates=function(){var e=E.default.wrapTemplate(["<% var shown = Math.max( view.views.length, history.contents_active.active ) %>","<% if( shown ){ %>",'',"<%- shown %> ",(0,M.default)("shown"),"","<% } %>","<% if( history.contents_active.deleted ){ %>",'',"<% if( view.model.contents.includeDeleted ){ %>",'',(0,M.default)("hide deleted"),"","<% } else { %>","<%- history.contents_active.deleted %> ",'',(0,M.default)("deleted"),"","<% } %>","","<% } %>","<% if( history.contents_active.hidden ){ %>",'',"<% if( view.model.contents.includeHidden ){ %>",'',(0,M.default)("hide hidden"),"","<% } else { %>","<%- history.contents_active.hidden %> ",'',(0,M.default)("hidden"),"","<% } %>","","<% } %>"],"history"),t=E.default.wrapTemplate([(0,M.default)("Found")," <%- view.views.length %>, ","<% if( history.contents_active.deleted ){ %>","<% if( view.model.contents.includeDeleted ){ %>",'',(0,M.default)("hide deleted"),", ","<% } else { %>",'',(0,M.default)("show deleted"),", ","<% } %>","<% } %>","<% if( history.contents_active.hidden ){ %>","<% if( view.model.contents.includeHidden ){ %>",'',(0,M.default)("hide hidden"),"","<% } else { %>",'',(0,M.default)("show hidden"),"","<% } %>","<% } %>"],"history");return n.extend(n.clone(I.prototype.templates),{counts:e,found:t})}(),t.default={HistoryViewEdit:j}}).call(t,i(0),i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(60),o=s(a),l=i(40),r=s(l),d=i(4),c=s(d),u=i(3),h=s(u),f=o.default.DatasetListItemEdit,p=f.extend({className:f.prototype.className+" history-content",_fetchModelDetails:function(){var t=this;return t.model.inReadyState()&&!t.model.hasDetails()?t.model.fetch({silent:!0}):t.model.has("rerunnable")?e.when():t.model.fetch({silent:!0,data:{keys:["rerunnable","creating_job"].join(",")}})},events:n.extend(n.clone(f.prototype.events),{"click .unhide-link":function(e){return this.model.unhide(),!1}}),toString:function(){return"HDAListItemEdit("+(this.model?""+this.model:"(no model)")+")"}});p.prototype.templates=function(){var e=n.extend({},f.prototype.templates.warnings,{hidden:c.default.wrapTemplate(["<% if( !dataset.visible ){ %>",'
      ',(0,h.default)("This dataset has been hidden"),'
      ',(0,h.default)("Unhide it"),"","
      ","<% } %>"],"dataset")});return n.extend({},f.prototype.templates,{titleBar:r.default.HDAListItemView.prototype.templates.titleBar,warnings:e})}(),t.default={HDAListItemEdit:p}}).call(t,i(0),i(1))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}function o(e,t){var i=e.toJSON();return v(i,{defaultHideSourceItems:t,creationFn:function(t,i,n){return t=[{name:"forward",src:"hda",id:t[0].id},{name:"reverse",src:"hda",id:t[1].id}],e.createHDCA(t,"paired",i,n)}})}Object.defineProperty(t,"__esModule",{value:!0});var l=i(28),r=a(l),d=i(20),c=a(d),u=i(4),h=a(u),f=i(3),p=a(f),m=e.View.extend(h.default.LoggableMixin).extend({_logNamespace:"collections",tagName:"li",className:"collection-element",initialize:function(e){this.element=e.element||{},this.identifier=e.identifier},render:function(){return this.$el.attr("data-element-id",this.element.id).html(this.template({identifier:this.identifier,element:this.element})),this},template:n.template(['<%- identifier %>','<%- element.name %>'].join("")),destroy:function(){this.off(),this.$el.remove()},toString:function(){return"DatasetCollectionElementView()"}}),g=r.default.ListCollectionCreator,_=g.extend({elementViewClass:m,collectionClass:c.default.HistoryDatasetCollection,className:"pair-collection-creator collection-creator flex-row-container",_mangleDuplicateNames:function(){},render:function(e,t){return 2===this.workingElements.length?g.prototype.render.call(this,e,t):this._renderInvalid(e,t)},_renderList:function(e,t){var i=this,a=s("
      "),o=i.$list();n.each(this.elementViews,function(e){e.destroy(),i.removeElementView(e)}),a.append(i._createForwardElementView().$el),a.append(i._createReverseElementView().$el),o.empty().append(a.children()),n.invoke(i.elementViews,"render")},_createForwardElementView:function(){return this._createElementView(this.workingElements[0],{identifier:"forward"})},_createReverseElementView:function(){return this._createElementView(this.workingElements[1],{identifier:"reverse"})},_createElementView:function(e,t){var i=new this.elementViewClass(n.extend(t,{element:e}));return this.elementViews.push(i),i},swap:function(){this.workingElements=[this.workingElements[1],this.workingElements[0]],this._renderList()},events:n.extend(n.clone(g.prototype.events),{"click .swap":"swap"}),templates:n.extend(n.clone(g.prototype.templates),{middle:n.template(['
      ','',(0,p.default)("Swap"),"","
      ",'
      ',"
      "].join("")),helpContent:n.template(["
      ",(0,p.default)(["Pair collections are permanent collections containing two datasets: one forward and one reverse. ","Often these are forward and reverse reads. The pair collections can be passed to tools and ","workflows in order to have analyses done on both datasets. This interface allows ","you to create a pair, name it, and swap which is forward and which reverse."].join("")),"
      ","
        ","
      • ",(0,p.default)(['Click the "Swap" link to make your forward dataset the reverse ',"and the reverse dataset forward."].join("")),"
        • ","
      • ",(0,p.default)(['Click the "Cancel" button to exit the interface.'].join("")),"
        • ","

      ","
      ",(0,p.default)(['Once your collection is complete, enter a name and ','click "Create list".'].join("")),"
      "].join("")),invalidInitial:n.template(['
      ','
      ','',"<% if( _.size( problems ) ){ %>",(0,p.default)("The following selections could not be included due to problems"),"
        <% _.each( problems, function( problem ){ %>","
      • <%- problem.element.name %>: <%- problem.text %>
        • ","<% }); %>
      ","<% } else if( _.size( elements ) === 0 ){ %>",(0,p.default)("No datasets were selected"),".","<% } else if( _.size( elements ) === 1 ){ %>",(0,p.default)("Only one dataset was selected"),": <%- elements[0].name %>","<% } else if( _.size( elements ) > 2 ){ %>",(0,p.default)("Too many datasets were selected"),': <%- _.pluck( elements, "name" ).join( ", ") %>',"<% } %>","
      ",(0,p.default)("Two (and only two) elements are needed for the pair"),". ",(0,p.default)("You may need to "),'',(0,p.default)("cancel")," ",(0,p.default)("and reselect new elements"),".","      ","
      ","
      ",'
      ','
      ','
      ','","
      ","
      ","
      "].join(""))}),toString:function(){return"PairCollectionCreator"}}),v=function(e,t){return t=t||{},t.title=(0,p.default)("Create a collection from a pair of datasets"),r.default.collectionCreatorModal(e,t,_)};t.default={PairCollectionCreator:_,pairCollectionCreatorModal:v,createPairCollection:o}}).call(t,i(2),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}}function l(e){function t(){return i.length||(i=[new RegExp(this.filters[0]),new RegExp(this.filters[1])]),i}e=e||{},e.createPair=e.createPair||function(e){e=e||{};var t=e.listA.splice(e.indexA,1)[0],i=e.listB.splice(e.indexB,1)[0],n=e.listB.indexOf(t),s=e.listA.indexOf(i);return-1!==n&&e.listB.splice(n,1),-1!==s&&e.listA.splice(s,1),this._pair(t,i,{silent:!0})};var i=[];return e.preprocessMatch=e.preprocessMatch||function(e){var i=t.call(this);return n.extend(e,{matchTo:e.matchTo.name.replace(i[0],""),possible:e.possible.name.replace(i[1],"")})},function(t){this.debug("autopair _strategy ---------------------------"),t=t||{};var i,n=t.listA,s=t.listB,a=0,o={score:0,index:null},l=[];for(this.debug("starting list lens:",n.length,s.length),this.debug("bestMatch (starting):",JSON.stringify(o,null,"  "));a=c?l.push(e.createPair.call(this,{listA:n,indexA:a,listB:s,indexB:o.index})):a+=1,!n.length||!s.length)return l}return this.debug("paired:",JSON.stringify(l,null,"  ")),this.debug("autopair _strategy ---------------------------"),l}}function r(e,t){var i=e.toJSON();return b(i,{historyId:e.historyId,defaultHideSourceItems:t})}Object.defineProperty(t,"__esModule",{value:!0});var d=i(99),c=o(d),u=i(53),h=o(u),f=i(52),p=o(f),m=i(4),g=o(m),_=i(3),v=o(_);i(54);var w=e.View.extend(g.default.LoggableMixin).extend({_logNamespace:"collections",tagName:"li",className:"dataset paired",initialize:function(e){this.pair=e.pair||{}},template:n.template(['<%- pair.forward.name %>','','<%- pair.name %>',"",'<%- pair.reverse.name %>'].join("")),render:function(){this.dragStartHandler=n.bind(this._dragstart,this),this.dragEndHandler=n.bind(this._dragend,this);var e=this.$el.attr("draggable",!0).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container").get(0);return e.addEventListener("dragstart",this.dragStartHandler,!1),e.addEventListener("dragend",this.dragEndHandler,!1),this},events:{dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(e){e.currentTarget.style.opacity="0.4",e.originalEvent&&(e=e.originalEvent),e.dataTransfer.effectAllowed="move",e.dataTransfer.setData("text/plain",JSON.stringify(this.pair)),this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(e){e.currentTarget.style.opacity="1.0",this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(e){this.$el.parent().trigger(e)},toString:function(){return"PairView("+this.pair.name+")"}}),y=e.View.extend(g.default.LoggableMixin).extend(p.default.CollectionCreatorMixin).extend({_logNamespace:"collections",className:"list-of-pairs-collection-creator collection-creator flex-row-container",initialize:function(e){this.metric("PairedCollectionCreator.initialize",e),e=n.defaults(e,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:!0,strategy:"lcs",matchPercentage:.9,twoPassAutopairing:!0}),this.initialList=e.datasets,this.historyId=e.historyId,this.filters=this.commonFilters[e.filters]||this.commonFilters[this.DEFAULT_FILTERS],n.isArray(e.filters)&&(this.filters=e.filters),this.automaticallyPair=e.automaticallyPair,this.strategy=this.strategies[e.strategy]||this.strategies[this.DEFAULT_STRATEGY],n.isFunction(e.strategy)&&(this.strategy=e.strategy),this.matchPercentage=e.matchPercentage,this.twoPassAutopairing=e.twoPassAutopairing,this.removeExtensions=!0,this.oncancel=e.oncancel,this.oncreate=e.oncreate,this.autoscrollDist=e.autoscrollDist||24,this.unpairedPanelHidden=!1,this.pairedPanelHidden=!1,this.$dragging=null,this.blocking=!1,this._setUpCommonSettings(e),this._setUpBehaviors(),this._dataSetUp()},commonFilters:{illumina:["_1","_2"],Rs:["_R1","_R2"]},DEFAULT_FILTERS:"illumina",strategies:{simple:"autopairSimple",lcs:"autopairLCS",levenshtein:"autopairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[],this.unpaired=[],this.selectedIds=[],this._sortInitialList(),this._ensureIds(),this.unpaired=this.initialList.slice(0),this.automaticallyPair&&(this.autoPair(),this.once("rendered:initial",function(){this.trigger("autopair")}))},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(e){return e.sort(function(e,t){return(0,h.default)(e.name,t.name)}),e},_ensureIds:function(){return this.initialList.forEach(function(e){e.hasOwnProperty("id")||(e.id=n.uniqueId())}),this.initialList},_splitByFilters:function(){function e(e,t){return t.test(e.name)}var t=this.filters.map(function(e){return new RegExp(e)}),i=[[],[]];return this.unpaired.forEach(function(n){t.forEach(function(t,s){e(n,t)&&i[s].push(n)})}),i},_addToUnpaired:function(e){var t=this;this.unpaired.splice(function i(n,s){if(n===s)return n;var a=Math.floor((s-n)/2)+n,o=(0,h.default)(e.name,t.unpaired[a].name);if(o<0)return i(n,a);if(o>0)return i(a+1,s);for(;t.unpaired[a]&&t.unpaired[a].name===e.name;)a++;return a}(0,this.unpaired.length),0,e)},autoPair:function(e){var t=this._splitByFilters(),i=[];return this.twoPassAutopairing&&(i=this.autopairSimple({listA:t[0],listB:t[1]}),t=this._splitByFilters()),e=e||this.strategy,t=this._splitByFilters(),i=i.concat(this[e].call(this,{listA:t[0],listB:t[1]}))},autopairSimple:l({scoreThreshold:function(){return.6},match:function(e){return e=e||{},e.matchTo===e.possible?{index:e.index,score:1}:e.bestMatch}}),autopairLevenshtein:l({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var t=(0,c.default)(e.matchTo,e.possible),i=1-t/Math.max(e.matchTo.length,e.possible.length);return i>e.bestMatch.score?{index:e.index,score:i}:e.bestMatch}}),autopairLCS:l({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var t=this._naiveStartingAndEndingLCS(e.matchTo,e.possible).length,i=t/Math.max(e.matchTo.length,e.possible.length);return i>e.bestMatch.score?{index:e.index,score:i}:e.bestMatch}}),_naiveStartingAndEndingLCS:function(e,t){for(var i="",n="",s=0,a=0;s=0&&a>=0&&e[s]===t[a];)n=[e[s],n].join(""),s-=1,a-=1;return i+n},_pair:function(e,t,i){i=i||{},this.debug("_pair:",e,t);var s=this._createPair(e,t,i.name);return this.paired.push(s),this.unpaired=n.without(this.unpaired,e,t),i.silent||this.trigger("pair:new",s),s},_createPair:function(e,t,i){if(!e||!t||e===t)throw new Error("Bad pairing: "+[JSON.stringify(e),JSON.stringify(t)]);return i=i||this._guessNameForPair(e,t),{forward:e,name:i,reverse:t}},_guessNameForPair:function(e,t,i){i=void 0!==i?i:this.removeExtensions;var n=e.name,s=t.name,a=this._naiveStartingAndEndingLCS(n.replace(new RegExp(this.filters[0]),""),s.replace(new RegExp(this.filters[1]),""));if(i){var o=a.lastIndexOf(".");if(o>0){var l=a.slice(o,a.length);a=a.replace(l,""),n=n.replace(l,""),s=s.replace(l,"")}}return a||n+" & "+s},_unpair:function(e,t){if(t=t||{},!e)throw new Error("Bad pair: "+JSON.stringify(e));return this.paired=n.without(this.paired,e),this._addToUnpaired(e.forward),this._addToUnpaired(e.reverse),t.silent||this.trigger("pair:unpair",[e]),e},unpairAll:function(){for(var e=[];this.paired.length;)e.push(this._unpair(this.paired[0],{silent:!0}));this.trigger("pair:unpair",e)},_pairToJSON:function(e,t){return t=t||"hda",{collection_type:"paired",src:"new_collection",name:e.name,element_identifiers:[{name:"forward",id:e.forward.id,src:t},{name:"reverse",id:e.reverse.id,src:t}]}},createList:function(e){var t=this,i=Galaxy.root+"api/histories/"+this.historyId+"/contents/dataset_collections",a={type:"dataset_collection",collection_type:"list:paired",hide_source_items:t.hideOriginals||!1,name:n.escape(e||t.$(".collection-name").val()),element_identifiers:t.paired.map(function(e){return t._pairToJSON(e)})};return 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+="
      "+JSON.stringify(e.responseJSON)+"
      ":s+=": "+i),n._showAlert(s,"alert-danger")},render:function(e,t){return this.$el.empty().html(this.templates.main()),this._renderHeader(e),this._renderMiddle(e),this._renderFooter(e),this._addPluginComponents(),this.trigger("rendered",this),this},_renderHeader:function(e,t){var i=this.$(".header").empty().html(this.templates.header()).find(".help-content").prepend(a(this.templates.helpContent()));return this._renderFilters(),i},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(e,t){var i=this.$(".middle").empty().html(this.templates.middle());return this.unpairedPanelHidden?this.$(".unpaired-columns").hide():this.pairedPanelHidden&&this.$(".paired-columns").hide(),this._renderUnpaired(),this._renderPaired(),i},_renderUnpaired:function(e,t){var i,n,s=this,a=[],o=this._splitByFilters();return this.$(".forward-column .title").text([o[0].length,(0,v.default)("unpaired forward")].join(" ")),this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-o[0].length)),this.$(".reverse-column .title").text([o[1].length,(0,v.default)("unpaired reverse")].join(" ")),this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-o[1].length)),this.$(".unpaired-columns .column-datasets").empty(),this.$(".autopair-link").toggle(0!==this.unpaired.length),0===this.unpaired.length?void this._renderUnpairedEmpty():(n=o[1].map(function(e,t){return void 0!==o[0][t]&&o[0][t]!==e&&a.push(s._renderPairButton()),s._renderUnpairedDataset(e)}),i=o[0].map(function(e){return s._renderUnpairedDataset(e)}),i.length||n.length?(this.$(".unpaired-columns .forward-column .column-datasets").append(i).add(this.$(".unpaired-columns .paired-column .column-datasets").append(a)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(n)),void this._adjUnpairedOnScrollbar()):void this._renderUnpairedNotShown())},_renderUnpairedDisplayStr:function(e){return["(",e," ",(0,v.default)("filtered out"),")"].join("")},_renderUnpairedDataset:function(e){return a("
    • ").attr("id","dataset-"+e.id).addClass("dataset unpaired").attr("draggable",!0).addClass(e.selected?"selected":"").append(a("").addClass("dataset-name").text(e.name)).data("dataset",e)},_renderPairButton:function(){return a("
    • ").addClass("dataset unpaired").append(a("").addClass("dataset-name").text((0,v.default)("Pair these datasets")))},_renderUnpairedEmpty:function(){var e=a('
      ').text("("+(0,v.default)("no remaining unpaired datasets")+")");return this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(e),e},_renderUnpairedNotShown:function(){var e=a('
      ').text("("+(0,v.default)("no datasets were found matching the current filters")+")");return this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(e),e},_adjUnpairedOnScrollbar:function(){var e=this.$(".unpaired-columns").last(),t=this.$(".unpaired-columns .reverse-column .dataset").first();if(t.length){var i=e.offset().left+e.outerWidth(),n=t.offset().left+t.outerWidth(),s=Math.floor(i)-Math.floor(n);this.$(".unpaired-columns .forward-column").css("margin-left",s>0?s:0)}},_renderPaired:function(e,t){if(this.$(".paired-column-title .title").text([this.paired.length,(0,v.default)("paired")].join(" ")),this.$(".unpair-all-link").toggle(0!==this.paired.length),0===this.paired.length)return void this._renderPairedEmpty();this.$(".remove-extensions-link").show(),this.$(".paired-columns .column-datasets").empty();var i=this;this.paired.forEach(function(e,t){var n=new w({pair:e});i.$(".paired-columns .column-datasets").append(n.render().$el).append(['"].join(""))})},_renderPairedEmpty:function(){var e=a('
      ').text("("+(0,v.default)("no paired datasets yet")+")");return this.$(".paired-columns .column-datasets").empty().prepend(e),e},footerSettings:{".hide-originals":"hideOriginals",".remove-extensions":"removeExtensions"},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link"),this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(e){function t(e,t){return['"].join("")}var i=a(n.template(['
      ','
      ',(0,v.default)("Choose from the following filters to change which unpaired reads are shown in the display"),":
      ",n.values(this.commonFilters).map(function(e){return t(e[0],e[1])}).join(""),"
      "].join(""))({}));return this.$(e).popover({container:".collection-creator",placement:"bottom",html:!0,content:i})},_validationWarning:function(e,t){"name"===e&&(e=this.$(".collection-name").add(this.$(".collection-name-prompt")),this.$(".collection-name").focus().select()),t?(e=e||this.$(".validation-warning"),e.removeClass("validation-warning")):e.addClass("validation-warning")},_setUpBehaviors:function(){return this.once("rendered",function(){this.trigger("rendered:initial",this)}),this.on("pair:new",function(){this._renderUnpaired(),this._renderPaired(),this.$(".paired-columns").scrollTop(8e6)}),this.on("pair:unpair",function(e){this._renderUnpaired(),this._renderPaired(),this.splitView()}),this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter input").val(),this.$(".reverse-unpaired-filter input").val()],this.metric("filter-change",this.filters),this._renderFilters(),this._renderUnpaired()}),this.on("autopair",function(){this._renderUnpaired(),this._renderPaired();var e,t=null;this.paired.length?(t="alert-success",e=this.paired.length+" "+(0,v.default)("pairs created"),this.unpaired.length||(e+=": "+(0,v.default)("all datasets have been successfully paired"),this.hideUnpaired(),this.$(".collection-name").focus())):e=(0,v.default)(["Could not automatically create any pairs from the given dataset names.","You may want to choose or enter different filters and try auto-pairing again.","Close this message using the X on the right to view more help."].join(" ")),this._showAlert(e,t)}),this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .main-help":"_toggleHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(e){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(e){a(e.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter input":function(e){this.trigger("filter-change")},"focus .reverse-unpaired-filter input":function(e){a(e.currentTarget).select()},"click .forward-column .dataset.unpaired":"_clickUnpairedDataset","click .reverse-column .dataset.unpaired":"_clickUnpairedDataset","click .paired-column .dataset.unpaired":"_clickPairRow","click .unpaired-columns":"clearSelectedUnpaired","mousedown .unpaired-columns .dataset":"_mousedownUnpaired","click .paired-column-title":"_clickShowOnlyPaired","mousedown .flexible-partition-drag":"_startPartitionDrag","click .paired-columns .dataset.paired":"selectPair","click .paired-columns":"clearSelectedPaired","click .paired-columns .pair-name":"_clickPairName","click .unpair-btn":"_clickUnpair","dragover .paired-columns .column-datasets":"_dragoverPairedColumns","drop .paired-columns .column-datasets":"_dropPairedColumns","pair.dragstart .paired-columns .column-datasets":"_pairDragstart","pair.dragend   .paired-columns .column-datasets":"_pairDragend","change .remove-extensions":function(e){this.toggleExtensions()},"change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","change .hide-originals":"_changeHideOriginals","click .cancel-create":"_cancelCreate","click .create-collection":"_clickCreate"},_clickShowOnlyUnpaired:function(e){this.$(".paired-columns").is(":visible")?this.hidePaired():this.splitView()},_clickShowOnlyPaired:function(e){this.$(".unpaired-columns").is(":visible")?this.hideUnpaired():this.splitView()},hideUnpaired:function(e,t){this.unpairedPanelHidden=!0,this.pairedPanelHidden=!1,this._renderMiddle(e,t)},hidePaired:function(e,t){this.unpairedPanelHidden=!1,this.pairedPanelHidden=!0,this._renderMiddle(e,t)},splitView:function(e,t){return this.unpairedPanelHidden=this.pairedPanelHidden=!1,this._renderMiddle(e,t),this},_clickUnpairAll:function(e){this.metric("unpairAll"),this.unpairAll()},_clickAutopair:function(e){var t=this.autoPair();this.metric("autopair",t.length,this.unpaired.length),this.trigger("autopair")},_clickFilterChoice:function(e){var t=a(e.currentTarget);this.$(".forward-unpaired-filter input").val(t.data("forward")),this.$(".reverse-unpaired-filter input").val(t.data("reverse")),this._hideChooseFilters(),this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide"),this.$(".popover").css("display","none")},_clearFilters:function(e){this.$(".forward-unpaired-filter input").val(""),this.$(".reverse-unpaired-filter input").val(""),this.trigger("filter-change")},_clickUnpairedDataset:function(e){return e.stopPropagation(),this.toggleSelectUnpaired(a(e.currentTarget))},toggleSelectUnpaired:function(e,t){t=t||{};var i=e.data("dataset"),n=void 0!==t.force?t.force:!e.hasClass("selected");return e.length&&void 0!==i?(n?(e.addClass("selected"),t.waitToPair||this.pairAllSelected()):e.removeClass("selected"),e):e},pairAllSelected:function(e){e=e||{};var t=this,i=[],n=[],s=[];return t.$(".unpaired-columns .forward-column .dataset.selected").each(function(){i.push(a(this).data("dataset"))}),t.$(".unpaired-columns .reverse-column .dataset.selected").each(function(){n.push(a(this).data("dataset"))}),i.length=n.length=Math.min(i.length,n.length),i.forEach(function(e,i){try{s.push(t._pair(e,n[i],{silent:!0}))}catch(e){t.error(e)}}),s.length&&!e.silent&&this.trigger("pair:new",s),s},clearSelectedUnpaired:function(){this.$(".unpaired-columns .dataset.selected").removeClass("selected")},_mousedownUnpaired:function(e){if(e.shiftKey){var t=this,i=a(e.target).addClass("selected"),n=function(e){t.$(e.target).filter(".dataset").addClass("selected")};i.parent().on("mousemove",n),a(document).one("mouseup",function(e){i.parent().off("mousemove",n),t.pairAllSelected()})}},_clickPairRow:function(e){var t=a(e.currentTarget).index(),i=a(".unpaired-columns .forward-column .dataset").eq(t).data("dataset"),n=a(".unpaired-columns .reverse-column .dataset").eq(t).data("dataset");this._pair(i,n)},_startPartitionDrag:function(e){function t(e){n.$(".flexible-partition-drag").css("color",""),a("body").css("cursor","").unbind("mousemove",i)}function i(e){var t=e.pageY-s;n.adjPartition(t)||a("body").trigger("mouseup"),n._adjUnpairedOnScrollbar(),s+=t}var n=this,s=e.pageY;a("body").css("cursor","ns-resize"),n.$(".flexible-partition-drag").css("color","black"),a("body").mousemove(i),a("body").one("mouseup",t)},adjPartition:function(e){var t=this.$(".unpaired-columns"),i=this.$(".paired-columns"),n=parseInt(t.css("height"),10),s=parseInt(i.css("height"),10);n=Math.max(10,n+e),s-=e;var a=e<0;if(a){if(this.unpairedPanelHidden)return!1;if(n<=10)return this.hideUnpaired(),!1}else this.unpairedPanelHidden&&(t.show(),this.unpairedPanelHidden=!1);if(a)this.pairedPanelHidden&&(i.show(),this.pairedPanelHidden=!1);else{if(this.pairedPanelHidden)return!1;if(s<=15)return this.hidePaired(),!1}return t.css({height:n+"px",flex:"0 0 auto"}),!0},selectPair:function(e){e.stopPropagation(),a(e.currentTarget).toggleClass("selected")},clearSelectedPaired:function(e){this.$(".paired-columns .dataset.selected").removeClass("selected")},_clickPairName:function(e){e.stopPropagation();var t=a(e.currentTarget),i=t.parent().parent(),n=i.index(".dataset.paired"),s=this.paired[n],o=prompt("Enter a new name for the pair:",s.name);o&&(s.name=o,s.customizedName=!0,t.text(s.name))},_clickUnpair:function(e){var t=Math.floor(a(e.currentTarget).index(".unpair-btn"));this._unpair(this.paired[t])},_dragoverPairedColumns:function(e){e.preventDefault();var t=this.$(".paired-columns .column-datasets");this._checkForAutoscroll(t,e.originalEvent.clientY);var i=this._getNearestPairedDatasetLi(e.originalEvent.clientY);a(".element-drop-placeholder").remove();var n=a('
      ');i.length?i.before(n):t.append(n)},_checkForAutoscroll:function(e,t){var i=e.offset(),n=e.scrollTop(),s=t-i.top,a=i.top+e.outerHeight()-t;s>=0&&s=0&&ae&&s-o",e.name)},toString:function(){return"PairedCollectionCreator"},templates:n.extend({},p.default.CollectionCreatorMixin._creatorTemplates,{header:n.template(['
      ','',(0,v.default)("More help"),"",'
      ','',(0,v.default)("Less"),"","
      ","
      ",'
      ','','',"
      ",'
      ','
      ','
      ','
      ','',(0,v.default)("Unpaired forward"),"",'',"
      ",'
      ','',"
      ","
      ","
      ",'
      ','
      ','',(0,v.default)("Choose filters"),"",'',(0,v.default)("Clear filters"),"
      ",'',(0,v.default)("Auto-pair"),"","
      ","
      ",'
      ','
      ','
      ','',(0,v.default)("Unpaired reverse"),"",'',"
      ",'
      ','',"
      ","
      ","
      ","
      "].join("")),middle:n.template(['
      ','
      ','
        ',"
        ",'
        ','
          ',"
          ",'
          ','
            ',"
            ","
            ",'
            ','
            ','
            ','
            ','',"
            ",'',(0,v.default)("Unpair all"),"","
            ","
            ",'
            ','
              ',"
              "].join("")),footer:n.template(['
              ','
              ','",'","
              ",'
              ','','
              ',(0,v.default)("Name"),":
              ","
              ","
              ",'
              ','
              ','",'
              ','",'","
              ","
              ",'
              ','","
              ","
              "].join("")),helpContent:n.template(["
              ",(0,v.default)(["Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ","These collections can be passed to tools and workflows in order to have analyses done on each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"
              ","
              ",(0,v.default)(['Unpaired datasets are shown in the unpaired section ',"(hover over the underlined words to highlight below). ",'Paired datasets are shown in the paired section.',"
                To pair datasets, you can:","
              • Click a dataset in the ",'forward column ',"to select it then click a dataset in the ",'reverse column.',"
                • ",'
              • Click one of the "Pair these datasets" buttons in the ','middle column ',"to pair the datasets in a particular row.","
                • ",'
              • Click "Auto-pair" ',"to have your datasets automatically paired based on name.","
                • ","
              "].join("")),"
              ","
              ",(0,v.default)(["
                You can filter what is shown in the unpaired sections by:","
              • Entering partial dataset names in either the ",'forward filter or ','reverse filter.',"
                • ","
              • Choosing from a list of preset filters by clicking the ",'"Choose filters" link.',"
                • ","
              • Entering regular expressions to match dataset names. See: ",'MDN\'s JavaScript Regular Expression Tutorial. ',"Note: forward slashes (\\) are not needed.","
                • ","
              • Clearing the filters by clicking the ",'"Clear filters" link.',"
                • ","
              "].join("")),"
              ","
              ",(0,v.default)(["To unpair individual dataset pairs, click the ",'unpair buttons (  ). ','Click the "Unpair all" link to unpair all pairs.'].join("")),"
              ","
              ",(0,v.default)(['You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the ','"Remove file extensions from pair names?" control.'].join("")),"
              ","
              ",(0,v.default)(['Once your collection is complete, enter a name and ','click "Create list". ',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"
              "].join(""))})}),b=function(e,t){var i,a=s.Deferred();if(t=n.defaults(t||{},{datasets:e,oncancel:function(){Galaxy.modal.hide(),a.reject("cancelled")},oncreate:function(e,t){Galaxy.modal.hide(),a.resolve(t)},title:(0,v.default)("Create a collection of paired datasets")}),!window.Galaxy||!Galaxy.modal)throw new Error("Galaxy or Galaxy.modal not found");return i=new y(t),Galaxy.modal.show({title:t.title,body:i.$el,width:"80%",height:"800px",closing_events:!0}),i.render(),window.creator=i,a};t.default={PairedCollectionCreator:y,pairedCollectionCreatorModal:b,createListOfPairsCollection:r}}).call(t,i(2),i(1),i(0),i(0))},,,,,,,,,,,,,,,function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(0),a=n(s),o=i(26),l=n(o),r=i(6),d=n(r),c=a.default,u=e.Router.extend({initialize:function(e,t){this.page=e,this.options=t},push:function(e,t){t=t||{},t.__identifer=Math.random().toString(36).substr(2),e+=-1==e.indexOf("?")?"?":"&",e+=c.param(t,!0),Galaxy.params=t,this.navigate(e,{trigger:!0})},execute:function(e,t,i){Galaxy.debug("router execute:",e,t,i);var n=l.default.parse(t.pop());t.push(n),e&&(this.authenticate(t,i)?e.apply(this,t):this.access_denied())},authenticate:function(e,t){return!0},access_denied:function(){this.page.display(new d.default.Message({status:"danger",message:"You must be logged in with proper credentials to make this request.",persistent:!0}))}});t.default=u}).call(t,i(2))},function(e,t,i){"use strict";(function(e,n,s){Object.defineProperty(t,"__esModule",{value:!0});var a=i(5);!function(e){e&&e.__esModule}(a);t.default=e.View.extend({options:{class_check:"fa-check-square-o",class_uncheck:"fa-square-o",parameters:[{id:"space_to_tab",title:"Convert spaces to tabs"},{id:"to_posix_lines",title:"Use POSIX standard"}]},initialize:function(e){this.model=e.model,this.setElement(n("
              ").addClass("upload-settings")),this.$el.append(n("
              ").addClass("upload-settings-cover")),this.$el.append(n("").addClass("upload-settings-table ui-table-striped").append("")),this.$cover=this.$(".upload-settings-cover"),this.$table=this.$(".upload-settings-table > tbody"),this.listenTo(this.model,"change",this.render,this),this.model.trigger("change")},render:function(){var e=this;this.$table.empty(),s.each(this.options.parameters,function(t){var i=n("
              ").addClass("upload-"+t.id+" upload-icon-button fa").addClass(e.model.get(t.id)&&e.options.class_check||e.options.class_uncheck).on("click",function(){e.model.get("enabled")&&e.model.set(t.id,!e.model.get(t.id))});e.$table.append(n("
              ").append(n(""},_template:function(){return'
              ").append(i)).append(n("").append(t.title)))}),this.$cover[this.model.get("enabled")&&"hide"||"show"]()}})}).call(t,i(2),i(0),i(1))},function(e,t,i){"use strict";(function(e,n,s){Object.defineProperty(t,"__esModule",{value:!0});var a=i(5),o=function(e){return e&&e.__esModule?e:{default:e}}(a);t.default=e.View.extend({initialize:function(t){this.model=new e.Model({cls:"upload-ftp",class_add:"upload-icon-button fa fa-square-o",class_remove:"upload-icon-button fa fa-check-square-o",class_partial:"upload-icon-button fa fa-minus-square-o",help_enabled:!0,help_text:"This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at "+t.ftp_upload_site+" using your Galaxy credentials.",collection:null,onchange:function(){},onadd:function(){},onremove:function(){}}).set(t),this.collection=this.model.get("collection"),this.setElement(this._template()),this.$content=this.$(".upload-ftp-content"),this.$wait=this.$(".upload-ftp-wait"),this.$help=this.$(".upload-ftp-help"),this.$number=this.$(".upload-ftp-number"),this.$disk=this.$(".upload-ftp-disk"),this.$body=this.$(".upload-ftp-body"),this.$warning=this.$(".upload-ftp-warning"),this.$select=this.$(".upload-ftp-select-all"),this.render()},render:function(){var e=this;this.$wait.show(),this.$content.hide(),this.$warning.hide(),this.$help.hide(),n.ajax({url:Galaxy.root+"api/remote_files",method:"GET",success:function(t){e.model.set("ftp_files",t),e._index(),e._renderTable()},error:function(){e._renderTable()}})},_renderTable:function(){var e=this,t=this.model.get("ftp_files");if(this.rows=[],t&&t.length>0){this.$body.empty();var i=0;s.each(t,function(t){e.rows.push(e._renderRow(t)),i+=t.size}),this.$number.html(t.length+" files"),this.$disk.html(o.default.bytesToString(i,!0)),this.collection&&(this.$("._has_collection").show(),this.$select.addClass(this.model.get("class_add")).off().on("click",function(){e._all()}),this._refresh()),this.$content.show()}else this.$warning.show();this.model.get("help_enabled")&&this.$help.show(),this.$wait.hide()},_renderRow:function(e){var t=this,i=this.model.attributes,s=n(this._templateRow(e)),a=s.find(".icon");if(this.$body.append(s),this.collection){var o=this.ftp_index[e.path];a.addClass(void 0===o?i.class_add:i.class_remove),s.on("click",function(){t._switch(a,e),t._refresh()})}else s.on("click",function(){i.onchange(e)});return a},_index:function(){var e=this;this.ftp_index={},this.collection&&this.collection.each(function(t){"ftp"==t.get("file_mode")&&(e.ftp_index[t.get("file_path")]=t.id)})},_all:function(){var e=this.model.attributes,t=this.model.get("ftp_files"),i=this.$select.hasClass(e.class_add);for(var n in t){var s=t[n],a=this.ftp_index[s.path];(void 0===a&&i||void 0!==a&&!i)&&this._switch(this.rows[n],s)}this._refresh()},_switch:function(e,t){e.removeClass();var i=this.model.attributes,n=this.ftp_index[t.path];if(void 0===n){var s=i.onadd(t);e.addClass(i.class_remove),this.ftp_index[t.path]=s}else i.onremove(n),e.addClass(i.class_add),this.ftp_index[t.path]=void 0},_refresh:function(){var e=s.reduce(this.ftp_index,function(e,t){return void 0!==t&&e++,e},0);this.$select.removeClass(),0==e?this.$select.addClass(this.model.get("class_add")):this.$select.addClass(e==this.rows.length?this.model.get("class_remove"):this.model.get("class_partial"))},_templateRow:function(e){return'
              '+s.escape(e.path)+''+o.default.bytesToString(e.size)+''+e.ctime+"
              NameSizeCreated
              Your FTP directory does not contain any files.
              '}})}).call(t,i(2),i(0),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(5),o=(s(a),i(27)),l=s(o);t.default=e.View.extend({initialize:function(t){this.model=new e.Model(t),this.setElement("
              "),this.render()},render:function(){var e=this.model.attributes,t=n.findWhere(e.list,{id:e.extension});this.extension_popup&&this.extension_popup.remove(),this.extension_popup=new l.default.View({placement:e.placement||"bottom",container:e.$el}),this.extension_popup.title(e.title),this.extension_popup.empty(),this.extension_popup.append(this._templateDescription(t)),this.extension_popup.show()},_templateDescription:function(e){if(e.description){var t=e.description;return e.description_url&&(t+=' (read more)'),t}return"There is no description available for this file extension."}})}).call(t,i(2),i(1))},function(e,t,i){"use strict";(function(e,t){!function(i){e.event.props.push("dataTransfer"),i.uploadpost=function(t){var n=i.extend({},{data:{},success:function(){},error:function(){},progress:function(){},url:null,maxfilesize:2048,error_filesize:"File exceeds 2GB. Please use a FTP client.",error_default:"Please make sure the file is available.",error_server:"Upload request failed.",error_login:"Uploads require you to log in."},t),s=n.data;if(s.error_message)return void n.error(s.error_message);var a=new FormData;for(var o in s.payload)a.append(o,s.payload[o]);var l=0;for(var o in s.files){var r=s.files[o];a.append(r.name,r.file,r.file.name),l+=r.file.size}if(l>1048576*n.maxfilesize)return void n.error(n.error_filesize);var d=new XMLHttpRequest;d.open("POST",n.url,!0),d.setRequestHeader("Accept","application/json"),d.setRequestHeader("Cache-Control","no-cache"),d.setRequestHeader("X-Requested-With","XMLHttpRequest"),d.onreadystatechange=function(){if(d.readyState==d.DONE){var t=null,i="";if(d.responseText)try{t=e.parseJSON(d.responseText),i=t.err_msg}catch(e){t=d.responseText,i=t}if(d.status<200||d.status>299){var s=d.statusText;403==d.status?s=n.error_login:0==d.status?s=n.error_server:s||(s=n.error_default),n.error(s+" ("+d.status+"). "+i)}else n.success(t)}},d.upload.addEventListener("progress",function(e){e.lengthComputable&&n.progress(Math.round(100*e.loaded/e.total))},!1),Galaxy.emit.debug("uploadbox::uploadpost()","Posting following data.",n),d.send(a)},i.fn.uploadinput=function(e){var t=this,n=i.extend({},{ondragover:function(){},ondragleave:function(){},onchange:function(){},multiple:!1},e),s=i('");return t.append(s.change(function(e){n.onchange(e.target.files),i(this).val("")})),t.on("drop",function(e){n.ondragleave(e),e.dataTransfer&&(n.onchange(e.dataTransfer.files),e.preventDefault())}),t.on("dragover",function(e){e.preventDefault(),n.ondragover(e)}),t.on("dragleave",function(e){e.stopPropagation(),n.ondragleave(e)}),{dialog:function(){s.trigger("click")}}},i.fn.uploadbox=function(e){function n(e){if(e&&e.length&&!g){var i=void 0;return t.each(e,function(e,i){"new"!==e.mode&&t.filter(f,function(t){return t.name===e.name&&t.size===e.size}).length&&(e.duplicate=!0)}),t.each(e,function(e){e.duplicate||(i=String(p++),f[i]=e,h.announce(i,f[i]),m++)}),i}}function s(e){f[e]&&(delete f[e],m--)}function a(){if(0==m||_)return _=!1,g=!1,void h.complete();g=!0;var e=-1;for(var t in f){e=t;break}f[e];s(e),i.uploadpost({url:h.url,data:h.initialize(e),success:function(t){h.success(e,t),a()},error:function(t){h.error(e,t),a()},progress:function(t){h.progress(e,t)}})}function o(){v.dialog()}function l(e){for(e in f)s(e)}function r(){g||(g=!0,a())}function d(){_=!0}function c(e){return h=i.extend({},h,e)}function u(){return window.File&&window.FormData&&window.XMLHttpRequest&&window.FileList}var h=i.extend({},{dragover:function(){},dragleave:function(){},announce:function(e){},initialize:function(e){},progress:function(e,t){},success:function(e,t){},error:function(e,t){alert(t)},complete:function(){}},e),f={},p=0,m=0,g=!1,_=!1,v=i(this).uploadinput({multiple:!0,onchange:function(e){n(e)},ondragover:e.ondragover,ondragleave:e.ondragleave});return{select:o,add:n,remove:s,start:r,stop:d,reset:l,configure:c,compatible:u}}}(e)}).call(t,i(0),i(1))},function(e,t,i){"use strict";Object.defineProperty(t,"__esModule",{value:!0}),t.default={tool:"fa-wrench",data_input:"fa-file-o",data_collection_input:"fa-folder-o",subworkflow:"fa-sitemap fa-rotate-270",pause:"fa-pause"}},function(e,t,i){"use strict";function n(e,t){function i(){var i=['
              ','
              ','','loading...',"
              ","
              "].join("\n"),n=o(i).hide().css(t.css||{position:"fixed"}),s=n.children(".loading-indicator-text");return t.cover?(n.css({"z-index":2,top:e.css("top"),bottom:e.css("bottom"),left:e.css("left"),right:e.css("right"),opacity:.5,"background-color":"white","text-align":"center"}),s=n.children(".loading-indicator-text").css({"margin-top":"20px"})):(s=n.children(".loading-indicator-text").css({margin:"12px 0px 0px 10px",opacity:"0.85",color:"grey"}),s.children(".loading-indicator-message").css({margin:"0px 8px 0px 0px","font-style":"italic"})),n}var n=this;return t=a.default.extend({cover:!1},t||{}),n.show=function(t,s,a){return t=t||"loading...",s=s||"fast",e.parent().find(".loading-indicator").remove(),n.$indicator=i().insertBefore(e),n.message(t),n.$indicator.fadeIn(s,a),n},n.message=function(e){n.$indicator.find("i").text(e)},n.hide=function(e,t){return e=e||"fast",n.$indicator&&n.$indicator.length?n.$indicator.fadeOut(e,function(){n.$indicator.remove(),t&&t()}):t&&t(),n},n}Object.defineProperty(t,"__esModule",{value:!0});var s=i(0),a=function(e){return e&&e.__esModule?e:{default:e}}(s),o=a.default;t.default=n},function(e,t,i){"use strict";function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(41),a=n(s),o=i(97),l=n(o),r=i(10),d=n(r),c=i(3),u=n(c),h=a.default.HDCAListItemView,f=h.extend({_getFoldoutPanelClass:function(){return l.default.CollectionViewEdit},_renderPrimaryActions:function(){return this.log(this+"._renderPrimaryActions"),h.prototype._renderPrimaryActions.call(this).concat([this._renderDeleteButton()])},_renderDeleteButton:function(){var e=this,t=this.model.get("deleted");return(0,d.default)({title:t?(0,u.default)("Dataset collection is already deleted"):(0,u.default)("Delete"),classes:"delete-btn",faIcon:"fa-times",disabled:t,onclick:function(){e.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},toString:function(){return"HDCAListItemEdit("+(this.model?""+this.model:"(no model)")+")"}});t.default={HDCAListItemEdit:f}},function(e,t,i){"use strict";function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(59),a=n(s),o=i(29),l=(n(o),i(98)),r=n(l),d=i(4),c=(n(d),i(22)),u=n(c),h=i(10),f=(n(h),i(3)),p=n(f);i(15);var m=a.default.CollectionView,g=m.extend({DatasetDCEViewClass:r.default.DatasetDCEListItemEdit,NestedDCDCEViewClass:r.default.NestedDCDCEListItemEdit,getNestedDCDCEViewClass:function(){return r.default.NestedDCDCEListItemEdit.extend({foldoutPanelClass:g})},initialize:function(e){m.prototype.initialize.call(this,e)},_setUpBehaviors:function(e){if(e=e||this.$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 u.default.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},usePrompt:!1}),this.tagsEditor.toggle(!0)}},toString:function(){return"CollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}});t.default={CollectionViewEdit:g}},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(33),o=s(a),l=i(60),r=s(l),d=i(4),c=(s(d),i(3)),u=(s(c),o.default.DCListItemView),h=u.extend({initialize:function(e){u.prototype.initialize.call(this,e)},toString:function(){return"DCListItemEdit("+(this.model?""+this.model:"(no model)")+")"}}),f=o.default.DCEListItemView,p=f.extend({initialize:function(e){f.prototype.initialize.call(this,e)},toString:function(){return"DCEListItemEdit("+(this.model?""+this.model:"(no model)")+")"}}),m=r.default.DatasetListItemEdit.extend({initialize:function(e){r.default.DatasetListItemEdit.prototype.initialize.call(this,e)},_fetchModelDetails:function(){var t=this;return t.model.inReadyState()&&!t.model.hasDetails()?t.model.fetch({silent:!0}):e.when()},_renderDeleteButton:function(){return null},toString:function(){return"DatasetDCEListItemEdit("+(this.model?""+this.model:"(no model)")+")"}});m.prototype.templates=function(){return n.extend({},r.default.DatasetListItemEdit.prototype.templates,{titleBar:o.default.DatasetDCEListItemView.prototype.templates.titleBar})}();var g=o.default.NestedDCDCEListItemView.extend({toString:function(){return"NestedDCDCEListItemEdit("+(this.model?""+this.model:"(no model)")+")"}});t.default={DCListItemEdit:h,DCEListItemEdit:p,DatasetDCEListItemEdit:m,NestedDCDCEListItemEdit:g}}).call(t,i(0),i(1))},function(e,t,i){"use strict";function n(e,t){if(0===e.length)return t.length;if(0===t.length)return e.length;var i,n=[];for(i=0;i<=t.length;i++)n[i]=[i];var s;for(s=0;s<=e.length;s++)n[0][s]=s;for(i=1;i<=t.length;i++)for(s=1;s<=e.length;s++)t.charAt(i-1)===e.charAt(s-1)?n[i][s]=n[i-1][s-1]:n[i][s]=Math.min(n[i-1][s-1]+1,Math.min(n[i][s-1]+1,n[i-1][s]+1));return n[t.length][e.length]}Object.defineProperty(t,"__esModule",{value:!0}),t.default=n},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(13),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(3),l=a(o),r=i(5),d=a(r),c=i(119),u=a(c),h=i(6),f=a(h),p=i(13),m=a(p),g=i(121),_=a(g),v=i(81),w=a(v),y=i(9),b=a(y),x=i(68),$=a(x),C=i(94),k=a(C),S=e.View.extend({initialize:function(t){var i=this;this.modal=parent.Galaxy.modal||new b.default.View,this.model=t&&t.model||new e.Model(t),this.deferred=new u.default,this.setElement(n("
              ").addClass("ui-form-composite").append(this.$message=n("
              ")).append(this.$header=n("
              ")).append(this.$steps=n("
              "))),n("body").append(this.$el),this._configure(),this.render(),n(window).resize(function(){i._refresh()})},_refresh:function(e){var t=s.reduce(this.$el.children(),function(e,t){return e+n(t).outerHeight()},0)-this.$steps.height()+90;this.$steps.css("height",n(window).height()-t)},_configure:function(){function e(e,n){for(var s,a=/\$\{(.+?)\}/g;s=a.exec(String(e));){var o=s[1];n(t.wp_inputs[o]=t.wp_inputs[o]||{label:o,name:o,type:"text",color:"hsl( "+100*++i+", 70%, 30% )",style:"ui-form-wp-source",links:[]})}}var t=this;this.forms=[],this.steps=[],this.links=[],this.parms=[],s.each(this.model.get("steps"),function(e,i){Galaxy.emit.debug("tool-form-composite::initialize()",i+" : Preparing workflow step.");var n=k.default[e.step_type],a=parseInt(i+1)+": "+(e.step_label||e.step_name);e.annotation&&(a+=" - "+e.annotation),e.step_version&&(a+=" (Galaxy Version "+e.step_version+")"),e=d.default.merge({index:i,fixed_title:s.escape(a),icon:n||"",help:null,citations:null,collapsible:!0,collapsed:i>0&&!t._isDataStep(e),sustain_version:!0,sustain_repeats:!0,sustain_conditionals:!0,narrow:!0,text_enable:"Edit",text_disable:"Undo",cls_enable:"fa fa-edit",cls_disable:"fa fa-undo",errors:e.messages,initial_errors:!0,cls:"ui-portlet-narrow",hide_operations:!0,needs_refresh:!1,always_refresh:"tool"!=e.step_type},e),t.steps[i]=e,t.links[i]=[],t.parms[i]={}}),s.each(this.steps,function(e,i){_.default.visitInputs(e.inputs,function(e,n){t.parms[i][n]=e})}),s.each(this.steps,function(e,i){s.each(e.output_connections,function(e){s.each(t.steps,function(n,s){n.step_index===e.input_step_index&&t.links[i].push(n)})})}),s.each(this.steps,function(e,i){s.each(t.steps,function(n,a){var o={};s.each(e.output_connections,function(e){n.step_index===e.input_step_index&&(o[e.input_name]=e)}),s.each(t.parms[a],function(t,n){var s=o[n];s&&(t.type="hidden",t.help=t.step_linked?t.help+", ":"",t.help+="Output dataset '"+s.output_name+"' from step "+(parseInt(i)+1),t.step_linked=t.step_linked||[],t.step_linked.push({index:e.index,step_type:e.step_type}))})})});var i=0;this.wp_inputs={},s.each(this.steps,function(i,n){s.each(t.parms[n],function(t,n){e(t.value,function(e){e.links.push(i),t.wp_linked=!0,t.type="text",t.backdrop=!0,t.style="ui-form-wp-target"})}),s.each(i.post_job_actions,function(t){s.each(t.action_arguments,function(t){e(t,function(){})})})}),s.each(this.steps,function(e,i){if("tool"==e.step_type){var n=!0;_.default.visitInputs(e.inputs,function(i,s,a){var o=i.value&&"RuntimeValue"==i.value.__class__,l=-1!=["data","data_collection"].indexOf(i.type),r=a[i.data_ref];i.step_linked&&!t._isDataStep(i.step_linked)&&(n=!1),i.options&&(0==i.options.length&&!n||i.wp_linked)&&(i.is_workflow=!0),r&&(i.is_workflow=r.step_linked&&!t._isDataStep(r.step_linked)||i.wp_linked),(l||i.value&&"RuntimeValue"==i.value.__class__&&!i.step_linked)&&(e.collapsed=!1),o&&(i.value=i.default_value),i.flavor="workflow",o||l||"hidden"===i.type||i.wp_linked||(i.optional||!d.default.isEmpty(i.value)&&""!==i.value)&&(i.collapsible_value=i.value,i.collapsible_preview=!0)})}})},render:function(){var e=this;this.deferred.reset(),this._renderHeader(),this._renderMessage(),this._renderParameters(),this._renderHistory(),this._renderUseCachedJob(),s.each(this.steps,function(t){e._renderStep(t)})},_renderHeader:function(){var e=this;this.execute_btn=new f.default.Button({icon:"fa-check",title:(0,l.default)("Run workflow"),cls:"btn btn-primary",onclick:function(){e._execute()}}),this.$header.addClass("ui-form-header").empty().append(new f.default.Label({title:"Workflow: "+this.model.get("name")}).$el).append(this.execute_btn.$el)},_renderMessage:function(){this.$message.empty(),this.model.get("has_upgrade_messages")&&this.$message.append(new f.default.Message({message:"Some tools in this workflow may have changed since it was last saved or some errors were found. The workflow may still run, but any new options will have default values. Please review the messages below to make a decision about whether the changes will affect your analysis.",status:"warning",persistent:!0,fade:!1}).$el);var e=this.model.get("step_version_changes");e&&e.length>0&&this.$message.append(new f.default.Message({message:"Some tools are being executed with different versions compared to those available when this workflow was last saved because the other versions are not or no longer available on this Galaxy instance. To upgrade your workflow and dismiss this message simply edit the workflow and re-save it.",status:"warning",persistent:!0,fade:!1}).$el)},_renderParameters:function(){var e=this;this.wp_form=null,s.isEmpty(this.wp_inputs)||(this.wp_form=new m.default({title:"Workflow Parameters",inputs:this.wp_inputs,cls:"ui-portlet-narrow",onchange:function(){s.each(e.wp_form.input_list,function(t,i){s.each(t.links,function(t){e._refreshStep(t)})})}}),this._append(this.$steps.empty(),this.wp_form.$el))},_renderHistory:function(){this.history_form=new m.default({cls:"ui-portlet-narrow",title:"History Options",inputs:[{type:"conditional",name:"new_history",test_param:{name:"check",label:"Send results to a new history",type:"boolean",value:"false",help:""},cases:[{value:"true",inputs:[{name:"name",label:"History name",type:"text",value:this.model.get("name")}]}]}]}),this._append(this.$steps,this.history_form.$el)},_renderUseCachedJob:function(){var e={};Galaxy.user.attributes.preferences&&"extra_user_preferences"in Galaxy.user.attributes.preferences&&(e=JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences));var t="use_cached_job|use_cached_job_checkbox"in e&&e["use_cached_job|use_cached_job_checkbox"];this.display_use_cached_job_checkbox="true"===t,this.display_use_cached_job_checkbox&&(this.job_options_form=new m.default({cls:"ui-portlet-narrow",title:"Job re-use Options",inputs:[{type:"conditional",name:"use_cached_job",test_param:{name:"check",label:"BETA: Attempt to reuse jobs with identical parameters?",type:"boolean",value:"false",help:"This may skip executing jobs that you have already run."}}]}),this._append(this.$steps,this.job_options_form.$el))},_renderStep:function(e){var t=this,i=null;this.deferred.execute(function(a){if(t.$steps.addClass("ui-steps"),"tool"==e.step_type)e.postchange=function(t,i){var s={tool_id:e.id,tool_version:e.version,inputs:n.extend(!0,{},i.data.create())};i.wait(!0),Galaxy.emit.debug("tool-form-composite::postchange()","Sending current state.",s),d.default.request({type:"POST",url:Galaxy.root+"api/tools/"+e.id+"/build",data:s,success:function(e){i.update(e),i.wait(!1),Galaxy.emit.debug("tool-form-composite::postchange()","Received new model.",e),t.resolve()},error:function(e){Galaxy.emit.debug("tool-form-composite::postchange()","Refresh request failed.",e),t.reject()}})},i=new w.default(e),e.post_job_actions&&e.post_job_actions.length&&i.portlet.append(n("
              ").addClass("ui-form-element-disabled").append(n("
              ").addClass("ui-form-title").html("Job Post Actions")).append(n("
              ").addClass("ui-form-preview").html(s.reduce(e.post_job_actions,function(e,t){return e+" "+t.short_str},""))));else{var o=-1!=["data_input","data_collection_input"].indexOf(e.step_type);s.each(e.inputs,function(e){e.flavor="module",e.hide_label=o}),i=new m.default(d.default.merge({title:e.fixed_title,onchange:function(){s.each(t.links[e.index],function(e){t._refreshStep(e)})},inputs:e.inputs&&e.inputs.length>0?e.inputs:[{type:"hidden",name:"No options available.",ignore:null}]},e))}t.forms[e.index]=i,t._append(t.$steps,i.$el),t._refresh(),e.needs_refresh&&t._refreshStep(e),i.portlet[t.show_progress?"disable":"enable"](),t.show_progress&&t.execute_btn.model.set({wait:!0,wait_text:"Preparing...",percentage:100*(e.index+1)/t.steps.length}),Galaxy.emit.debug("tool-form-composite::initialize()",e.index+" : Workflow step state ready.",e),setTimeout(function(){a.resolve()},0)})},_refreshStep:function(e){var t=this,i=this.forms[e.index];i?(s.each(t.parms[e.index],function(e,n){if(e.step_linked||e.wp_linked){var a=i.field_list[i.data.match(n)];if(a){var o=void 0;if(e.step_linked)o={values:[]},s.each(e.step_linked,function(e){if(t._isDataStep(e)){var i=t.forms[e.index].data.create().input;i&&s.each(i.values,function(e){o.values.push(e)})}}),!e.multiple&&o.values.length>0&&(o={values:[o.values[0]]});else if(e.wp_linked){o=e.value;for(var l,r=/\$\{(.+?)\}/g;l=r.exec(e.value);){var d=t.wp_form.field_list[t.wp_form.data.match(l[1])],c=d&&d.value();c&&(o=o.split(l[0]).join(c))}}void 0!==o&&a.value(o)}}}),i.trigger("change")):e.needs_refresh=!0},_refreshHistory:function(){var e=this,t=parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.model;this._refresh_history&&clearTimeout(this._refresh_history),t&&t.refresh().success(function(){0===t.numOfUnfinishedShownContents()&&(e._refresh_history=setTimeout(function(){e._refreshHistory()},t.UPDATE_DELAY))})},_execute:function(){var e=this;this.show_progress=!0,this._enabled(!1),this.deferred.execute(function(t){setTimeout(function(){t.resolve(),e._submit()},0)})},_submit:function(){var e=this,t=this.history_form.data.create(),i={new_history_name:t["new_history|name"]?t["new_history|name"]:null,history_id:t["new_history|name"]?null:this.model.get("history_id"),replacement_params:this.wp_form?this.wp_form.data.create():{},parameters:{},parameters_normalized:!0,batch:!0};this.display_use_cached_job_checkbox&&(i.use_cached_job="true"===this.job_options_form.data.create()["use_cached_job|check"]);var s=!0;for(var a in this.forms){var o=this.forms[a],r=o.data.create(),c=e.steps[a],u=c.step_index;o.trigger("reset");for(var h in r){var f=r[h],p=o.data.match(h),m=(o.field_list[p],o.input_list[p]);if(!m.step_linked){if(!(s=this._isDataStep(c)?f&&f.values&&f.values.length>0:m.optional||m.is_workflow&&""!==f||!m.is_workflow&&null!==f)){o.highlight(p);break}i.parameters[u]=i.parameters[u]||{},i.parameters[u][h]=r[h]}}if(!s)break}s?(Galaxy.emit.debug("tool-form-composite::submit()","Validation complete.",i),d.default.request({type:"POST",url:Galaxy.root+"api/workflows/"+this.model.id+"/invocations",data:i,success:function(t){if(Galaxy.emit.debug("tool-form-composite::submit","Submission successful.",t),e.$el.children().hide(),e.$el.append(e._templateSuccess(t)),n.isArray(t)&&t.length>0){e.$el.append(n("
              ",{id:"webhook-view"}));new $.default.WebhookView({urlRoot:Galaxy.root+"api/webhooks/workflow",toolId:i.tool_id,toolVersion:i.tool_version})}e._refreshHistory()},error:function(t){Galaxy.emit.debug("tool-form-composite::submit","Submission failed.",t);var n=!1;if(t&&t.err_data)for(var s in e.forms){var a=e.forms[s],o=t.err_data[a.model.get("step_index")];if(o){var r=a.data.matchResponse(o);for(var d in r){a.highlight(d,r[d]),n=!0;break}}}n||e.modal.show({title:(0,l.default)("Workflow submission failed"),body:e._templateError(i,t&&t.err_msg),buttons:{Close:function(){e.modal.hide()}}})},complete:function(){e._enabled(!0)}})):(e._enabled(!0),Galaxy.emit.debug("tool-form-composite::submit()","Validation failed.",i))},_append:function(e,t){e.append("
              ").append(t)},_enabled:function(e){this.execute_btn.model.set({wait:!e,wait_text:"Sending...",percentage:-1}),this.wp_form&&this.wp_form.portlet[e?"enable":"disable"](),this.history_form&&this.history_form.portlet[e?"enable":"disable"](),s.each(this.forms,function(t){t&&t.portlet[e?"enable":"disable"]()})},_isDataStep:function(e){for(var t=n.isArray(e)?e:[e],i=0;i0?n("
              ").addClass("donemessagelarge").append(n("
              ").html("Successfully invoked workflow "+d.default.sanitize(this.model.get("name"))+""+(e.length>1?" "+e.length+" times":"")+".")).append(n("
              ").append("").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")):this._templateError(e,"Invalid success response. No invocations found.")},_templateError:function(e,t){return n("
              ").addClass("errormessagelarge").append(n("
              ").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(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){function t(e){return e&&e.__esModule?e:{default:e}}var n=i(0),s=t(n),a=i(64),o=t(a),l=i(89),r=t(l),d=i(252),c=t(d),u=i(262),h=t(u),f=i(43),p=t(f),m=i(118),g=t(m),_=i(100),v=t(_),w=i(265),y=t(w),b=i(266),x=t(b),$=i(113),C=t($),k=i(25),S=t(k),T=i(268),P=t(T),D=i(269),E=t(D),A=i(271),M=t(A),I=i(276),j=t(I),O=i(136),L=t(O),V=i(26),H=t(V),N=i(5),G=t(N),F=i(6),U=t(F),z=i(277),R=t(z),B=i(278),W=t(B),J=i(122),q=t(J),Y=i(63),Q=t(Y),K=s.default;window.app=function(t,i){window.Galaxy=new o.default.GalaxyApp(t,i),Galaxy.debug("analysis app");var n=r.default.extend({routes:{"(/)":"home","(/)root*":"home","(/)tours(/)(:tour_id)":"show_tours","(/)user(/)":"show_user","(/)user(/)(:form_id)":"show_user_form","(/)openids(/)list":"show_openids","(/)pages(/)create(/)":"show_pages_create","(/)pages(/)edit(/)":"show_pages_edit","(/)pages(/)(:action_id)":"show_pages","(/)visualizations(/)edit(/)":"show_visualizations_edit","(/)visualizations/(:action_id)":"show_visualizations","(/)workflows/import_workflow":"show_import_workflow","(/)workflows/run(/)":"show_run","(/)workflows(/)list":"show_workflows","(/)workflows/list_published(/)":"show_workflows_published","(/)workflows/create(/)":"show_workflows_create","(/)histories(/)citations(/)":"show_history_citations","(/)histories(/)rename(/)":"show_histories_rename","(/)histories(/)import(/)":"show_histories_import","(/)histories(/)permissions(/)":"show_histories_permissions","(/)histories(/)(:action_id)":"show_histories","(/)datasets(/)list(/)":"show_datasets","(/)custom_builds":"show_custom_builds","(/)datasets/edit":"show_dataset_edit_attributes","(/)datasets/error":"show_dataset_error"},require_login:["show_user","show_user_form","show_workflows"],authenticate:function(e,t){return Galaxy.user&&Galaxy.user.id||-1==this.require_login.indexOf(t)},show_tours:function(e){e?C.default.giveTourById(e):this.page.display(new C.default.ToursView)},show_user:function(){this.page.display(new y.default.View)},show_user_form:function(e){var t=new y.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="+H.default.get("id"),redirect:"visualizations/list"}))},show_workflows_published:function(){this.page.display(new S.default({url_base:Galaxy.root+"workflow/list_published"}))},show_histories:function(e){this.page.display(new j.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:H.default.get("id"),source:"histories"}}).$mount(t)},show_histories_rename:function(){this.page.display(new v.default.View({url:"history/rename?id="+H.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).$mount(t)},show_histories_permissions:function(){this.page.display(new v.default.View({url:"history/permissions?id="+H.default.get("id"),redirect:"histories/list"}))},show_openids:function(){this.page.display(new S.default({url_base:Galaxy.root+"user/openids_list"}))},show_datasets:function(){this.page.display(new S.default({url_base:Galaxy.root+"dataset/list"}))},show_pages:function(e){this.page.display(new P.default.View({action_id:e,plural:"Pages",item:"page"}))},show_pages_create:function(){this.page.display(new v.default.View({url:"page/create",redirect:"pages/list"}))},show_pages_edit:function(){this.page.display(new v.default.View({url:"page/edit?id="+H.default.get("id"),redirect:"pages/list"}))},show_workflows:function(){this.page.display(new E.default.View)},show_workflows_create:function(){this.page.display(new v.default.View({url:"workflow/create",redirect:"workflow/editor"}))},show_run:function(){this._loadWorkflow()},show_import_workflow:function(){this.page.display(new E.default.ImportWorkflowView)},show_custom_builds:function(){var e=this,t=this.page.historyPanel.historyView;if(!t||!t.model||!t.model.id)return void window.setTimeout(function(){e.show_custom_builds()},500);this.page.display(new x.default.View)},show_dataset_edit_attributes:function(){this.page.display(new W.default.View)},show_dataset_error:function(){this.page.display(new R.default.View)},home:function(e){e.tool_id||e.job_id?"upload1"===e.tool_id?(this.page.toolPanel.upload.show(),this._loadCenterIframe("welcome")):this._loadToolForm(e):e.workflow_id?this._loadWorkflow():e.m_c?this._loadCenterIframe(e.m_c+"/"+e.m_a):this._loadCenterIframe("welcome")},_loadToolForm:function(e){e.id=decodeURIComponent(e.tool_id),this.page.display(new g.default.View(e))},_loadCenterIframe:function(e,t){t=t||Galaxy.root,e=t+e,this.page.$("#galaxy_main").prop("src",e)},_loadWorkflow:function(){var e=this;G.default.get({url:Galaxy.root+"api/workflows/"+G.default.getQueryString("id")+"/download?style=run",success:function(t){e.page.display(new L.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 strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(80),o=s(a),l=i(253),r=s(l),d=i(3),c=s(d),u=i(136),h=(s(u),e.View.extend({initialize:function(t,i){var n=i.config;this.root=i.root,this.stored_workflow_menu_entries=n.stored_workflow_menu_entries||[];var s=new o.default.ToolSearch({hidden:!1}),a=new o.default.ToolCollection(n.toolbox);this.tool_panel=new o.default.ToolPanel({tool_search:s,tools:a,layout:n.toolbox_in_panel}),this.tool_panel_view=new o.default.ToolPanelView({model:this.tool_panel}),this.upload_button=new r.default({nginx_upload_path:n.nginx_upload_path,ftp_upload_site:n.ftp_upload_site,default_genome:n.default_genome,default_extension:n.default_extension}),Galaxy.upload=this.upload_button,this.model=new e.Model({title:(0,c.default)("Tools"),buttons:[this.upload_button]}),this.setElement(this._template())},render:function(){var e=this;this.tool_panel.get("layout").size()>0&&(this.$el.prepend(this.tool_panel_view.$el),this.tool_panel_view.render()),e.$("#internal-workflows").append(e._templateAllWorkflow({title:(0,c.default)("All workflows"),href:"workflows/list"})),n.each(this.stored_workflow_menu_entries,function(t){e.$("#internal-workflows").append(e._templateWorkflowLink({title:t.stored_workflow.name,href:"workflows/run?id="+t.encoded_stored_workflow_id}))})},_templateTool:function(e){return['
              ','',e.title,"","
              "].join("")},_templateAllWorkflow:function(e){return['
              ','',e.title,"","
              "].join("")},_templateWorkflowLink:function(e){return['
              ','',e.title,"","
              "].join("")},_template:function(){return['
              ','",'
              ','
              ','
              ',"",(0,c.default)("Workflows"),"","
              ",'
              ','
              ',"
              ","
              "].join("")},toString:function(){return"toolPanel"}}));t.default=h}).call(t,i(2),i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),a=n(s),o=i(5),l=n(o),r=i(9),d=n(r),c=i(78),u=n(c),h=i(254),f=n(h),p=i(255),m=n(p),g=i(258),_=n(g),v=i(260),w=n(v);t.default=e.View.extend({options:{nginx_upload_path:"",ftp_upload_site:"n/a",default_genome:"?",default_extension:"auto",height:500,width:900,auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be.  You can also upload compressed files, which will automatically be decompressed."}},list_extensions:[],list_genomes:[],initialize:function(e){var t=this;this.options=l.default.merge(e,this.options),this.ui_button=new f.default.View({onclick:function(e){e.preventDefault(),t.show()},onunload:function(){var e=t.ui_button.model.get("percentage",0);if(e>0&&e<100)return"Several uploads are queued."}}),this.setElement(this.ui_button.$el);var t=this;l.default.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(e){for(var i in e)t.list_extensions.push({id:e[i].extension,text:e[i].extension,description:e[i].description,description_url:e[i].description_url,composite_files:e[i].composite_files});t.list_extensions.sort(function(e,t){var i=e.text&&e.text.toLowerCase(),n=t.text&&t.text.toLowerCase();return i>n?1:ii.text?1:e.text0){var n={file_count:e.length,dbkey:e[0].get("genome","?"),file_type:e[0].get("extension","auto")};for(var s in e){var a=e[s];if(a.set("status","running"),!(a.get("file_size")>0)){i.error_message="Upload content incomplete.",a.set("status","error"),a.set("info",i.error_message);break}var o="files_"+s+"|";switch(n[o+"type"]="upload_dataset",n[o+"space_to_tab"]=a.get("space_to_tab")&&"Yes"||null,n[o+"to_posix_lines"]=a.get("to_posix_lines")&&"Yes"||null,n[o+"dbkey"]=a.get("genome",null),n[o+"file_type"]=a.get("extension",null),a.get("file_mode")){case"new":n[o+"url_paste"]=a.get("url_paste");break;case"ftp":n[o+"ftp_files"]=a.get("file_path");break;case"local":i.files.push({name:o+"file_data",file:a.get("file_data")})}}i.payload.inputs=JSON.stringify(n)}return i}})}).call(t,i(2))},function(e,t,i){"use strict";(function(e,n){Object.defineProperty(t,"__esModule",{value:!0});var s=i(3),a=function(e){return e&&e.__esModule?e:{default:e}}(s),o=e.View.extend({initialize:function(t){var i=this;this.model=t&&t.model||new e.Model({icon:"fa-upload",tooltip:(0,a.default)("Download from URL or upload files from disk"),label:"Load Data",percentage:0,status:"",onunload:function(){},onclick:function(){}}).set(t),this.setElement(this._template()),this.$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.$progress.removeClass().addClass("progress-bar").addClass("progress-bar-notransition").addClass(""!=e.status&&"progress-bar-"+e.status).css({width:e.percentage+"%"})},_template:function(){return'
              '}});t.default={View:o}}).call(t,i(2),i(0))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),l=a(o),r=i(5),d=(a(r),i(49)),c=a(d),u=i(256),h=a(u),f=i(91),p=a(f),m=i(92),g=a(m),_=i(27),v=a(_),w=i(12),y=a(w),b=i(6),x=a(b),$=i(257),C=a($);i(93),t.default=e.View.extend({upload_size:0,collection:new c.default.Collection,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ui_button=e.ui_button,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.$uploadbox=this.$(".upload-box"),this.$uploadtable=this.$(".upload-table"),this.btnLocal=new x.default.Button({id:"btn-local",title:(0,l.default)("Choose local file"),onclick:function(){t.uploadbox.select()},icon:"fa fa-laptop"}),this.btnFtp=new x.default.Button({id:"btn-ftp",title:(0,l.default)("Choose FTP file"),onclick:function(){t._eventFtp()},icon:"fa fa-folder-open-o"}),this.btnCreate=new x.default.Button({id:"btn-new",title:"Paste/Fetch data",onclick:function(){t._eventCreate()},icon:"fa fa-edit"}),this.btnStart=new x.default.Button({id:"btn-start",title:(0,l.default)("Start"),onclick:function(){t._eventStart()}}),this.btnStop=new x.default.Button({id:"btn-stop",title:(0,l.default)("Pause"),onclick:function(){t._eventStop()}}),this.btnReset=new x.default.Button({id:"btn-reset",title:(0,l.default)("Reset"),onclick:function(){t._eventReset()}}),this.btnClose=new x.default.Button({id:"btn-close",title:(0,l.default)("Close"),onclick:function(){t.app.modal.hide()}}),n.each([this.btnLocal,this.btnFtp,this.btnCreate,this.btnStop,this.btnReset,this.btnStart,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.uploadbox=this.$uploadbox.uploadbox({url:this.app.options.nginx_upload_path,announce:function(e,i){t._eventAnnounce(e,i)},initialize:function(e){return t.app.toData([t.collection.get(e)],t.history_id)},progress:function(e,i){t._eventProgress(e,i)},success:function(e,i){t._eventSuccess(e,i)},error:function(e,i){t._eventError(e,i)},complete:function(){t._eventComplete()},ondragover:function(){t.$uploadbox.addClass("highlight")},ondragleave:function(){t.$uploadbox.removeClass("highlight")}}),this.ftp=new v.default.View({title:(0,l.default)("FTP files"),container:this.btnFtp.$el}),this.select_extension=new y.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-extension"),data:n.filter(this.list_extensions,function(e){return!e.composite_files}),value:this.options.default_extension,onchange:function(e){t._changeExtension(e)}}),this.$(".upload-footer-extension-info").on("click",function(e){new g.default({$el:s(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),list:t.list_extensions,placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new y.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome,onchange:function(e){t._changeGenome(e)}}),this.loader=new C.default({$container:this.$uploadbox,collection:this.collection,new_content:function(e){var i=new h.default(t,{model:e});return t.$uploadtable.find("> tbody:first").append(i.$el),i.render(),i}}),this.collection.on("remove",function(e){t._eventRemove(e)}),this.render()},render:function(){var e="";e=0==this.counter.announce?this.uploadbox.compatible()?" ":"Browser does not support Drag & Drop. Try Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.":0==this.counter.running?"You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed.":"Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining.",this.$(".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'
              Drop files here
              Type (set all): Genome (set all):
              '}})}).call(t,i(2),i(1),i(0))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),l=a(o),r=i(5),d=a(r),c=i(49),u=(a(c),i(90)),h=a(u),f=i(27),p=a(f),m=i(12),g=a(m);t.default=e.View.extend({status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template(t.model)),this.$mode=this.$(".upload-mode"),this.$title=this.$(".upload-title"),this.$text=this.$(".upload-text"),this.$size=this.$(".upload-size"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$text_content=this.$(".upload-text-content"),this.$settings=this.$(".upload-settings"),this.$symbol=this.$(".upload-symbol"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.settings=new p.default.View({title:(0,l.default)("Upload configuration"),container:this.$(".upload-settings"),placement:"bottom"});var s=this.app.select_genome.value(),a=this.app.select_extension.value();this.select_genome=new 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'
              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.