From 7a1d7fcaf4672c0a3ad382b07362b969180797d2 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 4 Dec 2017 12:45:45 -0500
Subject: [PATCH 1/6] download behaves badly on firefox, preventing right
 clicking to copy the url here

---
 client/galaxy/scripts/mvc/dataset/dataset-li.js | 14 ++++----------
 1 file changed, 4 insertions(+), 10 deletions(-)

diff --git a/client/galaxy/scripts/mvc/dataset/dataset-li.js b/client/galaxy/scripts/mvc/dataset/dataset-li.js
index 97f8b831b6e..db96fd99962 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-li.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-li.js
@@ -286,16 +286,10 @@ var DatasetListItemView = _super.extend(
                 return this._renderMetaFileDownloadButton();
             }
 
-            return $(
-                [
-                    '<a class="download-btn icon-btn" ',
-                    'href="',
-                    this.model.urls.download,
-                    `" title="${_l("Download")}" download>`,
-                    '<span class="fa fa-floppy-o"></span>',
-                    "</a>"
-                ].join("")
-            );
+            return $(`
+                <a class="download-btn icon-btn" href="${this.model.urls.download}" title="${_l("Download")}">
+                    <span class="fa fa-floppy-o"></span>
+                </a>`);
         },
 
         /** Render the download button which opens a dropdown with links to download assoc. meta files (indeces, etc.) */

From 0ab21a2f4ed195711d0a55fa369dbc2fc09b123a Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 4 Dec 2017 13:06:26 -0500
Subject: [PATCH 2/6] We preventdefault on this anyway, so the void(0) doesn't
 do anything.  This allows right click copy on primary dataset regardless of
 whether or not there are extra meta files.

---
 client/galaxy/scripts/mvc/dataset/dataset-li.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/mvc/dataset/dataset-li.js b/client/galaxy/scripts/mvc/dataset/dataset-li.js
index db96fd99962..b8684908b12 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-li.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-li.js
@@ -298,7 +298,7 @@ var DatasetListItemView = _super.extend(
             return $(
                 [
                     '<div class="metafile-dropdown dropdown">',
-                    '<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',
+                    `<a class="download-btn icon-btn" href="${this.model.urls.download}" data-toggle="dropdown"`,
                     ` title="${_l("Download")}">`,
                     '<span class="fa fa-floppy-o"></span>',
                     "</a>",

From ab084ffd4b9a797d3ccee35ffcdc1953970b88a0 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 4 Dec 2017 13:27:51 -0500
Subject: [PATCH 3/6] Convert download blob to template literals instead of
 array concats.

---
 .../galaxy/scripts/mvc/dataset/dataset-li.js  | 52 +++++++++----------
 1 file changed, 25 insertions(+), 27 deletions(-)

diff --git a/client/galaxy/scripts/mvc/dataset/dataset-li.js b/client/galaxy/scripts/mvc/dataset/dataset-li.js
index b8684908b12..d8369b2c686 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-li.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-li.js
@@ -292,35 +292,33 @@ var DatasetListItemView = _super.extend(
                 </a>`);
         },
 
-        /** Render the download button which opens a dropdown with links to download assoc. meta files (indeces, etc.) */
+        /** Render the download button which opens a dropdown with links to download assoc. meta files (indices, etc.) */
         _renderMetaFileDownloadButton: function() {
             var urls = this.model.urls;
-            return $(
-                [
-                    '<div class="metafile-dropdown dropdown">',
-                    `<a class="download-btn icon-btn" href="${this.model.urls.download}" data-toggle="dropdown"`,
-                    ` title="${_l("Download")}">`,
-                    '<span class="fa fa-floppy-o"></span>',
-                    "</a>",
-                    '<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">',
-                    `<li><a href="${urls.download}" download>`,
-                    _l("Download dataset"),
-                    "</a></li>",
-                    _.map(this.model.get("meta_files"), meta_file =>
-                        [
-                            '<li><a href="',
-                            urls.meta_download + meta_file.file_type,
-                            '">',
-                            _l("Download"),
-                            " ",
-                            meta_file.file_type,
-                            "</a></li>"
-                        ].join("")
-                    ).join("\n"),
-                    "</ul>",
-                    "</div>"
-                ].join("\n")
-            );
+            return $(`
+                <div class="metafile-dropdown dropdown">
+                    <a class="download-btn icon-btn" href="${
+                        this.model.urls.download
+                    }" data-toggle="dropdown" title="${_l("Download")}">
+                        <span class="fa fa-floppy-o"></span>
+                    </a>
+                    <ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">
+                        <li>
+                            <a href="${urls.download}">
+                                ${_l("Download dataset")}
+                            </a>
+                        </li>
+                        ${_.map(
+                            this.model.get("meta_files"),
+                            meta_file =>
+                                `<li>
+                                    <a href="${urls.meta_download + meta_file.file_type}">
+                                        ${_l("Download")} ${meta_file.file_type}
+                                    </a>
+                                </li>`
+                        )}
+                    </ul>
+                </div>`);
         },
 
         _renderNametags: function() {

From d3d6e723539618bea80a9f18b1895cc82aee280b Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 4 Dec 2017 14:10:05 -0500
Subject: [PATCH 4/6] Use the local var for urls.download

---
 client/galaxy/scripts/mvc/dataset/dataset-li.js | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/mvc/dataset/dataset-li.js b/client/galaxy/scripts/mvc/dataset/dataset-li.js
index d8369b2c686..66e2bf4b2f0 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-li.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-li.js
@@ -297,9 +297,7 @@ var DatasetListItemView = _super.extend(
             var urls = this.model.urls;
             return $(`
                 <div class="metafile-dropdown dropdown">
-                    <a class="download-btn icon-btn" href="${
-                        this.model.urls.download
-                    }" data-toggle="dropdown" title="${_l("Download")}">
+                    <a class="download-btn icon-btn" href="${urls.download}" data-toggle="dropdown" title="${_l("Download")}">
                         <span class="fa fa-floppy-o"></span>
                     </a>
                     <ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">

From d93a2b437972d08c3df38f2c8020b04fb659f696 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 18 Dec 2017 21:07:49 -0500
Subject: [PATCH 5/6] Client-format.

---
 client/galaxy/scripts/mvc/dataset/dataset-li.js | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/client/galaxy/scripts/mvc/dataset/dataset-li.js b/client/galaxy/scripts/mvc/dataset/dataset-li.js
index 66e2bf4b2f0..e1b54b1d0ce 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-li.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-li.js
@@ -297,7 +297,9 @@ var DatasetListItemView = _super.extend(
             var urls = this.model.urls;
             return $(`
                 <div class="metafile-dropdown dropdown">
-                    <a class="download-btn icon-btn" href="${urls.download}" data-toggle="dropdown" title="${_l("Download")}">
+                    <a class="download-btn icon-btn" href="${urls.download}" data-toggle="dropdown" title="${_l(
+                "Download"
+            )}">
                         <span class="fa fa-floppy-o"></span>
                     </a>
                     <ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">

From 202305687abcf887541d6d16fc71e96f9afb63d9 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 18 Dec 2017 21:08:34 -0500
Subject: [PATCH 6/6] Rebuild client again.

---
 static/scripts/bundled/analysis.bundled.js | 2 +-
 static/scripts/mvc/dataset/dataset-li.js   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/static/scripts/bundled/analysis.bundled.js b/static/scripts/bundled/analysis.bundled.js
index 198c7a6a0e4..df481305239 100644
--- a/static/scripts/bundled/analysis.bundled.js
+++ b/static/scripts/bundled/analysis.bundled.js
@@ -1,3 +1,3 @@
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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 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this.key=e.key,this._initStorage(),this.maxSize=e.maxSize||s.defaultOptions.maxSize,this},s.prototype._hasStorage=function(){try{return localStorage.setItem("test","test"),localStorage.removeItem("test"),!0}catch(e){return!1}},s.prototype._initStorage=function(){return null===localStorage.getItem(this.key)?this.empty():this},s.prototype.add=function(e){var t=this,i=t._fetchAndParse(),n=i.length+1-t.maxSize;return n>0&&i.splice(0,n),i.push(e),t._unparseAndStore(i),i.length},s.prototype._fetchAndParse=function(){var e=this;return JSON.parse(localStorage.getItem(e.key))},s.prototype._unparseAndStore=function(e){var t=this;return localStorage.setItem(t.key,JSON.stringify(e))},s.prototype.length=function(){return this._fetchAndParse().length},s.prototype.get=function(e){return this._fetchAndParse().slice(0,e)},s.prototype.remove=function(e){var t=this._fetchAndParse(),i=t.splice(0,e);return this._unparseAndStore(t),i},s.prototype.empty=function(){return localStorage.setItem(this.key,"[]"),this},s.prototype.stringify=function(e){return JSON.stringify(this.get(e))},s.prototype.print=function(){console.log(JSON.stringify(this._fetchAndParse(),null,"  "))},t.default={MetricsLogger:i,LoggingCache:s}}).call(t,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(34),l=a(o),r=i(23),d=a(r),c=i(8),u=a(c),h=i(4),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("<a/>").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['<div id="everything">','<div id="background"/>','<div id="masthead"/>','<div id="messagebox"/>','<div id="inactivebox" class="panel-warning-message" />','<div id="left" />','<div id="center" />','<div id="right" />',"</div>",'<div id="dd-helper" />'].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 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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){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var 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a=i(4);!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("<div/>").addClass("upload-settings")),this.$el.append(n("<div/>").addClass("upload-settings-cover")),this.$el.append(n("<table/>").addClass("upload-settings-table ui-table-striped").append("<tbody/>")),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.$table.empty(),s.each(this.options.parameters,function(t){var i=n("<div/>").addClass("upload-"+t.id+" upload-icon-button 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float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span class="upload-ftp-number"/>&nbsp;&nbsp;<span class="upload-icon fa fa-hdd-o"/><span class="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th class="_has_collection" style="display: none;"><div class="upload-ftp-select-all"></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody class="upload-ftp-body"/></table></div><div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'}})}).call(t,i(2),i(0),i(1))},function(e,t,i){"use strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(4),o=(s(a),i(16)),l=s(o);t.default=e.View.extend({initialize:function(t){this.model=new e.Model(t),this.setElement("<div/>"),this.render()},render:function(){var e=this.model.attributes,t=n.findWhere(e.list,{id:e.extension});this.extension_popup&&this.extension_popup.remove(),this.extension_popup=new l.default.View({placement:e.placement||"bottom",container:e.$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+='&nbsp;(<a href="'+e.description_url+'" target="_blank">read more</a>)'),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. 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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(['<a class="name" title="',(0,w.default)("Click to rename"),'" href="javascript:void(0)">',"<%- element.name %>","</a>",'<button class="discard btn btn-sm" title="',(0,w.default)("Remove this dataset from the 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this.workingElements.length<this.minElements?this._renderInvalid(e,t):(this.$el.empty().html(this.templates.main()),this._renderHeader(e),this._renderMiddle(e),this._renderFooter(e),this._addPluginComponents(),this.$(".collection-name").focus(),this.trigger("rendered",this),this)},_renderInvalid:function(e,t){return this.$el.empty().html(this.templates.invalidInitial({problems:this.invalidElements,elements:this.workingElements})),"function"==typeof this.oncancel&&this.$(".cancel-create.btn").show(),this.trigger("rendered",this),this},_renderHeader:function(e,t){var i=this.$(".header").empty().html(this.templates.header()).find(".help-content").prepend(s(this.templates.helpContent()));return this.invalidElements.length&&this._invalidElementsAlert(),i},_renderMiddle:function(e,t){var i=this.$(".middle").empty().html(this.templates.middle());return this._renderList(e),i},_addPluginComponents:function(){this.$(".help-content 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i=e.offset(),n=e.scrollTop(),s=t-i.top,a=i.top+e.outerHeight()-t;s>=0&&s<this.autoscrollDist?e.scrollTop(n-2):a>=0&&a<this.autoscrollDist&&e.scrollTop(n+2)},_getNearestElement:function(e){for(var t=this.$(".collection-elements li.collection-element").toArray(),i=0;i<t.length;i++){var n=s(t[i]),a=n.offset().top,o=Math.floor(n.outerHeight()/2)+4;if(a+o>e&&a-o<e)return n}return s()},_dropElements:function(e){e.originalEvent&&(e=e.originalEvent),e.preventDefault(),e.dataTransfer.dropEffect="move";var t=this._getNearestElement(e.clientY);return t.length?this.$dragging.insertBefore(t):this.$dragging.insertAfter(this.$(".collection-elements .collection-element").last()),this._syncOrderToDom(),!1},_syncOrderToDom:function(){var e=this,t=[];this.$(".collection-elements .collection-element").each(function(){var i=s(this).attr("data-element-id"),a=n.findWhere(e.workingElements,{id:i});a?t.push(a):console.error("missing element: 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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){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(61),a=n(s),o=i(107),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){function a(e){return 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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";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(e,n,s,a){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var l=i(64),r=o(l),d=i(65),c=(o(d),i(114)),u=o(c),h=i(4),f=o(h),p=i(5),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 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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")+")"}})),y=u.default.InfinitelyScrollingCollection,w=y.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),y.prototype.initialize.call(this,e,t),this.includeDeleted=t.includeDeleted||!1,this.currentHistoryId=t.currentHistoryId,this.setUpListeners()},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot},setUpListeners:function(){return this.on({"change:deleted":function(e){this.debug("change:deleted",this.includeDeleted,e.get("deleted")),!this.includeDeleted&&e.get("deleted")&&this.remove(e)},copied:function(e,t){this.setCurrent(new v(t,[]))},"set-as-current":function(e){var t=this.currentHistoryId;this.trigger("no-longer-current",t),this.currentHistoryId=e.id}})},_buildFetchData:function(e){return s.extend(y.prototype._buildFetchData.call(this,e),{view:"dev-detailed"})},_buildFetchFilters:function(e){var t=y.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=y.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(y.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 y.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:w}}).call(t,i(2),i(0),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(114),l=a(o),r=i(115),d=a(r),c=i(60),u=a(c),h=i(65),f=a(h),p=i(253),m=a(p),g=i(5),_=a(g),v=i(116),y=a(v),w=500;try{w=localStorage.getItem("historyContentsLimitPerPageDefault")||w}catch(e){}var b=l.default.PaginatedCollection,x=b.extend(_.default.LoggableMixin).extend({_logNamespace:"history",limitPerPage:w,limitPerProgressiveFetch:w,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 y.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){Object.defineProperty(t,"__esModule",{value:!0});var n=i(5),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,n,s,a){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var l=i(5),r=o(l),d=i(3),c=(o(d),e.View.extend(r.default.LoggableMixin).extend({_logNamespace:"list",initialize:function(e){this.expanded=e.expanded||!1,this.log("\t expanded:",this.expanded),this.fxSpeed=void 0!==e.fxSpeed?e.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(e){var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){var e=n(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(e).replaceWith(this._renderDetails().show()),e},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;0===t?(i._swapNewRender(e),i.trigger("rendered",i)):n(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",s.isFunction(this.className)?this.className():this.className).append(e.children())},_setUpBehaviors:function(e){e=e||this.$el,e.find("[title]").tooltip({placement:"bottom"})},$details:function(e){return e=e||this.$el,e.find("> .details")},_renderDetails:function(){var e=n(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(e),e},toggleExpanded:function(e){return e=void 0===e?!this.expanded:e,e?this.expand():this.collapse(),this},expand:function(){var e=this;return e._fetchModelDetails().always(function(){e._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?a.when():this.model.fetch()},_expand:function(){var e=this,t=e._renderDetails();e.$details().replaceWith(t),e.expanded=!0,e.$details().slideDown(e.fxSpeed,function(){e.trigger("expanded",e)})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var e=this;e.expanded=!1,this.$details().slideUp(e.fxSpeed,function(){e.trigger("collapsed",e)})}})),u=c.extend(r.default.mixin(r.default.SelectableViewMixin,r.default.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){c.prototype.initialize.call(this,e),r.default.SelectableViewMixin.initialize.call(this,e),r.default.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(e){e?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var e=c.prototype._buildNewRender.call(this);return e.children(".warnings").replaceWith(this._renderWarnings()),e.children(".title-bar").replaceWith(this._renderTitleBar()),e.children(".primary-actions").append(this._renderPrimaryActions()),e.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),e},_swapNewRender:function(e){return c.prototype._swapNewRender.call(this,e),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var e=this,t=n('<div class="warnings"></div>'),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(['<div class="list-element">','<div class="warnings"></div>','<div class="selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="primary-actions"></div>','<div class="title-bar"></div>','<div class="details"></div>',"</div>"]),warnings:{},titleBar:r.default.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element"),subtitle:r.default.wrapTemplate(['<div class="subtitle"></div>']),details:r.default.wrapTemplate(['<div class="details"></div>'])}}();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.$el)},expand:function(){var e=this;return e._fetchModelDetails().always(function(){"foldout"===e.foldoutStyle?e._expand():"drilldown"===e.foldoutStyle&&e._expandByDrilldown()})},_expandByDrilldown:function(){var e=this;e.listenTo(e.foldout,"close",function(){e.trigger("collapsed:drilldown",e,e.foldout)}),e.trigger("expanded:drilldown",e,e.foldout)}});h.prototype.templates=function(){var e=r.default.wrapTemplate(['<div class="details">',"</div>"],"collection");return s.extend({},u.prototype.templates,{details:e})}(),t.default={ExpandableView:c,ListItemView:u,FoldoutListItemView:h}}).call(t,i(2),i(0),i(1),i(0))},function(e,t,i){"use strict";(function(e,n,s,a){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var l=i(66),r=o(l),d=i(17),c=o(d),u=i(22),h=o(u),f=i(5),p=o(f),m=i(3),g=o(m),_=r.default.ListItemView,v=_.extend({_logNamespace:"dataset",className:_.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log(this+".initialize:",e),_.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_setUpListeners:function(){_.prototype._setUpListeners.call(this);var t=this;return t.listenTo(t.model,{change:function(i){t.model.changedAttributes().state&&t.model.inReadyState()&&t.expanded&&!t.model.hasDetails()?t.model.fetch({silent:!0}).done(function(){t.render()}):e.has(i.changed,"tags")&&1===e.keys(i.changed).length?t.$(".nametags").html(t._renderNametags()):t.render()}})},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):n.when()},remove:function(e,t){var i=this;e=e||this.fxSpeed,this.$el.fadeOut(e,function(){s.View.prototype.remove.call(i),t&&t.call(i)})},_swapNewRender:function(e){return _.prototype._swapNewRender.call(this,e),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var e=this.model.get("state");if(e===c.default.NOT_VIEWABLE||e===c.default.DISCARDED||!this.model.get("accessible"))return null;var t={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))t.disabled=!0,t.title=(0,g.default)("Cannot display datasets removed from disk");else if(e===c.default.UPLOAD)t.disabled=!0,t.title=(0,g.default)("This dataset must finish uploading before it can be viewed");else if(e===c.default.NEW)t.disabled=!0,t.title=(0,g.default)("This dataset is not yet viewable");else{t.title=(0,g.default)("View data"),t.href=this.model.urls.display;var i=this;t.onclick=function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.addDataset(i.model.get("id")),e.preventDefault())}}return t.faIcon="fa-eye",(0,h.default)(t)},_renderDetails:function(){if(this.model.get("state")===c.default.NOT_VIEWABLE)return a(this.templates.noAccess(this.model.toJSON(),this));var e=_.prototype._renderDetails.call(this);return e.find(".actions .left").empty().append(this._renderSecondaryActions()),e.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),e.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(e),e},_renderSummary:function(){var e=this.model.toJSON(),t=this.templates.summaries[e.state];return(t=t||this.templates.summaries.unknown)(e,this)},_renderDetailMessages:function(){var t=this,i=a('<div class="detail-messages"></div>'),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(['<a class="download-btn icon-btn" ','href="',this.model.urls.download,'" title="'+(0,g.default)("Download")+'" download>','<span class="fa fa-floppy-o"></span>',"</a>"].join("")):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var t=this.model.urls;return a(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+(0,g.default)("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+t.download+'" download>',(0,g.default)("Download dataset"),"</a></li>",e.map(this.model.get("meta_files"),function(e){return['<li><a href="',t.meta_download+e.file_type,'">',(0,g.default)("Download")," ",e.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},_renderNametags:function(){return e.template(["<% _.each(_.sortBy(_.uniq(tags), function(x) { return x }), function(tag){ %>",'<% if (tag.indexOf("name:") == 0){ %>','<span class="label label-info"><%- tag.slice(5) %></span>',"<% } %>","<% }); %>"].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" ){ %>','<div class="warningmessagesmall">',(0,g.default)("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:p.default.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',(0,g.default)("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:p.default.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',(0,g.default)("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:p.default.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,g.default)("This dataset has been deleted"),"</div>","<% } %>"])}),i=p.default.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset"),n=p.default.wrapTemplate(['<div class="details">','<div class="summary">',(0,g.default)("You do not have permission to view this dataset"),"</div>","</div>"],"dataset"),s={};s[c.default.OK]=s[c.default.FAILED_METADATA]=p.default.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.file_ext ){ %>",'<div class="datatype">','<label class="prompt">',(0,g.default)("format"),"</label>",'<span class="value"><%- dataset.file_ext %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',(0,g.default)("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset"),s[c.default.NEW]=p.default.wrapTemplate(["<div>",(0,g.default)("This 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Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset"),s[c.default.ERROR]=p.default.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',(0,g.default)("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset"),s[c.default.EMPTY]=p.default.wrapTemplate(["<div>",(0,g.default)("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset"),s.unknown=p.default.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var a={resubmitted:p.default.wrapTemplate(["<% if( model.resubmitted ){ %>",'<div class="resubmitted-msg infomessagesmall">',(0,g.default)("The job creating this dataset has been resubmitted"),"</div>","<% } %>"])},o=p.default.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%- link.target %>" href="<%- link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return e.extend({},_.prototype.templates,{warnings:t,details:i,noAccess:n,summaries:s,detailMessages:a,displayApplications:o})}(),t.default={DatasetListItemView:v}}).call(t,i(1),i(0),i(2),i(0))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(66),l=a(o),r=i(67),d=a(r),c=i(5),u=a(c),h=i(3),f=a(h),p=l.default.FoldoutListItemView,m=l.default.ListItemView,g=p.extend({className:p.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},initialize:function(e){this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,p.prototype.initialize.call(this,e)},_setUpListeners:function(){p.prototype._setUpListeners.call(this),this.listenTo(this.model,"change",function(t,i){e.has(t.changed,"deleted")?this.render():e.has(t.changed,"element_count")&&this.$("> .title-bar .subtitle").replaceWith(this._renderSubtitle())})},_renderSubtitle:function(){return n(this.templates.subtitle(this.model.toJSON(),this))},_getFoldoutPanelOptions:function(){var t=p.prototype._getFoldoutPanelOptions.call(this);return e.extend(t,{linkTarget:this.linkTarget,hasUser:this.hasUser})},$selector:function(){return this.$("> .selector")},toString:function(){return"DCListItemView("+(this.model?""+this.model:"(no model)")+")"}});g.prototype.templates=function(){var t=e.extend({},p.prototype.templates.warnings,{error:u.default.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',(0,f.default)("There was an error getting the data for this collection"),": <%- model.error %>","</div>","<% } %>"]),purged:u.default.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',(0,f.default)("This collection has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:u.default.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,f.default)("This collection has been deleted"),"</div>","<% } %>"])}),i=u.default.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- collection.element_identifier || collection.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"collection"),n=u.default.wrapTemplate(['<div class="subtitle">','<% 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"),"<% } %>","</div>"],"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(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"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(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>","</div>"],"element");return e.extend({},d.default.DatasetListItemView.prototype.templates,{titleBar:t})}();var y=g.extend({className:g.prototype.className+" dataset-collection-element",_swapNewRender:function(e){g.prototype._swapNewRender.call(this,e);var t=this.model.get("state")||"ok";return this.$el.addClass("state-"+t),this.$el},toString:function(){return"NestedDCDCEListItemView("+(this.model?""+this.model:"(no model)")+")"}});t.default={DCListItemView:g,DCEListItemView:_,DatasetDCEListItemView:v,NestedDCDCEListItemView:y}}).call(t,i(1),i(0),i(0))},function(e,t,i){"use strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(11),o=s(a),l=i(6),r=s(l),d=e.View.extend({initialize:function(t){this.model=new e.Model(t),this.url=this.model.get("url"),this.redirect=this.model.get("redirect"),this.setElement("<div/>"),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.$el.parents().filter(function(){return-1!=["auto","scroll"].indexOf(n(this).css("overflow"))}).first().animate({scrollTop:0},500),e.message.update(t)}});t.default={View:d}}).call(t,i(2),i(0))},,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(17),l=a(o),r=i(5),d=a(r),c=i(3),u=a(c),h=d.default.SearchableModelMixin,f=e.Model.extend(d.default.LoggableMixin).extend(d.default.mixin(h,{_logNamespace:"dataset",defaults:{state:l.default.NEW,deleted:!1,purged:!1,name:"(unnamed dataset)",accessible:!0,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(e,t){this.debug(this+"(Dataset).initialize",e,t),
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e=this;this.$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.$input.off(),this.stopListening(this.model),e.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",""+this.model,")"].join("")}});t.default={TagsEditor:d}}).call(t,i(2),i(1))},,,,,,,,,,,,,,function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(0),a=n(s),o=i(15),l=n(o),r=i(6),d=n(r),c=a.default,u=e.Router.extend({initialize:function(e,t){this.page=e,this.options=t},push:function(e,t){t=t||{},t.__identifer=Math.random().toString(36).substr(2),c.isEmptyObject(t)||(e+=-1==e.indexOf("?")?"?":"&",e+=c.param(t,!0)),Galaxy.params=t,this.navigate(e,{trigger:!0})},execute:function(e,t,i){Galaxy.debug("router execute:",e,t,i);var n=l.default.parse(t.pop());t.push(n),e&&(this.authenticate(t,i)?e.apply(this,t):this.access_denied())},authenticate:function(e,t){return!0},access_denied:function(){this.page.display(new d.default.Message({status:"danger",message:"You must be logged in with proper credentials to make this request.",persistent:!0}))}});t.default=u}).call(t,i(2))},function(e,t,i){"use strict";(function(e,n,s){Object.defineProperty(t,"__esModule",{value:!0});var a=i(4);!function(e){e&&e.__esModule}(a);t.default=e.View.extend({options:{class_check:"fa-check-square-o",class_uncheck:"fa-square-o",parameters:[{id:"space_to_tab",title:"Convert spaces to tabs"},{id:"to_posix_lines",title:"Use POSIX standard"}]},initialize:function(e){this.model=e.model,this.setElement(n("<div/>").addClass("upload-settings")),this.$el.append(n("<div/>").addClass("upload-settings-cover")),this.$el.append(n("<table/>").addClass("upload-settings-table ui-table-striped").append("<tbody/>")),this.$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("<div/>").addClass("upload-"+t.id+" upload-icon-button 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To upload some files, log in to the FTP server at <strong>"+t.ftp_upload_site+"</strong> 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'<tr class="upload-ftp-row"><td class="_has_collection" style="display: none;"><div class="icon"/></td><td class="ftp-name">'+s.escape(e.path)+'</td><td class="ftp-size">'+o.default.bytesToString(e.size)+'</td><td class="ftp-time">'+e.ctime+"</td></tr>"},_template:function(){return'<div class="'+this.model.get("cls")+'"><div class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">'+this.model.get("help_text")+'</div><div class="upload-ftp-content"><span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span class="upload-ftp-number"/>&nbsp;&nbsp;<span class="upload-icon fa fa-hdd-o"/><span class="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th class="_has_collection" style="display: none;"><div class="upload-ftp-select-all"></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody class="upload-ftp-body"/></table></div><div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'}})}).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(4),o=(s(a),i(16)),l=s(o);t.default=e.View.extend({initialize:function(t){this.model=new e.Model(t),this.setElement("<div/>"),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.$el}),this.extension_popup.title(e.title),this.extension_popup.empty(),this.extension_popup.append(this._templateDescription(t)),this.extension_popup.show()},_templateDescription:function(e){if(e.description){var t=e.description;return e.description_url&&(t+='&nbsp;(<a href="'+e.description_url+'" target="_blank">read more</a>)'),t}return"There is no description available for this file extension."}})}).call(t,i(2),i(1))},function(e,t,i){"use strict";(function(e,t){!function(i){e.event.props.push("dataTransfer"),i.uploadpost=function(t){var n=i.extend({},{data:{},success:function(){},error:function(){},progress:function(){},url:null,maxfilesize:2048,error_filesize:"File exceeds 2GB. 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b=e.View.extend(f.default.LoggableMixin).extend({_logNamespace:"collections",tagName:"li",className:"collection-element",initialize:function(e){this.element=e.element||{},this.selected=e.selected||!1},render:function(){this.dragStartHandler=n.bind(this._dragstart,this),this.dragEndHandler=n.bind(this._dragend,this);var e=this.$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.$el.addClass("selected"),this},template:n.template(['<a class="name" title="',(0,w.default)("Click to rename"),'" href="javascript:void(0)">',"<%- element.name %>","</a>",'<button class="discard btn btn-sm" title="',(0,w.default)("Remove this dataset from the list"),'">',(0,w.default)("Discard"),"</button>"].join("")),select:function(e){this.$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,w.default)("Enter a new name for the element"),":\n(",(0,w.default)("Note that changing the name here will not rename the dataset"),")"].join(""),prompt((0,w.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"!==e.history_content_type?(0,w.default)("is not a dataset"):e.state===u.default.OK||n.contains(u.default.NOT_READY_STATES,e.state)?e.deleted||e.purged?(0,w.default)("has been deleted or purged"):null:(0,w.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<this.minElements?this._renderInvalid(e,t):(this.$el.empty().html(this.templates.main()),this._renderHeader(e),this._renderMiddle(e),this._renderFooter(e),this._addPluginComponents(),this.$(".collection-name").focus(),this.trigger("rendered",this),this)},_renderInvalid:function(e,t){return this.$el.empty().html(this.templates.invalidInitial({problems:this.invalidElements,elements:this.workingElements})),"function"==typeof this.oncancel&&this.$(".cancel-create.btn").show(),this.trigger("rendered",this),this},_renderHeader:function(e,t){var i=this.$(".header").empty().html(this.templates.header()).find(".help-content").prepend(s(this.templates.helpContent()));return this.invalidElements.length&&this._invalidElementsAlert(),i},_renderMiddle:function(e,t){var i=this.$(".middle").empty().html(this.templates.middle());return this._renderList(e),i},_addPluginComponents:function(){this.$(".help-content 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0px"):o.css("border-width","0px")},_createElementView:function(e){var t=new this.elementViewClass({element:e,selected:n.has(this.selectedIds,e.id)});return this.elementViews.push(t),this._listenToElementView(t),t},_listenToElementView:function(e){var t=this;t.listenTo(e,{select:function(e){var i=e.source.element;e.selected?t.selectedIds[i.id]=!0:delete t.selectedIds[i.id],t.trigger("elements:select",e)},discard:function(e){t.trigger("elements:discard",e)}})},addElementView:function(e){},removeElementView:function(e){delete this.selectedIds[e.element.id],this._renderClearSelected(),this.elementViews=n.without(this.elementViews,e),this.stopListening(e)},_renderNoElementsLeft:function(){this._disableNameAndCreate(!0),this.$(".collection-elements").append(this.templates.noElementsLeft())},_elementToJSON:function(e){return e},createList:function(e){if(!this.workingElements.length){var t=(0,w.default)("No valid elements for final list")+". ";return t+='<a class="cancel-create" href="javascript:void(0);">'+(0,w.default)("Cancel")+"</a> ",t+=(0,w.default)("or"),t+=' <a class="reset" href="javascript:void(0);">'+(0,w.default)("start over")+"</a>.",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,w.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,w.default)("An error occurred");if(e.xhr){var n=e.xhr,s=e.message;0===n.readyState&&0===n.status?i+=": "+(0,w.default)("Galaxy could not be reached and may be updating.")+(0,w.default)(" Try again in a few minutes."):n.responseJSON?i+=":<br /><pre>"+JSON.stringify(n.responseJSON)+"</pre>":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 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"),(0,w.default)("Would you like to "),'<a class="reset" href="javascript:void(0)">',(0,w.default)("start over"),"</a>?","</li>"].join("")),invalidInitial:n.template(['<div class="header flex-row no-flex">','<div class="alert alert-warning" style="display: block">','<span class="alert-message">',"<% if( _.size( problems ) ){ %>",(0,w.default)("The following selections could not be included due to problems"),":","<ul><% _.each( problems, function( problem ){ %>","<li><b><%- problem.element.name %></b>: <%- problem.text %></li>","<% }); %></ul>","<% } else if( _.size( elements ) < 1 ){ %>",(0,w.default)("No datasets were selected"),".","<% } %>","<br />",(0,w.default)("At least one element is needed for the collection"),". 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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 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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 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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")+")"}})),y=u.default.InfinitelyScrollingCollection,w=y.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),y.prototype.initialize.call(this,e,t),this.includeDeleted=t.includeDeleted||!1,this.currentHistoryId=t.currentHistoryId,this.setUpListeners()},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot},setUpListeners:function(){return 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e=e||{},e.offset=0,t.fetchMore(e)})},comparators:s.extend(s.clone(y.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 y.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:w}}).call(t,i(2),i(0),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(114),l=a(o),r=i(115),d=a(r),c=i(60),u=a(c),h=i(65),f=a(h),p=i(253),m=a(p),g=i(5),_=a(g),v=i(116),y=a(v),w=500;try{w=localStorage.getItem("historyContentsLimitPerPageDefault")||w}catch(e){}var b=l.default.PaginatedCollection,x=b.extend(_.default.LoggableMixin).extend({_logNamespace:"history",limitPerPage:w,limitPerProgressiveFetch:w,order:"hid",urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(e,t){this.on({"sync 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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 y.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){Object.defineProperty(t,"__esModule",{value:!0});var n=i(5),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,n,s,a){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var l=i(5),r=o(l),d=i(3),c=(o(d),e.View.extend(r.default.LoggableMixin).extend({_logNamespace:"list",initialize:function(e){this.expanded=e.expanded||!1,this.log("\t expanded:",this.expanded),this.fxSpeed=void 0!==e.fxSpeed?e.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(e){var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){var e=n(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(e).replaceWith(this._renderDetails().show()),e},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;0===t?(i._swapNewRender(e),i.trigger("rendered",i)):n(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",s.isFunction(this.className)?this.className():this.className).append(e.children())},_setUpBehaviors:function(e){e=e||this.$el,e.find("[title]").tooltip({placement:"bottom"})},$details:function(e){return e=e||this.$el,e.find("> .details")},_renderDetails:function(){var e=n(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(e),e},toggleExpanded:function(e){return e=void 0===e?!this.expanded:e,e?this.expand():this.collapse(),this},expand:function(){var e=this;return e._fetchModelDetails().always(function(){e._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?a.when():this.model.fetch()},_expand:function(){var e=this,t=e._renderDetails();e.$details().replaceWith(t),e.expanded=!0,e.$details().slideDown(e.fxSpeed,function(){e.trigger("expanded",e)})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var e=this;e.expanded=!1,this.$details().slideUp(e.fxSpeed,function(){e.trigger("collapsed",e)})}})),u=c.extend(r.default.mixin(r.default.SelectableViewMixin,r.default.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){c.prototype.initialize.call(this,e),r.default.SelectableViewMixin.initialize.call(this,e),r.default.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(e){e?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var e=c.prototype._buildNewRender.call(this);return e.children(".warnings").replaceWith(this._renderWarnings()),e.children(".title-bar").replaceWith(this._renderTitleBar()),e.children(".primary-actions").append(this._renderPrimaryActions()),e.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),e},_swapNewRender:function(e){return c.prototype._swapNewRender.call(this,e),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var e=this,t=n('<div class="warnings"></div>'),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(['<div class="list-element">','<div class="warnings"></div>','<div class="selector">','<span class="fa fa-2x fa-square-o"></span>',"</div>",'<div class="primary-actions"></div>','<div class="title-bar"></div>','<div class="details"></div>',"</div>"]),warnings:{},titleBar:r.default.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element"),subtitle:r.default.wrapTemplate(['<div class="subtitle"></div>']),details:r.default.wrapTemplate(['<div class="details"></div>'])}}();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(['<div class="details">',"</div>"],"collection");return s.extend({},u.prototype.templates,{details:e})}(),t.default={ExpandableView:c,ListItemView:u,FoldoutListItemView:h}}).call(t,i(2),i(0),i(1),i(0))},function(e,t,i){"use strict";(function(e,n,s,a){function o(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var l=i(66),r=o(l),d=i(17),c=o(d),u=i(22),h=o(u),f=i(5),p=o(f),m=i(3),g=o(m),_=r.default.ListItemView,v=_.extend({_logNamespace:"dataset",className:_.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log(this+".initialize:",e),_.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_setUpListeners:function(){_.prototype._setUpListeners.call(this);var t=this;return t.listenTo(t.model,{change:function(i){t.model.changedAttributes().state&&t.model.inReadyState()&&t.expanded&&!t.model.hasDetails()?t.model.fetch({silent:!0}).done(function(){t.render()}):e.has(i.changed,"tags")&&1===e.keys(i.changed).length?t.$(".nametags").html(t._renderNametags()):t.render()}})},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):n.when()},remove:function(e,t){var i=this;e=e||this.fxSpeed,this.$el.fadeOut(e,function(){s.View.prototype.remove.call(i),t&&t.call(i)})},_swapNewRender:function(e){return _.prototype._swapNewRender.call(this,e),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var e=this.model.get("state");if(e===c.default.NOT_VIEWABLE||e===c.default.DISCARDED||!this.model.get("accessible"))return null;var t={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))t.disabled=!0,t.title=(0,g.default)("Cannot display datasets removed from disk");else if(e===c.default.UPLOAD)t.disabled=!0,t.title=(0,g.default)("This dataset must finish uploading before it can be viewed");else if(e===c.default.NEW)t.disabled=!0,t.title=(0,g.default)("This dataset is not yet viewable");else{t.title=(0,g.default)("View data"),t.href=this.model.urls.display;var i=this;t.onclick=function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.addDataset(i.model.get("id")),e.preventDefault())}}return t.faIcon="fa-eye",(0,h.default)(t)},_renderDetails:function(){if(this.model.get("state")===c.default.NOT_VIEWABLE)return a(this.templates.noAccess(this.model.toJSON(),this));var e=_.prototype._renderDetails.call(this);return e.find(".actions .left").empty().append(this._renderSecondaryActions()),e.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),e.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(e),e},_renderSummary:function(){var e=this.model.toJSON(),t=this.templates.summaries[e.state];return(t=t||this.templates.summaries.unknown)(e,this)},_renderDetailMessages:function(){var t=this,i=a('<div class="detail-messages"></div>'),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                <a class="download-btn icon-btn" href="'+this.model.urls.download+'" title="'+(0,g.default)("Download")+'">\n                    <span class="fa fa-floppy-o"></span>\n                </a>'):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var t=this.model.urls;return a('\n                <div class="metafile-dropdown dropdown">\n                    <a class="download-btn icon-btn" href="'+t.download+'" data-toggle="dropdown" title="'+(0,g.default)("Download")+'">\n                        <span class="fa fa-floppy-o"></span>\n                    </a>\n                    <ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">\n                        <li>\n                            <a href="'+t.download+'">\n                                '+(0,g.default)("Download dataset")+"\n                            </a>\n                        </li>\n                        "+e.map(this.model.get("meta_files"),function(e){return'<li>\n                                    <a href="'+(t.meta_download+e.file_type)+'">\n                                        '+(0,g.default)("Download")+" "+e.file_type+"\n                                    </a>\n                                </li>"})+"\n                    </ul>\n                </div>")},_renderNametags:function(){return e.template(["<% _.each(_.sortBy(_.uniq(tags), function(x) { return x }), function(tag){ %>",'<% if (tag.indexOf("name:") == 0){ %>','<span class="label label-info"><%- tag.slice(5) %></span>',"<% } %>","<% }); %>"].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" ){ %>','<div class="warningmessagesmall">',(0,g.default)("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:p.default.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',(0,g.default)("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:p.default.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',(0,g.default)("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:p.default.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,g.default)("This dataset has been deleted"),"</div>","<% } %>"])}),i=p.default.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset"),n=p.default.wrapTemplate(['<div class="details">','<div class="summary">',(0,g.default)("You do not have permission to view this dataset"),"</div>","</div>"],"dataset"),s={};s[c.default.OK]=s[c.default.FAILED_METADATA]=p.default.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.file_ext ){ %>",'<div class="datatype">','<label class="prompt">',(0,g.default)("format"),"</label>",'<span class="value"><%- dataset.file_ext %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',(0,g.default)("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset"),s[c.default.NEW]=p.default.wrapTemplate(["<div>",(0,g.default)("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset"),s[c.default.NOT_VIEWABLE]=p.default.wrapTemplate(["<div>",(0,g.default)("You do not have permission to view this dataset"),"</div>"],"dataset"),s[c.default.DISCARDED]=p.default.wrapTemplate(["<div>",(0,g.default)("The job creating this dataset was cancelled before completion"),"</div>"],"dataset"),s[c.default.QUEUED]=p.default.wrapTemplate(["<div>",(0,g.default)("This job is waiting to run"),"</div>"],"dataset"),s[c.default.RUNNING]=p.default.wrapTemplate(["<div>",(0,g.default)("This job is currently running"),"</div>"],"dataset"),s[c.default.UPLOAD]=p.default.wrapTemplate(["<div>",(0,g.default)("This dataset is currently uploading"),"</div>"],"dataset"),s[c.default.SETTING_METADATA]=p.default.wrapTemplate(["<div>",(0,g.default)("Metadata is being auto-detected"),"</div>"],"dataset"),s[c.default.PAUSED]=p.default.wrapTemplate(["<div>",(0,g.default)('This job is paused. 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this.get("name")&&(e='"'+this.get("name")+'",'+e),"Dataset("+e+")"}})),p=e.Collection.extend(d.default.LoggableMixin).extend({_logNamespace:"dataset",model:f,urlRoot:Galaxy.root+"api/datasets",url:function(){return this.urlRoot},ids:function(){return this.map(function(e){return e.get("id")})},notReady:function(){return this.filter(function(e){return!e.inReadyState()})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},ajaxQueue:function(e,t){var i=s.Deferred(),n=this.length,a=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(s,l){return function(){var r=e.call(s,t);r.done(function(e){i.notify({curr:l,total:n,response:e,model:s})}),r.always(function(e){a.push(e),o.length?o.shift()():i.resolve(a)})}}).value();return o.shift()(),i},matches:function(e){return this.filter(function(t){return t.matches(e)})},toString:function(){return["DatasetAssociationCollection(",this.length,")"].join("")}});t.default={DatasetAssociation:f,DatasetAssociationCollection:p}}).call(t,i(2),i(1),i(0))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(17),a=(n(s),i(5)),o=(n(a),i(3)),l=(n(o),1e3);try{l=localStorage.getItem("collectionFuzzyCountDefault")||l}catch(e){}var r={defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",hidden:function(){return!this.get("visible")},isVisible:function(e,t){var i=!0;return e||!this.get("deleted")&&!this.get("purged")||(i=!1),t||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var e=this.get("history_content_type"),t=this.get("history_id"),i=this.get("id"),n=""+this.urlRoot+t+"/contents/"+e+"s/"+i;return"dataset_collection"==e&&(n=n+"?view=element-reference&fuzzy_count="+l),n},hide:function(t){return this.get("visible")?this.save({visible:!1},t):e.when()},unhide:function(t){return this.get("visible")?e.when():this.save({visible:!0},t)},toString:function(){return[this.get("type_id"),this.get("hid"),this.get("name")].join(":")}};t.default={HistoryContentMixin:r}}).call(t,i(0))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var 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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(['<div class="header flex-row no-flex"></div>','<div class="middle flex-row flex-row-container"></div>','<div class="footer flex-row no-flex"></div>'].join(""))}};t.default={CollectionCreatorMixin:i}}).call(t,i(1))},function(e,t,i){"use strict";function n(e,t){var i=/(-?[0-9\.]+)/g,n=e.toString().toLowerCase()||"",s=t.toString().toLowerCase()||"",a=String.fromCharCode(0),o=n.replace(i,a+"$1"+a).split(a),l=s.replace(i,a+"$1"+a).split(a),r=new Date(n).getTime(),d=r?new Date(s).getTime():null;if(d){if(r<d)return-1;if(r>d)return 1}for(var c,u,h=0,f=Math.max(o.length,l.length);h<f;h++){if(c=parseFloat(o[h])||o[h],u=parseFloat(l[h])||l[h],c<u)return-1;if(c>u)return 1}return 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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 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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<n)&&(i.allFetched=!0,i.trigger("all-fetched",this))})},fetchAll:function(e){e=e||{};var t=this;return e=a.pick(e,"silent"),e.filters={},t.fetch(e).done(function(){t.allFetched=!0,t.trigger("all-fetched",t)})}});t.default={ControlledFetchCollection:c,PaginatedCollection:u,InfinitelyScrollingCollection:h}}).call(t,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(106),a=n(s),o=i(107),l=n(o),r=i(5),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){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 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this.deferred.always(e)}},{key:"progress",value:function(e){return this.deferred.progress(e)}}],[{key:"create",value:function(e){return new t(e).deferred}}]),t}(),r=function(e){function t(e){s(this,t);var n=i(this,(t.__proto__||Object.getPrototypeOf(t)).call(this,e));return n.names={},n}return n(t,e),o(t,[{key:"add",value:function(e){if(!e.hasOwnProperty("name")||!e.hasOwnProperty("fn"))throw new Error('NamedAjaxQueue.add requires an object with both "name" and "fn": '+JSON.stringify(e));if(!this.names.hasOwnProperty(e.name))return this.names[e.name]=!0,a(t.prototype.__proto__||Object.getPrototypeOf(t.prototype),"add",this).call(this,e.fn)}},{key:"clear",value:function(){return this.names={},this}}],[{key:"create",value:function(e){return new t(e).deferred}}]),t}(l);t.default={AjaxQueue:l,NamedAjaxQueue:r}}).call(t,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(66),l=a(o),r=i(256),d=a(r),c=i(5),u=a(c),h=i(3),f=a(h);i(118);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(['<div class="list-action-menu btn-group">','<button class="list-action-menu-btn btn btn-default dropdown-toggle" data-toggle="dropdown">',(0,f.default)("For all selected"),"...","</button>",'<ul class="dropdown-menu pull-right" role="menu">',"</ul>","</div>"].join("")),a=i.map(function(e){var t=['<li><a href="javascript:void(0);">',e.html,"</a></li>"].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<n?this.views.slice(i,n+1):this.views.slice(n,i+1)},_renderSearch:function(e){return e.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:n.bind(this._firstSearch,this),onsearch:n.bind(this.searchItems,this),onclear:n.bind(this.clearSearch,this)}),e},_firstSearch:function(e){return this.log("onFirstSearch",e),this.searchItems(e)},searchItems:function(e,t){if(this.log("searchItems",e,this.searchFor,t),!t&&this.searchFor===e)return this;this.searchFor=e,this.renderItems(),this.trigger("search:searching",e,this);var i=this.$("> .controls .search-query");return i.val()!==e&&i.val(e),this},clearSearch:function(e){return this.searchFor="",this.trigger("search:clear",this),this.$("> .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(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]),controls:u.default.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%- view.title %></div>',"</div>",'<div class="subtitle"><%- view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',(0,f.default)("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',(0,f.default)("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>","</div>"])}}();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(['<div class="controls">','<div class="title">','<div class="name"><%- model.name %></div>',"</div>",'<div class="subtitle"><%- view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',(0,f.default)("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',(0,f.default)("None"),"</button>","</div>",'<div class="list-action-menu btn-group">',"</div>","</div>","</div>"]);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['<input type="text" name="',t.name,'" placeholder="',t.placeholder,'" ','class="search-query ',t.classes,'" ',"/>"].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(['<span class="search-clear fa fa-times-circle" ','title="',l("clear search (esc)"),'"></span>'].join("")).tooltip({placement:"bottom"}).click(function(e){i.call(this,e)})}(),function(){return o(['<span class="search-loading fa fa-spinner fa-spin" ','title="',l("loading..."),'"></span>'].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(67),a=n(s),o=i(5),l=n(o),r=i(120),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        <div class="title-bar clear" tabindex="0">\n            <span class="state-icon"></span>\n            <div class="title">\n                <span class="hid">'+t.hid+'</span>\n                <span class="name">'+e.escape(t.name)+"</span>\n            </div>\n            </br>\n            "+d.default.nametagTemplate(t)+"\n        </div>\n    "},i=e.extend({},h.prototype.templates.warnings,{hidden:l.default.wrapTemplate(["<% if( !dataset.visible ){ %>",'<div class="hidden-msg warningmessagesmall">',(0,u.default)("This dataset has been hidden"),"</div>","<% } %>"],"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 i(t){return 0==t.indexOf("name:")?'<span class="label label-info">'+e.escape(t.slice(5))+"</span>":""}function n(t){return'<span class="nametags">'+e.sortBy(e.uniq(t.tags)).map(i).join("")+"</span>"}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}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(17),a=n(s),o=i(68),l=n(o),r=i(122),d=n(r),c=i(5),u=(n(c),i(120)),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                        <div class="progress state-progress">\n                            <span class="note">Creating jobs.<span class="blinking">..</span></span>\n                            <div class="progress-bar info" style="width:100%">\n                        </div>';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                        <div class="progress state-progress">\n                            <span class="note">'+(o&&o>1?o+" jobs":"a job")+" generating a "+i+'</span>\n                            <div class="progress-bar ok" style="width:'+100*c+'%"></div>\n                            <div class="progress-bar running" style="width:'+100*u+'%"></div>\n                            <div class="progress-bar new" style="width:'+100*h+'%">\n                        </div>'}return'\n                    <div class="progress state-progress">\n                        <span class="note">Loading job data for '+i+'.<span class="blinking">..</span></span>\n                        <div class="progress-bar info" style="width:100%">\n                    </div>'}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        <div class="title-bar clear" tabindex="0">\n            <span class="state-icon"></span>\n            <div class="title">\n                <span class="hid">'+t.hid+'</span>\n                <span class="name">'+e.escape(t.name)+'</span>\n            </div>\n            <div class="state-description">\n            </div>\n            '+h.default.nametagTemplate(t)+"\n        </div>\n    "};return e.extend({},m.prototype.templates,{warnings:t,titleBar:i})}(),t.default={HDCAListItemView:g}}).call(t,i(1))},function(e,t,i){"use strict";(function(e){function n(e){return e&&e.__esModule?e:{default:e}}function s(e){var t=e.get("collection_type");return"list"==t?(0,f.default)("list"):"paired"==t?(0,f.default)("dataset pair"):"list:paired"==t?(0,f.default)("list of pairs"):(0,f.default)("nested list")}function a(e){var t=e.get("element_count"),i="a "+s(e);if(t){var n;1==t?n="with 1 item":t&&(n="with "+t+" items"),i=i+" "+(0,f.default)(n)}return i}Object.defineProperty(t,"__esModule",{value:!0});var o=i(117),l=n(o),r=i(61),d=(n(r),i(68)),c=n(d),u=i(5),h=(n(u),i(3)),f=n(h),p=l.default.ModelListPanel,m=p.extend({_logNamespace:"collections",className:p.prototype.className+" dataset-collection-panel",DatasetDCEViewClass:c.default.DatasetDCEListItemView,modelCollectionKey:"elements",initialize:function(e){p.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,this.panelStack=[],this.parentName=e.parentName,this.foldoutStyle=e.foldoutStyle||"foldout",this.downloadUrl=Galaxy.root+"api/dataset_collections/"+this.model.attributes.id+"/download"},getNestedDCDCEViewClass:function(){return c.default.NestedDCDCEListItemView.extend({foldoutPanelClass:m})},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;this.handleWarning(e),i.log("_queueNewRender:",e,t),i._swapNewRender(e),i.trigger("rendered",i)},handleWarning:function(e){var t=this.views.length,i=this.model.get("element_count");if(i&&i!==t){var n=(0,f.default)("displaying only "+t+" of "+i+" items");e.find(".elements-warning").html('<div class="warningmessagesmall">'+n+"</div>")}},_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        <div class="controls">\n            <div class="navigation">\n            <a class="back" href="javascript:void(0)">\n                <span class="fa fa-icon fa-angle-left"></span>\n                '+(0,f.default)("Back to ")+"\n                "+e.escape(i.parentName)+'\n            </a>\n            </div>\n            <div class="title">\n                <div class="name">'+(e.escape(t.name)||e.escape(t.element_identifier))+'</div>\n                <div class="subtitle">\n                    '+n+'\n                </div>\n            </div>\n            <div class="elements-warning">\n            </div>\n            <div class="tags-display"></div>\n            <div class="actions">\n                <a class="download-btn icon-btn" href="'+i.downloadUrl+'"\n                   title="" download="" data-original-title="Download Collection">\n                   <span class="fa fa-floppy-o"></span>\n                </a>\n            </div>\n        </div>'};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(17),o=s(a),l=i(67),r=s(l),d=i(40),c=s(d),u=i(124),h=s(u),f=i(22),p=s(f),m=i(5),g=s(m),_=i(3),v=s(_),y=r.default.DatasetListItemView,w=y.extend({initialize:function(e){y.prototype.initialize.call(this,e),this.hasUser=e.hasUser,this.purgeAllowed=e.purgeAllowed||!1,this.tagsEditorShown=e.tagsEditorShown||!1,this.annotationEditorShown=e.annotationEditorShown||!1},_renderPrimaryActions:function(){var e=y.prototype._renderPrimaryActions.call(this);return this.model.get("state")===o.default.NOT_VIEWABLE?e:y.prototype._renderPrimaryActions.call(this).concat([this._renderEditButton(),this._renderDeleteButton()])},_renderEditButton:function(){var t=this;if(this.model.get("state")===o.default.DISCARDED||!this.model.get("accessible"))return null;var i=this.model.get("purged"),n=this.model.get("deleted"),s={title:(0,v.default)("Edit attributes"),href:Galaxy.root+"datasets/edit?dataset_id="+this.model.attributes.id,faIcon:"fa-pencil",classes:"edit-btn",onclick:function(e){Galaxy.router&&(e.preventDefault(),Galaxy.router.push("datasets/edit",{dataset_id:t.model.attributes.id}))}};return n||i?(s.disabled=!0,i?s.title=(0,v.default)("Cannot edit attributes of datasets removed from disk"):n&&(s.title=(0,v.default)("Undelete dataset to edit attributes"))):e.contains([o.default.UPLOAD,o.default.NEW],this.model.get("state"))&&(s.disabled=!0,s.title=(0,v.default)("This dataset is not yet editable")),(0,p.default)(s)},_renderDeleteButton:function(){if(!this.model.get("accessible"))return null;var e=this,t=this.model.isDeletedOrPurged();return(0,p.default)({title:t?(0,v.default)("Dataset is already deleted"):(0,v.default)("Delete"),disabled:t,faIcon:"fa-times",classes:"delete-btn",onclick:function(){e.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},_renderDetails:function(){var t=y.prototype._renderDetails.call(this),i=this.model.get("state");return!this.model.isDeletedOrPurged()&&e.contains([o.default.OK,o.default.FAILED_METADATA],i)&&(this._renderTags(t),this._renderAnnotation(t),this._makeDbkeyEditLink(t)),this._setUpBehaviors(t),t},_renderToolHelpButton:function(){var e=this.model.attributes.dataset_id,t=this.model.attributes.creating_job,i=this,s=function(t){var s='<div id="thdiv-'+e+'" class="toolhelp">';t.name&&t.help?(s+="<strong>Tool help for "+t.name+"</strong><hr/>",s+=t.help):s+="<strong>Tool help is unavailable for this dataset.</strong><hr/>",s+="</div>",i.$el.find(".details").append(n.parseHTML(s))},a=function(e){n.ajax({url:Galaxy.root+"api/tools/"+e.tool_id+"/build"}).done(function(e){s(e)}).fail(function(){s({})})};return null===Galaxy.user.id?null:(0,p.default)({title:(0,v.default)("Tool Help"),classes:"icon-btn",href:"#",faIcon:"fa-question",onclick:function(){i.$el.find(".toolhelp").length>0?i.$el.find(".toolhelp").toggle():n.ajax({url:Galaxy.root+"api/jobs/"+t}).done(function(e){a(e)}).fail(function(){console.log('Failed at recovering job information from the  Galaxy API for job id "'+t+'".')})}})},_renderSecondaryActions:function(){var e=y.prototype._renderSecondaryActions.call(this);switch(this.model.get("state")){case o.default.UPLOAD:case o.default.NOT_VIEWABLE:return e;case o.default.ERROR:return e.unshift(this._renderErrButton()),e.concat([this._renderRerunButton(),this._renderToolHelpButton()]);case o.default.OK:case o.default.FAILED_METADATA:return e.concat([this._renderRerunButton(),this._renderVisualizationsButton(),this._renderToolHelpButton()])}return e.concat([this._renderRerunButton(),this._renderToolHelpButton()])},_renderErrButton:function(){var e=this;return(0,p.default)({title:(0,v.default)("View or report this error"),href:Galaxy.root+"datasets/error?dataset_id="+this.model.attributes.id,classes:"report-error-btn",faIcon:"fa-bug",onclick:function(t){Galaxy.router&&(t.preventDefault(),Galaxy.router.push("datasets/error",{dataset_id:e.model.attributes.id}))}})},_renderRerunButton:function(){var e=this.model.get("creating_job");if(this.model.get("rerunnable"))return(0,p.default)({title:(0,v.default)("Run this job again"),href:this.model.urls.rerun,classes:"rerun-btn",target:this.linkTarget,faIcon:"fa-refresh",onclick:function(t){Galaxy.router&&(t.preventDefault(),Galaxy.router.push("/",{job_id:e}))}})},_renderVisualizationsButton:function(){var t=this.model.get("visualizations");if(this.model.isDeletedOrPurged()||!this.hasUser||!this.model.hasData()||e.isEmpty(t))return null;if(!e.isObject(t[0]))return this.warn("Visualizations have been switched off"),null;var i=n(this.templates.visualizations(t,this));return i.find('[target="galaxy_main"]').attr("target",this.linkTarget),this._addScratchBookFn(i.find(".visualization-link").addBack(".visualization-link")),i},_addScratchBookFn:function(e){e.click(function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:(0,v.default)("Visualization"),url:n(this).attr("href")}),e.preventDefault(),e.stopPropagation())})},_renderTags:function(e){if(this.hasUser){var t=this;this.tagsEditor=new c.default.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.tagsEditorShown=!0},onhide:function(){t.tagsEditorShown=!1},$activator:(0,p.default)({title:(0,v.default)("Edit dataset tags"),classes:"tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".actions .right"))}),this.tagsEditorShown&&this.tagsEditor.toggle(!0)}},_renderAnnotation:function(e){if(this.hasUser){var t=this;this.annotationEditor=new h.default.AnnotationEditor({model:this.model,el:e.find(".annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.annotationEditorShown=!0},onhide:function(){t.annotationEditorShown=!1},$activator:(0,p.default)({title:(0,v.default)("Edit dataset annotation"),classes:"annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".actions .right"))}),this.annotationEditorShown&&this.annotationEditor.toggle(!0)}},_makeDbkeyEditLink:function(e){if("?"===this.model.get("metadata_dbkey")&&!this.model.isDeletedOrPurged()){var t=n('<a class="value">?</a>').attr("href",this.model.urls.edit).attr("target","_top");e.find(".dbkey .value").replaceWith(t)}},events:e.extend(e.clone(y.prototype.events),{"click .undelete-link":"_clickUndeleteLink","click .purge-link":"_clickPurgeLink","click .edit-btn":function(e){this.trigger("edit",this,e)},"click .delete-btn":function(e){this.trigger("delete",this,e)},"click .rerun-btn":function(e){this.trigger("rerun",this,e)},"click .report-err-btn":function(e){this.trigger("report-err",this,e)},"click .visualization-btn":function(e){this.trigger("visualize",this,e)},"click .dbkey a":function(e){this.trigger("edit",this,e)}}),_clickUndeleteLink:function(e){return this.model.undelete(),!1},_clickPurgeLink:function(e){return confirm((0,v.default)("This will permanently remove the data in your dataset. Are you sure?"))&&this.model.purge(),!1},toString:function(){return"HDAEditView("+(this.model?""+this.model:"(no model)")+")"}});w.prototype.templates=function(){var t=e.extend({},y.prototype.templates.warnings,{failed_metadata:g.default.wrapTemplate(['<% if( dataset.state === "failed_metadata" ){ %>','<div class="failed_metadata-warning warningmessagesmall">',(0,v.default)("An error occurred setting the metadata for this dataset"),'<br /><a href="<%- dataset.urls.edit %>" target="_top">',(0,v.default)("Set it manually or retry auto-detection"),"</a>","</div>","<% } %>"],"dataset"),deleted:g.default.wrapTemplate(["<% if( dataset.deleted && !dataset.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,v.default)("This dataset has been deleted"),'<br /><a class="undelete-link" href="javascript:void(0);">',(0,v.default)("Undelete it"),"</a>","<% if( view.purgeAllowed ){ %>",'<br /><a class="purge-link" href="javascript:void(0);">',(0,v.default)("Permanently remove it from disk"),"</a>","<% } %>","</div>","<% } %>"],"dataset")}),i=g.default.wrapTemplate(["<% if( visualizations.length === 1 ){ %>",'<a class="visualization-link icon-btn" href="<%- visualizations[0].href %>"',' target="<%- visualizations[0].target %>" title="',(0,v.default)("Visualize in"),' <%- visualizations[0].html %>">','<span class="fa fa-bar-chart-o"></span>',"</a>","<% } else { %>",'<div class="visualizations-dropdown dropdown icon-btn">','<a data-toggle="dropdown" title="',(0,v.default)("Visualize"),'">','<span class="fa fa-bar-chart-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu">',"<% _.each( visualizations, function( visualization ){ %>",'<li><a class="visualization-link" href="<%- visualization.href %>"',' target="<%- visualization.target %>">',"<%- visualization.html %>","</a></li>","<% }); %>","</ul>","</div>","<% } %>"],"visualizations");return e.extend({},y.prototype.templates,{warnings:t,visualizations:i})}(),t.default={DatasetListItemEdit:w}}).call(t,i(1),i(0))},function(e,t,i){"use strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(5),o=s(a),l=i(3),r=s(l);i(21);var d=e.View.extend(o.default.LoggableMixin).extend(o.default.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(e){e=e||{},this.tooltipConfig=e.tooltipConfig||{placement:"bottom"},this.listenTo(this.model,"change:annotation",function(){this.render()}),this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.$el.html(this._template()),this.$annotation().make_text_editable({use_textarea:!0,on_finish:function(t){e.$annotation().text(t),e.model.save({annotation:t},{silent:!0}).fail(function(){e.$annotation().text(e.model.previous("annotation"))})}}),this},_template:function(){var 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system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be.  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e)t.list_genomes.push({id:e[i][1],text:e[i][0]});t.list_genomes.sort(function(e,i){return e.id==t.options.default_genome?-1:i.id==t.options.default_genome?1:e.text>i.text?1:e.text<i.text?-1:0})}})},show:function(){var e=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model)return void window.setTimeout(function(){e.show()},500);this.current_user=Galaxy.user.id,this.modal||(this.tabs=new u.default.View,this.default_view=new m.default(this),this.tabs.add({id:"regular",title:(0,a.default)("Regular"),$el:this.default_view.$el}),this.composite_view=new _.default(this),this.tabs.add({id:"composite",title:(0,a.default)("Composite"),$el:this.composite_view.$el}),this.collection_view=new y.default(this),this.tabs.add({id:"collection",title:(0,a.default)("Collection"),$el:this.collection_view.$el}),this.modal=new d.default.View({title:(0,a.default)("Download from web or upload from 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t.app.toData([t.collection.get(e)],t.history_id)},progress:function(e,i){t._eventProgress(e,i)},success:function(e,i){t._eventSuccess(e,i)},error:function(e,i){t._eventError(e,i)},complete:function(){t._eventComplete()},ondragover:function(){t.$uploadbox.addClass("highlight")},ondragleave:function(){t.$uploadbox.removeClass("highlight")}}),this.ftp=new v.default.View({title:(0,l.default)("FTP files"),container:this.btnFtp.$el}),this.select_extension=new w.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-extension"),data:n.filter(this.list_extensions,function(e){return!e.composite_files}),value:this.options.default_extension,onchange:function(e){t._changeExtension(e)}}),this.$(".upload-footer-extension-info").on("click",function(e){new g.default({$el:s(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),list:t.list_extensions,placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new w.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome,onchange:function(e){t._changeGenome(e)}}),this.loader=new $.default({$container:this.$uploadbox,collection:this.collection,new_content:function(e){var i=new h.default(t,{model:e});return t.$uploadtable.find("> tbody:first").append(i.$el),i.render(),i}}),this.collection.on("remove",function(e){t._eventRemove(e)}),this.render()},render:function(){var e="";e=0==this.counter.announce?this.uploadbox.compatible()?"&nbsp;":"Browser does not support Drag & Drop. 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Add more files or click 'Start' to proceed.":"Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining.",this.$(".upload-top-info").html(e);var t=0==this.counter.running&&this.counter.announce+this.counter.success+this.counter.error>0,i=0==this.counter.running&&this.counter.announce>0,n=0==this.counter.running,s=this.counter.announce+this.counter.success+this.counter.error>0;this.btnReset[t?"enable":"disable"](),this.btnStart[i?"enable":"disable"](),this.btnStart.$el[i?"addClass":"removeClass"]("btn-primary"),this.btnStop[this.counter.running>0?"enable":"disable"](),this.btnLocal[n?"enable":"disable"](),this.btnFtp[n?"enable":"disable"](),this.btnCreate[n?"enable":"disable"](),this.btnFtp.$el[this.ftp_upload_site?"show":"hide"](),this.$(".upload-table")[s?"show":"hide"](),this.$(".upload-helper")[s?"hide":"show"]()},_eventAnnounce:function(e,t){this.counter.announce++;var i=new c.default.Model({id:e,file_name:t.name,file_size:t.size,file_mode:t.mode||"local",file_path:t.path,file_data:t});this.render(),this.collection.add(i)},_eventProgress:function(e,t){var i=this.collection.get(e);i.set("percentage",t),this.ui_button.model.set("percentage",this._uploadPercentage(t,i.get("file_size")))},_eventSuccess:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"success"}),this.ui_button.model.set("percentage",this._uploadPercentage(100,i.get("file_size"))),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.success++,this.render(),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(e,t){var i=this.collection.get(e);i.set({percentage:100,status:"error",info:t}),this.ui_button.model.set({percentage:this._uploadPercentage(100,i.get("file_size")),status:"danger"}),this.upload_completed+=100*i.get("file_size"),this.counter.announce--,this.counter.error++,this.render()},_eventComplete:function(){this.collection.each(function(e){"queued"==e.get("status")&&e.set("status","init")}),this.counter.running=0,this.render()},_eventRemove:function(e){var t=e.get("status");"success"==t?this.counter.success--:"error"==t?this.counter.error--:this.counter.announce--,this.uploadbox.remove(e.id),this.render()},_eventFtp:function(){if(this.ftp.visible)this.ftp.hide();else{this.ftp.empty();var e=this;this.ftp.append(new p.default({collection:this.collection,ftp_upload_site:this.ftp_upload_site,onadd:function(t){return e.uploadbox.add([{mode:"ftp",name:t.path,size:t.size,path:t.path}])},onremove:function(t){e.collection.remove(t)}}).$el),this.ftp.show()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(0!=this.counter.announce&&0==this.counter.running){var e=this;this.upload_size=0,this.upload_completed=0,this.collection.each(function(t){"init"==t.get("status")&&(t.set("status","queued"),e.upload_size+=t.get("file_size"))}),this.ui_button.model.set({percentage:0,status:"success"}),this.counter.running=this.counter.announce,this.history_id=this.app.currentHistory(),this._uploadFtp(),this.uploadbox.start(),this.render()}},_eventStop:function(){this.counter.running>0&&(this.ui_button.model.set("status","info"),s(".upload-top-info").html("Queue will pause after completing the current file..."),this.uploadbox.stop())},_eventReset:function(){if(0==this.counter.running){this.collection.reset(),this.counter.reset(),this.uploadbox.reset(),this.select_extension.value(this.options.default_extension),this.select_genome.value(this.options.default_genome),this.ui_button.model.set("percentage",0),this.render()}},_changeExtension:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("extension")!=i.options.default_extension&&t||n.set("extension",e)})},_changeGenome:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("genome")!=i.options.default_genome&&t||n.set("genome",e)})},_uploadFtp:function(){var e=this,t=[];this.collection.each(function(i){"queued"==i.get("status")&&"ftp"==i.get("file_mode")&&(e.uploadbox.remove(i.id),t.push(i))}),t.length>0&&s.uploadpost({data:this.app.toData(t),url:this.app.options.nginx_upload_path,success:function(i){n.each(t,function(t){e._eventSuccess(t.id)})},error:function(i){n.each(t,function(t){e._eventError(t.id,i)})}})},_uploadPercentage:function(e,t){return(this.upload_completed+e*t)/this.upload_size},_template:function(){return'<div class="upload-view-default"><div class="upload-top"><h6 class="upload-top-info"/></div><div class="upload-box"><div class="upload-helper"><i class="fa fa-files-o"/>Drop files here</div><table class="upload-table ui-table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th/></tr></thead><tbody/></table></div><div class="upload-footer"><span class="upload-footer-title">Type (set all):</span><span class="upload-footer-extension"/><span class="upload-footer-extension-info upload-icon-button fa fa-search"/> <span class="upload-footer-title">Genome (set all):</span><span class="upload-footer-genome"/></div><div class="upload-buttons"/></div>'}})}).call(t,i(2),i(1),i(0))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),l=a(o),r=i(4),d=a(r),c=i(30),u=(a(c),i(55)),h=a(u),f=i(16),p=a(f),m=i(10),g=a(m);t.default=e.View.extend({status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template(t.model)),this.$mode=this.$(".upload-mode"),this.$title=this.$(".upload-title"),this.$text=this.$(".upload-text"),this.$size=this.$(".upload-size"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$text_content=this.$(".upload-text-content"),this.$settings=this.$(".upload-settings"),this.$symbol=this.$(".upload-symbol"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.settings=new p.default.View({title:(0,l.default)("Upload configuration"),container:this.$(".upload-settings"),placement:"bottom"});var s=this.app.select_genome.value(),a=this.app.select_extension.value();this.select_genome=new g.default.View({css:"upload-genome",data:i.app.list_genomes,container:this.$(".upload-genome"),value:s,onchange:function(e){i.model.set("genome",e)}}),this.select_extension=new g.default.View({css:"upload-extension",data:i.app.list_extensions,container:this.$(".upload-extension"),value:a,onchange:function(e){i.model.set("extension",e)}}),this.model.set({genome:s,extension:a}),this.$symbol.on("click",function(){i._removeRow()}),this.$(".upload-extension-info").on("click",function(e){i.app.showExtensionInfo({$el:n(e.target),title:i.select_extension.text(),extension:i.select_extension.value()})}).on("mousedown",function(e){e.preventDefault()}),this.$settings.on("click",function(e){i._showSettings()}).on("mousedown",function(e){e.preventDefault()}),this.$text_content.on("change input",function(e){i.model.set({url_paste:n(e.target).val(),file_size:n(e.target).val().length})}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:genome",function(){i._refreshGenome()}),this.listenTo(this.model,"change:extension",function(){i._refreshExtension()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()})},render:function(){this._refreshType(),this._refreshPercentage(),this._refreshStatus(),this._refreshInfo(),this._refreshGenome(),this._refreshExtension(),this._refreshFileSize()},remove:function(){this.select_genome.remove(),this.select_extension.remove(),e.View.prototype.remove.apply(this)},_refreshType:function(){var e=this.model.attributes;this.$title.html(s.escape(e.file_name)),this.$size.html(d.default.bytesToString(e.file_size)),this.$mode.removeClass().addClass("upload-mode").addClass("text-primary"),"new"==e.file_mode?(this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$mode.addClass("fa fa-edit")):"local"==e.file_mode?this.$mode.addClass("fa fa-laptop"):"ftp"==e.file_mode&&this.$mode.addClass("fa fa-folder-open-o")},_refreshExtension:function(){this.select_extension.value(this.model.get("extension"))},_refreshGenome:function(){this.select_genome.value(this.model.get("genome"))},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("<strong>Failed: </strong>"+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).$el),this.settings.show())},_template:function(e){return'<tr id="upload-row-'+e.id+'" class="upload-row"><td><div class="upload-text-column"><div class="upload-mode"/><div class="upload-title"/><div class="upload-text"><div class="upload-text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea class="upload-text-content form-control"/></div></div></td><td><div class="upload-size"/></td><td><div class="upload-extension" style="float: left;"/>&nbsp;&nbsp<div class="upload-extension-info upload-icon-button fa fa-search"/></td><td><div class="upload-genome"/></td><td><div class="upload-settings upload-icon-button fa fa-gear"/></td><td><div class="upload-info"><div class="upload-info-text"/><div class="upload-info-progress progress"><div class="upload-progress-bar progress-bar progress-bar-success"/><div class="upload-percentage">0%</div></div></div></td><td><div class="upload-symbol '+this.status_classes.init+'"/></td></tr>'}})}).call(t,i(2),i(0),i(1))},function(e,t,i){"use strict";(function(e,i,n){Object.defineProperty(t,"__esModule",{value:!0}),t.default=e.View.extend({initialize:function(e){this.$container=e.$container,this.collection=e.collection,this.new_content=e.new_content,this.max=e.max||50,this.content_list={},this.$message=i("<div/>").addClass("ui-limitloader").append("...only the first "+this.max+" entries are visible."),this.$container.append(this.$message),this.listenTo(this.collection,"reset",this._reset,this),this.listenTo(this.collection,"add",this._refresh,this),this.listenTo(this.collection,"remove",this._remove,this)},_done:function(){var e=n.size(this.content_list)>this.max;return this.$message[e?"show":"hide"](),e},_reset:function(){n.each(this.content_list,function(e){e.remove()}),this.content_list={},this.$message.hide()},_remove:function(e){var t=e.id,i=this.content_list[t];i&&(i.remove(),delete this.content_list[t]),this._refresh()},_refresh:function(){if(!this._done())for(var e in this.collection.models){var t=this.collection.models[e];this.content_list[t.id];if(!this.content_list[t.id]){var i=this.new_content(t);if(this.content_list[t.id]=i,this._done())break}}}})}).call(t,i(2),i(0),i(1))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),l=a(o),r=i(4),d=(a(r),i(30)),c=a(d),u=i(247),h=a(u),f=i(57),p=a(f),m=i(16),g=(a(m),i(10)),_=a(g),v=i(6),y=a(v);t.default=e.View.extend({collection:new c.default.Collection,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.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.btnStart=new y.default.Button({title:(0,l.default)("Start"),onclick:function(){t._eventStart()}}),this.btnClose=new y.default.Button({title:(0,l.default)("Close"),onclick:function(){t.app.modal.hide()}}),n.each([this.btnStart,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.select_extension=new _.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-extension"),data:n.filter(this.list_extensions,function(e){return e.composite_files}),onchange:function(e){t.collection.reset();var i=n.findWhere(t.list_extensions,{id:e});i&&i.composite_files&&n.each(i.composite_files,function(e){t.collection.add({id:t.collection.size(),file_desc:e.description||e.name})})}}),this.$(".upload-footer-extension-info").on("click",function(e){new p.default({$el:s(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),list:t.list_extensions,placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new _.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome}),this.listenTo(this.collection,"add",function(e){t._eventAnnounce(e)}),this.listenTo(this.collection,"change add",function(){t.render()}),this.select_extension.options.onchange(this.select_extension.value()),this.render()},render:function(){var e=this.collection.first();e&&"running"==e.get("status")?(this.select_genome.disable(),this.select_extension.disable()):(this.select_genome.enable(),this.select_extension.enable()),this.collection.where({status:"ready"}).length==this.collection.length&&this.collection.length>0?(this.btnStart.enable(),this.btnStart.$el.addClass("btn-primary")):(this.btnStart.disable(),this.btnStart.$el.removeClass("btn-primary")),this.$(".upload-table")[this.collection.length>0?"show":"hide"]()},_eventAnnounce:function(e){var t=new h.default(this,{model:e});this.$(".upload-table > tbody:first").append(t.$el),this.$(".upload-table")[this.collection.length>0?"show":"hide"](),t.render()},_eventStart:function(){var e=this;this.collection.each(function(t){t.set({genome:e.select_genome.value(),extension:e.select_extension.value()})}),s.uploadpost({url:this.app.options.nginx_upload_path,data:this.app.toData(this.collection.filter()),success:function(t){e._eventSuccess(t)},error:function(t){e._eventError(t)},progress:function(t){e._eventProgress(t)}})},_eventProgress:function(e){this.collection.each(function(t){t.set("percentage",e)})},_eventSuccess:function(e){this.collection.each(function(e){e.set("status","success")}),Galaxy.currHistoryPanel.refreshContents()},_eventError:function(e){this.collection.each(function(t){t.set({status:"error",info:e})})},_template:function(){return'<div class="upload-view-composite"><div class="upload-top"><h6 class="upload-top-info"/></div><div class="upload-box"><table class="upload-table ui-table-striped" style="display: none;"><thead><tr><th/><th/><th>Description</th><th>Name</th><th>Size</th><th>Settings</th><th>Status</th></tr></thead><tbody/></table></div><div class="upload-footer"><span class="upload-footer-title">Composite Type:</span><span class="upload-footer-extension"/><span class="upload-footer-extension-info upload-icon-button fa fa-search"/> <span class="upload-footer-title">Genome/Build:</span><span class="upload-footer-genome"/></div><div class="upload-buttons"/></div>'}})}).call(t,i(2),i(1),i(0))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),l=a(o),r=i(4),d=a(r),c=i(55),u=a(c),h=i(56),f=a(h),p=i(16),m=a(p),g=i(6),_=a(g),v=i(10);a(v);i(58),t.default=e.View.extend({status_classes:{init:"upload-mode fa fa-exclamation text-primary",ready:"upload-mode fa fa-check text-success",running:"upload-mode fa fa-spinner fa-spin",success:"upload-mode fa fa-check",error:"upload-mode fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template()),this.$source=this.$(".upload-source"),this.$settings=this.$(".upload-settings"),this.$status=this.$(".upload-status"),this.$text=this.$(".upload-text"),this.$text_content=this.$(".upload-text-content"),this.$info_text=this.$(".upload-info-text"),this.$info_progress=this.$(".upload-info-progress"),this.$file_name=this.$(".upload-file-name"),this.$file_desc=this.$(".upload-file-desc"),this.$file_size=this.$(".upload-file-size"),this.$progress_bar=this.$(".upload-progress-bar"),this.$percentage=this.$(".upload-percentage"),this.uploadinput=this.$el.uploadinput({ondragover:function(){i.model.get("enabled")&&i.$el.addClass("warning")},ondragleave:function(){i.$el.removeClass("warning")},onchange:function(e){"running"!=i.model.get("status")&&e&&e.length>0&&(i.model.reset({file_data:e[0],file_name:e[0].name,file_size:e[0].size,file_mode:e[0].mode||"local"}),i._refreshReady())}}),this.button_menu=new _.default.ButtonMenu({icon:"fa-caret-down",title:(0,l.default)("Select"),pull:"left"}),this.$source.append(this.button_menu.$el),this.button_menu.addMenu({icon:"fa-laptop",title:(0,l.default)("Choose local file"),onclick:function(){i.uploadinput.dialog()}}),this.app.ftp_upload_site&&this.button_menu.addMenu({icon:"fa-folder-open-o",title:(0,l.default)("Choose FTP file"),onclick:function(){i._showFtp()}}),this.button_menu.addMenu({icon:"fa-edit",title:"Paste/Fetch data",onclick:function(){i.model.reset({file_mode:"new",file_name:"New File"})}}),this.ftp=new m.default.View({title:"Choose FTP file:",container:this.$source.find(".ui-button-menu"),placement:"right"}),this.settings=new m.default.View({title:(0,l.default)("Upload configuration"),container:this.$settings,placement:"bottom"}),this.$text_content.on("change input",function(e){i.model.set({url_paste:n(e.target).val(),file_size:n(e.target).val().length}),i._refreshReady()}),this.$settings.on("click",function(e){i._showSettings()}).on("mousedown",function(e){e.preventDefault()}),this.listenTo(this.model,"change:percentage",function(){i._refreshPercentage()}),this.listenTo(this.model,"change:status",function(){i._refreshStatus()}),this.listenTo(this.model,"change:info",function(){i._refreshInfo()}),this.listenTo(this.model,"change:file_name",function(){i._refreshFileName()}),this.listenTo(this.model,"change:file_mode",function(){i._refreshMode()}),this.listenTo(this.model,"change:file_size",function(){i._refreshFileSize()}),this.listenTo(this.model,"remove",function(){i.remove()}),this.app.collection.on("reset",function(){i.remove()})},render:function(){this.$el.attr("id","upload-row-"+this.model.id),this.$file_name.html(s.escape(this.model.get("file_name")||"-")),this.$file_desc.html(this.model.get("file_desc")||"Unavailable"),this.$file_size.html(d.default.bytesToString(this.model.get("file_size"))),this.$status.removeClass().addClass(this.status_classes.init)},remove:function(){e.View.prototype.remove.apply(this)},_refreshReady:function(){this.app.collection.each(function(e){e.set("status",e.get("file_size")>0&&"ready"||"init")})},_refreshMode:function(){"new"==this.model.get("file_mode")?(this.height=this.$el.height(),this.$text.css({width:this.$el.width()-16+"px",top:this.$el.height()-8+"px"}).show(),this.$el.height(this.$el.height()-8+this.$text.height()+16),this.$text_content.val("").trigger("keyup")):(this.$el.height(this.height),this.$text.hide())},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("<strong>Failed: </strong>"+e).show():this.$info_text.hide()},_refreshPercentage:function(){var e=parseInt(this.model.get("percentage"));0!=e?this.$progress_bar.css({width:e+"%"}):(this.$progress_bar.addClass("no-transition"),this.$progress_bar.css({width:"0%"}),this.$progress_bar[0].offsetHeight,this.$progress_bar.removeClass("no-transition")),this.$percentage.html(100!=e?e+"%":"Adding to history...")},_refreshStatus:function(){var e=this.model.get("status");this.$status.removeClass().addClass(this.status_classes[e]),this.model.set("enabled","running"!=e),this.$text_content.attr("disabled",!this.model.get("enabled")),this.$el.removeClass("success danger warning"),"running"!=e&&"ready"!=e||this.model.set("percentage",0),this.$source.find(".button")["running"==e?"addClass":"removeClass"]("disabled"),"success"==e&&(this.$el.addClass("success"),this.model.set("percentage",100),this.$percentage.html("100%")),"error"==e?(this.$el.addClass("danger"),this.model.set("percentage",0),this.$info_progress.hide(),this.$info_text.show()):(this.$info_progress.show(),this.$info_text.hide())},_refreshFileName:function(){this.$file_name.html(this.model.get("file_name")||"-")},_refreshFileSize:function(){this.$file_size.html(d.default.bytesToString(this.model.get("file_size")))},_showFtp:function(){if(this.ftp.visible)this.ftp.hide();else{var e=this;this.ftp.empty(),this.ftp.append(new f.default({ftp_upload_site:this.app.ftp_upload_site,onchange:function(t){e.ftp.hide(),"running"!=e.model.get("status")&&t&&(e.model.reset({file_mode:"ftp",file_name:t.path,file_size:t.size,file_path:t.path}),e._refreshReady())}}).$el),this.ftp.show()}},_showSettings:function(){this.settings.visible?this.settings.hide():(this.settings.empty(),this.settings.append(new u.default(this).$el),this.settings.show())},_template:function(){return'<tr class="upload-row"><td><div class="upload-source"/><div class="upload-text-column"><div class="upload-text"><div class="upload-text-info">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.</div><textarea class="upload-text-content form-control"/></div></div></td><td><div class="upload-status"/></td><td><div class="upload-file-desc upload-title"/></td><td><div class="upload-file-name upload-title"/></td><td><div class="upload-file-size upload-size"/></td><td><div class="upload-settings upload-icon-button fa fa-gear"/></td><td><div class="upload-info"><div class="upload-info-text"/><div class="upload-info-progress progress"><div class="upload-progress-bar progress-bar progress-bar-success"/><div class="upload-percentage">0%</div></div></div></td></tr>'}})}).call(t,i(2),i(0),i(1))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),l=a(o),r=i(4),d=(a(r),i(30)),c=a(d),u=i(249),h=a(u),f=i(56),p=a(f),m=i(57),g=a(m),_=i(16),v=a(_),y=i(10),w=a(y),b=i(6),x=a(b),C=i(59);a(C);i(58),t.default=e.View.extend({upload_size:0,collection:new c.default.Collection,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(e){var t=this;this.app=e,this.options=e.options,this.list_extensions=e.list_extensions,this.list_genomes=e.list_genomes,this.ui_button=e.ui_button,this.ftp_upload_site=e.currentFtp(),this.setElement(this._template()),this.btnLocal=new x.default.Button({id:"btn-local",title:(0,l.default)("Choose local files"),onclick:function(){t.uploadbox.select()},icon:"fa fa-laptop"}),this.btnFtp=new x.default.Button({id:"btn-ftp",title:(0,l.default)("Choose FTP files"),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.btnBuild=new x.default.Button({id:"btn-build",title:(0,l.default)("Build"),onclick:function(){t._eventBuild()}}),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.btnBuild,this.btnClose],function(e){t.$(".upload-buttons").prepend(e.$el)}),this.uploadbox=this.$(".upload-box").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.$(".upload-box").addClass("highlight")},ondragleave:function(){t.$(".upload-box").removeClass("highlight")}}),this.ftp=new v.default.View({title:(0,l.default)("FTP files"),container:this.btnFtp.$el}),this.select_extension=new w.default.View({css:"upload-footer-selection-compressed",container:this.$(".upload-footer-extension"),data:n.filter(this.list_extensions,function(e){return!e.composite_files}),value:this.options.default_extension,onchange:function(e){t.updateExtension(e)}}),this.collectionType="list",this.select_collection=new w.default.View({css:"upload-footer-selection-compressed",container:this.$(".upload-footer-collection-type"),data:[{id:"list",text:"List"},{id:"paired",text:"Paired"},{id:"list:paired",text:"List of Pairs"}],value:"list",onchange:function(e){t.updateCollectionType(e)}}),this.$(".upload-footer-extension-info").on("click",function(e){new g.default({$el:s(e.target),title:t.select_extension.text(),extension:t.select_extension.value(),list:t.list_extensions,placement:"top"})}).on("mousedown",function(e){e.preventDefault()}),this.select_genome=new w.default.View({css:"upload-footer-selection",container:this.$(".upload-footer-genome"),data:this.list_genomes,value:this.options.default_genome,onchange:function(e){t.updateGenome(e)}}),this.collection.on("remove",function(e){t._eventRemove(e)}),this._updateScreen()},_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,extension:this.select_extension.value(),genome:this.select_genome.value()});this.collection.add(i);var n=new h.default(this,{model:i});this.$(".upload-table > tbody:first").append(n.$el),this._updateScreen(),n.render()},_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=n.pluck(t.outputs,"hid"),s=this.collection.get(e);s.set({percentage:100,status:"success",hids:i}),this.ui_button.model.set("percentage",this._uploadPercentage(100,s.get("file_size"))),this.upload_completed+=100*s.get("file_size"),this.counter.announce--,this.counter.success++,this._updateScreen(),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._updateScreen()},_eventComplete:function(){this.collection.each(function(e){"queued"==e.get("status")&&e.set("status","init")}),this.counter.running=0,this._updateScreen()},_eventBuild:function(){var e=[];n.forEach(this.collection.models,function(t){e.push.apply(e,t.get("hids"))});var t=n.map(e,function(e){return Galaxy.currHistoryPanel.collection.getByHid(e)}),i=new Galaxy.currHistoryPanel.collection.constructor(t);i.historyId=Galaxy.currHistoryPanel.collection.historyId,Galaxy.currHistoryPanel.buildCollection(this.collectionType,i,!0),this.counter.running=0,this._updateScreen(),this._eventReset(),this.app.modal.hide()},_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._updateScreen()},_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)}}).$el),this.ftp.show()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(!(0==this.counter.announce||this.counter.running>0)){var e=this;this.upload_size=0,this.upload_completed=0,this.collection.each(function(t){"init"==t.get("status")&&(t.set("status","queued"),e.upload_size+=t.get("file_size"))}),this.ui_button.model.set({percentage:0,status:"success"}),this.counter.running=this.counter.announce,this.history_id=this.app.currentHistory(),this.uploadbox.start(),this._updateScreen()}},_eventStop:function(){this.counter.running>0&&(this.ui_button.model.set("status","info"),s(".upload-top-info").html("Queue will pause after completing the current file..."),this.uploadbox.stop())},_eventReset:function(){0==this.counter.running&&(this.collection.reset(),this.counter.reset(),this.uploadbox.reset(),this.select_extension.value(this.options.default_extension),this.select_genome.value(this.options.default_genome),this.ui_button.model.set("percentage",0),this._updateScreen())},updateExtension:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("extension")!=i.options.default_extension&&t||n.set("extension",e)})},updateCollectionType:function(e){this.collectionType=e},updateGenome:function(e,t){var i=this;this.collection.each(function(n){"init"!=n.get("status")||n.get("genome")!=i.options.default_genome&&t||n.set("genome",e)})},_updateScreen:function(){var e="";e=0==this.counter.announce?this.uploadbox.compatible()?"&nbsp;":"Browser does not support Drag & Drop. Try Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.":0==this.counter.running?"You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed.":"Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining.",this.$(".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&&0==this.counter.announce&&this.counter.success>0&&0==this.counter.error,s=0==this.counter.running,a=this.counter.announce+this.counter.success+this.counter.error>0;this.btnReset[t?"enable":"disable"](),this.btnStart[i?"enable":"disable"](),this.btnStart.$el[i?"addClass":"removeClass"]("btn-primary"),this.btnBuild[n?"enable":"disable"](),this.btnBuild.$el[n?"addClass":"removeClass"]("btn-primary"),this.btnStop[this.counter.running>0?"enable":"disable"](),this.btnLocal[s?"enable":"disable"](),this.btnFtp[s?"enable":"disable"](),this.btnCreate[s?"enable":"disable"](),this.btnFtp.$el[this.ftp_upload_site?"show":"hide"](),this.$(".upload-table")[a?"show":"hide"](),this.$(".upload-helper")[a?"hide":"show"]()},_uploadPercentage:function(e,t){return(this.upload_completed+e*t)/this.upload_size},_template:function(){return'<div class="upload-view-default"><div class="upload-top"><h6 class="upload-top-info"/></div><div class="upload-box"><div class="upload-helper"><i class="fa fa-files-o"/>Drop files here</div><table class="upload-table ui-table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Status</th><th/></tr></thead><tbody/></table></div><div class="upload-footer"><span class="upload-footer-title-compressed">Collection Type:</span><span class="upload-footer-collection-type"/><span class="upload-footer-title-compressed">File Type:</span><span class="upload-footer-extension"/><span class="upload-footer-extension-info upload-icon-button fa fa-search"/> <span class="upload-footer-title-compressed">Genome (set all):</span><span class="upload-footer-genome"/></div><div class="upload-buttons"/></div>'}})}).call(t,i(2),i(1),i(0))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),l=a(o),r=i(4),d=a(r),c=i(30),u=(a(c),i(55)),h=a(u),f=i(16),p=a(f),m=i(10);a(m);t.default=e.View.extend({status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},initialize:function(e,t){var i=this;this.app=e,this.model=t.model,this.setElement(this._template(t.model)),this.$mode=this.$(".upload-mode"),this.$title=this.$(".upload-title-extended"),this.$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.$(".upload-text-content"),this.$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"});this.app.select_genome.value(),this.app.select_extension.value();this.$symbol.on("click",function(){i._removeRow()}),this.$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:file_size",function(){i._refreshFileSize()}),this.listenTo(this.model,"remove",function(){i.remove()}),this.app.collection.on("reset",function(){i.remove()})},render: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")},_refreshInfo:function(){var e=this.model.get("info");e?this.$info_text.html("<strong>Failed: </strong>"+e).show():this.$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),"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'<tr id="upload-row-'+e.id+'" class="upload-row"><td><div class="upload-text-column"><div class="upload-mode"/><div class="upload-title-extended"/><div class="upload-text"><div class="upload-text-info">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.</div><textarea class="upload-text-content form-control"/></div></div></td><td><div class="upload-size"/></td><td><div class="upload-info"><div class="upload-info-text"/><div class="upload-info-progress progress"><div class="upload-progress-bar progress-bar progress-bar-success"/><div class="upload-percentage">0%</div></div></div></td><td><div class="upload-symbol '+this.status_classes.init+'"/></td></tr>'}})}).call(t,i(2),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(6),a=n(s),o=i(251),l=n(o),r=i(252),d=n(r),c=i(3),u=n(c),h=e.View.extend({initialize:function(t,i){var n=this;this.userIsAnonymous=Galaxy.user.isAnonymous(),this.allow_user_dataset_purge=i.config.allow_user_dataset_purge,this.root=i.root,this.historyView=new d.default.CurrentHistoryView({className:d.default.CurrentHistoryView.prototype.className+" middle",purgeAllowed:this.allow_user_dataset_purge,linkTarget:"galaxy_main"}),Galaxy.currHistoryPanel=this.historyView,Galaxy.currHistoryPanel.listenToGalaxy(Galaxy),this.buttonRefresh=new a.default.ButtonLink({id:"history-refresh-button",title:(0,u.default)("Refresh history"),cls:"panel-header-button",icon:"fa fa-refresh",onclick:function(){n.historyView.loadCurrentHistory()}}),this.buttonOptions=new a.default.ButtonLink({id:"history-options-button",title:(0,u.default)("History options"),cls:"panel-header-button",target:"galaxy_main",icon:"fa fa-cog",href:this.root+"root/history_options"}),this.buttonViewMulti=new a.default.ButtonLink({id:"history-view-multi-button",title:(0,u.default)("View all histories"),cls:"panel-header-button",icon:"fa fa-columns",href:this.root+"history/view_multiple"}),this.model=new e.Model({cls:"history-right-panel",title:(0,u.default)("History"),buttons:[this.buttonRefresh,this.buttonOptions,this.buttonViewMulti]}),this.setElement(this._template()),this.historyView.setElement(this.$el),this.historyView.connectToQuotaMeter(Galaxy.quotaMeter),this.historyView.loadCurrentHistory(),Galaxy.listenTo(this.historyView,"history-size-change",function(){Galaxy.user.fetch({url:Galaxy.user.urlRoot()+"/"+(Galaxy.user.id||"current")})})},render:function(){this.optionsMenu=(0,l.default)(this.buttonOptions.$el,{anonymous:this.userIsAnonymous,purgeAllowed:this.allow_user_dataset_purge,root:this.root}),this.buttonViewMulti.$el[this.userIsAnonymous?"hide":"show"]()},_template:function(e){return['<div id="current-history-panel" class="history-panel middle"/>'].join("")},toString:function(){return"historyPanel"}});t.default=h}).call(t,i(2))},function(e,t,i){"use strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}function a(e,t,i){return n.clone(m).filter(function(n){return!(e&&!n.anon)&&(!(!t&&n.purge)&&(n.href&&(n.href=i+n.href,n.target=n.target||"galaxy_main"),n.confirm&&(n.func=function(){confirm(n.confirm)&&(galaxy_main.location=n.href)}),!0))})}Object.defineProperty(t,"__esModule",{value:!0});var o=i(43),l=s(o),r=i(112),d=s(r),c=i(5),u=(s(c),i(3)),h=s(u),f=i(35),p=s(f),m=[{html:(0,h.default)("History Lists"),header:!0},{html:(0,h.default)("Saved Histories"),href:"histories/list",target:"_top"},{html:(0,h.default)("Histories Shared with Me"),href:"histories/list_shared",target:"_top"},{html:(0,h.default)("Current History"),header:!0,anon:!0},{html:(0,h.default)("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:(0,h.default)("Copy History"),func:function(){(0,d.default)(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Share or Publish"),href:"history/sharing"},{html:(0,h.default)("Show Structure"),href:"history/display_structured",anon:!0},{html:(0,h.default)("Extract Workflow"),href:"workflow/build_from_current_history"},{html:(0,h.default)("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,h.default)("Really delete the current history?"))&&Galaxy.currHistoryPanel.model._delete().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,h.default)("Really delete the current history permanently? This cannot be undone."))&&Galaxy.currHistoryPanel.model.purge().done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Dataset Actions"),header:!0,anon:!0},{html:(0,h.default)("Copy Datasets"),href:"dataset/copy_datasets"},{html:(0,h.default)("Dataset Security"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/permissions?id="+Galaxy.currHistoryPanel.model.id)}},{html:(0,h.default)("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:(0,h.default)("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:(0,h.default)("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,h.default)("Really unhide all hidden datasets?"))&&e.post(Galaxy.root+"history/adjust_hidden",{user_action:"unhide"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm((0,h.default)("Really delete all hidden datasets?"))&&e.post(Galaxy.root+"history/adjust_hidden",{user_action:"delete"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:(0,h.default)("Purge Deleted Datasets"),confirm:(0,h.default)("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:(0,h.default)("Downloads"),header:!0},{html:(0,h.default)("Export Tool Citations"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.router&&Galaxy.router.push("/histories/citations?id="+Galaxy.currHistoryPanel.model.id)}},{html:(0,h.default)("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:(0,h.default)("Other Actions"),header:!0},{html:(0,h.default)("Import from File"),href:"histories/import",target:"_top"}];p.default.add({url:"api/webhooks/history-menu/all",async:!1,callback:function(t){var i=[];e.each(t.models,function(e,t){var n=t.toJSON();n.activate&&i.push({html:(0,h.default)(n.config.title),anon:!0})}),i.length>0&&(i.unshift({html:(0,h.default)("Webhooks"),header:!0}),e.merge(m,i))}});var g=function(e,t){t=t||{};var i=void 0===t.anonymous||t.anonymous,n=t.purgeAllowed||!1,s=a(i,n,Galaxy.root);return new l.default(e,s)};t.default=g}).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}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(63),l=(a(o),i(254)),r=a(l),d=i(5),c=a(d),u=i(3),h=a(u),f=c.default.SessionStorageModel.extend({defaults:{tagsEditorShown:!1,annotationEditorShown:!1,scrollPosition:0},toString:function(){return"HistoryViewPrefs("+JSON.stringify(this.toJSON())+")"}});f.storageKey=function(){return"history-panel"};var p=r.default.HistoryViewEdit,m=p.extend({className:p.prototype.className+" current-history-panel",HDCAViewClass:p.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),emptyMsg:[(0,h.default)("This history is empty"),". ",(0,h.default)("You can "),'<a class="uploader-link" href="javascript:void(0)">',(0,h.default)("load your own data"),"</a>",(0,h.default)(" or "),'<a class="get-data-link" href="javascript:void(0)">',(0,h.default)("get data from an external source"),"</a>"].join(""),initialize:function(t){t=t||{},this.preferences=new f(e.extend({id:f.storageKey()},e.pick(t,e.keys(f.prototype.defaults)))),p.prototype.initialize.call(this,t),this.panelStack=[],this.currentContentId=t.currentContentId||null},_setUpListeners:function(){p.prototype._setUpListeners.call(this);var e=this;this.on("new-model",function(){e.preferences.set("scrollPosition",0)})},loadCurrentHistory:function(){return this.loadHistory(null,{url:Galaxy.root+"history/current_history_json"})},switchToHistory:function(e,t){return Galaxy.user.isAnonymous()?(this.trigger("error",(0,h.default)("You must be logged in to switch histories"),(0,h.default)("Anonymous user")),n.when()):this.loadHistory(e,{url:Galaxy.root+"history/set_as_current?id="+e})},createNewHistory:function(e){return Galaxy.user.isAnonymous()?(this.trigger("error",(0,h.default)("You must be logged in to create histories"),(0,h.default)("Anonymous user")),n.when()):this.loadHistory(null,{url:Galaxy.root+"history/create_new_current"})},setModel:function(e,t,i){return p.prototype.setModel.call(this,e,t,i),this.model&&this.model.id&&(this.log("checking for updates"),this.model.checkForUpdates()),this},_setUpModelListeners:function(){return p.prototype._setUpModelListeners.call(this),this.listenTo(this.model,{"change:nice_size change:size":function(){this.trigger("history-size-change",this,this.model,arguments)},"change:id":function(){this.once("loading-done",function(){this.model.checkForUpdates()})}})},_setUpCollectionListeners:function(){p.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,"state:ready",function(e,t,i){e.get("visible")||this.collection.storage.includeHidden()||this.removeItemView(e)})},_setUpBehaviors:function(t){t=t||this.$el;var i=this;return p.prototype._setUpBehaviors.call(i,t),this._debouncedScrollCaptureHandler||(this._debouncedScrollCaptureHandler=e.debounce(function(){i.$el.is(":visible")&&i.preferences.set("scrollPosition",n(this).scrollTop())},40)),i.$scrollContainer(t).off("scroll",this._debouncedScrollCaptureHandler).on("scroll",this._debouncedScrollCaptureHandler),i},_buildNewRender:function(){if(!this.model)return n();var e=p.prototype._buildNewRender.call(this);return e.find(".search").prependTo(e.find("> .controls")),this._renderQuotaMessage(e),e},_renderQuotaMessage:function(e){return e=e||this.$el,n(this.templates.quotaMsg({},this)).prependTo(e.find(".messages"))},_renderTags:function(e){var t=this;p.prototype._renderTags.call(t,e),t.preferences.get("tagsEditorShown")&&t.tagsEditor.toggle(!0),t.listenTo(t.tagsEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(e){t.preferences.set("tagsEditorShown",e.hidden)})},_renderAnnotation:function(e){var t=this;p.prototype._renderAnnotation.call(t,e),t.preferences.get("annotationEditorShown")&&t.annotationEditor.toggle(!0),t.listenTo(t.annotationEditor,"hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(e){t.preferences.set("annotationEditorShown",e.hidden)})},_swapNewRender:function(t){p.prototype._swapNewRender.call(this,t);var i=this;return e.delay(function(){var e=i.preferences.get("scrollPosition");e&&i.scrollTo(e,0)},10),this},_attachItems:function(e){p.prototype._attachItems.call(this,e);var t=this;return t.currentContentId&&t._setCurrentContentById(t.currentContentId),this},addItemView:function(e,t,i){var n=p.prototype.addItemView.call(this,e,t,i);return n&&this.panelStack.length?this._collapseDrilldownPanel():n},_setUpItemViewListeners:function(e){var t=this;return p.prototype._setUpItemViewListeners.call(t,e),t.listenTo(e,{"expanded:drilldown":function(e,t){this._expandDrilldownPanel(t)},"collapsed:drilldown":function(e,t){this._collapseDrilldownPanel(t)}})},setCurrentContent:function(e){this.$(".history-content.current-content").removeClass("current-content"),e?(e.$el.addClass("current-content"),this.currentContentId=e.model.id):this.currentContentId=null},_setCurrentContentById:function(e){var t=this.viewFromModelId(e)||null;this.setCurrentContent(t)},_expandDrilldownPanel:function(e){this.panelStack.push(e),this.$controls().add(this.$list()).hide(),e.parentName=this.model.get("name"),e.delegateEvents().render().$el.appendTo(this.$el)},_collapseDrilldownPanel:function(e){this.panelStack.pop(),this.$controls().add(this.$list()).show()},events:e.extend(e.clone(p.prototype.events),{"click .uploader-link":function(e){Galaxy.upload.show(e)},"click .get-data-link":function(e){var t=n(".toolMenuContainer");t.parent().scrollTop(0),t.find('span:contains("Get Data")').click()}}),listenToGalaxy:function(t){this.listenTo(t,{"center-frame:load":function(t){var i=t.fullpath,n=null,s={display:/datasets\/([a-f0-9]+)\/display/,edit:/datasets\/([a-f0-9]+)\/edit/,report_error:/dataset\/errors\?id=([a-f0-9]+)/,rerun:/tool_runner\/rerun\?id=([a-f0-9]+)/,show_params:/datasets\/([a-f0-9]+)\/show_params/};e.find(s,function(t,s){return n=e.result(i.match(t),1)}),this._setCurrentContentById(n?"dataset-"+n:null)},"center-panel:load":function(e){this._setCurrentContentById()}})},connectToQuotaMeter:function(e){return e?(this.listenTo(e,"quota:over",this.showQuotaMessage),this.listenTo(e,"quota:under",this.hideQuotaMessage),this.on("rendered rendered:initial",function(){e&&e.isOverQuota()&&this.showQuotaMessage()}),this):this},clearMessages:function(t){var i=e.isUndefined(t)?this.$messages().children('[class$="message"]'):n(t.currentTarget);return i=i.not(".quota-message"),i.fadeOut(this.fxSpeed,function(){n(this).remove()}),this},showQuotaMessage:function(){var e=this.$(".quota-message");e.is(":hidden")&&e.slideDown(this.fxSpeed)},hideQuotaMessage:function(){var e=this.$(".quota-message");e.is(":hidden")||e.slideUp(this.fxSpeed)},unhideHidden:function(){var e=this;return confirm((0,h.default)("Really unhide all hidden datasets?"))?e.model.contents._filterAndUpdate({visible:!1,deleted:"",purged:""},{visible:!0}).done(function(){e.model.contents.includeHidden||e.renderItems()}):s.when()},deleteHidden:function(){var e=this;return confirm((0,h.default)("Really delete all hidden datasets?"))?e.model.contents._filterAndUpdate({visible:!1,deleted:"",purged:""},{deleted:!0,visible:!0}):s.when()},toString:function(){return"CurrentHistoryView("+(this.model?this.model.get("name"):"")+")"}});m.prototype.templates=function(){var t=c.default.wrapTemplate(['<div class="quota-message errormessage">',(0,h.default)("You are over your disk quota"),". ",(0,h.default)("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return e.extend(e.clone(p.prototype.templates),{quotaMsg:t})}(),t.default={CurrentHistoryView:m}}).call(t,i(1),i(0),i(0))},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(116),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(255),l=a(o),r=i(64),d=(a(r),i(17)),c=(a(d),i(115)),u=a(c),h=i(257),f=a(h),p=i(258),m=a(p),g=i(40),_=a(g),v=i(124),y=a(v),w=i(59),b=a(w),x=i(261),C=a(x),$=i(262),k=a($),S=i(22),T=a(S),P=i(43),E=(a(P),i(5)),D=a(E),A=i(3),M=a(A);i(21);var I=l.default.HistoryView,L=I.extend({HDAViewClass:f.default.HDAListItemEdit,HDCAViewClass:m.default.HDCAListItemEdit,initialize:function(e){e=e||{},I.prototype.initialize.call(this,e),this.tagsEditor=null,this.dragItems=!0,this.annotationEditor=null,this.purgeAllowed=e.purgeAllowed||!1,this.annotationEditorShown=e.annotationEditorShown||!1,this.tagsEditorShown=e.tagsEditorShown||!1},_setUpListeners:function(){return I.prototype._setUpListeners.call(this),this.on({"droptarget:drop":function(e,t){this.dataDropped(t),this.dropTargetOff()},"view:attached view:removed":function(){this._renderCounts()},"search:loading-progress":this._renderSearchProgress,"search:searching":this._renderSearchFindings})},_setUpModelListeners:function(){return I.prototype._setUpModelListeners.call(this),this.listenTo(this.model,"change:size",this.updateHistoryDiskSize),this},_setUpCollectionListeners:function(){return I.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"change:deleted":this._handleItemDeletedChange,"change:visible":this._handleItemVisibleChange,"change:purged":function(e){this.model.fetch()},"fetching-deleted":function(e){this.$("> .controls .deleted-count").html("<i>"+(0,M.default)("loading...")+"</i>")},"fetching-hidden":function(e){this.$("> .controls .hidden-count").html("<i>"+(0,M.default)("loading...")+"</i>")},"fetching-deleted-done fetching-hidden-done":this._renderCounts}),this},_buildNewRender:function(){var e=I.prototype._buildNewRender.call(this);return this.model?(Galaxy&&Galaxy.user&&Galaxy.user.id&&Galaxy.user.id===this.model.get("user_id")&&(this._renderTags(e),this._renderAnnotation(e)),e):e},updateHistoryDiskSize:function(){this.$(".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 y.default.AnnotationEditor({model:this.model,el:e.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){t.toggleHDAAnnotationEditors(!0,t.fxSpeed)},onhide:function(){t.toggleHDAAnnotationEditors(!1,t.fxSpeed)},$activator:(0,T.default)({title:(0,M.default)("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".controls .actions"))})},_setUpBehaviors:function(e){if(e=e||this.$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=C.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(["<i>",(0,M.default)("Searching "),i,"/",this.model.contentsShown(),"</i>"].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.$(".history-drop-target").remove(),s("<div/>").addClass("history-drop-target")},_renderDropTargetHelp:function(){return this.$(".history-drop-target-help").remove(),s("<div/>").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"):"")+")"}});L.prototype.templates=function(){var e=D.default.wrapTemplate(["<% var shown = Math.max( view.views.length, history.contents_active.active ) %>","<% if( shown ){ %>",'<span class="shown-count">',"<%- shown %> ",(0,M.default)("shown"),"</span>","<% } %>","<% if( history.contents_active.deleted ){ %>",'<span class="deleted-count">',"<% if( view.model.contents.includeDeleted ){ %>",'<a class="toggle-deleted-link" href="javascript:void(0);">',(0,M.default)("hide deleted"),"</a>","<% } else { %>","<%- history.contents_active.deleted %> ",'<a class="toggle-deleted-link" href="javascript:void(0);">',(0,M.default)("deleted"),"</a>","<% } %>","</span>","<% } %>","<% if( history.contents_active.hidden ){ %>",'<span class="hidden-count">',"<% if( view.model.contents.includeHidden ){ %>",'<a class="toggle-hidden-link" href="javascript:void(0);">',(0,M.default)("hide hidden"),"</a>","<% } else { %>","<%- history.contents_active.hidden %> ",'<a class="toggle-hidden-link" href="javascript:void(0);">',(0,M.default)("hidden"),"</a>","<% } %>","</span>","<% } %>"],"history"),t=D.default.wrapTemplate([(0,M.default)("Found")," <%- view.views.length %>, ","<% if( history.contents_active.deleted ){ %>","<% if( view.model.contents.includeDeleted ){ %>",'<a class="toggle-deleted-link" href="javascript:void(0);">',(0,M.default)("hide deleted"),"</a>, ","<% } else { %>",'<a class="toggle-deleted-link" href="javascript:void(0);">',(0,M.default)("show deleted"),"</a>, ","<% } %>","<% } %>","<% if( history.contents_active.hidden ){ %>","<% if( view.model.contents.includeHidden ){ %>",'<a class="toggle-hidden-link" href="javascript:void(0);">',(0,M.default)("hide hidden"),"</a>","<% } else { %>",'<a class="toggle-hidden-link" href="javascript:void(0);">',(0,M.default)("show hidden"),"</a>","<% } %>","<% } %>"],"history");return n.extend(n.clone(I.prototype.templates),{counts:e,found:t})}(),t.default={HistoryViewEdit:L}}).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(117),o=s(a),l=i(63),r=s(l),d=i(64),c=s(d),u=i(65),h=(s(u),i(119)),f=s(h),p=i(121),m=s(p),g=i(25),_=(s(g),i(113)),v=s(_),y=i(22),w=s(y),b=i(5),x=s(b),C=i(3),$=s(C);i(118);var k=o.default.ModelListPanel,S=k.extend({_logNamespace:"history",HDAViewClass:f.default.HDAListItemView,HDCAViewClass:m.default.HDCAListItemView,collectionClass:c.default.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:k.prototype.className+" history-panel",emptyMsg:(0,$.default)("This history is empty"),noneFoundMsg:(0,$.default)("No matching datasets found"),searchPlaceholder:(0,$.default)("search datasets"),initialize:function(e){k.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_createDefaultCollection:function(){return new this.collectionClass([],{history:this.model})},freeModel:function(){return k.prototype.freeModel.call(this),this.model&&this.model.stopPolling(),this},_setUpListeners:function(){k.prototype._setUpListeners.call(this),this.on({error:function(e,t,i,n,s){this.errorHandler(e,t,i,n,s)},"views:ready view:attached view:removed":function(e){this._renderSelectButton()},"view:attached":function(e){this.scrollTo(0)}})},loadHistory:function(t,i,n){var s=this;return n=e.extend(n||{silent:!0}),this.info("loadHistory:",t,i,n),this.setModel(new r.default.History({id:t})),n.silent=!0,this.trigger("loading"),this.model.fetchWithContents(i,n).always(function(){s.render(),s.trigger("loading-done")})},refreshContents:function(e){return this.model?this.model.refresh(e):n.when()},_setUpCollectionListeners:function(){return k.prototype._setUpCollectionListeners.call(this),this.listenTo(this.collection,{"fetching-more":function(){this._toggleContentsLoadingIndicator(!0),this.$emptyMessage().hide()},"fetching-more-done":function(){this._toggleContentsLoadingIndicator(!1)}})},_showLoadingIndicator:function(t,i,s){var a=n('<div class="loading-indicator"/>');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.$el,!this.multiselectActions().length)return null;if(!this.views.length)return this.hideSelectors(),e.find(".controls .actions .show-selectors-btn").remove(),null;var t=e.find(".controls .actions .show-selectors-btn");return t.length?t:(0,w.default)({title:(0,$.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('<div class="contents-loading-indicator"><span class="fa fa-2x fa-spinner fa-spin"/></div>'):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: 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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 ){ %>",'<div class="hidden-msg warningmessagesmall">',(0,h.default)("This dataset has been hidden"),'<br /><a class="unhide-link" a href="javascript:void(0);">',(0,h.default)("Unhide it"),"</a>","</div>","<% } %>"],"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 n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var s=i(121),a=n(s),o=i(259),l=n(o),r=i(22),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.$el.find(".icon-btn.delete-btn").trigger("mouseout"),e.model.delete()}})},toString:function(){return"HDCAListItemEdit("+(this.model?""+this.model:"(no model)")+")"}});t.default={HDCAListItemEdit:f}},function(e,t,i){"use strict";function n(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var 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.name").text(i)}}),this.tagsEditor=new u.default.TagsEditor({model:this.model,el:e.find(".tags-display"),onshowFirstTime:function(){this.render()},usePrompt:!1}),this.tagsEditor.toggle(!0)}},toString:function(){return"CollectionViewEdit("+(this.model?this.model.get("name"):"")+")"}});t.default={CollectionViewEdit:g}},function(e,t,i){"use strict";(function(e,n){function s(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var a=i(68),o=s(a),l=i(123),r=s(l),d=i(5),c=(s(d),i(3)),u=(s(c),o.default.DCListItemView),h=u.extend({initialize:function(e){u.prototype.initialize.call(this,e)},toString:function(){return"DCListItemEdit("+(this.model?""+this.model:"(no model)")+")"}}),f=o.default.DCEListItemView,p=f.extend({initialize:function(e){f.prototype.initialize.call(this,e)},toString:function(){return"DCEListItemEdit("+(this.model?""+this.model:"(no 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paired",initialize:function(e){this.pair=e.pair||{}},template:n.template(['<span class="forward-dataset-name flex-column"><%- pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%- pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%- pair.reverse.name %></span>'].join("")),render:function(){this.dragStartHandler=n.bind(this._dragstart,this),this.dragEndHandler=n.bind(this._dragend,this);var e=this.$el.attr("draggable",!0).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container").get(0);return e.addEventListener("dragstart",this.dragStartHandler,!1),e.addEventListener("dragend",this.dragEndHandler,!1),this},events:{dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(e){e.currentTarget.style.opacity="0.4",e.originalEvent&&(e=e.originalEvent),e.dataTransfer.effectAllowed="move",e.dataTransfer.setData("text/plain",JSON.stringify(this.pair)),this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(e){e.currentTarget.style.opacity="1.0",this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(e){this.$el.parent().trigger(e)},toString:function(){return"PairView("+this.pair.name+")"}}),w=e.View.extend(g.default.LoggableMixin).extend(p.default.CollectionCreatorMixin).extend({_logNamespace:"collections",className:"list-of-pairs-collection-creator collection-creator flex-row-container",initialize:function(e){this.metric("PairedCollectionCreator.initialize",e),e=n.defaults(e,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:!0,strategy:"lcs",matchPercentage:.9,twoPassAutopairing:!0}),this.initialList=e.datasets,this.historyId=e.historyId,this.filters=this.commonFilters[e.filters]||this.commonFilters[this.DEFAULT_FILTERS],n.isArray(e.filters)&&(this.filters=e.filters),this.automaticallyPair=e.automaticallyPair,this.strategy=this.strategies[e.strategy]||this.strategies[this.DEFAULT_STRATEGY],n.isFunction(e.strategy)&&(this.strategy=e.strategy),this.matchPercentage=e.matchPercentage,this.twoPassAutopairing=e.twoPassAutopairing,this.removeExtensions=!0,this.oncancel=e.oncancel,this.oncreate=e.oncreate,this.autoscrollDist=e.autoscrollDist||24,this.unpairedPanelHidden=!1,this.pairedPanelHidden=!1,this.$dragging=null,this.blocking=!1,this._setUpCommonSettings(e),this._setUpBehaviors(),this._dataSetUp()},commonFilters:{illumina:["_1","_2"],Rs:["_R1","_R2"]},DEFAULT_FILTERS:"illumina",strategies:{simple:"autopairSimple",lcs:"autopairLCS",levenshtein:"autopairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[],this.unpaired=[],this.selectedIds=[],this._sortInitialList(),this._ensureIds(),this.unpaired=this.initialList.slice(0),this.automaticallyPair&&(this.autoPair(),this.once("rendered:initial",function(){this.trigger("autopair")}))},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(e){return e.sort(function(e,t){return(0,h.default)(e.name,t.name)}),e},_ensureIds:function(){return this.initialList.forEach(function(e){e.hasOwnProperty("id")||(e.id=n.uniqueId())}),this.initialList},_splitByFilters:function(){function e(e,t){return t.test(e.name)}var t=this.filters.map(function(e){return new RegExp(e)}),i=[[],[]];return this.unpaired.forEach(function(n){t.forEach(function(t,s){e(n,t)&&i[s].push(n)})}),i},_addToUnpaired:function(e){var t=this;this.unpaired.splice(function i(n,s){if(n===s)return n;var a=Math.floor((s-n)/2)+n,o=(0,h.default)(e.name,t.unpaired[a].name);if(o<0)return i(n,a);if(o>0)return i(a+1,s);for(;t.unpaired[a]&&t.unpaired[a].name===e.name;)a++;return a}(0,this.unpaired.length),0,e)},autoPair:function(e){var t=this._splitByFilters(),i=[];return this.twoPassAutopairing&&(i=this.autopairSimple({listA:t[0],listB:t[1]}),t=this._splitByFilters()),e=e||this.strategy,t=this._splitByFilters(),i=i.concat(this[e].call(this,{listA:t[0],listB:t[1]}))},autopairSimple:l({scoreThreshold:function(){return.6},match:function(e){return e=e||{},e.matchTo===e.possible?{index:e.index,score:1}:e.bestMatch}}),autopairLevenshtein:l({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var t=(0,c.default)(e.matchTo,e.possible),i=1-t/Math.max(e.matchTo.length,e.possible.length);return i>e.bestMatch.score?{index:e.index,score:i}:e.bestMatch}}),autopairLCS:l({scoreThreshold:function(){return this.matchPercentage},match:function(e){e=e||{};var t=this._naiveStartingAndEndingLCS(e.matchTo,e.possible).length,i=t/Math.max(e.matchTo.length,e.possible.length);return i>e.bestMatch.score?{index:e.index,score:i}:e.bestMatch}}),_naiveStartingAndEndingLCS:function(e,t){for(var i="",n="",s=0,a=0;s<e.length&&s<t.length&&e[s]===t[s];)i+=e[s],s+=1;if(s===e.length)return e;if(s===t.length)return t;for(s=e.length-1,a=t.length-1;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.$(".collection-name").val()),element_identifiers:t.paired.map(function(e){return t._pairToJSON(e)})};return t.blocking=!0,s.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(a)}).always(function(){t.blocking=!1}).fail(function(e,i,n){t._ajaxErrHandler(e,i,n)}).done(function(e,i,n){t.trigger("collection:created",e,i,n),t.metric("collection:created",e),"function"==typeof t.oncreate&&t.oncreate.call(this,e,i,n)})},_ajaxErrHandler:function(e,t,i){this.error(e,t,i);var n=this,s=(0,v.default)("An error occurred while creating this collection");e&&(0===e.readyState&&0===e.status?s+=": "+(0,v.default)("Galaxy could not be reached and may be updating.")+(0,v.default)(" Try again in a few minutes."):e.responseJSON?s+="<br /><pre>"+JSON.stringify(e.responseJSON)+"</pre>":s+=": "+i),n._showAlert(s,"alert-danger")},render:function(e,t){return this.$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.$(".unpaired-columns .reverse-column .column-datasets").append(n)),void this._adjUnpairedOnScrollbar()):void this._renderUnpairedNotShown())},_renderUnpairedDisplayStr:function(e){return["(",e," ",(0,v.default)("filtered out"),")"].join("")},_renderUnpairedDataset:function(e){return a("<li/>").attr("id","dataset-"+e.id).addClass("dataset unpaired").attr("draggable",!0).addClass(e.selected?"selected":"").append(a("<span/>").addClass("dataset-name").text(e.name)).data("dataset",e)},_renderPairButton:function(){return a("<li/>").addClass("dataset unpaired").append(a("<span/>").addClass("dataset-name").text((0,v.default)("Pair these datasets")))},_renderUnpairedEmpty:function(){var e=a('<div class="empty-message"></div>').text("("+(0,v.default)("no remaining unpaired datasets")+")");return this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(e),e},_renderUnpairedNotShown:function(){var e=a('<div class="empty-message"></div>').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 y({pair:e});i.$(".paired-columns .column-datasets").append(n.render().$el).append(['<button class="unpair-btn">','<span class="fa fa-unlink" title="',(0,v.default)("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var e=a('<div class="empty-message"></div>').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['<button class="filter-choice btn" ','data-forward="',e,'" data-reverse="',t,'">',(0,v.default)("Forward"),": ",e,", ",(0,v.default)("Reverse"),": ",t,"</button>"].join("")}var i=a(n.template(['<div class="choose-filters">','<div class="help">',(0,v.default)("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",n.values(this.commonFilters).map(function(e){return t(e[0],e[1])}).join(""),"</div>"].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.$(".paired-columns .column-datasets");this._checkForAutoscroll(t,e.originalEvent.clientY);var i=this._getNearestPairedDatasetLi(e.originalEvent.clientY);a(".element-drop-placeholder").remove();var n=a('<div class="element-drop-placeholder"></div>');i.length?i.before(n):t.append(n)},_checkForAutoscroll:function(e,t){var i=e.offset(),n=e.scrollTop(),s=t-i.top,a=i.top+e.outerHeight()-t;s>=0&&s<this.autoscrollDist?e.scrollTop(n-2):a>=0&&a<this.autoscrollDist&&e.scrollTop(n+2)},_getNearestPairedDatasetLi:function(e){for(var t=this.$(".paired-columns .column-datasets li").toArray(),i=0;i<t.length;i++){var n=a(t[i]),s=n.offset().top,o=Math.floor(n.outerHeight()/2)+4;if(s+o>e&&s-o<e)return n}return a()},_dropPairedColumns:function(e){e.preventDefault(),e.dataTransfer.dropEffect="move";var t=this._getNearestPairedDatasetLi(e.originalEvent.clientY);return t.length?this.$dragging.insertBefore(t):this.$dragging.insertAfter(this.$(".paired-columns .unpair-btn").last()),this._syncPairsToDom(),!1},_syncPairsToDom:function(){var e=[];this.$(".paired-columns .dataset.paired").each(function(){e.push(a(this).data("pair"))}),this.paired=e,this._renderPaired()},_pairDragstart:function(e,t){t.$el.addClass("selected");var i=this.$(".paired-columns .dataset.selected");this.$dragging=i},_pairDragend:function(e,t){a(".element-drop-placeholder").remove(),this.$dragging=null},toggleExtensions:function(e){var t=this;t.removeExtensions=void 0!==e?e:!t.removeExtensions,n.each(t.paired,function(e){e.customizedName||(e.name=t._guessNameForPair(e.forward,e.reverse))}),t._renderPaired(),t._renderFooter()},_printList:function(e){var t=this;n.each(e,function(i){e===t.paired?t._printPair(i):t.debug(i)})},_printPair:function(e){this.debug(e.forward.name,e.reverse.name,": 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"+s),i.name=n,e.collection.create(i,{at:0,wait:!0,success:function(){l.success("Successfully copied workflow '"+t+"' to '"+n+"'")},error:function(e,t,i){l.error(i.errorThrown)}})}).error(function(e,t,i){l.error(e.responseJSON.err_msg)})},_rowTemplate:function(){var e=this.model.get("show_in_tool_panel"),t=this.model.id,i='<input id="show-in-tool-panel" type="checkbox" class="show-in-tool-panel" '+(e?'checked="'+e+'"':"")+' value="'+t+'">';return'<td><div class="dropdown"><button class="menubutton" type="button" data-toggle="dropdown">'+n.escape(this.model.get("name"))+'<span class="caret"></span></button>'+this._templateActions()+'</div></td><td><span><div class="'+t+' tags-display"></div></td><td>'+(this.model.get("owner")===Galaxy.user.attributes.username?"You":this.model.get("owner"))+"</span></td><td>"+this.model.get("number_of_steps")+"</td><td>"+(this.model.get("published")?"Yes":"No")+"</td><td>"+i+"</td>"},renderTagEditor:function(){var e=new d.default.TagsEditor({model:this.model,el:s.find("."+this.model.id+".tags-display"),workflow_mode:!0});e.toggle(!0),e.render()},_templateActions:function(){return this.model.get("owner")===Galaxy.user.attributes.username?'<ul class="dropdown-menu action-dpd"><li><a href="'+Galaxy.root+"workflow/editor?id="+this.model.id+'">Edit</a></li><li><a href="'+Galaxy.root+"workflows/run?id="+this.model.id+'">Run</a></li><li><a href="'+Galaxy.root+"workflow/sharing?id="+this.model.id+'">Share</a></li><li><a href="'+Galaxy.root+"api/workflows/"+this.model.id+'/download?format=json-download">Download</a></li><li><a id="copy-workflow" style="cursor: pointer;">Copy</a></li><li><a id="rename-workflow" style="cursor: pointer;">Rename</a></li><li><a href="'+Galaxy.root+"workflow/display_by_id?id="+this.model.id+'">View</a></li><li><a id="delete-workflow" style="cursor: pointer;">Delete</a></li></ul>':'<ul class="dropdown-menu action-dpd"><li><a href="'+Galaxy.root+"workflow/display_by_username_and_slug?username="+this.model.get("owner")+"&slug="+this.model.get("slug")+'">View</a></li><li><a href="'+Galaxy.root+"workflows/run?id="+this.model.id+'">Run</a></li><li><a id="copy-workflow" style="cursor: pointer;">Copy</a></li><li><a class="link-confirm-shared-'+this.model.id+'" href="'+Galaxy.root+"workflow/sharing?unshare_me=True&id="+this.model.id+'">Remove</a></li></ul>'}}),_=e.View.extend({title:(0,m.default)("Workflows"),initialize:function(){this.setElement("<div/>"),n.bindAll(this,"adjustActiondropdown"),this.collection=new u.default.WorkflowCollection,this.collection.fetch().done(this.render()),this.collection.bind("add",this.appendItem),this.collection.on("sync",this.render,this)},events:{dragleave:"unhighlightDropZone",drop:"drop",dragover:function(e){s(".hidden_description_layer").addClass("dragover"),s(".menubutton").addClass("background-none"),e.preventDefault()}},unhighlightDropZone:function(){s(".hidden_description_layer").removeClass("dragover"),s(".menubutton").removeClass("background-none")},drop:function(e){this.unhighlightDropZone(),e.preventDefault();for(var t,i=e.dataTransfer.files,n=this,s=0;t=i[s];s++)n.readWorkflowFiles(t)},readWorkflowFiles:function(e){var t=this,i=new FileReader;i.onload=function(n){var s;try{s=JSON.parse(i.result)}catch(t){l.error("Could not read file '"+e.name+"'. Verify it is a valid Galaxy workflow"),s=null}s&&t.collection.create(s,{at:0,wait:!0,success:function(){l.success("Successfully imported workflow '"+s.name+"'")},error:function(e,t,i){l.error(i.errorThrown)}})},i.readAsText(e,"utf-8")},_showArgErrors:n.once(function(){var e=f.default.get("message");"error"===f.default.get("status")?l.error(n.escape(e||"Unknown Error, please report this to an administrator.")):e&&l.info(n.escape(e))}),render:function(){var e=this._templateHeader(),t=this._templateActionButtons(),i=this._templateWorkflowTable();this.$el.html(e+t+i);var s=this;n(this.collection.models).each(function(e){s.appendItem(e),s.confirmDelete(e)},this);return this.searchWorkflow(this.$(".search-wf"),this.$(".workflow-search tr"),3),this.adjustActiondropdown(),this._showArgErrors(),this},appendItem:function(e){var t=new g({model:e,collection:this.collection});s(".workflow-search").append(t.render().el),t.renderTagEditor()},confirmDelete:function(e){this.$(".link-confirm-shared-"+e.id).click(function(){return window.confirm("Are you sure you want to remove the shared workflow '"+e.attributes.name+"'?")})},searchWorkflow:function(e,t,i){e.on("keyup",function(){var e=s(this).val();if(e.length>=i){var n=new RegExp(e,"i");t.hide(),t.filter(function(){return n.test(s(this).text())}).show()}else t.show()})},adjustActiondropdown:function(){s(this.el).on("show.bs.dropdown",function(){s(this.el).css("overflow","inherit")}),s(this.el).on("hide.bs.dropdown",function(){s(this.el).css("overflow","auto")})},_templateNoWorkflow:function(){return'<div class="wf-nodata"> You have no workflows. </div>'},_templateActionButtons:function(){return'<ul class="manage-table-actions"><li><input class="search-wf form-control" type="text" autocomplete="off" placeholder="search for workflow..."></li><li><a class="action-button fa fa-plus wf-action" id="new-workflow" title="Create new workflow" href="'+Galaxy.root+'workflows/create"></a></li><li><a class="action-button fa fa-upload wf-action" id="import-workflow" title="Upload or import workflow" href="'+Galaxy.root+'workflows/import_workflow"></a></li></ul>'},_templateWorkflowTable:function(){return'<table class="table colored"><thead><tr class="header"><th>Name</th><th>Tags</th><th>Owner</th><th># of Steps</th><th>Published</th><th>Show in tools panel</th></tr></thead><tbody class="workflow-search "><div class="hidden_description_layer"><p>Drop workflow files here to import</p></tbody></table></div>'},_templateHeader:function(){return'<div class="page-container"><div class="user-workflows wf"><div class="response-message"></div><h2>'+(0,m.default)("Your workflows")+"</h2></div></div>"}}),v=e.View.extend({initialize:function(){this.setElement("<div/>"),this.render()},render:function(){var e=this;s.getJSON(Galaxy.root+"workflow/upload_import_workflow",function(t){e.$el.empty().append(e._mainTemplate(t))})},_mainTemplate:function(e){return"<div class='toolForm'><div class='toolFormTitle'>Import Galaxy workflow</div><div class='toolFormBody'><form name='import_workflow' id='import_workflow' action='"+Galaxy.root+"workflow/upload_import_workflow' enctype='multipart/form-data' method='POST'><div class='form-row'><label>Galaxy workflow URL:</label><input type='text' name='url' class='input-url' value='"+e.url+"' size='40'><div class='toolParamHelp' style='clear: both;'>If the workflow is accessible via a URL, enter the URL above and click <b>Import</b>.</div><div style='clear: both'></div></div><div class='form-row'><label>Galaxy workflow file:</label><div class='form-row-input'><input type='file' name='file_data' class='input-file'/></div><div class='toolParamHelp' style='clear: both;'>If the workflow is in a file on your computer, choose it and then click <b>Import</b>.</div><div style='clear: both'></div></div><div class='form-row'><input type='submit' class='primary-button wf-import' name='import_button' value='Import'></div></form><hr/><div class='form-row'><label>Import a Galaxy workflow from myExperiment:</label><div class='form-row-input'><a href='"+e.myexperiment_target_url+"'> Visit myExperiment</a></div><div class='toolParamHelp' style='clear: both;'>Click the link above to visit myExperiment and browse for Galaxy workflows.</div><div style='clear: both'></div></div></div></div>"}});t.default={View:_,ImportWorkflowView:v}}).call(t,i(2),i(1),i(0))},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0});var n=i(5),s=function(e){return e&&e.__esModule?e:{default:e}}(n),a=e.Model.extend(s.default.LoggableMixin).extend({_logNamespace:"workflow",urlRoot:Galaxy.root+"api/workflows",toJSON:function(){return{workflow:this.attributes}}}),o=e.Collection.extend({model:a,url:Galaxy.root+"api/workflows"});t.default={WorkflowItem:a,WorkflowCollection:o}}).call(t,i(2))},function(e,t,i){"use strict";function n(e){i(270)}Object.defineProperty(t,"__esModule",{value:!0});var s=i(272),a=i.n(s),o=i(273),l=i(14),r=n,d=l(a.a,o.a,!1,r,null,null);t.default=d.exports},function(e,t,i){var n=i(271);"string"==typeof n&&(n=[[e.i,n,""]]),n.locals&&(e.exports=n.locals);i(48)("2fdc4394",n,!0)},function(e,t,i){t=e.exports=i(47)(void 0),t.push([e.i,".ui-message{display:block}",""])},function(e,t,i){"use strict";(function(e){Object.defineProperty(t,"__esModule",{value:!0}),t.default={data:function(){return{errormessage:null}},methods:{submit:function(){var t=this;e.ajax({url:Galaxy.root+"api/histories",data:new FormData(this.$refs.form),cache:!1,contentType:!1,processData:!1,method:"POST"}).done(function(e){window.location=Galaxy.root+"histories/list?message="+e.message+"&status=success"}).fail(function(e){var i=e.responseJSON&&e.responseJSON.err_msg;t.errormessage=i||"Import failed for unkown reason."})}}}}).call(t,i(0))},function(e,t,i){"use strict";var n=function(){var e=this,t=e.$createElement,i=e._self._c||t;return i("div",{staticClass:"ui-portlet-limited"},[e._m(0,!1,!1),e._v(" "),i("div",{staticClass:"portlet-content"},[e.errormessage?i("div",{staticClass:"ui-message alert alert-danger"},[e._v("\n            "+e._s(e.errormessage)+"\n        ")]):e._e(),e._v(" "),i("div",{staticClass:"portlet-body"},[i("form",{ref:"form"},[e._m(1,!1,!1),e._v(" "),e._m(2,!1,!1)])]),e._v(" "),i("div",{staticClass:"portlet-buttons"},[i("input",{staticClass:"btn btn-primary",attrs:{type:"button",value:"Import History"},on:{click:e.submit}})])])])},s=[function(){var e=this,t=e.$createElement,i=e._self._c||t;return i("div",{staticClass:"portlet-header"},[i("div",{staticClass:"portlet-title"},[i("i",{staticClass:"portlet-title-icon fa fa-upload"}),e._v(" "),i("span",{staticClass:"portlet-title-text"},[i("b",[e._v("Import a History from an Archive")])])])])},function(){var e=this,t=e.$createElement,i=e._self._c||t;return i("div",{staticClass:"ui-form-element"},[i("div",{staticClass:"ui-form-title"},[e._v("Archived History URL")]),e._v(" "),i("input",{staticClass:"ui-input",attrs:{type:"text",name:"archive_source"}})])},function(){var e=this,t=e.$createElement,i=e._self._c||t;return i("div",{staticClass:"ui-form-element"},[i("div",{staticClass:"ui-form-title"},[e._v("Archived History file")]),e._v(" "),i("input",{attrs:{type:"file",name:"archive_file"}})])}],a={render:n,staticRenderFns:s};t.a=a},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(3),o=s(a),l=i(4),r=s(l),d=i(20),c=s(d),u=i(63),h=s(u),f=i(112),p=s(f),m=c.default.extend({_showCopyDialog:function(e){var t=new h.default.History({id:e});t.fetch().fail(function(){alert("History could not be fetched. Please contact an administrator")}).done(function(){(0,p.default)(t,{}).done(function(){window.parent&&window.parent.Galaxy&&window.parent.Galaxy.currHistoryPanel&&window.parent.Galaxy.currHistoryPanel.loadCurrentHistory(),window.location.reload(!0)})})},_add_operation:function(t,i,n){var s=this,a=n.operation_config[i.label];"Copy"==i.label&&(i.onclick=function(e){s._showCopyDialog(e)}),a.allowed&&i.allow_popup&&t.addItem({html:i.label,href:a.url_args,target:a.target,confirmation_text:i.confirm,func:function(t){t.preventDefault();var a=e(t.target).html();i.onclick?i.onclick(n.encode_id):s.execute(this.findItemByHtml(a))}})}}),g=n.View.extend({title:(0,o.default)("Histories"),initialize:function(t){var i=this;this.setElement(e("<div/>")),this.model=new n.Model,r.default.get({url:Galaxy.root+"history/"+t.action_id+"?"+e.param(Galaxy.params),success:function(e){i.model.set(e),i.render()}})},render:function(){var e=new m(this.model.attributes);this.$el.empty().append(e.$el)}});t.default={View:g}}).call(t,i(0),i(2))},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(3),o=s(a),l=i(4),r=s(l),d=i(6),c=s(d),u=i(11),h=s(u),f=e.View.extend({initialize:function(){this.setElement("<div/>"),this.model=new e.Model({dataset_id:Galaxy.params.dataset_id}),this.render()},render:function(){var e=Galaxy.root+"api/datasets/"+this.model.get("dataset_id"),t=this;r.default.get({url:e,success:function(e){var i=Galaxy.root+"api/jobs/"+e.creating_job+"?full=True";r.default.get({url:i,success:function(i){Galaxy.root,e.creating_job;t.render_error_page(t,e,i)},error:function(e){var i={status:"error",message:"Error occured while loading the job.",persistent:!0,cls:"errormessage"};t.display_message(i,t.$(".response-message"))}})},error:function(e){var i={status:"error",message:"Error occured while loading the dataset.",persistent:!0,cls:"errormessage"};t.display_message(i,t.$(".response-message"))}})},render_error_page:function(e,t,i){e.$el.empty().append(e._templateHeader()),e.$el.append("<h2>Dataset Error</h2>"),e.$el.append("<p>An error occured while running the tool <b>"+i.tool_id+"</b>.</p>"),e.$el.append("<p>Tool execution generated the following messages:</p>"),e.$el.append('<pre class="code">'+i.stderr+"</pre>"),e.$el.append("<h2>Report This Error</pre>"),e.$el.append("<p>Usually the local Galaxy administrators regularly review errors that occur on the server. However, if you would like to provide additional information (such as what you were trying to do when the error occurred) and a contact e-mail address, we will be better able to investigate your problem and get back to you.</p>"),e.$el.append(e._getBugFormTemplate(t,i))},display_message:function(e,t,i,n){n?i?t.append(new c.default.UnescapedMessage(e).$el):t.empty().html(new c.default.UnescapedMessage(e).$el):i?t.append(new c.default.Message(e).$el):t.empty().html(new c.default.Message(e).$el)},_templateHeader:function(){return'<div class="page-container edit-attr"><div class="response-message"></div></div>'},_getBugFormTemplate:function(e,t){var i=this,n=[{help:(0,o.default)("Your email address"),options:[],type:"text",name:"email",label:"Your email",value:Galaxy.user.get("email")},{help:(0,o.default)("Any additional comments you can provide regarding what you were doing at the time of the bug."),options:[],type:"text",area:!0,name:"message",label:"Message"}],s=new h.default({title:(0,o.default)("Error Report"),inputs:n,buttons:{save:new c.default.Button({icon:"fa-bug",title:(0,o.default)("Report"),cls:"ui-button btn btn-primary",floating:"clear",onclick:function(){var n=s.data.create(),a=Galaxy.root+"api/jobs/"+t.id+"/error";n.dataset_id=e.id,i.submit(n,a)}})}});return s.$el},submit:function(e,t){var i=this;n.ajax({type:"POST",url:t,data:e,success:function(e){i.$el.empty().append(i._templateHeader()),e.messages.forEach(function(e){i.display_message({status:e[1],message:e[0],persistent:!0},i.$(".response-message"),!0,!0)})},error:function(e){var t={status:"error",message:"Error occured while saving. Please fill all the required fields and try again.",persistent:!0,cls:"errormessage"};i.display_message(t,i.$(".response-message"))}})}});t.default={View:f}}).call(t,i(2),i(0))},function(e,t,i){"use strict";(function(e,n,s){function a(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(t,"__esModule",{value:!0});var o=i(3),l=a(o),r=i(4),d=(a(r),i(44)),c=a(d),u=i(6),h=a(u),f=i(11),p=a(f),m=e.View.extend({initialize:function(){this.setElement("<div/>"),this.model=new e.Model({dataset_id:Galaxy.params.dataset_id}),this.message=new h.default.Message({persistent:!0}),this.tabs=this._createTabs(),this.$el.append(n("<h4/>").append("Edit dataset attributes")).append(this.message.$el).append("<p/>").append(this.tabs.$el).hide(),this.render()},render:function(){var e=this;n.ajax({url:Galaxy.root+"dataset/get_edit?dataset_id="+e.model.get("dataset_id"),success:function(t){!e.initial_message&&e.message.update(t),e.initial_message=!0,s.each(e.forms,function(e,i){e.model.set("inputs",t[i+"_inputs"]),e.model.set("hide_operations",t[i+"_disable"]),e.render()}),e.$el.show()},error:function(t){var i=t.responseJSON&&t.responseJSON.err_msg;e.message.update({status:"danger",message:i||"Error occured while loading the dataset."})}})},_submit:function(e,t){var i=this,s=t.data.create();s.dataset_id=this.model.get("dataset_id"),s.operation=e,n.ajax({type:"PUT",url:Galaxy.root+"dataset/set_edit",data:s,success:function(e){i.message.update(e),i.render(),i._reloadHistory()},error:function(e){var t=e.responseJSON&&e.responseJSON.err_msg;i.message.update({status:"danger",message:t||"Error occured while editing the dataset attributes."})}})},_createTabs:function(){this.forms={attribute:this._getAttribute(),conversion:this._getConversion(),datatype:this._getDatatype(),permission:this._getPermission()};var e=new c.default.View;return e.add({id:"attribute",title:(0,l.default)("Attributes"),icon:"fa fa-bars",tooltip:(0,l.default)("Edit dataset attributes"),$el:this.forms.attribute.$el}),e.add({id:"convert",title:(0,l.default)("Convert"),icon:"fa-gear",tooltip:(0,l.default)("Convert to new format"),$el:this.forms.conversion.$el}),e.add({id:"datatype",title:(0,l.default)("Datatypes"),icon:"fa-database",tooltip:(0,l.default)("Change data type"),$el:this.forms.datatype.$el}),e.add({id:"permissions",title:(0,l.default)("Permissions"),icon:"fa-user",tooltip:(0,l.default)("Permissions"),$el:this.forms.permission.$el}),e},_getAttribute:function(){var e=this,t=new p.default({title:(0,l.default)("Edit attributes"),operations:{submit_attributes:new h.default.ButtonIcon({tooltip:(0,l.default)("Save attributes of the dataset."),icon:"fa-floppy-o",title:(0,l.default)("Save"),onclick:function(){e._submit("attributes",t)}}),submit_autodetect:new h.default.ButtonIcon({tooltip:"This will inspect the dataset and attempt to correct the values of fields if they are not accurate.",icon:"fa-undo",title:"Auto-detect",onclick:function(){e._submit("autodetect",t)}})}});return t},_getConversion:function(){var e=this,t=new p.default({title:(0,l.default)("Convert to new format"),operations:{submit_conversion:new h.default.ButtonIcon({tooltip:(0,l.default)("Convert the datatype to a new format."),title:(0,l.default)("Convert datatype"),icon:"fa-exchange",onclick:function(){e._submit("conversion",t)}})}});return t},_getDatatype:function(){var e=this,t=new p.default({title:(0,l.default)("Change datatype"),operations:{submit_datatype:new h.default.ButtonIcon({tooltip:(0,l.default)("Change the datatype to a new type."),title:(0,l.default)("Change datatype"),icon:"fa-exchange",onclick:function(){e._submit("datatype",t)}})}});return t},_getPermission:function(){var e=this,t=new p.default({title:(0,l.default)("Manage dataset permissions"),operations:{submit_permission:new h.default.ButtonIcon({tooltip:(0,l.default)("Save permissions."),title:(0,l.default)("Save permissions"),icon:"fa-floppy-o ",onclick:function(){e._submit("permission",t)}})}});return t},_reloadHistory:function(){window.Galaxy&&window.Galaxy.currHistoryPanel.loadCurrentHistory()}});t.default={View:m}}).call(t,i(2),i(0),i(1))}],[239]);
\ No newline at end of file
diff --git a/static/scripts/mvc/dataset/dataset-li.js b/static/scripts/mvc/dataset/dataset-li.js
index 59a33660351..78a1bb963c4 100644
--- a/static/scripts/mvc/dataset/dataset-li.js
+++ b/static/scripts/mvc/dataset/dataset-li.js
@@ -1 +1 @@
-define("mvc/dataset/dataset-li",["exports","mvc/list/list-item","mvc/dataset/states","ui/fa-icon-button","mvc/base-mvc","utils/localization"],function(e,t,a,s,i,d){"use strict";function l(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(e,"__esModule",{value:!0});var n=l(t),r=l(a),o=l(s),u=l(i),p=l(d),f=n.default.ListItemView,c=f.extend({_logNamespace:"dataset",className:f.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),f.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_setUpListeners:function(){f.prototype._setUpListeners.call(this);var e=this;return e.listenTo(e.model,{change:function(t){e.model.changedAttributes().state&&e.model.inReadyState()&&e.expanded&&!e.model.hasDetails()?e.model.fetch({silent:!0}).done(function(){e.render()}):_.has(t.changed,"tags")&&1===_.keys(t.changed).length?e.$(".nametags").html(e._renderNametags()):e.render()}})},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):jQuery.when()},remove:function(e,t){var a=this;e=e||this.fxSpeed,this.$el.fadeOut(e,function(){Backbone.View.prototype.remove.call(a),t&&t.call(a)})},_swapNewRender:function(e){return f.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===r.default.NOT_VIEWABLE||e===r.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,p.default)("Cannot display datasets removed from disk");else if(e===r.default.UPLOAD)t.disabled=!0,t.title=(0,p.default)("This dataset must finish uploading before it can be viewed");else if(e===r.default.NEW)t.disabled=!0,t.title=(0,p.default)("This dataset is not yet viewable");else{t.title=(0,p.default)("View data"),t.href=this.model.urls.display;var a=this;t.onclick=function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.addDataset(a.model.get("id")),e.preventDefault())}}return t.faIcon="fa-eye",(0,o.default)(t)},_renderDetails:function(){if(this.model.get("state")===r.default.NOT_VIEWABLE)return $(this.templates.noAccess(this.model.toJSON(),this));var e=f.prototype._renderDetails.call(this);return e.find(".actions .left").empty().append(this._renderSecondaryActions()),e.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),e.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(e),e},_renderSummary:function(){var e=this.model.toJSON(),t=this.templates.summaries[e.state];return(t=t||this.templates.summaries.unknown)(e,this)},_renderDetailMessages:function(){var e=this,t=$('<div class="detail-messages"></div>'),a=e.model.toJSON();return _.each(e.templates.detailMessages,function(s){t.append($(s(a,e)))}),t},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case r.default.NOT_VIEWABLE:return[];case r.default.OK:case r.default.FAILED_METADATA:case r.default.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return(0,o.default)({title:(0,p.default)("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle",onclick:function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:(0,p.default)("Dataset details"),url:this.href}),e.preventDefault(),e.stopPropagation())}})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:_.isEmpty(this.model.get("meta_files"))?$(['<a class="download-btn icon-btn" ','href="',this.model.urls.download,'" title="'+(0,p.default)("Download")+'" download>','<span class="fa fa-floppy-o"></span>',"</a>"].join("")):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var e=this.model.urls;return $(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+(0,p.default)("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+e.download+'" download>',(0,p.default)("Download dataset"),"</a></li>",_.map(this.model.get("meta_files"),function(t){return['<li><a href="',e.meta_download+t.file_type,'">',(0,p.default)("Download")," ",t.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},_renderNametags:function(){return _.template(["<% _.each(_.sortBy(_.uniq(tags), function(x) { return x }), function(tag){ %>",'<% if (tag.indexOf("name:") == 0){ %>','<span class="label label-info"><%- tag.slice(5) %></span>',"<% } %>","<% }); %>"].join(""))({tags:this.model.get("tags")})},events:_.extend(_.clone(f.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)")+")"}});c.prototype.templates=function(){var e=_.extend({},f.prototype.templates.warnings,{failed_metadata:u.default.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',(0,p.default)("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:u.default.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',(0,p.default)("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:u.default.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',(0,p.default)("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:u.default.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,p.default)("This dataset has been deleted"),"</div>","<% } %>"])}),t=u.default.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset"),a=u.default.wrapTemplate(['<div class="details">','<div class="summary">',(0,p.default)("You do not have permission to view this dataset"),"</div>","</div>"],"dataset"),s={};s[r.default.OK]=s[r.default.FAILED_METADATA]=u.default.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.file_ext ){ %>",'<div class="datatype">','<label class="prompt">',(0,p.default)("format"),"</label>",'<span class="value"><%- dataset.file_ext %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',(0,p.default)("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset"),s[r.default.NEW]=u.default.wrapTemplate(["<div>",(0,p.default)("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset"),s[r.default.NOT_VIEWABLE]=u.default.wrapTemplate(["<div>",(0,p.default)("You do not have permission to view this dataset"),"</div>"],"dataset"),s[r.default.DISCARDED]=u.default.wrapTemplate(["<div>",(0,p.default)("The job creating this dataset was cancelled before completion"),"</div>"],"dataset"),s[r.default.QUEUED]=u.default.wrapTemplate(["<div>",(0,p.default)("This job is waiting to run"),"</div>"],"dataset"),s[r.default.RUNNING]=u.default.wrapTemplate(["<div>",(0,p.default)("This job is currently running"),"</div>"],"dataset"),s[r.default.UPLOAD]=u.default.wrapTemplate(["<div>",(0,p.default)("This dataset is currently uploading"),"</div>"],"dataset"),s[r.default.SETTING_METADATA]=u.default.wrapTemplate(["<div>",(0,p.default)("Metadata is being auto-detected"),"</div>"],"dataset"),s[r.default.PAUSED]=u.default.wrapTemplate(["<div>",(0,p.default)('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset"),s[r.default.ERROR]=u.default.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',(0,p.default)("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset"),s[r.default.EMPTY]=u.default.wrapTemplate(["<div>",(0,p.default)("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset"),s.unknown=u.default.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var i={resubmitted:u.default.wrapTemplate(["<% if( model.resubmitted ){ %>",'<div class="resubmitted-msg infomessagesmall">',(0,p.default)("The job creating this dataset has been resubmitted"),"</div>","<% } %>"])},d=u.default.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%- link.target %>" href="<%- link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},f.prototype.templates,{warnings:e,details:t,noAccess:a,summaries:s,detailMessages:i,displayApplications:d})}(),e.default={DatasetListItemView:c}});
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+define("mvc/dataset/dataset-li",["exports","mvc/list/list-item","mvc/dataset/states","ui/fa-icon-button","mvc/base-mvc","utils/localization"],function(e,t,a,s,i,d){"use strict";function l(e){return e&&e.__esModule?e:{default:e}}Object.defineProperty(e,"__esModule",{value:!0});var n=l(t),r=l(a),o=l(s),u=l(i),p=l(d),f=n.default.ListItemView,c=f.extend({_logNamespace:"dataset",className:f.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),f.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_setUpListeners:function(){f.prototype._setUpListeners.call(this);var e=this;return e.listenTo(e.model,{change:function(t){e.model.changedAttributes().state&&e.model.inReadyState()&&e.expanded&&!e.model.hasDetails()?e.model.fetch({silent:!0}).done(function(){e.render()}):_.has(t.changed,"tags")&&1===_.keys(t.changed).length?e.$(".nametags").html(e._renderNametags()):e.render()}})},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):jQuery.when()},remove:function(e,t){var a=this;e=e||this.fxSpeed,this.$el.fadeOut(e,function(){Backbone.View.prototype.remove.call(a),t&&t.call(a)})},_swapNewRender:function(e){return f.prototype._swapNewRender.call(this,e),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var e=this.model.get("state");if(e===r.default.NOT_VIEWABLE||e===r.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,p.default)("Cannot display datasets removed from disk");else if(e===r.default.UPLOAD)t.disabled=!0,t.title=(0,p.default)("This dataset must finish uploading before it can be viewed");else if(e===r.default.NEW)t.disabled=!0,t.title=(0,p.default)("This dataset is not yet viewable");else{t.title=(0,p.default)("View data"),t.href=this.model.urls.display;var a=this;t.onclick=function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.addDataset(a.model.get("id")),e.preventDefault())}}return t.faIcon="fa-eye",(0,o.default)(t)},_renderDetails:function(){if(this.model.get("state")===r.default.NOT_VIEWABLE)return $(this.templates.noAccess(this.model.toJSON(),this));var e=f.prototype._renderDetails.call(this);return e.find(".actions .left").empty().append(this._renderSecondaryActions()),e.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),e.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(e),e},_renderSummary:function(){var e=this.model.toJSON(),t=this.templates.summaries[e.state];return(t=t||this.templates.summaries.unknown)(e,this)},_renderDetailMessages:function(){var e=this,t=$('<div class="detail-messages"></div>'),a=e.model.toJSON();return _.each(e.templates.detailMessages,function(s){t.append($(s(a,e)))}),t},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case r.default.NOT_VIEWABLE:return[];case r.default.OK:case r.default.FAILED_METADATA:case r.default.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return(0,o.default)({title:(0,p.default)("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle",onclick:function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:(0,p.default)("Dataset details"),url:this.href}),e.preventDefault(),e.stopPropagation())}})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:_.isEmpty(this.model.get("meta_files"))?$('\n                <a class="download-btn icon-btn" href="'+this.model.urls.download+'" title="'+(0,p.default)("Download")+'">\n                    <span class="fa fa-floppy-o"></span>\n                </a>'):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var e=this.model.urls;return $('\n                <div class="metafile-dropdown dropdown">\n                    <a class="download-btn icon-btn" href="'+e.download+'" data-toggle="dropdown" title="'+(0,p.default)("Download")+'">\n                        <span class="fa fa-floppy-o"></span>\n                    </a>\n                    <ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">\n                        <li>\n                            <a href="'+e.download+'">\n                                '+(0,p.default)("Download dataset")+"\n                            </a>\n                        </li>\n                        "+_.map(this.model.get("meta_files"),function(t){return'<li>\n                                    <a href="'+(e.meta_download+t.file_type)+'">\n                                        '+(0,p.default)("Download")+" "+t.file_type+"\n                                    </a>\n                                </li>"})+"\n                    </ul>\n                </div>")},_renderNametags:function(){return _.template(["<% _.each(_.sortBy(_.uniq(tags), function(x) { return x }), function(tag){ %>",'<% if (tag.indexOf("name:") == 0){ %>','<span class="label label-info"><%- tag.slice(5) %></span>',"<% } %>","<% }); %>"].join(""))({tags:this.model.get("tags")})},events:_.extend(_.clone(f.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)")+")"}});c.prototype.templates=function(){var e=_.extend({},f.prototype.templates.warnings,{failed_metadata:u.default.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',(0,p.default)("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:u.default.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',(0,p.default)("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:u.default.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',(0,p.default)("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:u.default.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',(0,p.default)("This dataset has been deleted"),"</div>","<% } %>"])}),t=u.default.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset"),a=u.default.wrapTemplate(['<div class="details">','<div class="summary">',(0,p.default)("You do not have permission to view this dataset"),"</div>","</div>"],"dataset"),s={};s[r.default.OK]=s[r.default.FAILED_METADATA]=u.default.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.file_ext ){ %>",'<div class="datatype">','<label class="prompt">',(0,p.default)("format"),"</label>",'<span class="value"><%- dataset.file_ext %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',(0,p.default)("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset"),s[r.default.NEW]=u.default.wrapTemplate(["<div>",(0,p.default)("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset"),s[r.default.NOT_VIEWABLE]=u.default.wrapTemplate(["<div>",(0,p.default)("You do not have permission to view this dataset"),"</div>"],"dataset"),s[r.default.DISCARDED]=u.default.wrapTemplate(["<div>",(0,p.default)("The job creating this dataset was cancelled before completion"),"</div>"],"dataset"),s[r.default.QUEUED]=u.default.wrapTemplate(["<div>",(0,p.default)("This job is waiting to run"),"</div>"],"dataset"),s[r.default.RUNNING]=u.default.wrapTemplate(["<div>",(0,p.default)("This job is currently running"),"</div>"],"dataset"),s[r.default.UPLOAD]=u.default.wrapTemplate(["<div>",(0,p.default)("This dataset is currently uploading"),"</div>"],"dataset"),s[r.default.SETTING_METADATA]=u.default.wrapTemplate(["<div>",(0,p.default)("Metadata is being auto-detected"),"</div>"],"dataset"),s[r.default.PAUSED]=u.default.wrapTemplate(["<div>",(0,p.default)('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset"),s[r.default.ERROR]=u.default.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',(0,p.default)("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset"),s[r.default.EMPTY]=u.default.wrapTemplate(["<div>",(0,p.default)("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset"),s.unknown=u.default.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var i={resubmitted:u.default.wrapTemplate(["<% if( model.resubmitted ){ %>",'<div class="resubmitted-msg infomessagesmall">',(0,p.default)("The job creating this dataset has been resubmitted"),"</div>","<% } %>"])},d=u.default.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%- link.target %>" href="<%- link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},f.prototype.templates,{warnings:e,details:t,noAccess:a,summaries:s,detailMessages:i,displayApplications:d})}(),e.default={DatasetListItemView:c}});
\ No newline at end of file