From 980d37f50f324f097ca80b4508265c5160ac7ed0 Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Mon, 18 Apr 2016 15:14:06 -0400
Subject: [PATCH 1/3] fix a bug with missing history_id in libraries dataset
 import also allow creation of new histories as exists in the folderlist view

---
 .../mvc/library/library-dataset-view.js       | 101 ++++++++++++------
 .../mvc/library/library-dataset-view.js.map   |   2 +-
 .../mvc/library/library-dataset-view.js       |   2 +-
 3 files changed, 72 insertions(+), 33 deletions(-)

diff --git a/client/galaxy/scripts/mvc/library/library-dataset-view.js b/client/galaxy/scripts/mvc/library/library-dataset-view.js
index 44baf7c9022..9fefb6128f8 100644
--- a/client/galaxy/scripts/mvc/library/library-dataset-view.js
+++ b/client/galaxy/scripts/mvc/library/library-dataset-view.js
@@ -202,29 +202,47 @@ var LibraryDatasetView = Backbone.View.extend({
   },
 
   importCurrentIntoHistory: function(){
-      // var self = this;
-      var history_id = $(this.modal.elMain).find('select[name=dataset_import_single] option:selected').val();
-      var historyItem = new mod_library_model.HistoryItem();
-      historyItem.url = historyItem.urlRoot + history_id + '/contents';
-
-      // set the used history as current so user will see the last one
-      // that he imported into in the history panel on the 'analysis' page
-      jQuery.getJSON( Galaxy.root + 'history/set_as_current?id=' + history_id  );
-
-      // save the dataset into selected history
-      historyItem.save({ content : this.id, source : 'library' }, {
-        success : function(){
-            Galaxy.modal.hide();
-          mod_toastr.success('Dataset imported. Click this to start analyzing it.', '', {onclick: function() {window.location='/';}});
-        },
-        error : function(model, response){
-          if (typeof response.responseJSON !== "undefined"){
-            mod_toastr.error('Dataset not imported. ' + response.responseJSON.err_msg);
-          } else {
-            mod_toastr.error('An error occured. Dataset not imported. Please try again.');
-          }
-        }
+    this.modal.disableButton('Import');
+    var new_history_name = this.modal.$('input[name=history_name]').val();
+    var that = this;
+    if (new_history_name !== ''){
+      $.post( Galaxy.root + 'api/histories', {name: new_history_name})
+        .done(function( new_history ) {
+          that.processImportToHistory(new_history.id, new_history.name);
+        })
+        .fail(function( xhr, status, error ) {
+          mod_toastr.error('An error ocurred.');
+        })
+        .always(function() {
+          that.modal.enableButton('Import');
         });
+    } else {
+      var history_id = $(this.modal.$el).find('select[name=dataset_import_single] option:selected').val();
+      this.processImportToHistory( history_id );
+      this.modal.enableButton('Import');
+    }
+  },
+
+  processImportToHistory: function( history_id ){
+    var historyItem = new mod_library_model.HistoryItem();
+    historyItem.url = historyItem.urlRoot + history_id + '/contents';
+    // set the used history as current so user will see the last one
+    // that he imported into in the history panel on the 'analysis' page
+    jQuery.getJSON( Galaxy.root + 'history/set_as_current?id=' + history_id  );
+    // save the dataset into selected history
+    historyItem.save({ content : this.id, source : 'library' }, {
+      success : function(){
+        Galaxy.modal.hide();
+        mod_toastr.success('Dataset imported. Click this to start analyzing it.', '', {onclick: function() {window.location='/';}});
+      },
+      error : function(model, response){
+        if (typeof response.responseJSON !== "undefined"){
+          mod_toastr.error('Dataset not imported. ' + response.responseJSON.err_msg);
+        } else {
+          mod_toastr.error('An error occured. Dataset not imported. Please try again.');
+        }
+      }
+      });
   },
 
   shareDataset: function(){
@@ -1037,19 +1055,40 @@ var LibraryDatasetView = Backbone.View.extend({
     ].join(''));
   },
 
-  templateBulkImportInModal: function(){
+  // templateBulkImportInModal: function(){
+  //   return _.template([
+  //   '<span class="library-modal-item">',
+  //     'Select history: ',
+  //     '<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ',
+  //       '<% _.each(histories, function(history) { %>', //history select btn
+  //         '<option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>',
+  //       '<% }); %>',
+  //     '</select>',
+  //   '</span>'
+  //   ].join(''));
+  // },
+
+  templateBulkImportInModal : function(){
     return _.template([
-    '<span class="library-modal-item">',
-      'Select history: ',
-      '<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ',
-        '<% _.each(histories, function(history) { %>', //history select btn
-          '<option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>',
-        '<% }); %>',
-      '</select>',
-    '</span>'
+    '<div>',
+      '<div class="library-modal-item">',
+        'Select history: ',
+        '<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; " autofocus>',
+          '<% _.each(histories, function(history) { %>',
+            '<option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>',
+          '<% }); %>',
+        '</select>',
+      '</div>',
+      '<div class="library-modal-item">',
+        'or create new: ',
+        '<input type="text" name="history_name" value="" placeholder="name of the new history" style="width:50%;">',
+        '</input>',
+      '</div>',
+    '</div>'
     ].join(''));
   },
 
+
   templateAccessSelect: function(){
     return _.template([
     '<select id="access_select" multiple>',
diff --git a/static/maps/mvc/library/library-dataset-view.js.map b/static/maps/mvc/library/library-dataset-view.js.map
index 0be0a497e22..6aa420c6f87 100644
--- a/static/maps/mvc/library/library-dataset-view.js.map
+++ b/static/maps/mvc/library/library-dataset-view.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/static/scripts/mvc/library/library-dataset-view.js b/static/scripts/mvc/library/library-dataset-view.js
index 99cce9fbcf4..50cd004f992 100644
--- a/static/scripts/mvc/library/library-dataset-view.js
+++ b/static/scripts/mvc/library/library-dataset-view.js
@@ -1,2 +1,2 @@
-define(["libs/toastr","mvc/library/library-model","utils/utils","mvc/ui/ui-select"],function(a,b,c,d){var e=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon"},select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(a){this.options=_.extend(this.options,a),this.fetchExtAndGenomes(),this.options.id&&this.fetchDataset()},fetchDataset:function(c){this.options=_.extend(this.options,c),this.model=new b.Item({id:this.options.id});var d=this;this.model.fetch({success:function(){d.options.show_permissions?d.showPermissions():d.options.show_version?d.fetchVersion():d.render()},error:function(b,c){"undefined"!=typeof c.responseJSON?a.error(c.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}}):a.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}})},render:function(a){this.options=_.extend(this.options,a),$(".tooltip").remove();var b=this.templateDataset();this.$el.html(b({item:this.model})),$(".peek").html(this.model.get("peek")),$("#center [data-toggle]").tooltip()},fetchVersion:function(c){this.options=_.extend(this.options,c),that=this,this.options.ldda_id?(this.ldda=new b.Ldda({id:this.options.ldda_id}),this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id,this.ldda.fetch({success:function(){that.renderVersion()},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?c.responseJSON.err_msg:"An error ocurred.")}})):(this.render(),a.error("Library dataset version requested but no id provided."))},renderVersion:function(){$(".tooltip").remove();var a=this.templateVersion();this.$el.html(a({item:this.model,ldda:this.ldda})),$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var a=this.templateModifyDataset();this.$el.html(a({item:this.model})),this.renderSelectBoxes({genome_build:this.model.get("genome_build"),file_ext:this.model.get("file_ext")}),$(".peek").html(this.model.get("peek")),$("#center [data-toggle]").tooltip()},downloadDataset:function(){var a=Galaxy.root+"api/libraries/datasets/download/uncompressed",b={ld_ids:this.id};this.processDownload(a,b)},processDownload:function(b,c,d){if(b&&c){c="string"==typeof c?c:$.param(c);var e="";$.each(c.split("&"),function(){var a=this.split("=");e+='<input type="hidden" name="'+a[0]+'" value="'+a[1]+'" />'}),$('<form action="'+b+'" method="'+(d||"post")+'">'+e+"</form>").appendTo("body").submit().remove(),a.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(a){var b=a.templateBulkImportInModal();a.modal=Galaxy.modal,a.modal.show({closing_events:!0,title:"Import into History",body:b({histories:a.histories.models}),buttons:{Import:function(){a.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(c){var d=this;this.histories=new b.GalaxyHistories,this.histories.fetch({success:function(b){0===b.length?a.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location="/"}}):c(d)},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?c.responseJSON.err_msg:"An error ocurred.")}})},importCurrentIntoHistory:function(){var c=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val(),d=new b.HistoryItem;d.url=d.urlRoot+c+"/contents",jQuery.getJSON(Galaxy.root+"history/set_as_current?id="+c),d.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide(),a.success("Dataset imported. Click this to start analyzing it.","",{onclick:function(){window.location="/"}})},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?"Dataset not imported. "+c.responseJSON.err_msg:"An error occured. Dataset not imported. Please try again.")}})},shareDataset:function(){a.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(b){this.options=_.extend(this.options,b),$(".tooltip").remove(),void 0!==this.options.fetched_permissions&&this.model.set(0===this.options.fetched_permissions.access_dataset_roles.length?{is_unrestricted:!0}:{is_unrestricted:!1});var c=!1;Galaxy.user&&(c=Galaxy.user.isAdmin());var d=this.templateDatasetPermissions();this.$el.html(d({item:this.model,is_admin:c}));var e=this;void 0===this.options.fetched_permissions?$.get(Galaxy.root+"api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(a){e.prepareSelectBoxes({fetched_permissions:a,is_admin:c})}).fail(function(){a.error("An error occurred while attempting to fetch dataset permissions.")}):this.prepareSelectBoxes({is_admin:c}),$("#center [data-toggle]").tooltip(),$("#center").css("overflow","auto")},_serializeRoles:function(a){for(var b=[],c=0;c<a.length;c++)b.push(a[c][1]+":"+a[c][0]);return b},prepareSelectBoxes:function(b){this.options=_.extend(this.options,b);var c=this.options.fetched_permissions,e=this.options.is_admin,f=this,g=[],h=[],i=[];if(g=this._serializeRoles(c.access_dataset_roles),h=this._serializeRoles(c.modify_item_roles),i=this._serializeRoles(c.manage_dataset_roles),e){var j={minimumInputLength:0,css:"access_perm",multiple:!0,placeholder:"Click to select a role",container:f.$el.find("#access_perm"),ajax:{url:Galaxy.root+"api/libraries/datasets/"+f.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(a,b){return{q:a,page_limit:10,page:b}},results:function(a,b){var c=10*b<a.total;return{results:a.roles,more:c}}},formatResult:function(a){return a.name+" type: "+a.type},formatSelection:function(a){return a.name},initSelection:function(a,b){var c=[];$(a.val().split(",")).each(function(){var a=this.split(":");c.push({id:a[0],name:a[1]})}),b(c)},initialData:g.join(","),dropdownCssClass:"bigdrop"},k={minimumInputLength:0,css:"modify_perm",multiple:!0,placeholder:"Click to select a role",container:f.$el.find("#modify_perm"),ajax:{url:Galaxy.root+"api/libraries/datasets/"+f.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(a,b){return{q:a,page_limit:10,page:b}},results:function(a,b){var c=10*b<a.total;return{results:a.roles,more:c}}},formatResult:function(a){return a.name+" type: "+a.type},formatSelection:function(a){return a.name},initSelection:function(a,b){var c=[];$(a.val().split(",")).each(function(){var a=this.split(":");c.push({id:a[0],name:a[1]})}),b(c)},initialData:h.join(","),dropdownCssClass:"bigdrop"},l={minimumInputLength:0,css:"manage_perm",multiple:!0,placeholder:"Click to select a role",container:f.$el.find("#manage_perm"),ajax:{url:Galaxy.root+"api/libraries/datasets/"+f.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(a,b){return{q:a,page_limit:10,page:b}},results:function(a,b){var c=10*b<a.total;return{results:a.roles,more:c}}},formatResult:function(a){return a.name+" type: "+a.type},formatSelection:function(a){return a.name},initSelection:function(a,b){var c=[];$(a.val().split(",")).each(function(){var a=this.split(":");c.push({id:a[0],name:a[1]})}),b(c)},initialData:i.join(","),dropdownCssClass:"bigdrop"};f.accessSelectObject=new d.View(j),f.modifySelectObject=new d.View(k),f.manageSelectObject=new d.View(l)}else{var m=f.templateAccessSelect();$.get(Galaxy.root+"api/libraries/datasets/"+f.id+"/permissions?scope=available",function(a){$(".access_perm").html(m({options:a.roles})),f.accessSelectObject=$("#access_select").select2()}).fail(function(){a.error("An error occurred while attempting to fetch dataset permissions.")})}},comingSoon:function(){a.warning("Feature coming soon.")},copyToClipboard:function(){var a=Backbone.history.location.href;-1!==a.lastIndexOf("/permissions")&&(a=a.substr(0,a.lastIndexOf("/permissions"))),window.prompt("Copy to clipboard: Ctrl+C, Enter",a)},makeDatasetPrivate:function(){var b=this;$.post(Galaxy.root+"api/libraries/datasets/"+b.id+"/permissions?action=make_private").done(function(c){b.model.set({is_unrestricted:!1}),b.showPermissions({fetched_permissions:c}),a.success("The dataset is now private to you.")}).fail(function(){a.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var b=this;$.post(Galaxy.root+"api/libraries/datasets/"+b.id+"/permissions?action=remove_restrictions").done(function(c){b.model.set({is_unrestricted:!0}),b.showPermissions({fetched_permissions:c}),a.success("Access to this dataset is now unrestricted.")}).fail(function(){a.error("An error occurred while attempting to make dataset unrestricted.")})},_extractIds:function(a){ids_list=[];for(var b=a.length-1;b>=0;b--)ids_list.push(a[b].id);return ids_list},savePermissions:function(){var b=this,c=this._extractIds(this.accessSelectObject.$el.select2("data")),d=this._extractIds(this.manageSelectObject.$el.select2("data")),e=this._extractIds(this.modifySelectObject.$el.select2("data"));$.post(Galaxy.root+"api/libraries/datasets/"+b.id+"/permissions?action=set_permissions",{"access_ids[]":c,"manage_ids[]":d,"modify_ids[]":e}).done(function(c){b.showPermissions({fetched_permissions:c}),a.success("Permissions saved.")}).fail(function(){a.error("An error occurred while attempting to set dataset permissions.")})},fetchExtAndGenomes:function(){var a=this;c.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(b){for(key in b)a.list_extensions.push({id:b[key].extension,text:b[key].extension,description:b[key].description,description_url:b[key].description_url});a.list_extensions.sort(function(a,b){return a.id>b.id?1:a.id<b.id?-1:0}),a.list_extensions.unshift(a.auto)}}),c.get({url:Galaxy.root+"api/genomes",success:function(b){for(key in b)a.list_genomes.push({id:b[key][1],text:b[key][0]});a.list_genomes.sort(function(a,b){return a.id>b.id?1:a.id<b.id?-1:0})}})},renderSelectBoxes:function(a){var b="?",c="auto";"undefined"!=typeof a&&("undefined"!=typeof a.genome_build&&(b=a.genome_build),"undefined"!=typeof a.file_ext&&(c=a.file_ext));var e=this;this.select_genome=new d.View({css:"dataset-genome-select",data:e.list_genomes,container:e.$el.find("#dataset_genome_select"),value:b}),this.select_extension=new d.View({css:"dataset-extension-select",data:e.list_extensions,container:e.$el.find("#dataset_extension_select"),value:c})},templateDataset:function(){return _.template(['<div class="library_style_container">','<div id="library_toolbar">','<button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button toolbar-item" type="button">','<span class="fa fa-download"></span>',"&nbsp;Download","</button>",'<button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button toolbar-item" type="button">','<span class="fa fa-book"></span>',"&nbsp;to History","</button>",'<% if (item.get("can_user_modify")) { %>','<button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button toolbar-item" type="button">','<span class="fa fa-pencil"></span>',"&nbsp;Modify","</button>","<% } %>",'<% if (item.get("can_user_manage")) { %>','<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions">','<button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button toolbar-item" type="button">','<span class="fa fa-group"></span>',"&nbsp;Permissions","</button>","</a>","<% } %>","</div>",'<ol class="breadcrumb">','<li><a title="Return to the list of libraries" href="#">Libraries</a></li>','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'<li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',"<% } else { %>",'<li class="active"><span title="You are here"><%- path_item[1] %></span></li>',"<% } %>","<% }); %>","</ol>",'<% if (item.get("is_unrestricted")) { %>','<div class="alert alert-info">',"This dataset is unrestricted so everybody can access it. Just share the URL of this page. ",'<button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button">','<span class="fa fa-clipboard"></span>',"&nbsp;To Clipboard","</button> ","</div>","<% } %>",'<div class="dataset_table">','<table class="grid table table-striped table-condensed">',"<tr>",'<th class="dataset-first-column" scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>','<td><%= _.escape(item.get("name")) %></td>',"</tr>",'<% if (item.get("file_ext")) { %>',"<tr>",'<th scope="row">Data type</th>','<td><%= _.escape(item.get("file_ext")) %></td>',"</tr>","<% } %>",'<% if (item.get("genome_build")) { %>',"<tr>",'<th scope="row">Genome build</th>','<td><%= _.escape(item.get("genome_build")) %></td>',"</tr>","<% } %>",'<% if (item.get("file_size")) { %>',"<tr>",'<th scope="row">Size</th>','<td><%= _.escape(item.get("file_size")) %></td>',"</tr>","<% } %>",'<% if (item.get("date_uploaded")) { %>',"<tr>",'<th scope="row">Date uploaded (UTC)</th>','<td><%= _.escape(item.get("date_uploaded")) %></td>',"</tr>","<% } %>",'<% if (item.get("uploaded_by")) { %>',"<tr>",'<th scope="row">Uploaded by</th>','<td><%= _.escape(item.get("uploaded_by")) %></td>',"</tr>","<% } %>",'<% if (item.get("metadata_data_lines")) { %>',"<tr>",'<th scope="row">Data Lines</th>','<td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>',"</tr>","<% } %>",'<% if (item.get("metadata_comment_lines")) { %>',"<tr>",'<th scope="row">Comment Lines</th>','<td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>',"</tr>","<% } %>",'<% if (item.get("metadata_columns")) { %>',"<tr>",'<th scope="row">Number of Columns</th>','<td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>',"</tr>","<% } %>",'<% if (item.get("metadata_column_types")) { %>',"<tr>",'<th scope="row">Column Types</th>','<td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>',"</tr>","<% } %>",'<% if (item.get("message")) { %>',"<tr>",'<th scope="row">Message</th>','<td scope="row"><%= _.escape(item.get("message")) %></td>',"</tr>","<% } %>",'<% if (item.get("misc_blurb")) { %>',"<tr>",'<th scope="row">Miscellaneous blurb</th>','<td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>',"</tr>","<% } %>",'<% if (item.get("misc_info")) { %>',"<tr>",'<th scope="row">Miscellaneous information</th>','<td scope="row"><%= _.escape(item.get("misc_info")) %></td>',"</tr>","<% } %>","</table>","<div>",'<pre class="peek">',"</pre>","</div>",'<% if (item.get("has_versions")) { %>',"<div>","<h3>Expired versions:</h3>","<ul>",'<% _.each(item.get("expired_versions"), function(version) { %>','<li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>',"<% }) %>","<ul>","</div>","<% } %>","</div>","</div>"].join(""))},templateVersion:function(){return _.template(['<div class="library_style_container">','<div id="library_toolbar">','<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>">','<button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button toolbar-item" type="button">','<span class="fa fa-caret-left fa-lg"></span>',"&nbsp;Latest dataset","</button>","<a>","</div>",'<ol class="breadcrumb">','<li><a title="Return to the list of libraries" href="#">Libraries</a></li>','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'<li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',"<% } else { %>",'<li class="active"><span title="You are here"><%- path_item[1] %></span></li>',"<% } %>","<% }); %>","</ol>",'<div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>','<div class="dataset_table">','<table class="grid table table-striped table-condensed">',"<tr>",'<th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>','<td><%= _.escape(ldda.get("name")) %></td>',"</tr>",'<% if (ldda.get("file_ext")) { %>',"<tr>",'<th scope="row">Data type</th>','<td><%= _.escape(ldda.get("file_ext")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("genome_build")) { %>',"<tr>",'<th scope="row">Genome build</th>','<td><%= _.escape(ldda.get("genome_build")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("file_size")) { %>',"<tr>",'<th scope="row">Size</th>','<td><%= _.escape(ldda.get("file_size")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("date_uploaded")) { %>',"<tr>",'<th scope="row">Date uploaded (UTC)</th>','<td><%= _.escape(ldda.get("date_uploaded")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("uploaded_by")) { %>',"<tr>",'<th scope="row">Uploaded by</th>','<td><%= _.escape(ldda.get("uploaded_by")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("metadata_data_lines")) { %>',"<tr>",'<th scope="row">Data Lines</th>','<td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("metadata_comment_lines")) { %>',"<tr>",'<th scope="row">Comment Lines</th>','<td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("metadata_columns")) { %>',"<tr>",'<th scope="row">Number of Columns</th>','<td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("metadata_column_types")) { %>',"<tr>",'<th scope="row">Column Types</th>','<td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("message")) { %>',"<tr>",'<th scope="row">Message</th>','<td scope="row"><%= _.escape(ldda.get("message")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("misc_blurb")) { %>',"<tr>",'<th scope="row">Miscellaneous blurb</th>','<td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("misc_info")) { %>',"<tr>",'<th scope="row">Miscellaneous information</th>','<td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>',"</tr>","<% } %>","</table>","<div>",'<pre class="peek">',"</pre>","</div>","</div>","</div>"].join(""))},templateModifyDataset:function(){return _.template(['<div class="library_style_container">','<div id="library_toolbar">','<button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button toolbar-item" type="button">','<span class="fa fa-times"></span>',"&nbsp;Cancel","</button>",'<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button toolbar-item" type="button">','<span class="fa fa-floppy-o"></span>',"&nbsp;Save","</button>","</div>",'<ol class="breadcrumb">','<li><a title="Return to the list of libraries" href="#">Libraries</a></li>','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'<li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',"<% } else { %>",'<li class="active"><span title="You are here"><%- path_item[1] %></span></li>',"<% } %>","<% }); %>","</ol>",'<div class="dataset_table">','<p>For full editing options please import the dataset to history and use "Edit attributes" on it.</p>','<table class="grid table table-striped table-condensed">',"<tr>",'<th class="dataset-first-column" scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>','<td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>',"</tr>","<tr>",'<th scope="row">Data type</th>',"<td>",'<span id="dataset_extension_select" class="dataset-extension-select" />',"</td>","</tr>","<tr>",'<th scope="row">Genome build</th>',"<td>",'<span id="dataset_genome_select" class="dataset-genome-select" />',"</td>","</tr>","<tr>",'<th scope="row">Size</th>','<td><%= _.escape(item.get("file_size")) %></td>',"</tr>","<tr>",'<th scope="row">Date uploaded (UTC)</th>','<td><%= _.escape(item.get("date_uploaded")) %></td>',"</tr>","<tr>",'<th scope="row">Uploaded by</th>','<td><%= _.escape(item.get("uploaded_by")) %></td>',"</tr>",'<tr scope="row">','<th scope="row">Data Lines</th>','<td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>',"</tr>",'<th scope="row">Comment Lines</th>','<% if (item.get("metadata_comment_lines") === "") { %>','<td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>',"<% } else { %>",'<td scope="row">unknown</td>',"<% } %>","</tr>","<tr>",'<th scope="row">Number of Columns</th>','<td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>',"</tr>","<tr>",'<th scope="row">Column Types</th>','<td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>',"</tr>","<tr>",'<th scope="row">Message</th>','<td scope="row"><%= _.escape(item.get("message")) %></td>',"</tr>","<tr>",'<th scope="row">Miscellaneous information</th>','<td scope="row"><%= _.escape(item.get("misc_info")) %></td>',"</tr>","<tr>",'<th scope="row">Miscellaneous blurb</th>','<td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>',"</tr>","</table>","<div>",'<pre class="peek">',"</pre>","</div>","</div>","</div>"].join(""))},templateDatasetPermissions:function(){return _.template(['<div class="library_style_container">','<div id="library_toolbar">','<a href="#folders/<%- item.get("folder_id") %>">','<button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button toolbar-item" type="button">','<span class="fa fa-folder-open-o"></span>',"&nbsp;Containing Folder","</button>","</a>",'<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>">','<button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button toolbar-item" type="button">','<span class="fa fa-file-o"></span>',"&nbsp;Dataset Details","</button>","<a>","</div>",'<ol class="breadcrumb">','<li><a title="Return to the list of libraries" href="#">Libraries</a></li>','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'<li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',"<% } else { %>",'<li class="active"><span title="You are here"><%- path_item[1] %></span></li>',"<% } %>","<% }); %>","</ol>",'<h1>Dataset: <%= _.escape(item.get("name")) %></h1>','<div class="alert alert-warning">',"<% if (is_admin) { %>","You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.","<% } else { %>","You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.","<% } %>","</div>",'<div class="dataset_table">',"<h2>Library-related permissions</h2>","<h4>Roles that can modify the library item</h4>",'<div id="modify_perm" class="modify_perm roles-selection"></div>','<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>',"<hr/>","<h2>Dataset-related permissions</h2>",'<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>','<% if (!item.get("is_unrestricted")) { %>',"<p>You can remove all access restrictions on this dataset. ",'<button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">','<span class="fa fa-globe"></span>',"&nbsp;Remove restrictions","</button>","</p>","<% } else { %>","This dataset is unrestricted so everybody can access it. Just share the URL of this page.",'<button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button">','<span class="fa fa-clipboard"></span>',"&nbsp;To Clipboard","</button>","<p>You can make this dataset private to you. ",'<button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button">','<span class="fa fa-key"></span>',"&nbsp;Make Private","</button>","</p>","<% } %>","<h4>Roles that can access the dataset</h4>",'<div id="access_perm" class="access_perm roles-selection"></div>','<div class="alert alert-info roles-selection">',"User has to have <strong>all these roles</strong> in order to access this dataset."," Users without access permission <strong>cannot</strong> have other permissions on this dataset."," If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.","</div>","<h4>Roles that can manage permissions on the dataset</h4>",'<div id="manage_perm" class="manage_perm roles-selection"></div>','<div class="alert alert-info roles-selection">',"User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.","</div>",'<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button">','<span class="fa fa-floppy-o"></span>',"&nbsp;Save","</button>","</div>","</div>"].join(""))},templateBulkImportInModal:function(){return _.template(['<span class="library-modal-item">',"Select history: ",'<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ',"<% _.each(histories, function(history) { %>",'<option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>',"<% }); %>","</select>","</span>"].join(""))},templateAccessSelect:function(){return _.template(['<select id="access_select" multiple>',"<% _.each(options, function(option) { %>",'<option value="<%- option.name %>"><%- option.name %></option>',"<% }); %>","</select>"].join(""))}});return{LibraryDatasetView:e}});
+define(["libs/toastr","mvc/library/library-model","utils/utils","mvc/ui/ui-select"],function(a,b,c,d){var e=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon"},select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(a){this.options=_.extend(this.options,a),this.fetchExtAndGenomes(),this.options.id&&this.fetchDataset()},fetchDataset:function(c){this.options=_.extend(this.options,c),this.model=new b.Item({id:this.options.id});var d=this;this.model.fetch({success:function(){d.options.show_permissions?d.showPermissions():d.options.show_version?d.fetchVersion():d.render()},error:function(b,c){"undefined"!=typeof c.responseJSON?a.error(c.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}}):a.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}})},render:function(a){this.options=_.extend(this.options,a),$(".tooltip").remove();var b=this.templateDataset();this.$el.html(b({item:this.model})),$(".peek").html(this.model.get("peek")),$("#center [data-toggle]").tooltip()},fetchVersion:function(c){this.options=_.extend(this.options,c),that=this,this.options.ldda_id?(this.ldda=new b.Ldda({id:this.options.ldda_id}),this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id,this.ldda.fetch({success:function(){that.renderVersion()},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?c.responseJSON.err_msg:"An error ocurred.")}})):(this.render(),a.error("Library dataset version requested but no id provided."))},renderVersion:function(){$(".tooltip").remove();var a=this.templateVersion();this.$el.html(a({item:this.model,ldda:this.ldda})),$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var a=this.templateModifyDataset();this.$el.html(a({item:this.model})),this.renderSelectBoxes({genome_build:this.model.get("genome_build"),file_ext:this.model.get("file_ext")}),$(".peek").html(this.model.get("peek")),$("#center [data-toggle]").tooltip()},downloadDataset:function(){var a=Galaxy.root+"api/libraries/datasets/download/uncompressed",b={ld_ids:this.id};this.processDownload(a,b)},processDownload:function(b,c,d){if(b&&c){c="string"==typeof c?c:$.param(c);var e="";$.each(c.split("&"),function(){var a=this.split("=");e+='<input type="hidden" name="'+a[0]+'" value="'+a[1]+'" />'}),$('<form action="'+b+'" method="'+(d||"post")+'">'+e+"</form>").appendTo("body").submit().remove(),a.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(a){var b=a.templateBulkImportInModal();a.modal=Galaxy.modal,a.modal.show({closing_events:!0,title:"Import into History",body:b({histories:a.histories.models}),buttons:{Import:function(){a.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(c){var d=this;this.histories=new b.GalaxyHistories,this.histories.fetch({success:function(b){0===b.length?a.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location="/"}}):c(d)},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?c.responseJSON.err_msg:"An error ocurred.")}})},importCurrentIntoHistory:function(){this.modal.disableButton("Import");var b=this.modal.$("input[name=history_name]").val(),c=this;if(""!==b)$.post(Galaxy.root+"api/histories",{name:b}).done(function(a){c.processImportToHistory(a.id,a.name)}).fail(function(){a.error("An error ocurred.")}).always(function(){c.modal.enableButton("Import")});else{var d=$(this.modal.$el).find("select[name=dataset_import_single] option:selected").val();this.processImportToHistory(d),this.modal.enableButton("Import")}},processImportToHistory:function(c){var d=new b.HistoryItem;d.url=d.urlRoot+c+"/contents",jQuery.getJSON(Galaxy.root+"history/set_as_current?id="+c),d.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide(),a.success("Dataset imported. Click this to start analyzing it.","",{onclick:function(){window.location="/"}})},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?"Dataset not imported. "+c.responseJSON.err_msg:"An error occured. Dataset not imported. Please try again.")}})},shareDataset:function(){a.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(b){this.options=_.extend(this.options,b),$(".tooltip").remove(),void 0!==this.options.fetched_permissions&&this.model.set(0===this.options.fetched_permissions.access_dataset_roles.length?{is_unrestricted:!0}:{is_unrestricted:!1});var c=!1;Galaxy.user&&(c=Galaxy.user.isAdmin());var d=this.templateDatasetPermissions();this.$el.html(d({item:this.model,is_admin:c}));var e=this;void 0===this.options.fetched_permissions?$.get(Galaxy.root+"api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(a){e.prepareSelectBoxes({fetched_permissions:a,is_admin:c})}).fail(function(){a.error("An error occurred while attempting to fetch dataset permissions.")}):this.prepareSelectBoxes({is_admin:c}),$("#center [data-toggle]").tooltip(),$("#center").css("overflow","auto")},_serializeRoles:function(a){for(var b=[],c=0;c<a.length;c++)b.push(a[c][1]+":"+a[c][0]);return b},prepareSelectBoxes:function(b){this.options=_.extend(this.options,b);var c=this.options.fetched_permissions,e=this.options.is_admin,f=this,g=[],h=[],i=[];if(g=this._serializeRoles(c.access_dataset_roles),h=this._serializeRoles(c.modify_item_roles),i=this._serializeRoles(c.manage_dataset_roles),e){var j={minimumInputLength:0,css:"access_perm",multiple:!0,placeholder:"Click to select a role",container:f.$el.find("#access_perm"),ajax:{url:Galaxy.root+"api/libraries/datasets/"+f.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(a,b){return{q:a,page_limit:10,page:b}},results:function(a,b){var c=10*b<a.total;return{results:a.roles,more:c}}},formatResult:function(a){return a.name+" type: "+a.type},formatSelection:function(a){return a.name},initSelection:function(a,b){var c=[];$(a.val().split(",")).each(function(){var a=this.split(":");c.push({id:a[0],name:a[1]})}),b(c)},initialData:g.join(","),dropdownCssClass:"bigdrop"},k={minimumInputLength:0,css:"modify_perm",multiple:!0,placeholder:"Click to select a role",container:f.$el.find("#modify_perm"),ajax:{url:Galaxy.root+"api/libraries/datasets/"+f.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(a,b){return{q:a,page_limit:10,page:b}},results:function(a,b){var c=10*b<a.total;return{results:a.roles,more:c}}},formatResult:function(a){return a.name+" type: "+a.type},formatSelection:function(a){return a.name},initSelection:function(a,b){var c=[];$(a.val().split(",")).each(function(){var a=this.split(":");c.push({id:a[0],name:a[1]})}),b(c)},initialData:h.join(","),dropdownCssClass:"bigdrop"},l={minimumInputLength:0,css:"manage_perm",multiple:!0,placeholder:"Click to select a role",container:f.$el.find("#manage_perm"),ajax:{url:Galaxy.root+"api/libraries/datasets/"+f.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(a,b){return{q:a,page_limit:10,page:b}},results:function(a,b){var c=10*b<a.total;return{results:a.roles,more:c}}},formatResult:function(a){return a.name+" type: "+a.type},formatSelection:function(a){return a.name},initSelection:function(a,b){var c=[];$(a.val().split(",")).each(function(){var a=this.split(":");c.push({id:a[0],name:a[1]})}),b(c)},initialData:i.join(","),dropdownCssClass:"bigdrop"};f.accessSelectObject=new d.View(j),f.modifySelectObject=new d.View(k),f.manageSelectObject=new d.View(l)}else{var m=f.templateAccessSelect();$.get(Galaxy.root+"api/libraries/datasets/"+f.id+"/permissions?scope=available",function(a){$(".access_perm").html(m({options:a.roles})),f.accessSelectObject=$("#access_select").select2()}).fail(function(){a.error("An error occurred while attempting to fetch dataset permissions.")})}},comingSoon:function(){a.warning("Feature coming soon.")},copyToClipboard:function(){var a=Backbone.history.location.href;-1!==a.lastIndexOf("/permissions")&&(a=a.substr(0,a.lastIndexOf("/permissions"))),window.prompt("Copy to clipboard: Ctrl+C, Enter",a)},makeDatasetPrivate:function(){var b=this;$.post(Galaxy.root+"api/libraries/datasets/"+b.id+"/permissions?action=make_private").done(function(c){b.model.set({is_unrestricted:!1}),b.showPermissions({fetched_permissions:c}),a.success("The dataset is now private to you.")}).fail(function(){a.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var b=this;$.post(Galaxy.root+"api/libraries/datasets/"+b.id+"/permissions?action=remove_restrictions").done(function(c){b.model.set({is_unrestricted:!0}),b.showPermissions({fetched_permissions:c}),a.success("Access to this dataset is now unrestricted.")}).fail(function(){a.error("An error occurred while attempting to make dataset unrestricted.")})},_extractIds:function(a){ids_list=[];for(var b=a.length-1;b>=0;b--)ids_list.push(a[b].id);return ids_list},savePermissions:function(){var b=this,c=this._extractIds(this.accessSelectObject.$el.select2("data")),d=this._extractIds(this.manageSelectObject.$el.select2("data")),e=this._extractIds(this.modifySelectObject.$el.select2("data"));$.post(Galaxy.root+"api/libraries/datasets/"+b.id+"/permissions?action=set_permissions",{"access_ids[]":c,"manage_ids[]":d,"modify_ids[]":e}).done(function(c){b.showPermissions({fetched_permissions:c}),a.success("Permissions saved.")}).fail(function(){a.error("An error occurred while attempting to set dataset permissions.")})},fetchExtAndGenomes:function(){var a=this;c.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(b){for(key in b)a.list_extensions.push({id:b[key].extension,text:b[key].extension,description:b[key].description,description_url:b[key].description_url});a.list_extensions.sort(function(a,b){return a.id>b.id?1:a.id<b.id?-1:0}),a.list_extensions.unshift(a.auto)}}),c.get({url:Galaxy.root+"api/genomes",success:function(b){for(key in b)a.list_genomes.push({id:b[key][1],text:b[key][0]});a.list_genomes.sort(function(a,b){return a.id>b.id?1:a.id<b.id?-1:0})}})},renderSelectBoxes:function(a){var b="?",c="auto";"undefined"!=typeof a&&("undefined"!=typeof a.genome_build&&(b=a.genome_build),"undefined"!=typeof a.file_ext&&(c=a.file_ext));var e=this;this.select_genome=new d.View({css:"dataset-genome-select",data:e.list_genomes,container:e.$el.find("#dataset_genome_select"),value:b}),this.select_extension=new d.View({css:"dataset-extension-select",data:e.list_extensions,container:e.$el.find("#dataset_extension_select"),value:c})},templateDataset:function(){return _.template(['<div class="library_style_container">','<div id="library_toolbar">','<button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button toolbar-item" type="button">','<span class="fa fa-download"></span>',"&nbsp;Download","</button>",'<button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button toolbar-item" type="button">','<span class="fa fa-book"></span>',"&nbsp;to History","</button>",'<% if (item.get("can_user_modify")) { %>','<button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button toolbar-item" type="button">','<span class="fa fa-pencil"></span>',"&nbsp;Modify","</button>","<% } %>",'<% if (item.get("can_user_manage")) { %>','<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions">','<button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button toolbar-item" type="button">','<span class="fa fa-group"></span>',"&nbsp;Permissions","</button>","</a>","<% } %>","</div>",'<ol class="breadcrumb">','<li><a title="Return to the list of libraries" href="#">Libraries</a></li>','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'<li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',"<% } else { %>",'<li class="active"><span title="You are here"><%- path_item[1] %></span></li>',"<% } %>","<% }); %>","</ol>",'<% if (item.get("is_unrestricted")) { %>','<div class="alert alert-info">',"This dataset is unrestricted so everybody can access it. Just share the URL of this page. ",'<button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button">','<span class="fa fa-clipboard"></span>',"&nbsp;To Clipboard","</button> ","</div>","<% } %>",'<div class="dataset_table">','<table class="grid table table-striped table-condensed">',"<tr>",'<th class="dataset-first-column" scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>','<td><%= _.escape(item.get("name")) %></td>',"</tr>",'<% if (item.get("file_ext")) { %>',"<tr>",'<th scope="row">Data type</th>','<td><%= _.escape(item.get("file_ext")) %></td>',"</tr>","<% } %>",'<% if (item.get("genome_build")) { %>',"<tr>",'<th scope="row">Genome build</th>','<td><%= _.escape(item.get("genome_build")) %></td>',"</tr>","<% } %>",'<% if (item.get("file_size")) { %>',"<tr>",'<th scope="row">Size</th>','<td><%= _.escape(item.get("file_size")) %></td>',"</tr>","<% } %>",'<% if (item.get("date_uploaded")) { %>',"<tr>",'<th scope="row">Date uploaded (UTC)</th>','<td><%= _.escape(item.get("date_uploaded")) %></td>',"</tr>","<% } %>",'<% if (item.get("uploaded_by")) { %>',"<tr>",'<th scope="row">Uploaded by</th>','<td><%= _.escape(item.get("uploaded_by")) %></td>',"</tr>","<% } %>",'<% if (item.get("metadata_data_lines")) { %>',"<tr>",'<th scope="row">Data Lines</th>','<td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>',"</tr>","<% } %>",'<% if (item.get("metadata_comment_lines")) { %>',"<tr>",'<th scope="row">Comment Lines</th>','<td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>',"</tr>","<% } %>",'<% if (item.get("metadata_columns")) { %>',"<tr>",'<th scope="row">Number of Columns</th>','<td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>',"</tr>","<% } %>",'<% if (item.get("metadata_column_types")) { %>',"<tr>",'<th scope="row">Column Types</th>','<td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>',"</tr>","<% } %>",'<% if (item.get("message")) { %>',"<tr>",'<th scope="row">Message</th>','<td scope="row"><%= _.escape(item.get("message")) %></td>',"</tr>","<% } %>",'<% if (item.get("misc_blurb")) { %>',"<tr>",'<th scope="row">Miscellaneous blurb</th>','<td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>',"</tr>","<% } %>",'<% if (item.get("misc_info")) { %>',"<tr>",'<th scope="row">Miscellaneous information</th>','<td scope="row"><%= _.escape(item.get("misc_info")) %></td>',"</tr>","<% } %>","</table>","<div>",'<pre class="peek">',"</pre>","</div>",'<% if (item.get("has_versions")) { %>',"<div>","<h3>Expired versions:</h3>","<ul>",'<% _.each(item.get("expired_versions"), function(version) { %>','<li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>',"<% }) %>","<ul>","</div>","<% } %>","</div>","</div>"].join(""))},templateVersion:function(){return _.template(['<div class="library_style_container">','<div id="library_toolbar">','<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>">','<button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button toolbar-item" type="button">','<span class="fa fa-caret-left fa-lg"></span>',"&nbsp;Latest dataset","</button>","<a>","</div>",'<ol class="breadcrumb">','<li><a title="Return to the list of libraries" href="#">Libraries</a></li>','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'<li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',"<% } else { %>",'<li class="active"><span title="You are here"><%- path_item[1] %></span></li>',"<% } %>","<% }); %>","</ol>",'<div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>','<div class="dataset_table">','<table class="grid table table-striped table-condensed">',"<tr>",'<th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>','<td><%= _.escape(ldda.get("name")) %></td>',"</tr>",'<% if (ldda.get("file_ext")) { %>',"<tr>",'<th scope="row">Data type</th>','<td><%= _.escape(ldda.get("file_ext")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("genome_build")) { %>',"<tr>",'<th scope="row">Genome build</th>','<td><%= _.escape(ldda.get("genome_build")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("file_size")) { %>',"<tr>",'<th scope="row">Size</th>','<td><%= _.escape(ldda.get("file_size")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("date_uploaded")) { %>',"<tr>",'<th scope="row">Date uploaded (UTC)</th>','<td><%= _.escape(ldda.get("date_uploaded")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("uploaded_by")) { %>',"<tr>",'<th scope="row">Uploaded by</th>','<td><%= _.escape(ldda.get("uploaded_by")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("metadata_data_lines")) { %>',"<tr>",'<th scope="row">Data Lines</th>','<td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("metadata_comment_lines")) { %>',"<tr>",'<th scope="row">Comment Lines</th>','<td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("metadata_columns")) { %>',"<tr>",'<th scope="row">Number of Columns</th>','<td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("metadata_column_types")) { %>',"<tr>",'<th scope="row">Column Types</th>','<td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("message")) { %>',"<tr>",'<th scope="row">Message</th>','<td scope="row"><%= _.escape(ldda.get("message")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("misc_blurb")) { %>',"<tr>",'<th scope="row">Miscellaneous blurb</th>','<td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("misc_info")) { %>',"<tr>",'<th scope="row">Miscellaneous information</th>','<td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>',"</tr>","<% } %>","</table>","<div>",'<pre class="peek">',"</pre>","</div>","</div>","</div>"].join(""))},templateModifyDataset:function(){return _.template(['<div class="library_style_container">','<div id="library_toolbar">','<button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button toolbar-item" type="button">','<span class="fa fa-times"></span>',"&nbsp;Cancel","</button>",'<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button toolbar-item" type="button">','<span class="fa fa-floppy-o"></span>',"&nbsp;Save","</button>","</div>",'<ol class="breadcrumb">','<li><a title="Return to the list of libraries" href="#">Libraries</a></li>','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'<li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',"<% } else { %>",'<li class="active"><span title="You are here"><%- path_item[1] %></span></li>',"<% } %>","<% }); %>","</ol>",'<div class="dataset_table">','<p>For full editing options please import the dataset to history and use "Edit attributes" on it.</p>','<table class="grid table table-striped table-condensed">',"<tr>",'<th class="dataset-first-column" scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>','<td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>',"</tr>","<tr>",'<th scope="row">Data type</th>',"<td>",'<span id="dataset_extension_select" class="dataset-extension-select" />',"</td>","</tr>","<tr>",'<th scope="row">Genome build</th>',"<td>",'<span id="dataset_genome_select" class="dataset-genome-select" />',"</td>","</tr>","<tr>",'<th scope="row">Size</th>','<td><%= _.escape(item.get("file_size")) %></td>',"</tr>","<tr>",'<th scope="row">Date uploaded (UTC)</th>','<td><%= _.escape(item.get("date_uploaded")) %></td>',"</tr>","<tr>",'<th scope="row">Uploaded by</th>','<td><%= _.escape(item.get("uploaded_by")) %></td>',"</tr>",'<tr scope="row">','<th scope="row">Data Lines</th>','<td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>',"</tr>",'<th scope="row">Comment Lines</th>','<% if (item.get("metadata_comment_lines") === "") { %>','<td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>',"<% } else { %>",'<td scope="row">unknown</td>',"<% } %>","</tr>","<tr>",'<th scope="row">Number of Columns</th>','<td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>',"</tr>","<tr>",'<th scope="row">Column Types</th>','<td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>',"</tr>","<tr>",'<th scope="row">Message</th>','<td scope="row"><%= _.escape(item.get("message")) %></td>',"</tr>","<tr>",'<th scope="row">Miscellaneous information</th>','<td scope="row"><%= _.escape(item.get("misc_info")) %></td>',"</tr>","<tr>",'<th scope="row">Miscellaneous blurb</th>','<td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>',"</tr>","</table>","<div>",'<pre class="peek">',"</pre>","</div>","</div>","</div>"].join(""))},templateDatasetPermissions:function(){return _.template(['<div class="library_style_container">','<div id="library_toolbar">','<a href="#folders/<%- item.get("folder_id") %>">','<button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button toolbar-item" type="button">','<span class="fa fa-folder-open-o"></span>',"&nbsp;Containing Folder","</button>","</a>",'<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>">','<button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button toolbar-item" type="button">','<span class="fa fa-file-o"></span>',"&nbsp;Dataset Details","</button>","<a>","</div>",'<ol class="breadcrumb">','<li><a title="Return to the list of libraries" href="#">Libraries</a></li>','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'<li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',"<% } else { %>",'<li class="active"><span title="You are here"><%- path_item[1] %></span></li>',"<% } %>","<% }); %>","</ol>",'<h1>Dataset: <%= _.escape(item.get("name")) %></h1>','<div class="alert alert-warning">',"<% if (is_admin) { %>","You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.","<% } else { %>","You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.","<% } %>","</div>",'<div class="dataset_table">',"<h2>Library-related permissions</h2>","<h4>Roles that can modify the library item</h4>",'<div id="modify_perm" class="modify_perm roles-selection"></div>','<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>',"<hr/>","<h2>Dataset-related permissions</h2>",'<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>','<% if (!item.get("is_unrestricted")) { %>',"<p>You can remove all access restrictions on this dataset. ",'<button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">','<span class="fa fa-globe"></span>',"&nbsp;Remove restrictions","</button>","</p>","<% } else { %>","This dataset is unrestricted so everybody can access it. Just share the URL of this page.",'<button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button">','<span class="fa fa-clipboard"></span>',"&nbsp;To Clipboard","</button>","<p>You can make this dataset private to you. ",'<button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button">','<span class="fa fa-key"></span>',"&nbsp;Make Private","</button>","</p>","<% } %>","<h4>Roles that can access the dataset</h4>",'<div id="access_perm" class="access_perm roles-selection"></div>','<div class="alert alert-info roles-selection">',"User has to have <strong>all these roles</strong> in order to access this dataset."," Users without access permission <strong>cannot</strong> have other permissions on this dataset."," If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.","</div>","<h4>Roles that can manage permissions on the dataset</h4>",'<div id="manage_perm" class="manage_perm roles-selection"></div>','<div class="alert alert-info roles-selection">',"User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.","</div>",'<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button">','<span class="fa fa-floppy-o"></span>',"&nbsp;Save","</button>","</div>","</div>"].join(""))},templateBulkImportInModal:function(){return _.template(["<div>",'<div class="library-modal-item">',"Select history: ",'<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; " autofocus>',"<% _.each(histories, function(history) { %>",'<option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>',"<% }); %>","</select>","</div>",'<div class="library-modal-item">',"or create new: ",'<input type="text" name="history_name" value="" placeholder="name of the new history" style="width:50%;">',"</input>","</div>","</div>"].join(""))},templateAccessSelect:function(){return _.template(['<select id="access_select" multiple>',"<% _.each(options, function(option) { %>",'<option value="<%- option.name %>"><%- option.name %></option>',"<% }); %>","</select>"].join(""))}});return{LibraryDatasetView:e}});
 //# sourceMappingURL=../../../maps/mvc/library/library-dataset-view.js.map
\ No newline at end of file

From 35ab333c7e74275a1b31b49a805036a1e09938ec Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Mon, 18 Apr 2016 15:18:50 -0400
Subject: [PATCH 2/3] remove old template

---
 .../scripts/mvc/library/library-dataset-view.js     | 13 -------------
 static/maps/mvc/library/library-dataset-view.js.map |  2 +-
 2 files changed, 1 insertion(+), 14 deletions(-)

diff --git a/client/galaxy/scripts/mvc/library/library-dataset-view.js b/client/galaxy/scripts/mvc/library/library-dataset-view.js
index 9fefb6128f8..53ae6dda2e0 100644
--- a/client/galaxy/scripts/mvc/library/library-dataset-view.js
+++ b/client/galaxy/scripts/mvc/library/library-dataset-view.js
@@ -1055,19 +1055,6 @@ var LibraryDatasetView = Backbone.View.extend({
     ].join(''));
   },
 
-  // templateBulkImportInModal: function(){
-  //   return _.template([
-  //   '<span class="library-modal-item">',
-  //     'Select history: ',
-  //     '<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ',
-  //       '<% _.each(histories, function(history) { %>', //history select btn
-  //         '<option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>',
-  //       '<% }); %>',
-  //     '</select>',
-  //   '</span>'
-  //   ].join(''));
-  // },
-
   templateBulkImportInModal : function(){
     return _.template([
     '<div>',
diff --git a/static/maps/mvc/library/library-dataset-view.js.map b/static/maps/mvc/library/library-dataset-view.js.map
index 6aa420c6f87..32a5397875a 100644
--- a/static/maps/mvc/library/library-dataset-view.js.map
+++ b/static/maps/mvc/library/library-dataset-view.js.map
@@ -1 +1 @@
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\ No newline at end of file

From 642fccd288415b36c2e8a1a725191e4480e2d6d9 Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Mon, 18 Apr 2016 15:27:36 -0400
Subject: [PATCH 3/3] do not pass variable that is not used

---
 client/galaxy/scripts/mvc/library/library-dataset-view.js | 6 +++---
 static/maps/mvc/library/library-dataset-view.js.map       | 2 +-
 static/scripts/mvc/library/library-dataset-view.js        | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/client/galaxy/scripts/mvc/library/library-dataset-view.js b/client/galaxy/scripts/mvc/library/library-dataset-view.js
index 53ae6dda2e0..81cb6fd4e3d 100644
--- a/client/galaxy/scripts/mvc/library/library-dataset-view.js
+++ b/client/galaxy/scripts/mvc/library/library-dataset-view.js
@@ -208,7 +208,7 @@ var LibraryDatasetView = Backbone.View.extend({
     if (new_history_name !== ''){
       $.post( Galaxy.root + 'api/histories', {name: new_history_name})
         .done(function( new_history ) {
-          that.processImportToHistory(new_history.id, new_history.name);
+          that.processImportToHistory(new_history.id);
         })
         .fail(function( xhr, status, error ) {
           mod_toastr.error('An error ocurred.');
@@ -218,7 +218,7 @@ var LibraryDatasetView = Backbone.View.extend({
         });
     } else {
       var history_id = $(this.modal.$el).find('select[name=dataset_import_single] option:selected').val();
-      this.processImportToHistory( history_id );
+      this.processImportToHistory(history_id);
       this.modal.enableButton('Import');
     }
   },
@@ -1055,7 +1055,7 @@ var LibraryDatasetView = Backbone.View.extend({
     ].join(''));
   },
 
-  templateBulkImportInModal : function(){
+  templateBulkImportInModal: function(){
     return _.template([
     '<div>',
       '<div class="library-modal-item">',
diff --git a/static/maps/mvc/library/library-dataset-view.js.map b/static/maps/mvc/library/library-dataset-view.js.map
index 32a5397875a..b163f68e290 100644
--- a/static/maps/mvc/library/library-dataset-view.js.map
+++ b/static/maps/mvc/library/library-dataset-view.js.map
@@ -1 +1 @@
-{"version":3,"file":"library-dataset-view.js","sources":["../../../src/mvc/library/library-dataset-view.js"],"names":["define","mod_toastr","mod_library_model","mod_utils","mod_select","LibraryDatasetView","Backbone","View","extend","el","model","options","events","click .toolbtn_modify_dataset","click .toolbtn_cancel_modifications","click .toolbtn-download-dataset","click .toolbtn-import-dataset","click .toolbtn-share-dataset","click .btn-copy-link-to-clipboard","click .btn-make-private","click .btn-remove-restrictions","click .toolbtn_save_permissions","click 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\ No newline at end of file
diff --git a/static/scripts/mvc/library/library-dataset-view.js b/static/scripts/mvc/library/library-dataset-view.js
index 50cd004f992..219bd8ea73c 100644
--- a/static/scripts/mvc/library/library-dataset-view.js
+++ b/static/scripts/mvc/library/library-dataset-view.js
@@ -1,2 +1,2 @@
-define(["libs/toastr","mvc/library/library-model","utils/utils","mvc/ui/ui-select"],function(a,b,c,d){var e=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon"},select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(a){this.options=_.extend(this.options,a),this.fetchExtAndGenomes(),this.options.id&&this.fetchDataset()},fetchDataset:function(c){this.options=_.extend(this.options,c),this.model=new b.Item({id:this.options.id});var d=this;this.model.fetch({success:function(){d.options.show_permissions?d.showPermissions():d.options.show_version?d.fetchVersion():d.render()},error:function(b,c){"undefined"!=typeof c.responseJSON?a.error(c.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}}):a.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}})},render:function(a){this.options=_.extend(this.options,a),$(".tooltip").remove();var b=this.templateDataset();this.$el.html(b({item:this.model})),$(".peek").html(this.model.get("peek")),$("#center [data-toggle]").tooltip()},fetchVersion:function(c){this.options=_.extend(this.options,c),that=this,this.options.ldda_id?(this.ldda=new b.Ldda({id:this.options.ldda_id}),this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id,this.ldda.fetch({success:function(){that.renderVersion()},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?c.responseJSON.err_msg:"An error ocurred.")}})):(this.render(),a.error("Library dataset version requested but no id provided."))},renderVersion:function(){$(".tooltip").remove();var a=this.templateVersion();this.$el.html(a({item:this.model,ldda:this.ldda})),$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var a=this.templateModifyDataset();this.$el.html(a({item:this.model})),this.renderSelectBoxes({genome_build:this.model.get("genome_build"),file_ext:this.model.get("file_ext")}),$(".peek").html(this.model.get("peek")),$("#center [data-toggle]").tooltip()},downloadDataset:function(){var a=Galaxy.root+"api/libraries/datasets/download/uncompressed",b={ld_ids:this.id};this.processDownload(a,b)},processDownload:function(b,c,d){if(b&&c){c="string"==typeof c?c:$.param(c);var e="";$.each(c.split("&"),function(){var a=this.split("=");e+='<input type="hidden" name="'+a[0]+'" value="'+a[1]+'" />'}),$('<form action="'+b+'" method="'+(d||"post")+'">'+e+"</form>").appendTo("body").submit().remove(),a.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(a){var b=a.templateBulkImportInModal();a.modal=Galaxy.modal,a.modal.show({closing_events:!0,title:"Import into History",body:b({histories:a.histories.models}),buttons:{Import:function(){a.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(c){var d=this;this.histories=new b.GalaxyHistories,this.histories.fetch({success:function(b){0===b.length?a.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location="/"}}):c(d)},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?c.responseJSON.err_msg:"An error ocurred.")}})},importCurrentIntoHistory:function(){this.modal.disableButton("Import");var b=this.modal.$("input[name=history_name]").val(),c=this;if(""!==b)$.post(Galaxy.root+"api/histories",{name:b}).done(function(a){c.processImportToHistory(a.id,a.name)}).fail(function(){a.error("An error ocurred.")}).always(function(){c.modal.enableButton("Import")});else{var d=$(this.modal.$el).find("select[name=dataset_import_single] option:selected").val();this.processImportToHistory(d),this.modal.enableButton("Import")}},processImportToHistory:function(c){var d=new b.HistoryItem;d.url=d.urlRoot+c+"/contents",jQuery.getJSON(Galaxy.root+"history/set_as_current?id="+c),d.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide(),a.success("Dataset imported. Click this to start analyzing it.","",{onclick:function(){window.location="/"}})},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?"Dataset not imported. "+c.responseJSON.err_msg:"An error occured. Dataset not imported. Please try again.")}})},shareDataset:function(){a.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(b){this.options=_.extend(this.options,b),$(".tooltip").remove(),void 0!==this.options.fetched_permissions&&this.model.set(0===this.options.fetched_permissions.access_dataset_roles.length?{is_unrestricted:!0}:{is_unrestricted:!1});var c=!1;Galaxy.user&&(c=Galaxy.user.isAdmin());var d=this.templateDatasetPermissions();this.$el.html(d({item:this.model,is_admin:c}));var e=this;void 0===this.options.fetched_permissions?$.get(Galaxy.root+"api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(a){e.prepareSelectBoxes({fetched_permissions:a,is_admin:c})}).fail(function(){a.error("An error occurred while attempting to fetch dataset permissions.")}):this.prepareSelectBoxes({is_admin:c}),$("#center [data-toggle]").tooltip(),$("#center").css("overflow","auto")},_serializeRoles:function(a){for(var b=[],c=0;c<a.length;c++)b.push(a[c][1]+":"+a[c][0]);return b},prepareSelectBoxes:function(b){this.options=_.extend(this.options,b);var c=this.options.fetched_permissions,e=this.options.is_admin,f=this,g=[],h=[],i=[];if(g=this._serializeRoles(c.access_dataset_roles),h=this._serializeRoles(c.modify_item_roles),i=this._serializeRoles(c.manage_dataset_roles),e){var j={minimumInputLength:0,css:"access_perm",multiple:!0,placeholder:"Click to select a role",container:f.$el.find("#access_perm"),ajax:{url:Galaxy.root+"api/libraries/datasets/"+f.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(a,b){return{q:a,page_limit:10,page:b}},results:function(a,b){var c=10*b<a.total;return{results:a.roles,more:c}}},formatResult:function(a){return a.name+" type: "+a.type},formatSelection:function(a){return a.name},initSelection:function(a,b){var c=[];$(a.val().split(",")).each(function(){var a=this.split(":");c.push({id:a[0],name:a[1]})}),b(c)},initialData:g.join(","),dropdownCssClass:"bigdrop"},k={minimumInputLength:0,css:"modify_perm",multiple:!0,placeholder:"Click to select a role",container:f.$el.find("#modify_perm"),ajax:{url:Galaxy.root+"api/libraries/datasets/"+f.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(a,b){return{q:a,page_limit:10,page:b}},results:function(a,b){var c=10*b<a.total;return{results:a.roles,more:c}}},formatResult:function(a){return a.name+" type: "+a.type},formatSelection:function(a){return a.name},initSelection:function(a,b){var c=[];$(a.val().split(",")).each(function(){var a=this.split(":");c.push({id:a[0],name:a[1]})}),b(c)},initialData:h.join(","),dropdownCssClass:"bigdrop"},l={minimumInputLength:0,css:"manage_perm",multiple:!0,placeholder:"Click to select a role",container:f.$el.find("#manage_perm"),ajax:{url:Galaxy.root+"api/libraries/datasets/"+f.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(a,b){return{q:a,page_limit:10,page:b}},results:function(a,b){var c=10*b<a.total;return{results:a.roles,more:c}}},formatResult:function(a){return a.name+" type: "+a.type},formatSelection:function(a){return a.name},initSelection:function(a,b){var c=[];$(a.val().split(",")).each(function(){var a=this.split(":");c.push({id:a[0],name:a[1]})}),b(c)},initialData:i.join(","),dropdownCssClass:"bigdrop"};f.accessSelectObject=new d.View(j),f.modifySelectObject=new d.View(k),f.manageSelectObject=new d.View(l)}else{var m=f.templateAccessSelect();$.get(Galaxy.root+"api/libraries/datasets/"+f.id+"/permissions?scope=available",function(a){$(".access_perm").html(m({options:a.roles})),f.accessSelectObject=$("#access_select").select2()}).fail(function(){a.error("An error occurred while attempting to fetch dataset permissions.")})}},comingSoon:function(){a.warning("Feature coming soon.")},copyToClipboard:function(){var a=Backbone.history.location.href;-1!==a.lastIndexOf("/permissions")&&(a=a.substr(0,a.lastIndexOf("/permissions"))),window.prompt("Copy to clipboard: Ctrl+C, Enter",a)},makeDatasetPrivate:function(){var b=this;$.post(Galaxy.root+"api/libraries/datasets/"+b.id+"/permissions?action=make_private").done(function(c){b.model.set({is_unrestricted:!1}),b.showPermissions({fetched_permissions:c}),a.success("The dataset is now private to you.")}).fail(function(){a.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var b=this;$.post(Galaxy.root+"api/libraries/datasets/"+b.id+"/permissions?action=remove_restrictions").done(function(c){b.model.set({is_unrestricted:!0}),b.showPermissions({fetched_permissions:c}),a.success("Access to this dataset is now unrestricted.")}).fail(function(){a.error("An error occurred while attempting to make dataset unrestricted.")})},_extractIds:function(a){ids_list=[];for(var b=a.length-1;b>=0;b--)ids_list.push(a[b].id);return ids_list},savePermissions:function(){var b=this,c=this._extractIds(this.accessSelectObject.$el.select2("data")),d=this._extractIds(this.manageSelectObject.$el.select2("data")),e=this._extractIds(this.modifySelectObject.$el.select2("data"));$.post(Galaxy.root+"api/libraries/datasets/"+b.id+"/permissions?action=set_permissions",{"access_ids[]":c,"manage_ids[]":d,"modify_ids[]":e}).done(function(c){b.showPermissions({fetched_permissions:c}),a.success("Permissions saved.")}).fail(function(){a.error("An error occurred while attempting to set dataset permissions.")})},fetchExtAndGenomes:function(){var a=this;c.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(b){for(key in b)a.list_extensions.push({id:b[key].extension,text:b[key].extension,description:b[key].description,description_url:b[key].description_url});a.list_extensions.sort(function(a,b){return a.id>b.id?1:a.id<b.id?-1:0}),a.list_extensions.unshift(a.auto)}}),c.get({url:Galaxy.root+"api/genomes",success:function(b){for(key in b)a.list_genomes.push({id:b[key][1],text:b[key][0]});a.list_genomes.sort(function(a,b){return a.id>b.id?1:a.id<b.id?-1:0})}})},renderSelectBoxes:function(a){var b="?",c="auto";"undefined"!=typeof a&&("undefined"!=typeof a.genome_build&&(b=a.genome_build),"undefined"!=typeof a.file_ext&&(c=a.file_ext));var e=this;this.select_genome=new d.View({css:"dataset-genome-select",data:e.list_genomes,container:e.$el.find("#dataset_genome_select"),value:b}),this.select_extension=new d.View({css:"dataset-extension-select",data:e.list_extensions,container:e.$el.find("#dataset_extension_select"),value:c})},templateDataset:function(){return _.template(['<div class="library_style_container">','<div id="library_toolbar">','<button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button toolbar-item" type="button">','<span class="fa fa-download"></span>',"&nbsp;Download","</button>",'<button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button toolbar-item" type="button">','<span class="fa fa-book"></span>',"&nbsp;to History","</button>",'<% if (item.get("can_user_modify")) { %>','<button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button toolbar-item" type="button">','<span class="fa fa-pencil"></span>',"&nbsp;Modify","</button>","<% } %>",'<% if (item.get("can_user_manage")) { %>','<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions">','<button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button toolbar-item" type="button">','<span class="fa fa-group"></span>',"&nbsp;Permissions","</button>","</a>","<% } %>","</div>",'<ol class="breadcrumb">','<li><a title="Return to the list of libraries" href="#">Libraries</a></li>','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'<li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',"<% } else { %>",'<li class="active"><span title="You are here"><%- path_item[1] %></span></li>',"<% } %>","<% }); %>","</ol>",'<% if (item.get("is_unrestricted")) { %>','<div class="alert alert-info">',"This dataset is unrestricted so everybody can access it. Just share the URL of this page. ",'<button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button">','<span class="fa fa-clipboard"></span>',"&nbsp;To Clipboard","</button> ","</div>","<% } %>",'<div class="dataset_table">','<table class="grid table table-striped table-condensed">',"<tr>",'<th class="dataset-first-column" scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>','<td><%= _.escape(item.get("name")) %></td>',"</tr>",'<% if (item.get("file_ext")) { %>',"<tr>",'<th scope="row">Data type</th>','<td><%= _.escape(item.get("file_ext")) %></td>',"</tr>","<% } %>",'<% if (item.get("genome_build")) { %>',"<tr>",'<th scope="row">Genome build</th>','<td><%= _.escape(item.get("genome_build")) %></td>',"</tr>","<% } %>",'<% if (item.get("file_size")) { %>',"<tr>",'<th scope="row">Size</th>','<td><%= _.escape(item.get("file_size")) %></td>',"</tr>","<% } %>",'<% if (item.get("date_uploaded")) { %>',"<tr>",'<th scope="row">Date uploaded (UTC)</th>','<td><%= _.escape(item.get("date_uploaded")) %></td>',"</tr>","<% } %>",'<% if (item.get("uploaded_by")) { %>',"<tr>",'<th scope="row">Uploaded by</th>','<td><%= _.escape(item.get("uploaded_by")) %></td>',"</tr>","<% } %>",'<% if (item.get("metadata_data_lines")) { %>',"<tr>",'<th scope="row">Data Lines</th>','<td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>',"</tr>","<% } %>",'<% if (item.get("metadata_comment_lines")) { %>',"<tr>",'<th scope="row">Comment Lines</th>','<td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>',"</tr>","<% } %>",'<% if (item.get("metadata_columns")) { %>',"<tr>",'<th scope="row">Number of Columns</th>','<td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>',"</tr>","<% } %>",'<% if (item.get("metadata_column_types")) { %>',"<tr>",'<th scope="row">Column Types</th>','<td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>',"</tr>","<% } %>",'<% if (item.get("message")) { %>',"<tr>",'<th scope="row">Message</th>','<td scope="row"><%= _.escape(item.get("message")) %></td>',"</tr>","<% } %>",'<% if (item.get("misc_blurb")) { %>',"<tr>",'<th scope="row">Miscellaneous blurb</th>','<td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>',"</tr>","<% } %>",'<% if (item.get("misc_info")) { %>',"<tr>",'<th scope="row">Miscellaneous information</th>','<td scope="row"><%= _.escape(item.get("misc_info")) %></td>',"</tr>","<% } %>","</table>","<div>",'<pre class="peek">',"</pre>","</div>",'<% if (item.get("has_versions")) { %>',"<div>","<h3>Expired versions:</h3>","<ul>",'<% _.each(item.get("expired_versions"), function(version) { %>','<li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>',"<% }) %>","<ul>","</div>","<% } %>","</div>","</div>"].join(""))},templateVersion:function(){return _.template(['<div class="library_style_container">','<div id="library_toolbar">','<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>">','<button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button toolbar-item" type="button">','<span class="fa fa-caret-left fa-lg"></span>',"&nbsp;Latest dataset","</button>","<a>","</div>",'<ol class="breadcrumb">','<li><a title="Return to the list of libraries" href="#">Libraries</a></li>','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'<li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',"<% } else { %>",'<li class="active"><span title="You are here"><%- path_item[1] %></span></li>',"<% } %>","<% }); %>","</ol>",'<div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>','<div class="dataset_table">','<table class="grid table table-striped table-condensed">',"<tr>",'<th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>','<td><%= _.escape(ldda.get("name")) %></td>',"</tr>",'<% if (ldda.get("file_ext")) { %>',"<tr>",'<th scope="row">Data type</th>','<td><%= _.escape(ldda.get("file_ext")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("genome_build")) { %>',"<tr>",'<th scope="row">Genome build</th>','<td><%= _.escape(ldda.get("genome_build")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("file_size")) { %>',"<tr>",'<th scope="row">Size</th>','<td><%= _.escape(ldda.get("file_size")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("date_uploaded")) { %>',"<tr>",'<th scope="row">Date uploaded (UTC)</th>','<td><%= _.escape(ldda.get("date_uploaded")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("uploaded_by")) { %>',"<tr>",'<th scope="row">Uploaded by</th>','<td><%= _.escape(ldda.get("uploaded_by")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("metadata_data_lines")) { %>',"<tr>",'<th scope="row">Data Lines</th>','<td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("metadata_comment_lines")) { %>',"<tr>",'<th scope="row">Comment Lines</th>','<td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("metadata_columns")) { %>',"<tr>",'<th scope="row">Number of Columns</th>','<td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("metadata_column_types")) { %>',"<tr>",'<th scope="row">Column Types</th>','<td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("message")) { %>',"<tr>",'<th scope="row">Message</th>','<td scope="row"><%= _.escape(ldda.get("message")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("misc_blurb")) { %>',"<tr>",'<th scope="row">Miscellaneous blurb</th>','<td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("misc_info")) { %>',"<tr>",'<th scope="row">Miscellaneous information</th>','<td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>',"</tr>","<% } %>","</table>","<div>",'<pre class="peek">',"</pre>","</div>","</div>","</div>"].join(""))},templateModifyDataset:function(){return _.template(['<div class="library_style_container">','<div id="library_toolbar">','<button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button toolbar-item" type="button">','<span class="fa fa-times"></span>',"&nbsp;Cancel","</button>",'<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button toolbar-item" type="button">','<span class="fa fa-floppy-o"></span>',"&nbsp;Save","</button>","</div>",'<ol class="breadcrumb">','<li><a title="Return to the list of libraries" href="#">Libraries</a></li>','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'<li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',"<% } else { %>",'<li class="active"><span title="You are here"><%- path_item[1] %></span></li>',"<% } %>","<% }); %>","</ol>",'<div class="dataset_table">','<p>For full editing options please import the dataset to history and use "Edit attributes" on it.</p>','<table class="grid table table-striped table-condensed">',"<tr>",'<th class="dataset-first-column" scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>','<td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>',"</tr>","<tr>",'<th scope="row">Data type</th>',"<td>",'<span id="dataset_extension_select" class="dataset-extension-select" />',"</td>","</tr>","<tr>",'<th scope="row">Genome build</th>',"<td>",'<span id="dataset_genome_select" class="dataset-genome-select" />',"</td>","</tr>","<tr>",'<th scope="row">Size</th>','<td><%= _.escape(item.get("file_size")) %></td>',"</tr>","<tr>",'<th scope="row">Date uploaded (UTC)</th>','<td><%= _.escape(item.get("date_uploaded")) %></td>',"</tr>","<tr>",'<th scope="row">Uploaded by</th>','<td><%= _.escape(item.get("uploaded_by")) %></td>',"</tr>",'<tr scope="row">','<th scope="row">Data Lines</th>','<td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>',"</tr>",'<th scope="row">Comment Lines</th>','<% if (item.get("metadata_comment_lines") === "") { %>','<td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>',"<% } else { %>",'<td scope="row">unknown</td>',"<% } %>","</tr>","<tr>",'<th scope="row">Number of Columns</th>','<td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>',"</tr>","<tr>",'<th scope="row">Column Types</th>','<td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>',"</tr>","<tr>",'<th scope="row">Message</th>','<td scope="row"><%= _.escape(item.get("message")) %></td>',"</tr>","<tr>",'<th scope="row">Miscellaneous information</th>','<td scope="row"><%= _.escape(item.get("misc_info")) %></td>',"</tr>","<tr>",'<th scope="row">Miscellaneous blurb</th>','<td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>',"</tr>","</table>","<div>",'<pre class="peek">',"</pre>","</div>","</div>","</div>"].join(""))},templateDatasetPermissions:function(){return _.template(['<div class="library_style_container">','<div id="library_toolbar">','<a href="#folders/<%- item.get("folder_id") %>">','<button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button toolbar-item" type="button">','<span class="fa fa-folder-open-o"></span>',"&nbsp;Containing Folder","</button>","</a>",'<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>">','<button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button toolbar-item" type="button">','<span class="fa fa-file-o"></span>',"&nbsp;Dataset Details","</button>","<a>","</div>",'<ol class="breadcrumb">','<li><a title="Return to the list of libraries" href="#">Libraries</a></li>','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'<li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',"<% } else { %>",'<li class="active"><span title="You are here"><%- path_item[1] %></span></li>',"<% } %>","<% }); %>","</ol>",'<h1>Dataset: <%= _.escape(item.get("name")) %></h1>','<div class="alert alert-warning">',"<% if (is_admin) { %>","You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.","<% } else { %>","You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.","<% } %>","</div>",'<div class="dataset_table">',"<h2>Library-related permissions</h2>","<h4>Roles that can modify the library item</h4>",'<div id="modify_perm" class="modify_perm roles-selection"></div>','<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>',"<hr/>","<h2>Dataset-related permissions</h2>",'<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>','<% if (!item.get("is_unrestricted")) { %>',"<p>You can remove all access restrictions on this dataset. ",'<button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">','<span class="fa fa-globe"></span>',"&nbsp;Remove restrictions","</button>","</p>","<% } else { %>","This dataset is unrestricted so everybody can access it. Just share the URL of this page.",'<button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button">','<span class="fa fa-clipboard"></span>',"&nbsp;To Clipboard","</button>","<p>You can make this dataset private to you. ",'<button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button">','<span class="fa fa-key"></span>',"&nbsp;Make Private","</button>","</p>","<% } %>","<h4>Roles that can access the dataset</h4>",'<div id="access_perm" class="access_perm roles-selection"></div>','<div class="alert alert-info roles-selection">',"User has to have <strong>all these roles</strong> in order to access this dataset."," Users without access permission <strong>cannot</strong> have other permissions on this dataset."," If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.","</div>","<h4>Roles that can manage permissions on the dataset</h4>",'<div id="manage_perm" class="manage_perm roles-selection"></div>','<div class="alert alert-info roles-selection">',"User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.","</div>",'<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button">','<span class="fa fa-floppy-o"></span>',"&nbsp;Save","</button>","</div>","</div>"].join(""))},templateBulkImportInModal:function(){return _.template(["<div>",'<div class="library-modal-item">',"Select history: ",'<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; " autofocus>',"<% _.each(histories, function(history) { %>",'<option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>',"<% }); %>","</select>","</div>",'<div class="library-modal-item">',"or create new: ",'<input type="text" name="history_name" value="" placeholder="name of the new history" style="width:50%;">',"</input>","</div>","</div>"].join(""))},templateAccessSelect:function(){return _.template(['<select id="access_select" multiple>',"<% _.each(options, function(option) { %>",'<option value="<%- option.name %>"><%- option.name %></option>',"<% }); %>","</select>"].join(""))}});return{LibraryDatasetView:e}});
+define(["libs/toastr","mvc/library/library-model","utils/utils","mvc/ui/ui-select"],function(a,b,c,d){var e=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon"},select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(a){this.options=_.extend(this.options,a),this.fetchExtAndGenomes(),this.options.id&&this.fetchDataset()},fetchDataset:function(c){this.options=_.extend(this.options,c),this.model=new b.Item({id:this.options.id});var d=this;this.model.fetch({success:function(){d.options.show_permissions?d.showPermissions():d.options.show_version?d.fetchVersion():d.render()},error:function(b,c){"undefined"!=typeof c.responseJSON?a.error(c.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}}):a.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}})},render:function(a){this.options=_.extend(this.options,a),$(".tooltip").remove();var b=this.templateDataset();this.$el.html(b({item:this.model})),$(".peek").html(this.model.get("peek")),$("#center [data-toggle]").tooltip()},fetchVersion:function(c){this.options=_.extend(this.options,c),that=this,this.options.ldda_id?(this.ldda=new b.Ldda({id:this.options.ldda_id}),this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id,this.ldda.fetch({success:function(){that.renderVersion()},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?c.responseJSON.err_msg:"An error ocurred.")}})):(this.render(),a.error("Library dataset version requested but no id provided."))},renderVersion:function(){$(".tooltip").remove();var a=this.templateVersion();this.$el.html(a({item:this.model,ldda:this.ldda})),$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var a=this.templateModifyDataset();this.$el.html(a({item:this.model})),this.renderSelectBoxes({genome_build:this.model.get("genome_build"),file_ext:this.model.get("file_ext")}),$(".peek").html(this.model.get("peek")),$("#center [data-toggle]").tooltip()},downloadDataset:function(){var a=Galaxy.root+"api/libraries/datasets/download/uncompressed",b={ld_ids:this.id};this.processDownload(a,b)},processDownload:function(b,c,d){if(b&&c){c="string"==typeof c?c:$.param(c);var e="";$.each(c.split("&"),function(){var a=this.split("=");e+='<input type="hidden" name="'+a[0]+'" value="'+a[1]+'" />'}),$('<form action="'+b+'" method="'+(d||"post")+'">'+e+"</form>").appendTo("body").submit().remove(),a.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(a){var b=a.templateBulkImportInModal();a.modal=Galaxy.modal,a.modal.show({closing_events:!0,title:"Import into History",body:b({histories:a.histories.models}),buttons:{Import:function(){a.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(c){var d=this;this.histories=new b.GalaxyHistories,this.histories.fetch({success:function(b){0===b.length?a.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location="/"}}):c(d)},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?c.responseJSON.err_msg:"An error ocurred.")}})},importCurrentIntoHistory:function(){this.modal.disableButton("Import");var b=this.modal.$("input[name=history_name]").val(),c=this;if(""!==b)$.post(Galaxy.root+"api/histories",{name:b}).done(function(a){c.processImportToHistory(a.id)}).fail(function(){a.error("An error ocurred.")}).always(function(){c.modal.enableButton("Import")});else{var d=$(this.modal.$el).find("select[name=dataset_import_single] option:selected").val();this.processImportToHistory(d),this.modal.enableButton("Import")}},processImportToHistory:function(c){var d=new b.HistoryItem;d.url=d.urlRoot+c+"/contents",jQuery.getJSON(Galaxy.root+"history/set_as_current?id="+c),d.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide(),a.success("Dataset imported. Click this to start analyzing it.","",{onclick:function(){window.location="/"}})},error:function(b,c){a.error("undefined"!=typeof c.responseJSON?"Dataset not imported. "+c.responseJSON.err_msg:"An error occured. Dataset not imported. Please try again.")}})},shareDataset:function(){a.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(b){this.options=_.extend(this.options,b),$(".tooltip").remove(),void 0!==this.options.fetched_permissions&&this.model.set(0===this.options.fetched_permissions.access_dataset_roles.length?{is_unrestricted:!0}:{is_unrestricted:!1});var c=!1;Galaxy.user&&(c=Galaxy.user.isAdmin());var d=this.templateDatasetPermissions();this.$el.html(d({item:this.model,is_admin:c}));var e=this;void 0===this.options.fetched_permissions?$.get(Galaxy.root+"api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(a){e.prepareSelectBoxes({fetched_permissions:a,is_admin:c})}).fail(function(){a.error("An error occurred while attempting to fetch dataset permissions.")}):this.prepareSelectBoxes({is_admin:c}),$("#center [data-toggle]").tooltip(),$("#center").css("overflow","auto")},_serializeRoles:function(a){for(var b=[],c=0;c<a.length;c++)b.push(a[c][1]+":"+a[c][0]);return b},prepareSelectBoxes:function(b){this.options=_.extend(this.options,b);var c=this.options.fetched_permissions,e=this.options.is_admin,f=this,g=[],h=[],i=[];if(g=this._serializeRoles(c.access_dataset_roles),h=this._serializeRoles(c.modify_item_roles),i=this._serializeRoles(c.manage_dataset_roles),e){var j={minimumInputLength:0,css:"access_perm",multiple:!0,placeholder:"Click to select a role",container:f.$el.find("#access_perm"),ajax:{url:Galaxy.root+"api/libraries/datasets/"+f.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(a,b){return{q:a,page_limit:10,page:b}},results:function(a,b){var c=10*b<a.total;return{results:a.roles,more:c}}},formatResult:function(a){return a.name+" type: "+a.type},formatSelection:function(a){return a.name},initSelection:function(a,b){var c=[];$(a.val().split(",")).each(function(){var a=this.split(":");c.push({id:a[0],name:a[1]})}),b(c)},initialData:g.join(","),dropdownCssClass:"bigdrop"},k={minimumInputLength:0,css:"modify_perm",multiple:!0,placeholder:"Click to select a role",container:f.$el.find("#modify_perm"),ajax:{url:Galaxy.root+"api/libraries/datasets/"+f.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(a,b){return{q:a,page_limit:10,page:b}},results:function(a,b){var c=10*b<a.total;return{results:a.roles,more:c}}},formatResult:function(a){return a.name+" type: "+a.type},formatSelection:function(a){return a.name},initSelection:function(a,b){var c=[];$(a.val().split(",")).each(function(){var a=this.split(":");c.push({id:a[0],name:a[1]})}),b(c)},initialData:h.join(","),dropdownCssClass:"bigdrop"},l={minimumInputLength:0,css:"manage_perm",multiple:!0,placeholder:"Click to select a role",container:f.$el.find("#manage_perm"),ajax:{url:Galaxy.root+"api/libraries/datasets/"+f.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(a,b){return{q:a,page_limit:10,page:b}},results:function(a,b){var c=10*b<a.total;return{results:a.roles,more:c}}},formatResult:function(a){return a.name+" type: "+a.type},formatSelection:function(a){return a.name},initSelection:function(a,b){var c=[];$(a.val().split(",")).each(function(){var a=this.split(":");c.push({id:a[0],name:a[1]})}),b(c)},initialData:i.join(","),dropdownCssClass:"bigdrop"};f.accessSelectObject=new d.View(j),f.modifySelectObject=new d.View(k),f.manageSelectObject=new d.View(l)}else{var m=f.templateAccessSelect();$.get(Galaxy.root+"api/libraries/datasets/"+f.id+"/permissions?scope=available",function(a){$(".access_perm").html(m({options:a.roles})),f.accessSelectObject=$("#access_select").select2()}).fail(function(){a.error("An error occurred while attempting to fetch dataset permissions.")})}},comingSoon:function(){a.warning("Feature coming soon.")},copyToClipboard:function(){var a=Backbone.history.location.href;-1!==a.lastIndexOf("/permissions")&&(a=a.substr(0,a.lastIndexOf("/permissions"))),window.prompt("Copy to clipboard: Ctrl+C, Enter",a)},makeDatasetPrivate:function(){var b=this;$.post(Galaxy.root+"api/libraries/datasets/"+b.id+"/permissions?action=make_private").done(function(c){b.model.set({is_unrestricted:!1}),b.showPermissions({fetched_permissions:c}),a.success("The dataset is now private to you.")}).fail(function(){a.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var b=this;$.post(Galaxy.root+"api/libraries/datasets/"+b.id+"/permissions?action=remove_restrictions").done(function(c){b.model.set({is_unrestricted:!0}),b.showPermissions({fetched_permissions:c}),a.success("Access to this dataset is now unrestricted.")}).fail(function(){a.error("An error occurred while attempting to make dataset unrestricted.")})},_extractIds:function(a){ids_list=[];for(var b=a.length-1;b>=0;b--)ids_list.push(a[b].id);return ids_list},savePermissions:function(){var b=this,c=this._extractIds(this.accessSelectObject.$el.select2("data")),d=this._extractIds(this.manageSelectObject.$el.select2("data")),e=this._extractIds(this.modifySelectObject.$el.select2("data"));$.post(Galaxy.root+"api/libraries/datasets/"+b.id+"/permissions?action=set_permissions",{"access_ids[]":c,"manage_ids[]":d,"modify_ids[]":e}).done(function(c){b.showPermissions({fetched_permissions:c}),a.success("Permissions saved.")}).fail(function(){a.error("An error occurred while attempting to set dataset permissions.")})},fetchExtAndGenomes:function(){var a=this;c.get({url:Galaxy.root+"api/datatypes?extension_only=False",success:function(b){for(key in b)a.list_extensions.push({id:b[key].extension,text:b[key].extension,description:b[key].description,description_url:b[key].description_url});a.list_extensions.sort(function(a,b){return a.id>b.id?1:a.id<b.id?-1:0}),a.list_extensions.unshift(a.auto)}}),c.get({url:Galaxy.root+"api/genomes",success:function(b){for(key in b)a.list_genomes.push({id:b[key][1],text:b[key][0]});a.list_genomes.sort(function(a,b){return a.id>b.id?1:a.id<b.id?-1:0})}})},renderSelectBoxes:function(a){var b="?",c="auto";"undefined"!=typeof a&&("undefined"!=typeof a.genome_build&&(b=a.genome_build),"undefined"!=typeof a.file_ext&&(c=a.file_ext));var e=this;this.select_genome=new d.View({css:"dataset-genome-select",data:e.list_genomes,container:e.$el.find("#dataset_genome_select"),value:b}),this.select_extension=new d.View({css:"dataset-extension-select",data:e.list_extensions,container:e.$el.find("#dataset_extension_select"),value:c})},templateDataset:function(){return _.template(['<div class="library_style_container">','<div id="library_toolbar">','<button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button toolbar-item" type="button">','<span class="fa fa-download"></span>',"&nbsp;Download","</button>",'<button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button toolbar-item" type="button">','<span class="fa fa-book"></span>',"&nbsp;to History","</button>",'<% if (item.get("can_user_modify")) { %>','<button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button toolbar-item" type="button">','<span class="fa fa-pencil"></span>',"&nbsp;Modify","</button>","<% } %>",'<% if (item.get("can_user_manage")) { %>','<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions">','<button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button toolbar-item" type="button">','<span class="fa fa-group"></span>',"&nbsp;Permissions","</button>","</a>","<% } %>","</div>",'<ol class="breadcrumb">','<li><a title="Return to the list of libraries" href="#">Libraries</a></li>','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'<li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',"<% } else { %>",'<li class="active"><span title="You are here"><%- path_item[1] %></span></li>',"<% } %>","<% }); %>","</ol>",'<% if (item.get("is_unrestricted")) { %>','<div class="alert alert-info">',"This dataset is unrestricted so everybody can access it. Just share the URL of this page. ",'<button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button">','<span class="fa fa-clipboard"></span>',"&nbsp;To Clipboard","</button> ","</div>","<% } %>",'<div class="dataset_table">','<table class="grid table table-striped table-condensed">',"<tr>",'<th class="dataset-first-column" scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>','<td><%= _.escape(item.get("name")) %></td>',"</tr>",'<% if (item.get("file_ext")) { %>',"<tr>",'<th scope="row">Data type</th>','<td><%= _.escape(item.get("file_ext")) %></td>',"</tr>","<% } %>",'<% if (item.get("genome_build")) { %>',"<tr>",'<th scope="row">Genome build</th>','<td><%= _.escape(item.get("genome_build")) %></td>',"</tr>","<% } %>",'<% if (item.get("file_size")) { %>',"<tr>",'<th scope="row">Size</th>','<td><%= _.escape(item.get("file_size")) %></td>',"</tr>","<% } %>",'<% if (item.get("date_uploaded")) { %>',"<tr>",'<th scope="row">Date uploaded (UTC)</th>','<td><%= _.escape(item.get("date_uploaded")) %></td>',"</tr>","<% } %>",'<% if (item.get("uploaded_by")) { %>',"<tr>",'<th scope="row">Uploaded by</th>','<td><%= _.escape(item.get("uploaded_by")) %></td>',"</tr>","<% } %>",'<% if (item.get("metadata_data_lines")) { %>',"<tr>",'<th scope="row">Data Lines</th>','<td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>',"</tr>","<% } %>",'<% if (item.get("metadata_comment_lines")) { %>',"<tr>",'<th scope="row">Comment Lines</th>','<td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>',"</tr>","<% } %>",'<% if (item.get("metadata_columns")) { %>',"<tr>",'<th scope="row">Number of Columns</th>','<td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>',"</tr>","<% } %>",'<% if (item.get("metadata_column_types")) { %>',"<tr>",'<th scope="row">Column Types</th>','<td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>',"</tr>","<% } %>",'<% if (item.get("message")) { %>',"<tr>",'<th scope="row">Message</th>','<td scope="row"><%= _.escape(item.get("message")) %></td>',"</tr>","<% } %>",'<% if (item.get("misc_blurb")) { %>',"<tr>",'<th scope="row">Miscellaneous blurb</th>','<td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>',"</tr>","<% } %>",'<% if (item.get("misc_info")) { %>',"<tr>",'<th scope="row">Miscellaneous information</th>','<td scope="row"><%= _.escape(item.get("misc_info")) %></td>',"</tr>","<% } %>","</table>","<div>",'<pre class="peek">',"</pre>","</div>",'<% if (item.get("has_versions")) { %>',"<div>","<h3>Expired versions:</h3>","<ul>",'<% _.each(item.get("expired_versions"), function(version) { %>','<li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>',"<% }) %>","<ul>","</div>","<% } %>","</div>","</div>"].join(""))},templateVersion:function(){return _.template(['<div class="library_style_container">','<div id="library_toolbar">','<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>">','<button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button toolbar-item" type="button">','<span class="fa fa-caret-left fa-lg"></span>',"&nbsp;Latest dataset","</button>","<a>","</div>",'<ol class="breadcrumb">','<li><a title="Return to the list of libraries" href="#">Libraries</a></li>','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'<li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',"<% } else { %>",'<li class="active"><span title="You are here"><%- path_item[1] %></span></li>',"<% } %>","<% }); %>","</ol>",'<div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>','<div class="dataset_table">','<table class="grid table table-striped table-condensed">',"<tr>",'<th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>','<td><%= _.escape(ldda.get("name")) %></td>',"</tr>",'<% if (ldda.get("file_ext")) { %>',"<tr>",'<th scope="row">Data type</th>','<td><%= _.escape(ldda.get("file_ext")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("genome_build")) { %>',"<tr>",'<th scope="row">Genome build</th>','<td><%= _.escape(ldda.get("genome_build")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("file_size")) { %>',"<tr>",'<th scope="row">Size</th>','<td><%= _.escape(ldda.get("file_size")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("date_uploaded")) { %>',"<tr>",'<th scope="row">Date uploaded (UTC)</th>','<td><%= _.escape(ldda.get("date_uploaded")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("uploaded_by")) { %>',"<tr>",'<th scope="row">Uploaded by</th>','<td><%= _.escape(ldda.get("uploaded_by")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("metadata_data_lines")) { %>',"<tr>",'<th scope="row">Data Lines</th>','<td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("metadata_comment_lines")) { %>',"<tr>",'<th scope="row">Comment Lines</th>','<td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("metadata_columns")) { %>',"<tr>",'<th scope="row">Number of Columns</th>','<td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("metadata_column_types")) { %>',"<tr>",'<th scope="row">Column Types</th>','<td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("message")) { %>',"<tr>",'<th scope="row">Message</th>','<td scope="row"><%= _.escape(ldda.get("message")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("misc_blurb")) { %>',"<tr>",'<th scope="row">Miscellaneous blurb</th>','<td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>',"</tr>","<% } %>",'<% if (ldda.get("misc_info")) { %>',"<tr>",'<th scope="row">Miscellaneous information</th>','<td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>',"</tr>","<% } %>","</table>","<div>",'<pre class="peek">',"</pre>","</div>","</div>","</div>"].join(""))},templateModifyDataset:function(){return _.template(['<div class="library_style_container">','<div id="library_toolbar">','<button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button toolbar-item" type="button">','<span class="fa fa-times"></span>',"&nbsp;Cancel","</button>",'<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button toolbar-item" type="button">','<span class="fa fa-floppy-o"></span>',"&nbsp;Save","</button>","</div>",'<ol class="breadcrumb">','<li><a title="Return to the list of libraries" href="#">Libraries</a></li>','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'<li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',"<% } else { %>",'<li class="active"><span title="You are here"><%- path_item[1] %></span></li>',"<% } %>","<% }); %>","</ol>",'<div class="dataset_table">','<p>For full editing options please import the dataset to history and use "Edit attributes" on it.</p>','<table class="grid table table-striped table-condensed">',"<tr>",'<th class="dataset-first-column" scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>','<td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>',"</tr>","<tr>",'<th scope="row">Data type</th>',"<td>",'<span id="dataset_extension_select" class="dataset-extension-select" />',"</td>","</tr>","<tr>",'<th scope="row">Genome build</th>',"<td>",'<span id="dataset_genome_select" class="dataset-genome-select" />',"</td>","</tr>","<tr>",'<th scope="row">Size</th>','<td><%= _.escape(item.get("file_size")) %></td>',"</tr>","<tr>",'<th scope="row">Date uploaded (UTC)</th>','<td><%= _.escape(item.get("date_uploaded")) %></td>',"</tr>","<tr>",'<th scope="row">Uploaded by</th>','<td><%= _.escape(item.get("uploaded_by")) %></td>',"</tr>",'<tr scope="row">','<th scope="row">Data Lines</th>','<td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>',"</tr>",'<th scope="row">Comment Lines</th>','<% if (item.get("metadata_comment_lines") === "") { %>','<td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>',"<% } else { %>",'<td scope="row">unknown</td>',"<% } %>","</tr>","<tr>",'<th scope="row">Number of Columns</th>','<td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>',"</tr>","<tr>",'<th scope="row">Column Types</th>','<td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>',"</tr>","<tr>",'<th scope="row">Message</th>','<td scope="row"><%= _.escape(item.get("message")) %></td>',"</tr>","<tr>",'<th scope="row">Miscellaneous information</th>','<td scope="row"><%= _.escape(item.get("misc_info")) %></td>',"</tr>","<tr>",'<th scope="row">Miscellaneous blurb</th>','<td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>',"</tr>","</table>","<div>",'<pre class="peek">',"</pre>","</div>","</div>","</div>"].join(""))},templateDatasetPermissions:function(){return _.template(['<div class="library_style_container">','<div id="library_toolbar">','<a href="#folders/<%- item.get("folder_id") %>">','<button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button toolbar-item" type="button">','<span class="fa fa-folder-open-o"></span>',"&nbsp;Containing Folder","</button>","</a>",'<a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>">','<button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button toolbar-item" type="button">','<span class="fa fa-file-o"></span>',"&nbsp;Dataset Details","</button>","<a>","</div>",'<ol class="breadcrumb">','<li><a title="Return to the list of libraries" href="#">Libraries</a></li>','<% _.each(item.get("full_path"), function(path_item) { %>',"<% if (path_item[0] != item.id) { %>",'<li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> </li> ',"<% } else { %>",'<li class="active"><span title="You are here"><%- path_item[1] %></span></li>',"<% } %>","<% }); %>","</ol>",'<h1>Dataset: <%= _.escape(item.get("name")) %></h1>','<div class="alert alert-warning">',"<% if (is_admin) { %>","You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.","<% } else { %>","You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.","<% } %>","</div>",'<div class="dataset_table">',"<h2>Library-related permissions</h2>","<h4>Roles that can modify the library item</h4>",'<div id="modify_perm" class="modify_perm roles-selection"></div>','<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>',"<hr/>","<h2>Dataset-related permissions</h2>",'<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>','<% if (!item.get("is_unrestricted")) { %>',"<p>You can remove all access restrictions on this dataset. ",'<button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">','<span class="fa fa-globe"></span>',"&nbsp;Remove restrictions","</button>","</p>","<% } else { %>","This dataset is unrestricted so everybody can access it. Just share the URL of this page.",'<button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button">','<span class="fa fa-clipboard"></span>',"&nbsp;To Clipboard","</button>","<p>You can make this dataset private to you. ",'<button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button">','<span class="fa fa-key"></span>',"&nbsp;Make Private","</button>","</p>","<% } %>","<h4>Roles that can access the dataset</h4>",'<div id="access_perm" class="access_perm roles-selection"></div>','<div class="alert alert-info roles-selection">',"User has to have <strong>all these roles</strong> in order to access this dataset."," Users without access permission <strong>cannot</strong> have other permissions on this dataset."," If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.","</div>","<h4>Roles that can manage permissions on the dataset</h4>",'<div id="manage_perm" class="manage_perm roles-selection"></div>','<div class="alert alert-info roles-selection">',"User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.","</div>",'<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button">','<span class="fa fa-floppy-o"></span>',"&nbsp;Save","</button>","</div>","</div>"].join(""))},templateBulkImportInModal:function(){return _.template(["<div>",'<div class="library-modal-item">',"Select history: ",'<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; " autofocus>',"<% _.each(histories, function(history) { %>",'<option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>',"<% }); %>","</select>","</div>",'<div class="library-modal-item">',"or create new: ",'<input type="text" name="history_name" value="" placeholder="name of the new history" style="width:50%;">',"</input>","</div>","</div>"].join(""))},templateAccessSelect:function(){return _.template(['<select id="access_select" multiple>',"<% _.each(options, function(option) { %>",'<option value="<%- option.name %>"><%- option.name %></option>',"<% }); %>","</select>"].join(""))}});return{LibraryDatasetView:e}});
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