Webpack: correct tool menu template loading in requirejs/galaxy.panels.mako by using require.config.map; normalize galaxy_config.root and Galaxy.options.root to Galaxy.root across the templates and js

client/galaxy/scripts/galaxy-app-base.js

@@ -166,8 +166,6 @@ GalaxyApp.prototype._initUser = function _initUser( userJSON ){
     self.debug( '_initUser:', userJSON );
     self.user = new userModel.User( userJSON );
     self.user.logger = self.logger;
-    //TODO: temp - old alias
-    self.currUser = self.user;
     return self;
 };
 

client/galaxy/scripts/galaxy.library.js

@@ -83,7 +83,7 @@ var LibraryRouter = Backbone.Router.extend({
       url = "/" + url;
     }
     if ( typeof ga !== 'undefined' ) {
-      ga( 'send', 'pageview', galaxy_config.root + 'library/list' + url );
+      ga( 'send', 'pageview', Galaxy.root + 'library/list' + url );
     }
   }
 });

client/galaxy/scripts/layout/masthead.js

@@ -150,7 +150,7 @@ var GalaxyMasthead = Backbone.View.extend({
                     '</div>' +
                    '<div class="navbar-brand">' +
                         '<a href="' + options.logo_url + '">' +
-                            '<img style="margin-left: 0.35em;" border="0" src="' + galaxy_config.root + 'static/images/galaxyIcon_noText.png">' +
+                            '<img style="margin-left: 0.35em;" border="0" src="' + Galaxy.root + 'static/images/galaxyIcon_noText.png">' +
                             '<span id="brand"> Galaxy ' + brand_text + '</span>' +
                         '</a>' +
                     '</div>' +

client/galaxy/scripts/layout/menu.js

@@ -350,7 +350,7 @@ var GalaxyMastheadTab = Backbone.View.extend({
 
         // update url
         if ( this.options.content !== undefined && this.options.content.indexOf( '//' ) === -1 ){
-            this.options.content = galaxy_config.root + this.options.content;
+            this.options.content = Galaxy.root + this.options.content;
         }
 
         // add template for tab
@@ -397,7 +397,7 @@ var GalaxyMastheadTab = Backbone.View.extend({
 
         // update url
         if (menuOptions.content && menuOptions.content.indexOf('//') === -1)
-            menuOptions.content = galaxy_config.root + menuOptions.content;
+            menuOptions.content = Galaxy.root + menuOptions.content;
 
         // check if submenu element is available
         if (!this.$menu){
@@ -455,7 +455,7 @@ var GalaxyMastheadTab = Backbone.View.extend({
         var $popover_element = $(this.el).find('.head');
         $popover_element.popover({
             html: true,
-            content: 'Please <a href="' + galaxy_config.root + 'user/login?use_panels=True">log in</a> or <a href="' + galaxy_config.root + 'user/create?use_panels=True">register</a> to use this feature.',
+            content: 'Please <a href="' + Galaxy.root + 'user/login?use_panels=True">log in</a> or <a href="' + Galaxy.root + 'user/create?use_panels=True">register</a> to use this feature.',
             placement: 'bottom'
         }).on('shown.bs.popover', function() { // hooking on bootstrap event to automatically hide popovers after delay
             setTimeout(function() {

client/galaxy/scripts/layout/scratchbook.js

@@ -109,7 +109,7 @@ var GalaxyFrame = Backbone.View.extend({
                 else {
                     _.extend(frame_config, {
                         type: 'url',
-                        content: galaxy_config.root + 'datasets/' +
+                        content: Galaxy.root + 'datasets/' +
                                  dataset.id + '/display/?preview=True'
                     });
                 }
@@ -129,7 +129,7 @@ var GalaxyFrame = Backbone.View.extend({
         require(['viz/visualization', 'viz/trackster'], function(visualization, trackster) {
             var viz = new visualization.Visualization({id: viz_id});
             $.when( viz.fetch() ).then( function() {
-                var ui = new trackster.TracksterUI(galaxy_config.root);
+                var ui = new trackster.TracksterUI(Galaxy.root);
 
                 // Construct frame config based on dataset's type.
                 var frame_config = {

client/galaxy/scripts/mvc/citation/citation-model.js

@@ -41,7 +41,7 @@ var BaseCitationCollection = Backbone.Collection.extend( baseMVC.LoggableMixin )
     _logNamespace : logNamespace,
 
     /** root api url */
-    urlRoot : galaxy_config.root + 'api',
+    urlRoot : Galaxy.root + 'api',
     partial : true, // Assume some tools in history/workflow may not be properly annotated yet.
     model : Citation,
 } );

client/galaxy/scripts/mvc/collection/collection-model.js

@@ -133,14 +133,13 @@ var DatasetDCE = DATASET_MODEL.DatasetAssociation.extend( BASE_MVC.mixin( Datase
 
     /** url fn */
     url : function(){
-        var galaxyRoot = (( window.galaxy_config && galaxy_config.root )?( galaxy_config.root ):( '/' ));
         // won't always be an hda
         if( !this.has( 'history_id' ) ){
             console.warn( 'no endpoint for non-hdas within a collection yet' );
             // (a little silly since this api endpoint *also* points at hdas)
-            return galaxyRoot + 'api/datasets';
+            return Galaxy.root + 'api/datasets';
         }
-        return galaxyRoot + 'api/histories/' + this.get( 'history_id' ) + '/contents/' + this.get( 'id' );
+        return Galaxy.root + 'api/histories/' + this.get( 'history_id' ) + '/contents/' + this.get( 'id' );
     },
 
     defaults : _.extend( {},

client/galaxy/scripts/mvc/collection/collection-view-edit.js

@@ -41,7 +41,7 @@ var CollectionViewEdit = _super.extend(
         if( !this.model ){ return; }
 
         // anon users shouldn't have access to any of the following
-        if( !Galaxy.currUser || Galaxy.currUser.isAnonymous() ){
+        if( !Galaxy.user || Galaxy.user.isAnonymous() ){
             return;
         }
 

client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js

@@ -572,8 +572,7 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte
      */
     createList : function( name ){
         var creator = this,
-            root = ( window.Galaxy && Galaxy.options.root )? Galaxy.options.root : '/',
-            url = root + 'api/histories/' + this.historyId + '/contents/dataset_collections';
+            url = Galaxy.root + 'api/histories/' + this.historyId + '/contents/dataset_collections';
 
         //TODO: use ListPairedCollection.create()
         var ajaxData = {

client/galaxy/scripts/mvc/dataset/data.js

@@ -54,7 +54,7 @@ var Dataset = Backbone.Model.extend({
         return this.attributes.metadata.get(attribute);
     },
 
-    urlRoot: galaxy_config.root + "api/datasets"
+    urlRoot: Galaxy.root + "api/datasets"
 });
 
 /**
@@ -73,8 +73,8 @@ var TabularDataset = Dataset.extend({
 
         // If first data chunk is available, next chunk is 1.
         this.attributes.chunk_index = (this.attributes.first_data_chunk ? 1 : 0);
-        this.attributes.chunk_url = galaxy_config.root + 'dataset/display?dataset_id=' + this.id;
-        this.attributes.url_viz = galaxy_config.root + 'visualization';
+        this.attributes.chunk_url = Galaxy.root + 'dataset/display?dataset_id=' + this.id;
+        this.attributes.url_viz = Galaxy.root + 'visualization';
     },
 
     /**

client/galaxy/scripts/mvc/dataset/dataset-model.js

@@ -79,9 +79,8 @@ var DatasetAssociation = Backbone.Model
             'meta_download' : 'dataset/get_metadata_file?hda_id=' + id + '&metadata_name='
         };
 //TODO: global
-        var root = ( window.galaxy_config && galaxy_config.root )?( galaxy_config.root ):( '/' );
         _.each( urls, function( value, key ){
-            urls[ key ] = root + value;
+            urls[ key ] = Galaxy.root + value;
         });
         this.urls = urls;
         return urls;
@@ -251,12 +250,11 @@ var DatasetAssociationCollection = Backbone.Collection.extend( BASE_MVC.Loggable
     model : DatasetAssociation,
 
     /** root api url */
-    urlRoot : (( window.galaxy_config && galaxy_config.root )?( galaxy_config.root ):( '/' ))
-        + 'api/datasets',
+    urlRoot : Galaxy.root + 'api/datasets',
 
     /** url fn */
     url : function(){
-        return this.urlRoot
+        return this.urlRoot;
     },
 
     // ........................................................................ common queries

client/galaxy/scripts/mvc/history/history-content-model.js

@@ -94,7 +94,7 @@ var HistoryContentMixin = {
 //TODO: global
 //TODO: these are probably better done on the leaf classes
     /** history content goes through the 'api/histories' API */
-    urlRoot: ( window.Galaxy? Galaxy.options.root : '/' ) + 'api/histories/',
+    urlRoot: Galaxy.root + 'api/histories/',
 
     /** full url spec. for this content */
     url : function(){

client/galaxy/scripts/mvc/history/history-contents.js

@@ -71,7 +71,7 @@ var HistoryContents = Backbone.Collection
     },
 
     /** root api url */
-    urlRoot : galaxy_config.root + 'api/histories',
+    urlRoot : Galaxy.root + 'api/histories',
     /** complete api url */
     url : function(){
         return this.urlRoot + '/' + this.historyId + '/contents';

client/galaxy/scripts/mvc/history/history-model.js

@@ -30,7 +30,7 @@ var History = Backbone.Model
     },
 
     // ........................................................................ urls
-    urlRoot: galaxy_config.root + 'api/histories',
+    urlRoot: Galaxy.root + 'api/histories',
 
     // ........................................................................ set up/tear down
     /** Set up the model
@@ -116,16 +116,16 @@ var History = Backbone.Model
     },
 
     // ........................................................................ common queries
-    /** T/F is this history owned by the current user (Galaxy.currUser)
+    /** T/F is this history owned by the current user (Galaxy.user)
      *      Note: that this will return false for an anon user even if the history is theirs.
      */
     ownedByCurrUser : function(){
         // no currUser
-        if( !Galaxy || !Galaxy.currUser ){
+        if( !Galaxy || !Galaxy.user ){
             return false;
         }
         // user is anon or history isn't owned
-        if( Galaxy.currUser.isAnonymous() || Galaxy.currUser.id !== this.get( 'user_id' ) ){
+        if( Galaxy.user.isAnonymous() || Galaxy.user.id !== this.get( 'user_id' ) ){
             return false;
         }
         return true;
@@ -277,7 +277,7 @@ var History = Backbone.Model
 
     setAsCurrent : function(){
         var history = this,
-            xhr = jQuery.getJSON( galaxy_config.root + 'history/set_as_current?id=' + this.id );
+            xhr = jQuery.getJSON( Galaxy.root + 'history/set_as_current?id=' + this.id );
 
         xhr.done( function(){
             history.trigger( 'set-as-current', history );
@@ -310,9 +310,9 @@ History.getHistoryData = function getHistoryData( historyId, options ){
     function getHistory( id ){
         // get the history data
         if( historyId === 'current' ){
-            return jQuery.getJSON( galaxy_config.root + 'history/current_history_json' );
+            return jQuery.getJSON( Galaxy.root + 'history/current_history_json' );
         }
-        return jQuery.ajax( galaxy_config.root + 'api/histories/' + historyId );
+        return jQuery.ajax( Galaxy.root + 'api/histories/' + historyId );
     }
     function isEmpty( historyData ){
         // get the number of hdas accrd. to the history
@@ -338,7 +338,7 @@ History.getHistoryData = function getHistoryData( historyId, options ){
             // by frontend.
             data.dataset_collection_details = hdcaDetailIds.join( ',' );
         }
-        return jQuery.ajax( galaxy_config.root + 'api/histories/' + historyData.id + '/contents', { data: data });
+        return jQuery.ajax( Galaxy.root + 'api/histories/' + historyData.id + '/contents', { data: data });
     }
 
     // getting these concurrently is 400% slower (sqlite, local, vanilla) - so:
@@ -501,7 +501,7 @@ var HistoryCollection = Backbone.Collection
         this.setUpListeners();
     },
 
-    urlRoot : ( window.galaxy_config? galaxy_config.root : '/' ) + 'api/histories',
+    urlRoot : Galaxy.root + 'api/histories',
     url     : function(){ return this.urlRoot; },
 
     /** returns map of default filters and settings for fetching from the API */
@@ -609,7 +609,7 @@ var HistoryCollection = Backbone.Collection
     create : function create( data, hdas, historyOptions, xhrOptions ){
         //TODO: .create is actually a collection function that's overridden here
         var collection = this,
-            xhr = jQuery.getJSON( galaxy_config.root + 'history/create_new_current'  );
+            xhr = jQuery.getJSON( Galaxy.root + 'history/create_new_current'  );
         return xhr.done( function( newData ){
             collection.setCurrent( new History( newData, [], historyOptions || {} ) );
         });

client/galaxy/scripts/mvc/history/history-view-edit-current.js

@@ -110,7 +110,7 @@ var CurrentHistoryView = _super.extend(
         var panel = this,
             historyFn = function(){
                 // make this current and get history data with one call
-                return jQuery.getJSON( galaxy_config.root + 'history/set_as_current?id=' + historyId  );
+                return jQuery.getJSON( Galaxy.root + 'history/set_as_current?id=' + historyId  );
                 //    method  : 'PUT'
                 //});
             };
@@ -122,14 +122,14 @@ var CurrentHistoryView = _super.extend(
 
     /** creates a new history on the server and sets it as the user's current history */
     createNewHistory : function( attributes ){
-        if( !Galaxy || !Galaxy.currUser || Galaxy.currUser.isAnonymous() ){
+        if( !Galaxy || !Galaxy.user || Galaxy.user.isAnonymous() ){
             this.displayMessage( 'error', _l( 'You must be logged in to create histories' ) );
             return $.when();
         }
         var panel = this,
             historyFn = function(){
                 // create a new history and save: the server will return the proper JSON
-                return jQuery.getJSON( galaxy_config.root + 'history/create_new_current'  );
+                return jQuery.getJSON( Galaxy.root + 'history/create_new_current'  );
             };
 
         // id undefined bc there is no historyId yet - the server will provide

client/galaxy/scripts/mvc/history/history-view-edit.js

@@ -121,7 +121,7 @@ var HistoryViewEdit = _super.extend(
         var $newRender = _super.prototype._buildNewRender.call( this );
         if( !this.model ){ return $newRender; }
 
-        if( Galaxy && Galaxy.currUser && Galaxy.currUser.id && Galaxy.currUser.id === this.model.get( 'user_id' ) ){
+        if( Galaxy && Galaxy.user && Galaxy.user.id && Galaxy.user.id === this.model.get( 'user_id' ) ){
             this._renderTags( $newRender );
             this._renderAnnotation( $newRender );
         }
@@ -216,8 +216,8 @@ var HistoryViewEdit = _super.extend(
         if( !this.model ){ return; }
 
         // anon users shouldn't have access to any of the following
-        if( ( !Galaxy.currUser || Galaxy.currUser.isAnonymous() )
-        ||  ( Galaxy.currUser.id !== this.model.get( 'user_id' ) ) ){
+        if( ( !Galaxy.user || Galaxy.user.isAnonymous() )
+        ||  ( Galaxy.user.id !== this.model.get( 'user_id' ) ) ){
             return;
         }
 

client/galaxy/scripts/mvc/history/history-view.js

@@ -502,7 +502,7 @@ var HistoryView = _super.extend(
         //if( xhr.responseText ){
         //    xhr.responseText = _.escape( xhr.responseText );
         //}
-        var user = Galaxy.currUser,
+        var user = Galaxy.user,
             // add the args (w/ some extra info) into an obj
             parsed = {
                 message : this._bePolite( msg ),

client/galaxy/scripts/mvc/history/multi-panel.js

@@ -779,13 +779,7 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({
 
     close : function( ev ){
         //TODO: switch to pushState/router
-        var destination = '/';
-        if( Galaxy && Galaxy.options && Galaxy.options.root ){
-            destination = Galaxy.options.root;
-        } else if( galaxy_config && galaxy_config.root ){
-            destination = galaxy_config.root;
-        }
-        window.location = destination;
+        window.location = Galaxy.root;
     },
 
     _clickToggleDeletedHistories : function( ev ){
@@ -795,9 +789,9 @@ var MultiPanelColumns = Backbone.View.extend( baseMVC.LoggableMixin ).extend({
     /** Include deleted histories in the collection */
     toggleDeletedHistories : function( show ){
         if( show ){
-            window.location = Galaxy.options.root + 'history/view_multiple?include_deleted_histories=True';
+            window.location = Galaxy.root + 'history/view_multiple?include_deleted_histories=True';
         } else {
-            window.location = Galaxy.options.root + 'history/view_multiple';
+            window.location = Galaxy.root + 'history/view_multiple';
         }
     },
 

client/galaxy/scripts/mvc/history/options-menu.js

@@ -175,8 +175,7 @@ var create = function( $button, options ){
     options = options || {};
     var isAnon = options.anonymous === undefined? true : options.anonymous,
         purgeAllowed = options.purgeAllowed || false,
-        root = options.root || ( ( Galaxy && Galaxy.options )? Galaxy.options.root: '/' ),
-        menu = buildMenu( isAnon, purgeAllowed, root );
+        menu = buildMenu( isAnon, purgeAllowed, Galaxy.root );
     //console.debug( 'menu:', menu );
     return new PopupMenu( $button, menu );
 };

client/galaxy/scripts/mvc/job/job-model.js

@@ -86,7 +86,7 @@ var Job = Backbone.Model
 
     // ........................................................................ ajax
     /** root api url */
-    urlRoot : (( window.galaxy_config && galaxy_config.root )?( galaxy_config.root ):( '/' )) + 'api/jobs',
+    urlRoot : Galaxy.root + 'api/jobs',
     //url : function(){ return this.urlRoot; },
 
     // ........................................................................ searching
@@ -115,7 +115,7 @@ var JobCollection = Backbone.Collection
     model : Job,
 
     /** root api url */
-    urlRoot : (( window.galaxy_config && galaxy_config.root )?( galaxy_config.root ):( '/' )) + 'api/jobs',
+    urlRoot : Galaxy.root + 'api/jobs',
     url : function(){ return this.urlRoot; },
 
     intialize : function( models, options ){

client/galaxy/scripts/mvc/library/library-dataset-view.js

@@ -116,7 +116,7 @@ var LibraryDatasetView = Backbone.View.extend({
   },
 
   downloadDataset: function(){
-    var url = ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/download/uncompressed';
+    var url = Galaxy.root + 'api/libraries/datasets/download/uncompressed';
     var data = {'ld_ids' : this.id};
     this.processDownload(url, data);
   },
@@ -135,7 +135,7 @@ var LibraryDatasetView = Backbone.View.extend({
           //send request
           $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>')
           .appendTo('body').submit().remove();
-          
+
           mod_toastr.info('Your download will begin soon.');
         }
    },
@@ -183,16 +183,16 @@ var LibraryDatasetView = Backbone.View.extend({
       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 
+      // 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_config.root + 'history/set_as_current?id=' + history_id  );
+      jQuery.getJSON( Galaxy.root + 'history/set_as_current?id=' + history_id  );
 
       // save the dataset into selected history
-      historyItem.save({ content : this.id, source : 'library' }, { 
+      historyItem.save({ content : this.id, source : 'library' }, {
         success : function(){
             Galaxy.modal.hide();
           mod_toastr.success('Dataset imported. Click this to start analysing it.', '', {onclick: function() {window.location='/';}});
-        }, 
+        },
         error : function(model, response){
           if (typeof response.responseJSON !== "undefined"){
             mod_toastr.error('Dataset not imported. ' + response.responseJSON.err_msg);
@@ -224,15 +224,15 @@ var LibraryDatasetView = Backbone.View.extend({
     }
     // Select works different for admins
     var is_admin = false;
-    if (Galaxy.currUser){
-      is_admin = Galaxy.currUser.isAdmin();
+    if (Galaxy.user){
+      is_admin = Galaxy.user.isAdmin();
     }
     var template = this.templateDatasetPermissions();
     this.$el.html(template({item: this.model, is_admin: is_admin}));
 
     var self = this;
     if (this.options.fetched_permissions === undefined){
-      $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) {
+      $.get( Galaxy.root + "api/libraries/datasets/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) {
         self.prepareSelectBoxes({fetched_permissions:fetched_permissions, is_admin:is_admin});
       }).fail(function(){
           mod_toastr.error('An error occurred while attempting to fetch dataset permissions.');
@@ -263,7 +263,7 @@ var LibraryDatasetView = Backbone.View.extend({
         for (var i = 0; i < fetched_permissions.manage_dataset_roles.length; i++) {
             selected_manage_dataset_roles.push(fetched_permissions.manage_dataset_roles[i] + ':' + fetched_permissions.manage_dataset_roles[i]);
         }
-        
+
         // ACCESS PERMISSIONS
         if (is_admin){ // Admin has a special select that allows AJAX searching
             var access_select_options = {
@@ -273,7 +273,7 @@ var LibraryDatasetView = Backbone.View.extend({
               placeholder: 'Click to select a role',
               container: self.$el.find('#access_perm'),
               ajax: {
-                  url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available",
+                  url: Galaxy.root + "api/libraries/datasets/" + self.id + "/permissions?scope=available",
                   dataType: 'json',
                   quietMillis: 100,
                   data: function (term, page) { // page is the one-based page number tracked by Select2
@@ -320,7 +320,7 @@ var LibraryDatasetView = Backbone.View.extend({
               placeholder: 'Click to select a role',
               container: self.$el.find('#modify_perm'),
               ajax: {
-                  url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available",
+                  url: Galaxy.root + "api/libraries/datasets/" + self.id + "/permissions?scope=available",
                   dataType: 'json',
                   quietMillis: 100,
                   data: function (term, page) { // page is the one-based page number tracked by Select2
@@ -367,7 +367,7 @@ var LibraryDatasetView = Backbone.View.extend({
               placeholder: 'Click to select a role',
               container: self.$el.find('#manage_perm'),
               ajax: {
-                  url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available",
+                  url: Galaxy.root + "api/libraries/datasets/" + self.id + "/permissions?scope=available",
                   dataType: 'json',
                   quietMillis: 100,
                   data: function (term, page) { // page is the one-based page number tracked by Select2
@@ -413,7 +413,7 @@ var LibraryDatasetView = Backbone.View.extend({
             self.manageSelectObject = new mod_select.View(manage_select_options);
         } else { // Non-admins have select with pre-loaded options
             var template = self.templateAccessSelect();
-            $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available", function( data ) {
+            $.get( Galaxy.root + "api/libraries/datasets/" + self.id + "/permissions?scope=available", function( data ) {
                 $('.access_perm').html(template({options:data.roles}));
                 self.accessSelectObject = $('#access_select').select2();
             }).fail(function() {
@@ -436,7 +436,7 @@ var LibraryDatasetView = Backbone.View.extend({
 
   makeDatasetPrivate: function(){
     var self = this;
-    $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) {
+    $.post( Galaxy.root + "api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) {
       self.model.set({is_unrestricted:false});
       self.showPermissions({fetched_permissions:fetched_permissions})
       mod_toastr.success('The dataset is now private to you.');
@@ -447,7 +447,7 @@ var LibraryDatasetView = Backbone.View.extend({
 
   removeDatasetRestrictions: function(){
     var self = this;
-    $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions")
+    $.post( Galaxy.root + "api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions")
     .done(function(fetched_permissions) {
       self.model.set({is_unrestricted:true});
       self.showPermissions({fetched_permissions:fetched_permissions})
@@ -478,7 +478,7 @@ var LibraryDatasetView = Backbone.View.extend({
       modify_ids.push(modify_roles[i].id);
     };
 
-    $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } )
+    $.post( Galaxy.root + "api/libraries/datasets/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } )
     .done(function(fetched_permissions){
       //fetch dataset again
       self.showPermissions({fetched_permissions:fetched_permissions})
@@ -501,7 +501,7 @@ var LibraryDatasetView = Backbone.View.extend({
     tmpl_array.push('   <% if (item.get("can_user_modify")) { %>');
     tmpl_array.push('   <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');
     tmpl_array.push('   <% } %>');
-    
+
     tmpl_array.push('   <% if (item.get("can_user_manage")) { %>');
     tmpl_array.push('   <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" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');
     // tmpl_array.push('   <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');
@@ -644,7 +644,7 @@ var LibraryDatasetView = Backbone.View.extend({
     tmpl_array.push('</div>');
 
     return _.template(tmpl_array.join(''));
-  }, 
+  },
 
   templateVersion : function(){
     var tmpl_array = [];
@@ -668,7 +668,7 @@ var LibraryDatasetView = Backbone.View.extend({
     tmpl_array.push('</ol>');
 
     tmpl_array.push('  <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');
-    
+
     tmpl_array.push('<div class="dataset_table">');
 
     tmpl_array.push('   <table class="grid table table-striped table-condensed">');
@@ -847,7 +847,7 @@ var LibraryDatasetView = Backbone.View.extend({
     tmpl_array.push('       <tr>');
     tmpl_array.push('           <th scope="row">Message</th>');
     tmpl_array.push('           <td scope="row"><%= _.escape(item.get("message")) %></td>');
-    tmpl_array.push('       </tr>');    
+    tmpl_array.push('       </tr>');
     tmpl_array.push('       <tr>');
     tmpl_array.push('           <th scope="row">Miscellaneous information</th>');
     tmpl_array.push('           <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');
@@ -855,7 +855,7 @@ var LibraryDatasetView = Backbone.View.extend({
     tmpl_array.push('       <tr>');
     tmpl_array.push('           <th scope="row">Miscellaneous blurb</th>');
     tmpl_array.push('           <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');
-    tmpl_array.push('       </tr>');    
+    tmpl_array.push('       </tr>');
     tmpl_array.push('   </table>');
     tmpl_array.push('<div>');
     tmpl_array.push('   <pre class="peek">');
@@ -901,7 +901,7 @@ var LibraryDatasetView = Backbone.View.extend({
     tmpl_array.push('You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.');
     tmpl_array.push('<% } %>');
     tmpl_array.push('</div>');
-    
+
     tmpl_array.push('<div class="dataset_table">');
 
     tmpl_array.push('<h2>Library-related permissions</h2>');
@@ -966,7 +966,7 @@ var LibraryDatasetView = Backbone.View.extend({
 
     tmpl_array.push('<select id="access_select" multiple>');
 
-    tmpl_array.push('   <% _.each(options, function(option) { %>');    
+    tmpl_array.push('   <% _.each(options, function(option) { %>');
     tmpl_array.push('       <option value="<%- option.name %>"><%- option.name %></option>');
     tmpl_array.push('   <% }); %>');
 

client/galaxy/scripts/mvc/library/library-folder-view.js

@@ -73,15 +73,15 @@ var FolderView = Backbone.View.extend({
     $(".tooltip").remove();
 
     var is_admin = false;
-    if (Galaxy.currUser){
-      is_admin = Galaxy.currUser.isAdmin();
-    } 
+    if (Galaxy.user){
+      is_admin = Galaxy.user.isAdmin();
+    }
     var template = this.templateFolderPermissions();
     this.$el.html(template({folder: this.model, is_admin:is_admin}));
 
     var self = this;
     if (this.options.fetched_permissions === undefined){
-      $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/folders/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) {
+      $.get( Galaxy.root + "api/folders/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) {
         self.prepareSelectBoxes({fetched_permissions:fetched_permissions});
       }).fail(function(){
           mod_toastr.error('An error occurred while attempting to fetch folder permissions.');
@@ -125,7 +125,7 @@ var FolderView = Backbone.View.extend({
       placeholder: 'Click to select a role',
       container: self.$el.find('#' + id),
       ajax: {
-          url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/folders/" + self.id + "/permissions?scope=available",
+          url: Galaxy.root + "api/folders/" + self.id + "/permissions?scope=available",
           dataType: 'json',
           quietMillis: 100,
           data: function (term, page) { // page is the one-based page number tracked by Select2
@@ -195,7 +195,7 @@ var FolderView = Backbone.View.extend({
     var manage_ids = this._extractIds(this.manageSelectObject.$el.select2('data'));
     var modify_ids = this._extractIds(this.modifySelectObject.$el.select2('data'));
 
-    $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/folders/" + self.id + "/permissions?action=set_permissions", { 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } )
+    $.post( Galaxy.root + "api/folders/" + self.id + "/permissions?action=set_permissions", { 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } )
     .done(function(fetched_permissions){
       //fetch dataset again
       self.showPermissions({fetched_permissions:fetched_permissions})
@@ -252,7 +252,7 @@ var FolderView = Backbone.View.extend({
     var tmpl_array = [];
     // CONTAINER START
     tmpl_array.push('<div class="library_style_container">');
-    
+
 
     tmpl_array.push('  <div id="library_toolbar">');
     tmpl_array.push('   <a href="#/folders/<%= folder.get("parent_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to the parent folder" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Parent folder</span></button></a>');
@@ -267,7 +267,7 @@ var FolderView = Backbone.View.extend({
     tmpl_array.push('You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.');
     tmpl_array.push('<% }%>');
     tmpl_array.push('</div>');
-    
+
     tmpl_array.push('<div class="dataset_table">');
 
     tmpl_array.push('<h2>Folder permissions</h2>');

client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js

@@ -82,9 +82,9 @@ var FolderToolbarView = Backbone.View.extend({
         is_anonym: true,
         mutiple_add_dataset_options: false
     }
-    if (Galaxy.currUser){
-      template_defaults.is_admin = Galaxy.currUser.isAdmin();
-      template_defaults.is_anonym = Galaxy.currUser.isAnonymous();
+    if (Galaxy.user){
+      template_defaults.is_admin = Galaxy.user.isAdmin();
+      template_defaults.is_anonym = Galaxy.user.isAnonymous();
       if ( Galaxy.config.user_library_import_dir !== null || Galaxy.config.allow_library_path_paste !== false || Galaxy.config.library_import_dir !== null ){
         template_defaults.mutiple_add_dataset_options = true;
       }
@@ -117,8 +117,8 @@ var FolderToolbarView = Backbone.View.extend({
       $('.add-library-items').hide();
     }
     if (this.options.contains_file_or_folder === true){
-      if (Galaxy.currUser){
-        if (!Galaxy.currUser.isAnonymous()){
+      if (Galaxy.user){
+        if (!Galaxy.user.isAnonymous()){
           $('.logged-dataset-manipulation').show();
           $('.dataset-manipulation').show();
         } else {
@@ -283,7 +283,7 @@ var FolderToolbarView = Backbone.View.extend({
     this.initChainCallControl( { length: datasets_to_import.length, action: 'to_history', history_name: history_name } );
     // 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_config.root + 'history/set_as_current?id=' + history_id  );
+    jQuery.getJSON( Galaxy.root + 'history/set_as_current?id=' + history_id  );
     this.chainCallImportingIntoHistory( datasets_to_import, history_name );
   },
 
@@ -312,7 +312,7 @@ var FolderToolbarView = Backbone.View.extend({
                 folder_ids.push( this.parentElement.parentElement.id );
             }
         } );
-    var url = ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/download/' + format;
+    var url = Galaxy.root + 'api/libraries/datasets/download/' + format;
     var data = { 'ld_ids' : dataset_ids, 'folder_ids' : folder_ids };
     this.processDownload( url, data, 'get' );
   },
@@ -404,7 +404,7 @@ var FolderToolbarView = Backbone.View.extend({
   fetchExtAndGenomes: function(){
     var that = this;
     mod_utils.get({
-        url      :  ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/datatypes?extension_only=False",
+        url      :  Galaxy.root + "api/datatypes?extension_only=False",
         success  :  function( datatypes ) {
                         for (key in datatypes) {
                             that.list_extensions.push({
@@ -421,8 +421,8 @@ var FolderToolbarView = Backbone.View.extend({
                     }
       });
     mod_utils.get({
-        url:    ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/genomes",
-        success: function( genomes ) {
+        url     :    Galaxy.root + "api/genomes",
+        success : function( genomes ) {
                     for ( key in genomes ) {
                         that.list_genomes.push({
                             id      : genomes[key][1],
@@ -707,7 +707,7 @@ var FolderToolbarView = Backbone.View.extend({
       for ( var i = history_dataset_ids.length - 1; i >= 0; i-- ) {
         history_dataset_id = history_dataset_ids[i];
         var folder_item = new mod_library_model.Item();
-        folder_item.url = ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/folders/' + this.options.id + '/contents';
+        folder_item.url = Galaxy.root + 'api/folders/' + this.options.id + '/contents';
         folder_item.set( { 'from_hda_id':history_dataset_id } );
         hdas_to_add.push( folder_item );
       }
@@ -767,7 +767,7 @@ var FolderToolbarView = Backbone.View.extend({
       }
       return true;
     }
-    var promise = $.when( $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets?encoded_folder_id=' + that.id +
+    var promise = $.when( $.post( Galaxy.root + 'api/libraries/datasets?encoded_folder_id=' + that.id +
                                                        '&source=' + options.source +
                                                        '&path=' + popped_item +
                                                        '&file_type=' + options.file_type +
@@ -806,7 +806,7 @@ var FolderToolbarView = Backbone.View.extend({
       }
       return true;
     }
-    var promise = $.when( $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets?encoded_folder_id=' + that.id +
+    var promise = $.when( $.post( Galaxy.root + 'api/libraries/datasets?encoded_folder_id=' + that.id +
                                                           '&source=' + options.source +
                                                           '&path=' + popped_item +
                                                           '&preserve_dirs=' + options.preserve_dirs +

client/galaxy/scripts/mvc/library/library-library-view.js

@@ -79,15 +79,15 @@ var LibraryView = Backbone.View.extend({
       }
     }
     var is_admin = false;
-    if (Galaxy.currUser){
-      is_admin = Galaxy.currUser.isAdmin();
-    } 
+    if (Galaxy.user){
+      is_admin = Galaxy.user.isAdmin();
+    }
     var template = this.templateLibraryPermissions();
     this.$el.html(template({library: this.model, is_admin:is_admin}));
 
     var self = this;
     if (this.options.fetched_permissions === undefined){
-      $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) {
+      $.get( Galaxy.root + "api/libraries/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) {
         self.prepareSelectBoxes({fetched_permissions:fetched_permissions});
       }).fail(function(){
           mod_toastr.error('An error occurred while attempting to fetch library permissions.');
@@ -134,7 +134,7 @@ var LibraryView = Backbone.View.extend({
       placeholder: 'Click to select a role',
       container: self.$el.find('#' + id),
       ajax: {
-          url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/" + self.id + "/permissions?scope=available&is_library_access=" + is_library_access,
+          url: Galaxy.root + "api/libraries/" + self.id + "/permissions?scope=available&is_library_access=" + is_library_access,
           dataType: 'json',
           quietMillis: 100,
           data: function (term, page) { // page is the one-based page number tracked by Select2
@@ -193,7 +193,7 @@ var LibraryView = Backbone.View.extend({
 
   makeDatasetPrivate: function(){
     var self = this;
-    $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) {
+    $.post( Galaxy.root + "api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) {
       self.model.set({is_unrestricted:false});
       self.showPermissions({fetched_permissions:fetched_permissions})
       mod_toastr.success('The dataset is now private to you.');
@@ -204,7 +204,7 @@ var LibraryView = Backbone.View.extend({
 
   removeDatasetRestrictions: function(){
     var self = this;
-    $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions")
+    $.post( Galaxy.root + "api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions")
     .done(function(fetched_permissions) {
       self.model.set({is_unrestricted:true});
       self.showPermissions({fetched_permissions:fetched_permissions})
@@ -230,7 +230,7 @@ var LibraryView = Backbone.View.extend({
     var manage_ids = this._extractIds(this.manageSelectObject.$el.select2('data'));
     var modify_ids = this._extractIds(this.modifySelectObject.$el.select2('data'));
 
-    $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } )
+    $.post( Galaxy.root + "api/libraries/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } )
     .done(function(fetched_permissions){
       //fetch dataset again
       self.showPermissions({fetched_permissions:fetched_permissions})
@@ -287,7 +287,7 @@ var LibraryView = Backbone.View.extend({
     var tmpl_array = [];
     // CONTAINER START
     tmpl_array.push('<div class="library_style_container">');
-    
+
 
     tmpl_array.push('  <div id="library_toolbar">');
     tmpl_array.push('   <a href="#"><button data-toggle="tooltip" data-placement="top" title="Go back to the list of Libraries" class="btn btn-default primary-button" type="button"><span class="fa fa-list"></span> Libraries</span></button></a>');
@@ -302,7 +302,7 @@ var LibraryView = Backbone.View.extend({
     tmpl_array.push('You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.');
     tmpl_array.push('<% }%>');
     tmpl_array.push('</div>');
-    
+
     tmpl_array.push('<div class="dataset_table">');
 
     tmpl_array.push('<h2>Library permissions</h2>');
@@ -310,7 +310,7 @@ var LibraryView = Backbone.View.extend({
     tmpl_array.push('<h4>Roles that can access the library</h4>');
     tmpl_array.push('<div id="access_perm" class="access_perm roles-selection"></div>');
     tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can access this library. If there are no access roles set on the library it is considered <strong>unrestricted</strong>.</div>');
-    
+
     tmpl_array.push('<h4>Roles that can manage permissions on this library</h4>');
     tmpl_array.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');
     tmpl_array.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions on this library (includes giving access).</div>');

client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js

@@ -30,9 +30,9 @@ var LibraryToolbarView = Backbone.View.extend({
     var toolbar_template = this.templateToolBar();
     var is_admin = false;
     var is_anonym = true;
-    if ( Galaxy.currUser ){
-      is_admin = Galaxy.currUser.isAdmin();
-      is_anonym = Galaxy.currUser.isAnonymous();
+    if ( Galaxy.user ){
+      is_admin = Galaxy.user.isAdmin();
+      is_anonym = Galaxy.user.isAnonymous();
     }
     this.$el.html(toolbar_template( { admin_user: is_admin, anon_user: is_anonym } ) );
     if ( is_admin ){
@@ -46,7 +46,7 @@ var LibraryToolbarView = Backbone.View.extend({
   renderPaginator: function( options ){
     this.options = _.extend( this.options, options );
     var paginator_template = this.templatePaginator();
-    this.$el.find( '#library_paginator' ).html( paginator_template({ 
+    this.$el.find( '#library_paginator' ).html( paginator_template({
       show_page: parseInt( this.options.show_page ),
       page_count: parseInt( this.options.page_count ),
       total_libraries_count: this.options.total_libraries_count,

client/galaxy/scripts/mvc/library/library-model.js

@@ -4,7 +4,7 @@ define([], function() {
 // LIBRARY RELATED MODELS
 
     var Library = Backbone.Model.extend({
-      urlRoot: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/',
+      urlRoot: Galaxy.root + 'api/libraries/',
 
       /** based on show_deleted would this lib show in the list of lib's?
        *  @param {Boolean} show_deleted are we including deleted libraries?
@@ -19,7 +19,7 @@ define([], function() {
     });
 
     var Libraries = Backbone.Collection.extend({
-      url: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries',
+      url: Galaxy.root + 'api/libraries',
 
       model: Library,
 
@@ -60,7 +60,7 @@ define([], function() {
       },
 
       /** Sort collection by library name (ascending) and return the sorted
-       *  collection 
+       *  collection
        */
       sortByNameAsc: function(){
         this.comparator = function(libraryA, libraryB){
@@ -77,7 +77,7 @@ define([], function() {
       },
 
       /** Sort collection by library name (descending) and return the sorted
-       *  collection 
+       *  collection
        */
       sortByNameDesc: function(){
         this.comparator = function(libraryA, libraryB){
@@ -102,18 +102,18 @@ define([], function() {
     });
 
     var Ldda = LibraryItem.extend({
-      urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/'
+      urlRoot : Galaxy.root + 'api/libraries/datasets/'
     });
 
     var FolderAsModel = LibraryItem.extend({
-      urlRoot: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/folders/'
+      urlRoot: Galaxy.root + 'api/folders/'
     });
 
     var Folder = Backbone.Collection.extend({
       model: LibraryItem,
 
       /** Sort collection by item name (ascending) and return the sorted
-       *  collection. Folders go before datasets. 
+       *  collection. Folders go before datasets.
        */
       sortByNameAsc: function(){
         this.comparator = function(itemA, itemB){
@@ -138,7 +138,7 @@ define([], function() {
       },
 
       /** Sort collection by item name (descending) and return the sorted
-       *  collection. Folders go before datasets. 
+       *  collection. Folders go before datasets.
        */
       sortByNameDesc: function(){
         this.comparator = function(itemA, itemB){
@@ -166,7 +166,7 @@ define([], function() {
     var FolderContainer = Backbone.Model.extend({
       defaults : {
           folder : new Folder(),
-          urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/folders/',
+          urlRoot : Galaxy.root + 'api/folders/',
           id : "unknown"
       },
       parse : function(obj) {
@@ -195,11 +195,11 @@ define([], function() {
 // TODO UNITE
 
     var HistoryItem = Backbone.Model.extend({
-      urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories/'
+      urlRoot : Galaxy.root + 'api/histories/'
     });
 
     var HistoryContents = Backbone.Collection.extend({
-      urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories/',
+      urlRoot : Galaxy.root + 'api/histories/',
       initialize: function(options){
         this.id = options.id;
       },
@@ -210,22 +210,22 @@ define([], function() {
     });
 
     var GalaxyHistory = Backbone.Model.extend({
-      urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories/'
+      urlRoot : Galaxy.root + 'api/histories/'
     });
 
     var GalaxyHistories = Backbone.Collection.extend({
-      url : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories',
+      url : Galaxy.root + 'api/histories',
       model : GalaxyHistory
     });
 
 // ============================================================================
 // JSTREE MODEL
     /** Represents folder structure parsable by the jstree component.
-     * 
+     *
      */
-    
+
     var Jstree = Backbone.Model.extend({
-      urlRoot: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/remote_files'
+      urlRoot: Galaxy.root + 'api/remote_files'
     });
 
 return {

client/galaxy/scripts/mvc/tag.js

@@ -71,7 +71,7 @@ var TagsEditor = Backbone.View
     /** @returns {String[]} all tags used by the current user */
     _getTagsUsed : function(){
 //TODO: global
-        return Galaxy.currUser.get( 'tags_used' );
+        return Galaxy.user.get( 'tags_used' );
     },
 
     /** set up any event listeners on the view's DOM (mostly handled by select2) */
@@ -94,11 +94,11 @@ var TagsEditor = Backbone.View
      */
     _addNewTagToTagsUsed : function( newTag ){
 //TODO: global
-        var tagsUsed = Galaxy.currUser.get( 'tags_used' );
+        var tagsUsed = Galaxy.user.get( 'tags_used' );
         if( !_.contains( tagsUsed, newTag ) ){
             tagsUsed.push( newTag );
             tagsUsed.sort();
-            Galaxy.currUser.set( 'tags_used', tagsUsed );
+            Galaxy.user.set( 'tags_used', tagsUsed );
         }
     },
 

client/galaxy/scripts/mvc/tool/tools-form-workflow.js

@@ -33,10 +33,10 @@ define(['utils/utils', 'mvc/tool/tools-form-base'],
                 cls             : 'ui-portlet-narrow',
 
                 // configure model update
-                update_url      : galaxy_config.root + 'api/workflows/build_module',
+                update_url      : Galaxy.root + 'api/workflows/build_module',
                 update          : function(data) {
                     self.node.update_field_data(data);
-                    self.form.errors(data && data.tool_model)
+                    self.form.errors(data && data.tool_model);
                 }
             });
 

client/galaxy/scripts/mvc/tool/tools-jobs.js

@@ -30,7 +30,7 @@ return {
         // post job
         Utils.request({
             type    : 'POST',
-            url     : galaxy_config.root + 'api/tools',
+            url     : Galaxy.root + 'api/tools',
             data    : job_def,
             success : function(response) {
                 callback && callback();

client/galaxy/scripts/mvc/tool/tools.js

@@ -132,7 +132,7 @@ var Tool = Backbone.Model.extend({
         outputs: []
     },
 
-    urlRoot: galaxy_config.root + 'api/tools',
+    urlRoot: Galaxy.root + 'api/tools',
 
     initialize: function(options) {
 
@@ -362,7 +362,7 @@ var ToolSearch = Backbone.Model.extend({
         clear_key: 27
     },
 
-    urlRoot: galaxy_config.root + 'api/tools',
+    urlRoot: Galaxy.root + 'api/tools',
 
     initialize: function() {
         this.on("change:query", this.do_search);
@@ -393,7 +393,7 @@ var ToolSearch = Backbone.Model.extend({
         this.timer = setTimeout(function () {
             // log the search to analytics if present
             if ( typeof ga !== 'undefined' ) {
-                ga( 'send', 'pageview', galaxy_config.root + '?q=' + q );
+                ga( 'send', 'pageview', Galaxy.root + '?q=' + q );
             }
             $.get( self.urlRoot, { q: q }, function (data) {
                 self.set("results", data);

client/galaxy/scripts/mvc/ui/ui-select-ftp.js

@@ -26,7 +26,7 @@ var View = Backbone.View.extend({
 
         // initial fetch of ftps
         Utils.get({
-            url     : galaxy_config.root + 'api/remote_files',
+            url     : Galaxy.root + 'api/remote_files',
             success : function(response) {
                 var data = [];
                 for (var i in response) {

client/galaxy/scripts/mvc/ui/ui-select-library.js

@@ -4,7 +4,7 @@ define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-table', 'mvc/ui/ui-list'],
 
 // collection of libraries
 var Libraries = Backbone.Collection.extend({
-    url: galaxy_config.root + 'api/libraries?deleted=false'
+    url: Galaxy.root + 'api/libraries?deleted=false'
 });
 
 // collection of dataset
@@ -17,7 +17,7 @@ var LibraryDatasets = Backbone.Collection.extend({
         });
     },
     url: function() {
-        return galaxy_config.root + 'api/libraries/' + this.config.get('library_id') + '/contents'
+        return Galaxy.root + 'api/libraries/' + this.config.get('library_id') + '/contents';
     }
 });
 

client/galaxy/scripts/mvc/upload/upload-ftp.js

@@ -28,7 +28,7 @@ return Backbone.View.extend({
 
         // load extension
         Utils.get({
-            url     : galaxy_config.root + 'api/remote_files',
+            url     : Galaxy.root + 'api/remote_files',
             success : function(ftp_files) { self._fill(ftp_files); },
             error   : function() { self._fill(); }
         });

client/galaxy/scripts/mvc/upload/upload-view.js

@@ -74,7 +74,7 @@ return Backbone.View.extend({
         // load extensions
         var self = this;
         Utils.get({
-            url     : galaxy_config.root + 'api/datatypes?extension_only=False',
+            url     : Galaxy.root + 'api/datatypes?extension_only=False',
             success : function( datatypes ) {
                 for ( key in datatypes ) {
                     self.list_extensions.push({
@@ -98,7 +98,7 @@ return Backbone.View.extend({
 
         // load genomes
         Utils.get({
-            url     : galaxy_config.root + 'api/genomes',
+            url     : Galaxy.root + 'api/genomes',
             success : function( genomes ) {
                 for ( key in genomes ) {
                     self.list_genomes.push({

client/galaxy/scripts/mvc/user/user-model.js

@@ -15,7 +15,7 @@ var User = Backbone.Model.extend( baseMVC.LoggableMixin ).extend(
     _logNamespace : logNamespace,
 
     /** API location for this resource */
-    urlRoot : function(){ return Galaxy.options.root + 'api/users'; },
+    urlRoot : function(){ return Galaxy.root + 'api/users'; },
 
     /** Model defaults
      *  Note: don't check for anon-users with the username as the default is '(anonymous user)'
@@ -115,7 +115,7 @@ User.getCurrentUserFromApi = function( options ){
 // (stub) collection for users (shouldn't be common unless admin UI)
 var UserCollection = Backbone.Collection.extend( baseMVC.LoggableMixin ).extend({
     model   : User,
-    urlRoot : function(){ return Galaxy.options.root + 'api/users'; },
+    urlRoot : function(){ return Galaxy.root + 'api/users'; },
     //logger  : console,
 });
 

client/galaxy/scripts/mvc/visualization/visualization-model.js

@@ -19,10 +19,10 @@ var Visualization = Backbone.Model.extend(
         config : {}
     },
 
-    /** override urlRoot to handle presence/absence of galaxy_config */
+    /** override urlRoot to handle prefix */
     urlRoot : function(){
         var apiUrl = '/api/visualizations';
-        return (( window.galaxy_config && galaxy_config.root )?( galaxy_config.root + apiUrl ):( apiUrl ));
+        return Galaxy.root + apiUrl;
     },
 
     /** Set up the model, determine if accessible, bind listeners
@@ -89,7 +89,7 @@ var VisualizationCollection = Backbone.Collection.extend(
     //logger              : console,
 
     url : function(){
-        return galaxy_config.root + 'api/visualizations';
+        return Galaxy.root + 'api/visualizations';
     },
 
     /** Set up.

client/galaxy/scripts/mvc/workflow/workflow-manager.js

@@ -121,8 +121,8 @@ define(['mvc/workflow/workflow-connector'], function( Connector ) {
                 if (node.post_job_actions){
                     $.each( node.post_job_actions, function ( i, act ) {
                         var pja = {
-                            action_type : act.action_type, 
-                            output_name : act.output_name, 
+                            action_type : act.action_type,
+                            output_name : act.output_name,
                             action_arguments : act.action_arguments
                         }
                         post_job_actions[ act.action_type + act.output_name ] = null;
@@ -205,7 +205,7 @@ define(['mvc/workflow/workflow-connector'], function( Connector ) {
                         if(node.post_job_actions['HideDatasetAction'+ot.name] === undefined){
                             node.workflow_outputs.push(ot.name);
                             callout = $(node.element).find('.callout.'+ot.name);
-                            callout.find('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small.png');
+                            callout.find('img').attr('src', Galaxy.root + 'static/images/fugue/asterisk-small.png');
                             wf.has_changes = true;
                         }
                     });
@@ -285,7 +285,7 @@ define(['mvc/workflow/workflow-connector'], function( Connector ) {
                     if ( n_pred[ pred_k ] == 0 ) {
                         level_parents.push( pred_k );
                     }
-                }        
+                }
                 if ( level_parents.length == 0 ) {
                     break;
                 }
@@ -307,7 +307,7 @@ define(['mvc/workflow/workflow-connector'], function( Connector ) {
             // Layout each level
             var all_nodes = this.nodes;
             var h_pad = 80; v_pad = 30;
-            var left = h_pad;        
+            var left = h_pad;
             $.each( node_ids_by_level, function( i, ids ) {
                 // We keep nodes in the same order in a level to give the user
                 // some control over ordering

client/galaxy/scripts/mvc/workflow/workflow-view-data.js

@@ -82,13 +82,13 @@ define(['mvc/workflow/workflow-globals'], function( Globals ){
                 .css( { display: 'none' } )
                 .append(
                     $("<div class='buttons'></div>").append(
-                        $("<img/>").attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small-outline.png').click( function() {
+                        $("<img/>").attr('src', Galaxy.root + 'static/images/fugue/asterisk-small-outline.png').click( function() {
                             if ($.inArray(view.output.name, view.node.workflow_outputs) != -1){
                                 view.node.workflow_outputs.splice($.inArray(view.output.name, view.node.workflow_outputs), 1);
-                                view.$('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small-outline.png');
+                                view.$('img').attr('src', Galaxy.root + 'static/images/fugue/asterisk-small-outline.png');
                             }else{
                                 view.node.workflow_outputs.push(view.output.name);
-                                view.$('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small.png');
+                                view.$('img').attr('src', Galaxy.root + 'static/images/fugue/asterisk-small.png');
                             }
                             Globals.workflow.has_changes = true;
                             Globals.canvas_manager.draw_overview();
@@ -106,14 +106,14 @@ define(['mvc/workflow/workflow-globals'], function( Globals ){
 
         resetImage: function() {
             if ($.inArray( this.output.name, this.node.workflow_outputs) === -1){
-                this.$('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small-outline.png');
+                this.$('img').attr('src', Galaxy.root + 'static/images/fugue/asterisk-small-outline.png');
             } else{
-                this.$('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small.png');
+                this.$('img').attr('src', Galaxy.root + 'static/images/fugue/asterisk-small.png');
             }
         },
 
         hoverImage: function() {
-            this.$('img').attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small-yellow.png');
+            this.$('img').attr('src', Galaxy.root + 'static/images/fugue/asterisk-small-yellow.png');
         }
     });
 

client/galaxy/scripts/mvc/workflow/workflow-view.js

@@ -220,13 +220,13 @@ function reset_tool_search( initValue ) {
 
             // get available datatypes for post job action options
             this.datatypes = JSON.parse($.ajax({
-                url     : galaxy_config.root + 'api/datatypes',
+                url     : Galaxy.root + 'api/datatypes',
                 async   : false
             }).responseText);
 
             // get datatype mapping options
             this.datatypes_mapping = JSON.parse($.ajax({
-                url     : galaxy_config.root + 'api/datatypes/mapping',
+                url     : Galaxy.root + 'api/datatypes/mapping',
                 async   : false
             }).responseText);
 
@@ -700,7 +700,7 @@ function reset_tool_search( initValue ) {
             f.append( title );
             f.css( "left", $(window).scrollLeft() + 20 ); f.css( "top", $(window).scrollTop() + 20 );
             var b = $("<div class='toolFormBody'></div>");
-            var tmp = "<div><img height='16' align='middle' src='" + galaxy_config.root + "static/images/loading_small_white_bg.gif'/> loading tool info...</div>";
+            var tmp = "<div><img height='16' align='middle' src='" + Galaxy.root + "static/images/loading_small_white_bg.gif'/> loading tool info...</div>";
             b.append( tmp );
             node.form_html = tmp;
             f.append( b );

client/galaxy/scripts/utils/utils.js

@@ -175,7 +175,7 @@ function cssGetAttribute (classname, name) {
  */
 function cssLoadFile (url) {
     if (!$('link[href^="' + url + '"]').length) {
-        $('<link href="' + galaxy_config.root + url + '" rel="stylesheet">').appendTo('head');
+        $('<link href="' + Galaxy.root + url + '" rel="stylesheet">').appendTo('head');
     }
 };
 

client/galaxy/scripts/viz/circster.js

@@ -1084,7 +1084,7 @@ var Circster = Backbone.View.extend(
         {
             icon_class: 'plus-button', title: 'Add tracks', on_click: function()
             {
-                visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", vis.get('dbkey'), function(tracks)
+                visualization.select_datasets(Galaxy.root + "visualization/list_current_history_datasets", Galaxy.root + "api/datasets", vis.get('dbkey'), function(tracks)
                 {
                     vis.add_tracks(tracks);
                 });
@@ -1107,7 +1107,7 @@ var Circster = Backbone.View.extend(
 
                 // send to server
                 $.ajax({
-                    url: galaxy_config.root + "visualization/save",
+                    url: Galaxy.root + "visualization/save",
                     type: "POST",
                     dataType: "json",
                     data: {
@@ -1133,7 +1133,7 @@ var Circster = Backbone.View.extend(
         {
             icon_class: 'cross-circle', title: 'Close', on_click: function()
             {
-                window.location = galaxy_config.root + "visualization/list";
+                window.location = Galaxy.root + "visualization/list";
             }
         }], { tooltip_config: { placement: 'bottom' } });
 

client/galaxy/scripts/viz/sweepster.js

@@ -270,8 +270,8 @@ var SweepsterTrack = Backbone.Model.extend({
         if (options.track) {
             // FIXME: find a better way to deal with needed URLs:
             var track_config = _.extend({
-                                    data_url: galaxy_config.root + 'dummy1',
-                                    converted_datasets_state_url: galaxy_config.root + 'dummy2'
+                                    data_url: Galaxy.root + 'dummy1',
+                                    converted_datasets_state_url: Galaxy.root + 'dummy2'
                                 }, options.track);
             this.set('track', tracks.object_from_template(track_config, {}, null));
         }
@@ -407,7 +407,7 @@ var SweepsterTrackView = Backbone.View.extend({
         // Render tile placeholders.
         this.model.get('regions').each(function() {
             self.$el.append($('<td/>').addClass('tile').html(
-                $('<img/>').attr('src', galaxy_config.root + 'images/loading_large_white_bg.gif')
+                $('<img/>').attr('src', Galaxy.root + 'images/loading_large_white_bg.gif')
             ));
         });
 

client/galaxy/scripts/viz/trackster.js

@@ -84,7 +84,7 @@ var TracksterUI = Base.extend({
 
         // Make call to save visualization.
         return $.ajax({
-            url: galaxy_config.root + "visualization/save",
+            url: Galaxy.root + "visualization/save",
             type: "POST",
             dataType: "json",
             data: {
@@ -118,7 +118,7 @@ var TracksterUI = Base.extend({
         var self = this,
             menu = mod_icon_btn.create_icon_buttons_menu([
             { icon_class: 'plus-button', title: 'Add tracks', on_click: function() {
-                visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey },
+                visualization.select_datasets(Galaxy.root + "visualization/list_current_history_datasets", Galaxy.root + "api/datasets", { 'f-dbkey': view.dbkey },
                 function(new_tracks) {
                     _.each(new_tracks, function(track) {
                         view.add_drawable( tracks.object_from_template(track, view, view) );
@@ -373,11 +373,11 @@ var TracksterUI = Base.extend({
                     "Cancel": function() { Galaxy.modal.hide(); },
                     "Leave without Saving" : function() {
                         $(window).off('beforeunload');
-                        window.location = galaxy_config.root + 'visualization';
+                        window.location = Galaxy.root + 'visualization';
                     },
                     "Save" : function() {
                         $.when(self.save_viz()).then(function() {
-                            window.location = galaxy_config.root + 'visualization';
+                            window.location = Galaxy.root + 'visualization';
                         });
                     }
                 }
@@ -385,7 +385,7 @@ var TracksterUI = Base.extend({
 
         }
         else {
-            window.location = galaxy_config.root + 'visualization';
+            window.location = Galaxy.root + 'visualization';
         }
     }
 
@@ -397,7 +397,7 @@ var TracksterView = Backbone.View.extend(
     initialize : function ()
     {
         // load ui
-        ui = new TracksterUI(galaxy_config.root);
+        ui = new TracksterUI(Galaxy.root);
 
         // create button menu
         ui.createButtonMenu();
@@ -442,7 +442,7 @@ var TracksterView = Backbone.View.extend(
             listTracksParams[ 'f-dbkey' ] = dbkey;
         }
         $.ajax({
-            url: galaxy_config.root + 'visualization/list_tracks?' + $.param( listTracksParams ),
+            url: Galaxy.root + 'visualization/list_tracks?' + $.param( listTracksParams ),
             dataType: "html",
             error: function() { alert( "Could not add this dataset to browser." ); },
 
@@ -462,7 +462,7 @@ var TracksterView = Backbone.View.extend(
                                 $(parent.document).find('input[name=id]:checked').each(function() {
                                     var vis_id = $(this).val();
                                     dataset_params.id = vis_id;
-                                    window.location = galaxy_config.root + "visualization/trackster?" + $.param(dataset_params);
+                                    window.location = Galaxy.root + "visualization/trackster?" + $.param(dataset_params);
                                 });
                             }
                         }
@@ -482,7 +482,7 @@ var TracksterView = Backbone.View.extend(
                         ),
                         buttons : {
                             "Cancel": function() {
-                                window.location = galaxy_config.root + "visualization/list";
+                                window.location = Galaxy.root + "visualization/list";
                             },
                             "View in saved visualization": function() {
                                 view_in_saved();
@@ -533,7 +533,7 @@ var TracksterView = Backbone.View.extend(
         // ajax
         $.ajax(
         {
-            url: galaxy_config.root + "api/genomes?chrom_info=True",
+            url: Galaxy.root + "api/genomes?chrom_info=True",
             data: {},
             error: function() { alert( "Couldn't create new browser." ); },
             success: function(response)
@@ -543,7 +543,7 @@ var TracksterView = Backbone.View.extend(
                     title   : "New Visualization",
                     body    : self.template_view_new(response),
                     buttons : {
-                        "Cancel": function() { window.location = galaxy_config.root + "visualization/list"; },
+                        "Cancel": function() { window.location = Galaxy.root + "visualization/list"; },
                         "Create": function() { self.create_browser($("#new-title").val(), $("#new-dbkey").val()); Galaxy.modal.hide(); }
                     }
                 });
@@ -593,7 +593,7 @@ var TracksterView = Backbone.View.extend(
                         '</div>' +
                         '<div class="form-row">' +
                             'Is the build not listed here? ' +
-                            '<a href="' + galaxy_config.root + 'user/dbkeys?use_panels=True">Add a Custom Build</a>' +
+                            '<a href="' + Galaxy.root + 'user/dbkeys?use_panels=True">Add a Custom Build</a>' +
                         '</div>' +
                     '</form>';
 
@@ -629,7 +629,7 @@ var TracksterView = Backbone.View.extend(
         // add dataset
         if (galaxy_config.app.add_dataset)
             $.ajax({
-                url: galaxy_config.root + "api/datasets/" + galaxy_config.app.add_dataset,
+                url: Galaxy.root + "api/datasets/" + galaxy_config.app.add_dataset,
                 data: { hda_ldda: 'hda', data_type: 'track_config' },
                 dataType: "json",
                 success: function(track_data) { view.add_drawable( tracks.object_from_template(track_data, view, view) ); }

client/galaxy/scripts/viz/trackster/tracks.js

@@ -889,7 +889,7 @@ var TracksterView = Backbone.View.extend({
         // Introduction div shown when there are no tracks.
         this.intro_div = $("<div/>").addClass("intro").appendTo(this.viewport_container);
         var add_tracks_button = $("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function () {
-            visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey }, function(tracks) {
+            visualization.select_datasets(Galaxy.root + "visualization/list_current_history_datasets", Galaxy.root + "api/datasets", { 'f-dbkey': view.dbkey }, function(tracks) {
                 _.each(tracks, function(track) {
                     view.add_drawable( object_from_template(track, view, view) );
                 });
@@ -1186,7 +1186,7 @@ extend( TracksterView.prototype, DrawableCollection.prototype, {
             view = this,
             chrom_data = $.Deferred();
         $.ajax({
-            url: galaxy_config.root + "api/genomes/" + this.dbkey,
+            url: Galaxy.root + "api/genomes/" + this.dbkey,
             data: url_parms,
             dataType: "json",
             success: function (result) {
@@ -1835,7 +1835,7 @@ var TracksterToolView = Backbone.View.extend({
         url_params.inputs = this.model.get_inputs_dict();
         var ss_deferred = new util.ServerStateDeferred({
             ajax_settings: {
-                url: galaxy_config.root + "api/tools",
+                url: Galaxy.root + "api/tools",
                 data: JSON.stringify(url_params),
                 dataType: "json",
                 contentType: 'application/json',
@@ -2257,7 +2257,7 @@ extend(Track.prototype, Drawable.prototype, {
 
                         // Go to visualization.
                         window.location.href =
-                            galaxy_config.root + "visualization/sweepster" + "?" +
+                            Galaxy.root + "visualization/sweepster" + "?" +
                             $.param({
                                 dataset_id: track.dataset.id,
                                 hda_ldda: track.dataset.get('hda_ldda'),
@@ -3506,7 +3506,7 @@ var ReferenceTrack = function (view) {
     // Use offset to ensure that bases at tile edges are drawn.
     this.left_offset = view.canvas_manager.char_width_px;
     this.container_div.addClass("reference-track");
-    this.data_url = galaxy_config.root + "api/genomes/" + this.view.dbkey;
+    this.data_url = Galaxy.root + "api/genomes/" + this.view.dbkey;
     this.data_url_extra_params = {reference: true};
     this.data_manager = new visualization.GenomeReferenceDataManager({
         data_url: this.data_url,

client/galaxy/scripts/viz/visualization.js

@@ -115,7 +115,7 @@ _.extend( CanvasManager.prototype, {
         var patterns = this.patterns,
             dummy_context = this.dummy_context,
             image = new Image();
-        image.src = galaxy_config.root + "static/images" + path;
+        image.src = Galaxy.root + "static/images" + path;
         image.onload = function() {
             patterns[key] = dummy_context.createPattern( image, "repeat" );
         };
@@ -958,7 +958,7 @@ var Visualization = Backbone.Model.extend({
         type: ''
     },
 
-    urlRoot: galaxy_config.root + "api/visualizations",
+    urlRoot: Galaxy.root + "api/visualizations",
 
     /**
      * POSTs visualization's JSON to its URL using the parameter 'vis_json'

static/maps/galaxy-app-base.js.map

@@ -1 +1 @@
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static/maps/layout/masthead.js.map

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static/maps/layout/scratchbook.js.map

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static/maps/mvc/citation/citation-model.js.map

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static/maps/mvc/collection/collection-view-edit.js.map

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static/maps/mvc/history/history-content-model.js.map

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static/maps/mvc/history/options-menu.js.map

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static/maps/mvc/job/job-model.js.map

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static/maps/mvc/library/library-librarytoolbar-view.js.map

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static/maps/mvc/library/library-model.js.map

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static/maps/mvc/tag.js.map

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static/maps/mvc/tool/tools-form-workflow.js.map

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static/maps/mvc/tool/tools-jobs.js.map

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static/maps/mvc/ui/ui-select-ftp.js.map

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static/maps/mvc/ui/ui-select-library.js.map

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static/maps/mvc/upload/upload-ftp.js.map

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static/maps/mvc/upload/upload-view.js.map

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static/maps/mvc/user/user-model.js.map

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static/maps/mvc/visualization/visualization-model.js.map

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static/maps/mvc/workflow/workflow-view-data.js.map

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static/scripts/bundled/analysis.bundled.js

@@ -362,7 +362,7 @@ webpackJsonp([0],[
 	        outputs: []
 	    },
 	
-	    urlRoot: galaxy_config.root + 'api/tools',
+	    urlRoot: Galaxy.root + 'api/tools',
 	
 	    initialize: function(options) {
 	
@@ -592,7 +592,7 @@ webpackJsonp([0],[
 	        clear_key: 27
 	    },
 	
-	    urlRoot: galaxy_config.root + 'api/tools',
+	    urlRoot: Galaxy.root + 'api/tools',
 	
 	    initialize: function() {
 	        this.on("change:query", this.do_search);
@@ -623,7 +623,7 @@ webpackJsonp([0],[
 	        this.timer = setTimeout(function () {
 	            // log the search to analytics if present
 	            if ( typeof ga !== 'undefined' ) {
-	                ga( 'send', 'pageview', galaxy_config.root + '?q=' + q );
+	                ga( 'send', 'pageview', Galaxy.root + '?q=' + q );
 	            }
 	            $.get( self.urlRoot, { q: q }, function (data) {
 	                self.set("results", data);
@@ -1243,7 +1243,7 @@ webpackJsonp([0],[
 	        return this.attributes.metadata.get(attribute);
 	    },
 	
-	    urlRoot: galaxy_config.root + "api/datasets"
+	    urlRoot: Galaxy.root + "api/datasets"
 	});
 	
 	/**
@@ -1262,8 +1262,8 @@ webpackJsonp([0],[
 	
 	        // If first data chunk is available, next chunk is 1.
 	        this.attributes.chunk_index = (this.attributes.first_data_chunk ? 1 : 0);
-	        this.attributes.chunk_url = galaxy_config.root + 'dataset/display?dataset_id=' + this.id;
-	        this.attributes.url_viz = galaxy_config.root + 'visualization';
+	        this.attributes.chunk_url = Galaxy.root + 'dataset/display?dataset_id=' + this.id;
+	        this.attributes.url_viz = Galaxy.root + 'visualization';
 	    },
 	
 	    /**
@@ -3562,7 +3562,7 @@ webpackJsonp([0],[
 	 */
 	function cssLoadFile (url) {
 	    if (!$('link[href^="' + url + '"]').length) {
-	        $('<link href="' + galaxy_config.root + url + '" rel="stylesheet">').appendTo('head');
+	        $('<link href="' + Galaxy.root + url + '" rel="stylesheet">').appendTo('head');
 	    }
 	};
 	
@@ -8103,7 +8103,7 @@ webpackJsonp([0],[
 	
 	// collection of libraries
 	var Libraries = Backbone.Collection.extend({
-	    url: galaxy_config.root + 'api/libraries?deleted=false'
+	    url: Galaxy.root + 'api/libraries?deleted=false'
 	});
 	
 	// collection of dataset
@@ -8116,7 +8116,7 @@ webpackJsonp([0],[
 	        });
 	    },
 	    url: function() {
-	        return galaxy_config.root + 'api/libraries/' + this.config.get('library_id') + '/contents'
+	        return Galaxy.root + 'api/libraries/' + this.config.get('library_id') + '/contents';
 	    }
 	});
 	
@@ -8428,7 +8428,7 @@ webpackJsonp([0],[
 	
 	        // initial fetch of ftps
 	        Utils.get({
-	            url     : galaxy_config.root + 'api/remote_files',
+	            url     : Galaxy.root + 'api/remote_files',
 	            success : function(response) {
 	                var data = [];
 	                for (var i in response) {
@@ -9006,7 +9006,7 @@ webpackJsonp([0],[
 	    _logNamespace : logNamespace,
 	
 	    /** root api url */
-	    urlRoot : galaxy_config.root + 'api',
+	    urlRoot : Galaxy.root + 'api',
 	    partial : true, // Assume some tools in history/workflow may not be properly annotated yet.
 	    model : Citation,
 	} );
@@ -11149,7 +11149,7 @@ webpackJsonp([0],[
 	        // post job
 	        Utils.request({
 	            type    : 'POST',
-	            url     : galaxy_config.root + 'api/tools',
+	            url     : Galaxy.root + 'api/tools',
 	            data    : job_def,
 	            success : function(response) {
 	                callback && callback();
@@ -12686,7 +12686,7 @@ webpackJsonp([0],[
 	        // load extensions
 	        var self = this;
 	        Utils.get({
-	            url     : galaxy_config.root + 'api/datatypes?extension_only=False',
+	            url     : Galaxy.root + 'api/datatypes?extension_only=False',
 	            success : function( datatypes ) {
 	                for ( key in datatypes ) {
 	                    self.list_extensions.push({
@@ -12710,7 +12710,7 @@ webpackJsonp([0],[
 	
 	        // load genomes
 	        Utils.get({
-	            url     : galaxy_config.root + 'api/genomes',
+	            url     : Galaxy.root + 'api/genomes',
 	            success : function( genomes ) {
 	                for ( key in genomes ) {
 	                    self.list_genomes.push({
@@ -14473,7 +14473,7 @@ webpackJsonp([0],[
 	
 	        // load extension
 	        Utils.get({
-	            url     : galaxy_config.root + 'api/remote_files',
+	            url     : Galaxy.root + 'api/remote_files',
 	            success : function(ftp_files) { self._fill(ftp_files); },
 	            error   : function() { self._fill(); }
 	        });
@@ -15858,8 +15858,7 @@ webpackJsonp([0],[
 	    options = options || {};
 	    var isAnon = options.anonymous === undefined? true : options.anonymous,
 	        purgeAllowed = options.purgeAllowed || false,
-	        root = options.root || ( ( Galaxy && Galaxy.options )? Galaxy.options.root: '/' ),
-	        menu = buildMenu( isAnon, purgeAllowed, root );
+	        menu = buildMenu( isAnon, purgeAllowed, Galaxy.root );
 	    //console.debug( 'menu:', menu );
 	    return new PopupMenu( $button, menu );
 	};
@@ -16314,7 +16313,7 @@ webpackJsonp([0],[
 	        var panel = this,
 	            historyFn = function(){
 	                // make this current and get history data with one call
-	                return jQuery.getJSON( galaxy_config.root + 'history/set_as_current?id=' + historyId  );
+	                return jQuery.getJSON( Galaxy.root + 'history/set_as_current?id=' + historyId  );
 	                //    method  : 'PUT'
 	                //});
 	            };
@@ -16326,14 +16325,14 @@ webpackJsonp([0],[
 	
 	    /** creates a new history on the server and sets it as the user's current history */
 	    createNewHistory : function( attributes ){
-	        if( !Galaxy || !Galaxy.currUser || Galaxy.currUser.isAnonymous() ){
+	        if( !Galaxy || !Galaxy.user || Galaxy.user.isAnonymous() ){
 	            this.displayMessage( 'error', _l( 'You must be logged in to create histories' ) );
 	            return $.when();
 	        }
 	        var panel = this,
 	            historyFn = function(){
 	                // create a new history and save: the server will return the proper JSON
-	                return jQuery.getJSON( galaxy_config.root + 'history/create_new_current'  );
+	                return jQuery.getJSON( Galaxy.root + 'history/create_new_current'  );
 	            };
 	
 	        // id undefined bc there is no historyId yet - the server will provide
@@ -16731,7 +16730,7 @@ webpackJsonp([0],[
 	    },
 	
 	    // ........................................................................ urls
-	    urlRoot: galaxy_config.root + 'api/histories',
+	    urlRoot: Galaxy.root + 'api/histories',
 	
 	    // ........................................................................ set up/tear down
 	    /** Set up the model
@@ -16817,16 +16816,16 @@ webpackJsonp([0],[
 	    },
 	
 	    // ........................................................................ common queries
-	    /** T/F is this history owned by the current user (Galaxy.currUser)
+	    /** T/F is this history owned by the current user (Galaxy.user)
 	     *      Note: that this will return false for an anon user even if the history is theirs.
 	     */
 	    ownedByCurrUser : function(){
 	        // no currUser
-	        if( !Galaxy || !Galaxy.currUser ){
+	        if( !Galaxy || !Galaxy.user ){
 	            return false;
 	        }
 	        // user is anon or history isn't owned
-	        if( Galaxy.currUser.isAnonymous() || Galaxy.currUser.id !== this.get( 'user_id' ) ){
+	        if( Galaxy.user.isAnonymous() || Galaxy.user.id !== this.get( 'user_id' ) ){
 	            return false;
 	        }
 	        return true;
@@ -16978,7 +16977,7 @@ webpackJsonp([0],[
 	
 	    setAsCurrent : function(){
 	        var history = this,
-	            xhr = jQuery.getJSON( galaxy_config.root + 'history/set_as_current?id=' + this.id );
+	            xhr = jQuery.getJSON( Galaxy.root + 'history/set_as_current?id=' + this.id );
 	
 	        xhr.done( function(){
 	            history.trigger( 'set-as-current', history );
@@ -17011,9 +17010,9 @@ webpackJsonp([0],[
 	    function getHistory( id ){
 	        // get the history data
 	        if( historyId === 'current' ){
-	            return jQuery.getJSON( galaxy_config.root + 'history/current_history_json' );
+	            return jQuery.getJSON( Galaxy.root + 'history/current_history_json' );
 	        }
-	        return jQuery.ajax( galaxy_config.root + 'api/histories/' + historyId );
+	        return jQuery.ajax( Galaxy.root + 'api/histories/' + historyId );
 	    }
 	    function isEmpty( historyData ){
 	        // get the number of hdas accrd. to the history
@@ -17039,7 +17038,7 @@ webpackJsonp([0],[
 	            // by frontend.
 	            data.dataset_collection_details = hdcaDetailIds.join( ',' );
 	        }
-	        return jQuery.ajax( galaxy_config.root + 'api/histories/' + historyData.id + '/contents', { data: data });
+	        return jQuery.ajax( Galaxy.root + 'api/histories/' + historyData.id + '/contents', { data: data });
 	    }
 	
 	    // getting these concurrently is 400% slower (sqlite, local, vanilla) - so:
@@ -17202,7 +17201,7 @@ webpackJsonp([0],[
 	        this.setUpListeners();
 	    },
 	
-	    urlRoot : ( window.galaxy_config? galaxy_config.root : '/' ) + 'api/histories',
+	    urlRoot : Galaxy.root + 'api/histories',
 	    url     : function(){ return this.urlRoot; },
 	
 	    /** returns map of default filters and settings for fetching from the API */
@@ -17310,7 +17309,7 @@ webpackJsonp([0],[
 	    create : function create( data, hdas, historyOptions, xhrOptions ){
 	        //TODO: .create is actually a collection function that's overridden here
 	        var collection = this,
-	            xhr = jQuery.getJSON( galaxy_config.root + 'history/create_new_current'  );
+	            xhr = jQuery.getJSON( Galaxy.root + 'history/create_new_current'  );
 	        return xhr.done( function( newData ){
 	            collection.setCurrent( new History( newData, [], historyOptions || {} ) );
 	        });
@@ -17430,7 +17429,7 @@ webpackJsonp([0],[
 	    },
 	
 	    /** root api url */
-	    urlRoot : galaxy_config.root + 'api/histories',
+	    urlRoot : Galaxy.root + 'api/histories',
 	    /** complete api url */
 	    url : function(){
 	        return this.urlRoot + '/' + this.historyId + '/contents';
@@ -17787,7 +17786,7 @@ webpackJsonp([0],[
 	//TODO: global
 	//TODO: these are probably better done on the leaf classes
 	    /** history content goes through the 'api/histories' API */
-	    urlRoot: ( window.Galaxy? Galaxy.options.root : '/' ) + 'api/histories/',
+	    urlRoot: Galaxy.root + 'api/histories/',
 	
 	    /** full url spec. for this content */
 	    url : function(){
@@ -18059,9 +18058,8 @@ webpackJsonp([0],[
 	            'meta_download' : 'dataset/get_metadata_file?hda_id=' + id + '&metadata_name='
 	        };
 	//TODO: global
-	        var root = ( window.galaxy_config && galaxy_config.root )?( galaxy_config.root ):( '/' );
 	        _.each( urls, function( value, key ){
-	            urls[ key ] = root + value;
+	            urls[ key ] = Galaxy.root + value;
 	        });
 	        this.urls = urls;
 	        return urls;
@@ -18231,12 +18229,11 @@ webpackJsonp([0],[
 	    model : DatasetAssociation,
 	
 	    /** root api url */
-	    urlRoot : (( window.galaxy_config && galaxy_config.root )?( galaxy_config.root ):( '/' ))
-	        + 'api/datasets',
+	    urlRoot : Galaxy.root + 'api/datasets',
 	
 	    /** url fn */
 	    url : function(){
-	        return this.urlRoot
+	        return this.urlRoot;
 	    },
 	
 	    // ........................................................................ common queries
@@ -18606,14 +18603,13 @@ webpackJsonp([0],[
 	
 	    /** url fn */
 	    url : function(){
-	        var galaxyRoot = (( window.galaxy_config && galaxy_config.root )?( galaxy_config.root ):( '/' ));
 	        // won't always be an hda
 	        if( !this.has( 'history_id' ) ){
 	            console.warn( 'no endpoint for non-hdas within a collection yet' );
 	            // (a little silly since this api endpoint *also* points at hdas)
-	            return galaxyRoot + 'api/datasets';
+	            return Galaxy.root + 'api/datasets';
 	        }
-	        return galaxyRoot + 'api/histories/' + this.get( 'history_id' ) + '/contents/' + this.get( 'id' );
+	        return Galaxy.root + 'api/histories/' + this.get( 'history_id' ) + '/contents/' + this.get( 'id' );
 	    },
 	
 	    defaults : _.extend( {},
@@ -19116,7 +19112,7 @@ webpackJsonp([0],[
 	        var $newRender = _super.prototype._buildNewRender.call( this );
 	        if( !this.model ){ return $newRender; }
 	
-	        if( Galaxy && Galaxy.currUser && Galaxy.currUser.id && Galaxy.currUser.id === this.model.get( 'user_id' ) ){
+	        if( Galaxy && Galaxy.user && Galaxy.user.id && Galaxy.user.id === this.model.get( 'user_id' ) ){
 	            this._renderTags( $newRender );
 	            this._renderAnnotation( $newRender );
 	        }
@@ -19211,8 +19207,8 @@ webpackJsonp([0],[
 	        if( !this.model ){ return; }
 	
 	        // anon users shouldn't have access to any of the following
-	        if( ( !Galaxy.currUser || Galaxy.currUser.isAnonymous() )
-	        ||  ( Galaxy.currUser.id !== this.model.get( 'user_id' ) ) ){
+	        if( ( !Galaxy.user || Galaxy.user.isAnonymous() )
+	        ||  ( Galaxy.user.id !== this.model.get( 'user_id' ) ) ){
 	            return;
 	        }
 	
@@ -21204,7 +21200,7 @@ webpackJsonp([0],[
 	        //if( xhr.responseText ){
 	        //    xhr.responseText = _.escape( xhr.responseText );
 	        //}
-	        var user = Galaxy.currUser,
+	        var user = Galaxy.user,
 	            // add the args (w/ some extra info) into an obj
 	            parsed = {
 	                message : this._bePolite( msg ),
@@ -25025,7 +25021,7 @@ webpackJsonp([0],[
 	    /** @returns {String[]} all tags used by the current user */
 	    _getTagsUsed : function(){
 	//TODO: global
-	        return Galaxy.currUser.get( 'tags_used' );
+	        return Galaxy.user.get( 'tags_used' );
 	    },
 	
 	    /** set up any event listeners on the view's DOM (mostly handled by select2) */
@@ -25048,11 +25044,11 @@ webpackJsonp([0],[
 	     */
 	    _addNewTagToTagsUsed : function( newTag ){
 	//TODO: global
-	        var tagsUsed = Galaxy.currUser.get( 'tags_used' );
+	        var tagsUsed = Galaxy.user.get( 'tags_used' );
 	        if( !_.contains( tagsUsed, newTag ) ){
 	            tagsUsed.push( newTag );
 	            tagsUsed.sort();
-	            Galaxy.currUser.set( 'tags_used', tagsUsed );
+	            Galaxy.user.set( 'tags_used', tagsUsed );
 	        }
 	    },
 	
@@ -25426,7 +25422,7 @@ webpackJsonp([0],[
 	        if( !this.model ){ return; }
 	
 	        // anon users shouldn't have access to any of the following
-	        if( !Galaxy.currUser || Galaxy.currUser.isAnonymous() ){
+	        if( !Galaxy.user || Galaxy.user.isAnonymous() ){
 	            return;
 	        }
 	
@@ -26529,8 +26525,7 @@ webpackJsonp([0],[
 	     */
 	    createList : function( name ){
 	        var creator = this,
-	            root = ( window.Galaxy && Galaxy.options.root )? Galaxy.options.root : '/',
-	            url = root + 'api/histories/' + this.historyId + '/contents/dataset_collections';
+	            url = Galaxy.root + 'api/histories/' + this.historyId + '/contents/dataset_collections';
 	
 	        //TODO: use ListPairedCollection.create()
 	        var ajaxData = {
@@ -28065,7 +28060,7 @@ webpackJsonp([0],[
 	                    '</div>' +
 	                   '<div class="navbar-brand">' +
 	                        '<a href="' + options.logo_url + '">' +
-	                            '<img style="margin-left: 0.35em;" border="0" src="' + galaxy_config.root + 'static/images/galaxyIcon_noText.png">' +
+	                            '<img style="margin-left: 0.35em;" border="0" src="' + Galaxy.root + 'static/images/galaxyIcon_noText.png">' +
 	                            '<span id="brand"> Galaxy ' + brand_text + '</span>' +
 	                        '</a>' +
 	                    '</div>' +
@@ -28445,7 +28440,7 @@ webpackJsonp([0],[
 	
 	        // update url
 	        if ( this.options.content !== undefined && this.options.content.indexOf( '//' ) === -1 ){
-	            this.options.content = galaxy_config.root + this.options.content;
+	            this.options.content = Galaxy.root + this.options.content;
 	        }
 	
 	        // add template for tab
@@ -28492,7 +28487,7 @@ webpackJsonp([0],[
 	
 	        // update url
 	        if (menuOptions.content && menuOptions.content.indexOf('//') === -1)
-	            menuOptions.content = galaxy_config.root + menuOptions.content;
+	            menuOptions.content = Galaxy.root + menuOptions.content;
 	
 	        // check if submenu element is available
 	        if (!this.$menu){
@@ -28550,7 +28545,7 @@ webpackJsonp([0],[
 	        var $popover_element = $(this.el).find('.head');
 	        $popover_element.popover({
 	            html: true,
-	            content: 'Please <a href="' + galaxy_config.root + 'user/login?use_panels=True">log in</a> or <a href="' + galaxy_config.root + 'user/create?use_panels=True">register</a> to use this feature.',
+	            content: 'Please <a href="' + Galaxy.root + 'user/login?use_panels=True">log in</a> or <a href="' + Galaxy.root + 'user/create?use_panels=True">register</a> to use this feature.',
 	            placement: 'bottom'
 	        }).on('shown.bs.popover', function() { // hooking on bootstrap event to automatically hide popovers after delay
 	            setTimeout(function() {
@@ -28717,7 +28712,7 @@ webpackJsonp([0],[
 	                else {
 	                    _.extend(frame_config, {
 	                        type: 'url',
-	                        content: galaxy_config.root + 'datasets/' +
+	                        content: Galaxy.root + 'datasets/' +
 	                                 dataset.id + '/display/?preview=True'
 	                    });
 	                }
@@ -28738,7 +28733,7 @@ webpackJsonp([0],[
 	        __webpack_require__.e/* require */(1, function(__webpack_require__) { /* WEBPACK VAR INJECTION */(function($, _) {var __WEBPACK_AMD_REQUIRE_ARRAY__ = [__webpack_require__(/*! viz/visualization */ 123), __webpack_require__(/*! viz/trackster */ 125)]; (function(visualization, trackster) {
 	            var viz = new visualization.Visualization({id: viz_id});
 	            $.when( viz.fetch() ).then( function() {
-	                var ui = new trackster.TracksterUI(galaxy_config.root);
+	                var ui = new trackster.TracksterUI(Galaxy.root);
 	
 	                // Construct frame config based on dataset's type.
 	                var frame_config = {

static/scripts/bundled/galaxy.bundled.js

@@ -188,8 +188,6 @@ webpackJsonp([3],{
 	    self.debug( '_initUser:', userJSON );
 	    self.user = new userModel.User( userJSON );
 	    self.user.logger = self.logger;
-	    //TODO: temp - old alias
-	    self.currUser = self.user;
 	    return self;
 	};
 	

static/scripts/galaxy-app-base.js

@@ -1,2 +1,2 @@
-define(["libs/underscore","libs/backbone","mvc/base-mvc","mvc/user/user-model","utils/metrics-logger","utils/add-logging","utils/localization"],function(a,b,c,d,e,f,g){function h(a,b){var c=this;return c._init(a||{},b||{})}f(h,"GalaxyApp");var i="galaxy:debug",j=i+":namespaces",k=!1;try{k="true"==localStorage.getItem(i)}catch(l){console.log(g("localStorage not available for debug flag retrieval"))}return h.prototype._init=function(c,d){var e=this;return a.extend(e,b.Events),k&&(e.logger=console,console.debug("debugging galaxy:","options:",c,"bootstrapped:",d)),e._processOptions(c),e.root=c.root||"/",e._initConfig(c.config||d.config||{}),e._patchGalaxy(window.Galaxy),e._initLogger(e.options.loggerOptions||{}),e.debug("GalaxyApp.options: ",e.options),e.debug("GalaxyApp.config: ",e.config),e.debug("GalaxyApp.logger: ",e.logger),e._initLocale(),e.debug("GalaxyApp.localize: ",e.localize),e.config=c.config||{},e.debug("GalaxyApp.config: ",e.config),e._initUser(c.user||{}),e.debug("GalaxyApp.user: ",e.user),e._setUpListeners(),e.trigger("ready",e),e},h.prototype.defaultOptions={patchExisting:!0,root:"/"},h.prototype._processOptions=function(a){var b=this,c=b.defaultOptions;b.options={};for(var d in c)c.hasOwnProperty(d)&&(b.options[d]=a.hasOwnProperty(d)?a[d]:c[d]);return b},h.prototype._initConfig=function(a){var b=this;return b.config=a,b.config.debug=k||b.config.debug,b},h.prototype._patchGalaxy=function(a){var b=this;if(b.options.patchExisting&&a)for(var c in a)a.hasOwnProperty(c)&&(b[c]=a[c])},h.prototype._initLogger=function(a){var b=this;if(b.config.debug){a.consoleLogger=a.consoleLogger||console,a.consoleLevel=a.consoleLevel||e.MetricsLogger.ALL;try{a.consoleNamespaceWhitelist=localStorage.getItem(j).split(",")}catch(d){}}return b.logger=new e.MetricsLogger(a),b.emit={},["log","debug","info","warn","error","metric"].map(function(a){b.emit[a]=function(){b.logger.emit(a,arguments[0],Array.prototype.slice.call(arguments,1))}}),b.config.debug&&(c.LoggableMixin.logger=b.logger),b},h.prototype._initLocale=function(a){var b=this;return b.debug("_initLocale:",a),b.localize=g,window._l=b.localize,b},h.prototype._initUser=function(a){var b=this;return b.debug("_initUser:",a),b.user=new d.User(a),b.user.logger=b.logger,b.currUser=b.user,b},h.prototype._setUpListeners=function(){var a=this;return a.lastAjax={},$(document).bind("ajaxSend",function(b,c,d){var e=d.data;try{e=JSON.parse(e)}catch(f){}a.lastAjax={url:location.href.slice(0,-1)+d.url,data:e}}),a},h.prototype.debugging=function(a){var b=this;try{if(void 0===a)return"true"===localStorage.getItem(i);if(a)return localStorage.setItem(i,!0),!0;localStorage.removeItem(i),b.debuggingNamespaces(null)}catch(c){console.log(g("localStorage not available for debug flag retrieval"))}return!1},h.prototype.debuggingNamespaces=function(a){var b=this;try{if(void 0===a){var c=localStorage.getItem(j);return"string"==typeof c?c.split(","):[]}null===a?localStorage.removeItem(j):localStorage.setItem(j,a);var d=b.debuggingNamespaces();return b.logger&&(b.logger.options.consoleNamespaceWhitelist=d),d}catch(e){console.log(g("localStorage not available for debug namespace retrieval"))}},h.prototype.toString=function(){var a=this.user?this.user.get("email")||"(anonymous)":"uninitialized";return"GalaxyApp("+a+")"},{GalaxyApp:h}});
+define(["libs/underscore","libs/backbone","mvc/base-mvc","mvc/user/user-model","utils/metrics-logger","utils/add-logging","utils/localization"],function(a,b,c,d,e,f,g){function h(a,b){var c=this;return c._init(a||{},b||{})}f(h,"GalaxyApp");var i="galaxy:debug",j=i+":namespaces",k=!1;try{k="true"==localStorage.getItem(i)}catch(l){console.log(g("localStorage not available for debug flag retrieval"))}return h.prototype._init=function(c,d){var e=this;return a.extend(e,b.Events),k&&(e.logger=console,console.debug("debugging galaxy:","options:",c,"bootstrapped:",d)),e._processOptions(c),e.root=c.root||"/",e._initConfig(c.config||d.config||{}),e._patchGalaxy(window.Galaxy),e._initLogger(e.options.loggerOptions||{}),e.debug("GalaxyApp.options: ",e.options),e.debug("GalaxyApp.config: ",e.config),e.debug("GalaxyApp.logger: ",e.logger),e._initLocale(),e.debug("GalaxyApp.localize: ",e.localize),e.config=c.config||{},e.debug("GalaxyApp.config: ",e.config),e._initUser(c.user||{}),e.debug("GalaxyApp.user: ",e.user),e._setUpListeners(),e.trigger("ready",e),e},h.prototype.defaultOptions={patchExisting:!0,root:"/"},h.prototype._processOptions=function(a){var b=this,c=b.defaultOptions;b.options={};for(var d in c)c.hasOwnProperty(d)&&(b.options[d]=a.hasOwnProperty(d)?a[d]:c[d]);return b},h.prototype._initConfig=function(a){var b=this;return b.config=a,b.config.debug=k||b.config.debug,b},h.prototype._patchGalaxy=function(a){var b=this;if(b.options.patchExisting&&a)for(var c in a)a.hasOwnProperty(c)&&(b[c]=a[c])},h.prototype._initLogger=function(a){var b=this;if(b.config.debug){a.consoleLogger=a.consoleLogger||console,a.consoleLevel=a.consoleLevel||e.MetricsLogger.ALL;try{a.consoleNamespaceWhitelist=localStorage.getItem(j).split(",")}catch(d){}}return b.logger=new e.MetricsLogger(a),b.emit={},["log","debug","info","warn","error","metric"].map(function(a){b.emit[a]=function(){b.logger.emit(a,arguments[0],Array.prototype.slice.call(arguments,1))}}),b.config.debug&&(c.LoggableMixin.logger=b.logger),b},h.prototype._initLocale=function(a){var b=this;return b.debug("_initLocale:",a),b.localize=g,window._l=b.localize,b},h.prototype._initUser=function(a){var b=this;return b.debug("_initUser:",a),b.user=new d.User(a),b.user.logger=b.logger,b},h.prototype._setUpListeners=function(){var a=this;return a.lastAjax={},$(document).bind("ajaxSend",function(b,c,d){var e=d.data;try{e=JSON.parse(e)}catch(f){}a.lastAjax={url:location.href.slice(0,-1)+d.url,data:e}}),a},h.prototype.debugging=function(a){var b=this;try{if(void 0===a)return"true"===localStorage.getItem(i);if(a)return localStorage.setItem(i,!0),!0;localStorage.removeItem(i),b.debuggingNamespaces(null)}catch(c){console.log(g("localStorage not available for debug flag retrieval"))}return!1},h.prototype.debuggingNamespaces=function(a){var b=this;try{if(void 0===a){var c=localStorage.getItem(j);return"string"==typeof c?c.split(","):[]}null===a?localStorage.removeItem(j):localStorage.setItem(j,a);var d=b.debuggingNamespaces();return b.logger&&(b.logger.options.consoleNamespaceWhitelist=d),d}catch(e){console.log(g("localStorage not available for debug namespace retrieval"))}},h.prototype.toString=function(){var a=this.user?this.user.get("email")||"(anonymous)":"uninitialized";return"GalaxyApp("+a+")"},{GalaxyApp:h}});
 //# sourceMappingURL=../maps/galaxy-app-base.js.map

static/scripts/layout/masthead.js

@@ -1,2 +1,2 @@
-define(["utils/utils","layout/menu","layout/scratchbook","mvc/user/user-quotameter"],function(a,b,c,d){var e=Backbone.View.extend({el_masthead:"#everything",options:null,$background:null,list:[],initialize:function(a){this.options=a,$("body").off(),this.setElement($(this._template(a))),$(this.el_masthead).append($(this.el)),this.$background=$(this.el).find("#masthead-background");var e=this;$(window).on("beforeunload",function(){var a="";for(var b in e.list)if(e.list[b].options.onunload){var c=e.list[b].options.onunload();c&&(a+=c+" ")}return""!==a?a:void 0}),this.menu=Galaxy.menu=new b.GalaxyMenu({masthead:this,config:this.options}),this.frame=Galaxy.frame=new c.GalaxyFrame({masthead:this}),Galaxy.quotaMeter=new d.UserQuotaMeter({model:Galaxy.user,el:this.$(".quota-meter-container")}).render()},events:{click:"_click",mousedown:function(a){a.preventDefault()}},append:function(a){return this._add(a,!0)},prepend:function(a){return this._add(a,!1)},highlight:function(a){var b=$(this.el).find("#"+a+"> li");b&&b.addClass("active")},_add:function(a,b){var c=$(this.el).find("#"+a.location);if(c){var d=$(a.el);d.addClass("masthead-item"),b?c.append(d):c.prepend(d),this.list.push(a)}return null},_click:function(a){var b=$(this.el).find(".popup");b&&b.hide();var c=$(a.target).closest(".masthead-item").find(".popup");$(a.target).hasClass("head")?(c.show(),this.$background.show()):this.$background.hide()},_template:function(a){var b=a.brand?"/ "+a.brand:"";return'<div><div id="masthead" class="navbar navbar-fixed-top navbar-inverse"><div style="position: relative; right: -50%; float: left;"><div id="navbar" style="display: block; position: relative; right: 50%;"></div></div><div class="navbar-brand"><a href="'+a.logo_url+'"><img style="margin-left: 0.35em;" border="0" src="'+galaxy_config.root+'static/images/galaxyIcon_noText.png"><span id="brand"> Galaxy '+b+'</span></a></div><div class="quota-meter-container"></div><div id="iconbar" class="iconbar"></div></div><div id="masthead-background" style="display: none; position: absolute; top: 33px; width: 100%; height: 100%; z-index: 1010"></div></div>'}});return{GalaxyMasthead:e}});
+define(["utils/utils","layout/menu","layout/scratchbook","mvc/user/user-quotameter"],function(a,b,c,d){var e=Backbone.View.extend({el_masthead:"#everything",options:null,$background:null,list:[],initialize:function(a){this.options=a,$("body").off(),this.setElement($(this._template(a))),$(this.el_masthead).append($(this.el)),this.$background=$(this.el).find("#masthead-background");var e=this;$(window).on("beforeunload",function(){var a="";for(var b in e.list)if(e.list[b].options.onunload){var c=e.list[b].options.onunload();c&&(a+=c+" ")}return""!==a?a:void 0}),this.menu=Galaxy.menu=new b.GalaxyMenu({masthead:this,config:this.options}),this.frame=Galaxy.frame=new c.GalaxyFrame({masthead:this}),Galaxy.quotaMeter=new d.UserQuotaMeter({model:Galaxy.user,el:this.$(".quota-meter-container")}).render()},events:{click:"_click",mousedown:function(a){a.preventDefault()}},append:function(a){return this._add(a,!0)},prepend:function(a){return this._add(a,!1)},highlight:function(a){var b=$(this.el).find("#"+a+"> li");b&&b.addClass("active")},_add:function(a,b){var c=$(this.el).find("#"+a.location);if(c){var d=$(a.el);d.addClass("masthead-item"),b?c.append(d):c.prepend(d),this.list.push(a)}return null},_click:function(a){var b=$(this.el).find(".popup");b&&b.hide();var c=$(a.target).closest(".masthead-item").find(".popup");$(a.target).hasClass("head")?(c.show(),this.$background.show()):this.$background.hide()},_template:function(a){var b=a.brand?"/ "+a.brand:"";return'<div><div id="masthead" class="navbar navbar-fixed-top navbar-inverse"><div style="position: relative; right: -50%; float: left;"><div id="navbar" style="display: block; position: relative; right: 50%;"></div></div><div class="navbar-brand"><a href="'+a.logo_url+'"><img style="margin-left: 0.35em;" border="0" src="'+Galaxy.root+'static/images/galaxyIcon_noText.png"><span id="brand"> Galaxy '+b+'</span></a></div><div class="quota-meter-container"></div><div id="iconbar" class="iconbar"></div></div><div id="masthead-background" style="display: none; position: absolute; top: 33px; width: 100%; height: 100%; z-index: 1010"></div></div>'}});return{GalaxyMasthead:e}});
 //# sourceMappingURL=../../maps/layout/masthead.js.map

static/scripts/layout/scratchbook.js

@@ -1,2 +1,2 @@
-define(["mvc/ui/ui-frames"],function(a){var b=Backbone.View.extend({el_main:"body",active:!1,button_active:null,button_load:null,initialize:function(b){b=b||{};var d=this;this.frames=new a.View({visible:!1}),this.button_active=new c({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",onclick:function(){d._activate()},onunload:function(){return d.frames.length()>0?"You opened "+d.frames.length()+" frame(s) which will be lost.":void 0}}),this.button_load=new c({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",onclick:function(){d.frames.visible?d.frames.hide():d.frames.show()},with_number:!0}),b.masthead&&(b.masthead.append(this.button_active),b.masthead.append(this.button_load)),this.setElement(this.frames.$el),$(this.el_main).append(this.$el),this.frames.setOnChange(function(){d._refresh()}),this._refresh()},add_dataset:function(a){var b=this;require(["mvc/dataset/data"],function(c){var d=new c.Dataset({id:a});$.when(d.fetch()).then(function(){var a={title:d.get("name")},e=_.find(["tabular","interval"],function(a){return-1!==d.get("data_type").indexOf(a)});if(e){var f=new c.TabularDataset(d.toJSON());_.extend(a,{type:"other",content:function(a){c.createTabularDatasetChunkedView({model:f,parent_elt:a,embedded:!0,height:"100%"})}})}else _.extend(a,{type:"url",content:galaxy_config.root+"datasets/"+d.id+"/display/?preview=True"});b.add(a)})})},add_trackster_viz:function(a){var b=this;require(["viz/visualization","viz/trackster"],function(c,d){var e=new c.Visualization({id:a});$.when(e.fetch()).then(function(){var a=new d.TracksterUI(galaxy_config.root),c={title:e.get("name"),type:"other",content:function(b){var c={container:b,name:e.get("title"),id:e.id,dbkey:e.get("dbkey"),stand_alone:!1},d=e.get("latest_revision"),f=d.config.view.drawables;_.each(f,function(a){a.dataset={hda_ldda:a.hda_ldda,id:a.dataset_id}}),view=a.create_visualization(c,d.config.viewport,d.config.view.drawables,d.config.bookmarks,!1)}};b.add(c)})})},add:function(a){if("_blank"==a.target)return void window.open(a.content);if("_top"==a.target||"_parent"==a.target||"_self"==a.target)return void(window.location=a.content);if(this.active)this.frames.add(a);else{var b=$(window.parent.document).find("#galaxy_main");if("galaxy_main"==a.target||"center"==a.target)if(0===b.length){var c=a.content;c+=-1==c.indexOf("?")?"?":"&",c+="use_panels=True",window.location=c}else b.attr("src",a.content);else window.location=a.content}},_activate:function(){this.active?(this.active=!1,this.button_active.untoggle(),this.frames.hide()):(this.active=!0,this.button_active.toggle())},_refresh:function(){this.button_load.number(this.frames.length()),0===this.frames.length()?this.button_load.hide():this.button_load.show(),this.frames.visible?this.button_load.toggle():this.button_load.untoggle()}}),c=Backbone.View.extend({options:{id:"",icon:"fa-cog",tooltip:"",with_number:!1,onclick:function(){alert("clicked")},onunload:null,visible:!0},location:"iconbar",initialize:function(a){a&&(this.options=_.defaults(a,this.options)),this.setElement($(this._template(this.options)));var b=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",b.options.onclick),this.options.visible||this.hide()},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(a){$(this.el).find(".icon").removeClass(this.options.icon).addClass(a),this.options.icon=a},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(a){$(this.el).find(".number").text(a)},_template:function(a){var b='<div id="'+a.id+'" class="symbol"><div class="icon fa fa-2x '+a.icon+'"></div>';return a.with_number&&(b+='<div class="number"></div>'),b+="</div>"}});return{GalaxyFrame:b,GalaxyMastheadIcon:c}});
+define(["mvc/ui/ui-frames"],function(a){var b=Backbone.View.extend({el_main:"body",active:!1,button_active:null,button_load:null,initialize:function(b){b=b||{};var d=this;this.frames=new a.View({visible:!1}),this.button_active=new c({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",onclick:function(){d._activate()},onunload:function(){return d.frames.length()>0?"You opened "+d.frames.length()+" frame(s) which will be lost.":void 0}}),this.button_load=new c({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",onclick:function(){d.frames.visible?d.frames.hide():d.frames.show()},with_number:!0}),b.masthead&&(b.masthead.append(this.button_active),b.masthead.append(this.button_load)),this.setElement(this.frames.$el),$(this.el_main).append(this.$el),this.frames.setOnChange(function(){d._refresh()}),this._refresh()},add_dataset:function(a){var b=this;require(["mvc/dataset/data"],function(c){var d=new c.Dataset({id:a});$.when(d.fetch()).then(function(){var a={title:d.get("name")},e=_.find(["tabular","interval"],function(a){return-1!==d.get("data_type").indexOf(a)});if(e){var f=new c.TabularDataset(d.toJSON());_.extend(a,{type:"other",content:function(a){c.createTabularDatasetChunkedView({model:f,parent_elt:a,embedded:!0,height:"100%"})}})}else _.extend(a,{type:"url",content:Galaxy.root+"datasets/"+d.id+"/display/?preview=True"});b.add(a)})})},add_trackster_viz:function(a){var b=this;require(["viz/visualization","viz/trackster"],function(c,d){var e=new c.Visualization({id:a});$.when(e.fetch()).then(function(){var a=new d.TracksterUI(Galaxy.root),c={title:e.get("name"),type:"other",content:function(b){var c={container:b,name:e.get("title"),id:e.id,dbkey:e.get("dbkey"),stand_alone:!1},d=e.get("latest_revision"),f=d.config.view.drawables;_.each(f,function(a){a.dataset={hda_ldda:a.hda_ldda,id:a.dataset_id}}),view=a.create_visualization(c,d.config.viewport,d.config.view.drawables,d.config.bookmarks,!1)}};b.add(c)})})},add:function(a){if("_blank"==a.target)return void window.open(a.content);if("_top"==a.target||"_parent"==a.target||"_self"==a.target)return void(window.location=a.content);if(this.active)this.frames.add(a);else{var b=$(window.parent.document).find("#galaxy_main");if("galaxy_main"==a.target||"center"==a.target)if(0===b.length){var c=a.content;c+=-1==c.indexOf("?")?"?":"&",c+="use_panels=True",window.location=c}else b.attr("src",a.content);else window.location=a.content}},_activate:function(){this.active?(this.active=!1,this.button_active.untoggle(),this.frames.hide()):(this.active=!0,this.button_active.toggle())},_refresh:function(){this.button_load.number(this.frames.length()),0===this.frames.length()?this.button_load.hide():this.button_load.show(),this.frames.visible?this.button_load.toggle():this.button_load.untoggle()}}),c=Backbone.View.extend({options:{id:"",icon:"fa-cog",tooltip:"",with_number:!1,onclick:function(){alert("clicked")},onunload:null,visible:!0},location:"iconbar",initialize:function(a){a&&(this.options=_.defaults(a,this.options)),this.setElement($(this._template(this.options)));var b=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",b.options.onclick),this.options.visible||this.hide()},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(a){$(this.el).find(".icon").removeClass(this.options.icon).addClass(a),this.options.icon=a},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(a){$(this.el).find(".number").text(a)},_template:function(a){var b='<div id="'+a.id+'" class="symbol"><div class="icon fa fa-2x '+a.icon+'"></div>';return a.with_number&&(b+='<div class="number"></div>'),b+="</div>"}});return{GalaxyFrame:b,GalaxyMastheadIcon:c}});
 //# sourceMappingURL=../../maps/layout/scratchbook.js.map

static/scripts/mvc/citation/citation-model.js

@@ -1,2 +1,2 @@
-define(["libs/bibtex","mvc/base-mvc","utils/localization"],function(a,b){var c="citation",d=Backbone.Model.extend(b.LoggableMixin).extend({_logNamespace:c,initialize:function(){var a=this.attributes.content,b=new a.BibtexParser(a).entries[0];this.entry=b,this._fields={};var c=b.Fields;for(var d in c){var e=c[d],f=d.toLowerCase();this._fields[f]=e}},entryType:function(){return this.entry.EntryType},fields:function(){return this._fields}}),e=Backbone.Collection.extend(b.LoggableMixin).extend({_logNamespace:c,urlRoot:galaxy_config.root+"api",partial:!0,model:d}),f=e.extend({url:function(){return this.urlRoot+"/histories/"+this.history_id+"/citations"}}),g=e.extend({url:function(){return this.urlRoot+"/tools/"+this.tool_id+"/citations"},partial:!1});return{Citation:d,HistoryCitationCollection:f,ToolCitationCollection:g}});
+define(["libs/bibtex","mvc/base-mvc","utils/localization"],function(a,b){var c="citation",d=Backbone.Model.extend(b.LoggableMixin).extend({_logNamespace:c,initialize:function(){var a=this.attributes.content,b=new a.BibtexParser(a).entries[0];this.entry=b,this._fields={};var c=b.Fields;for(var d in c){var e=c[d],f=d.toLowerCase();this._fields[f]=e}},entryType:function(){return this.entry.EntryType},fields:function(){return this._fields}}),e=Backbone.Collection.extend(b.LoggableMixin).extend({_logNamespace:c,urlRoot:Galaxy.root+"api",partial:!0,model:d}),f=e.extend({url:function(){return this.urlRoot+"/histories/"+this.history_id+"/citations"}}),g=e.extend({url:function(){return this.urlRoot+"/tools/"+this.tool_id+"/citations"},partial:!1});return{Citation:d,HistoryCitationCollection:f,ToolCitationCollection:g}});
 //# sourceMappingURL=../../../maps/mvc/citation/citation-model.js.map