');
diff --git a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
index 9e9ebbf072c..eb841040d83 100644
--- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+++ b/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( $.post( Galaxy.root + 'api/libraries/datasets?encoded_folder_id=' + that.id +
'&source=' + options.source +
'&path=' + popped_item +
'&preserve_dirs=' + options.preserve_dirs +
diff --git a/client/galaxy/scripts/mvc/library/library-library-view.js b/client/galaxy/scripts/mvc/library/library-library-view.js
index a93f7bcba1e..1d9b5133cf2 100644
--- a/client/galaxy/scripts/mvc/library/library-library-view.js
+++ b/client/galaxy/scripts/mvc/library/library-library-view.js
@@ -79,15 +79,15 @@ var LibraryView = Backbone.View.extend({
}
}
var is_admin = false;
- if (Galaxy.currUser){
- is_admin = Galaxy.currUser.isAdmin();
- }
+ if (Galaxy.user){
+ is_admin = Galaxy.user.isAdmin();
+ }
var template = this.templateLibraryPermissions();
this.$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, } )
+ $.post( Galaxy.root + "api/libraries/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } )
.done(function(fetched_permissions){
//fetch dataset again
self.showPermissions({fetched_permissions:fetched_permissions})
@@ -287,7 +287,7 @@ var LibraryView = Backbone.View.extend({
var tmpl_array = [];
// CONTAINER START
tmpl_array.push('
');
-
+
tmpl_array.push('
');
-
+
tmpl_array.push('
');
tmpl_array.push('
Library permissions ');
@@ -310,7 +310,7 @@ var LibraryView = Backbone.View.extend({
tmpl_array.push('
Roles that can access the library ');
tmpl_array.push('
');
tmpl_array.push('
User with any of these roles can access this library. If there are no access roles set on the library it is considered unrestricted .
');
-
+
tmpl_array.push('
Roles that can manage permissions on this library ');
tmpl_array.push('
');
tmpl_array.push('
User with any of these roles can manage permissions on this library (includes giving access).
');
diff --git a/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js b/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
index 4ec97151890..66dbc809af6 100644
--- a/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
+++ b/client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
@@ -30,9 +30,9 @@ var LibraryToolbarView = Backbone.View.extend({
var toolbar_template = this.templateToolBar();
var is_admin = false;
var is_anonym = true;
- if ( Galaxy.currUser ){
- is_admin = Galaxy.currUser.isAdmin();
- is_anonym = Galaxy.currUser.isAnonymous();
+ if ( Galaxy.user ){
+ is_admin = Galaxy.user.isAdmin();
+ is_anonym = Galaxy.user.isAnonymous();
}
this.$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,
diff --git a/client/galaxy/scripts/mvc/library/library-model.js b/client/galaxy/scripts/mvc/library/library-model.js
index c63dba1e884..90eeed7e529 100644
--- a/client/galaxy/scripts/mvc/library/library-model.js
+++ b/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 {
diff --git a/client/galaxy/scripts/mvc/tag.js b/client/galaxy/scripts/mvc/tag.js
index 428f3af6f6b..e66e44da229 100644
--- a/client/galaxy/scripts/mvc/tag.js
+++ b/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 );
}
},
diff --git a/client/galaxy/scripts/mvc/tool/tools-form-workflow.js b/client/galaxy/scripts/mvc/tool/tools-form-workflow.js
index 8d5b5da2bb0..f133aeb8c11 100644
--- a/client/galaxy/scripts/mvc/tool/tools-form-workflow.js
+++ b/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);
}
});
diff --git a/client/galaxy/scripts/mvc/tool/tools-jobs.js b/client/galaxy/scripts/mvc/tool/tools-jobs.js
index 652c4fd78e8..89a0f995460 100644
--- a/client/galaxy/scripts/mvc/tool/tools-jobs.js
+++ b/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();
diff --git a/client/galaxy/scripts/mvc/tool/tools.js b/client/galaxy/scripts/mvc/tool/tools.js
index 14d7a44c232..a0d7da79d4d 100644
--- a/client/galaxy/scripts/mvc/tool/tools.js
+++ b/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);
diff --git a/client/galaxy/scripts/mvc/ui/ui-select-ftp.js b/client/galaxy/scripts/mvc/ui/ui-select-ftp.js
index 3f01cbac20b..ef8ea7cee7a 100644
--- a/client/galaxy/scripts/mvc/ui/ui-select-ftp.js
+++ b/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) {
diff --git a/client/galaxy/scripts/mvc/ui/ui-select-library.js b/client/galaxy/scripts/mvc/ui/ui-select-library.js
index 2df383b8eba..4cc6a492eb3 100644
--- a/client/galaxy/scripts/mvc/ui/ui-select-library.js
+++ b/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';
}
});
diff --git a/client/galaxy/scripts/mvc/upload/upload-ftp.js b/client/galaxy/scripts/mvc/upload/upload-ftp.js
index 044f73be3c6..2310ae37a3c 100644
--- a/client/galaxy/scripts/mvc/upload/upload-ftp.js
+++ b/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(); }
});
diff --git a/client/galaxy/scripts/mvc/upload/upload-view.js b/client/galaxy/scripts/mvc/upload/upload-view.js
index f4ba48fa004..472acade0ff 100644
--- a/client/galaxy/scripts/mvc/upload/upload-view.js
+++ b/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({
diff --git a/client/galaxy/scripts/mvc/user/user-model.js b/client/galaxy/scripts/mvc/user/user-model.js
index 3f6d5bd0b32..a49be5c5c69 100644
--- a/client/galaxy/scripts/mvc/user/user-model.js
+++ b/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,
});
diff --git a/client/galaxy/scripts/mvc/visualization/visualization-model.js b/client/galaxy/scripts/mvc/visualization/visualization-model.js
index 5d6e70e6f27..cb4179de734 100644
--- a/client/galaxy/scripts/mvc/visualization/visualization-model.js
+++ b/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.
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
index 26fa007231a..84200e7e388 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js
+++ b/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
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-data.js b/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
index ac8eda7726a..ddf372d4e7a 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-data.js
@@ -82,13 +82,13 @@ define(['mvc/workflow/workflow-globals'], function( Globals ){
.css( { display: 'none' } )
.append(
$("
").append(
- $("
").attr('src', galaxy_config.root + 'static/images/fugue/asterisk-small-outline.png').click( function() {
+ $("
").attr('src', Galaxy.root + 'static/images/fugue/asterisk-small-outline.png').click( function() {
if ($.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');
}
});
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view.js b/client/galaxy/scripts/mvc/workflow/workflow-view.js
index c757742fc17..066a756d41b 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view.js
+++ b/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 = $("
");
- var tmp = "
loading tool info...
";
+ var tmp = "
loading tool info...
";
b.append( tmp );
node.form_html = tmp;
f.append( b );
diff --git a/client/galaxy/scripts/utils/utils.js b/client/galaxy/scripts/utils/utils.js
index 2107fbcedd3..0cb34de55c7 100644
--- a/client/galaxy/scripts/utils/utils.js
+++ b/client/galaxy/scripts/utils/utils.js
@@ -175,7 +175,7 @@ function cssGetAttribute (classname, name) {
*/
function cssLoadFile (url) {
if (!$('link[href^="' + url + '"]').length) {
- $('
').appendTo('head');
+ $('
').appendTo('head');
}
};
diff --git a/client/galaxy/scripts/viz/circster.js b/client/galaxy/scripts/viz/circster.js
index 756d8e3f085..c994619b87d 100644
--- a/client/galaxy/scripts/viz/circster.js
+++ b/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
$.ajax({
- url: galaxy_config.root + "visualization/save",
+ url: Galaxy.root + "visualization/save",
type: "POST",
dataType: "json",
data: {
@@ -1133,7 +1133,7 @@ var Circster = Backbone.View.extend(
{
icon_class: 'cross-circle', title: 'Close', on_click: function()
{
- window.location = galaxy_config.root + "visualization/list";
+ window.location = Galaxy.root + "visualization/list";
}
}], { tooltip_config: { placement: 'bottom' } });
diff --git a/client/galaxy/scripts/viz/sweepster.js b/client/galaxy/scripts/viz/sweepster.js
index 36f512fba73..889435af435 100644
--- a/client/galaxy/scripts/viz/sweepster.js
+++ b/client/galaxy/scripts/viz/sweepster.js
@@ -270,8 +270,8 @@ var SweepsterTrack = Backbone.Model.extend({
if (options.track) {
// FIXME: find a better way to deal with needed URLs:
var track_config = _.extend({
- data_url: galaxy_config.root + 'dummy1',
- converted_datasets_state_url: galaxy_config.root + 'dummy2'
+ data_url: Galaxy.root + 'dummy1',
+ converted_datasets_state_url: Galaxy.root + 'dummy2'
}, options.track);
this.set('track', tracks.object_from_template(track_config, {}, null));
}
@@ -407,7 +407,7 @@ var SweepsterTrackView = Backbone.View.extend({
// Render tile placeholders.
this.model.get('regions').each(function() {
self.$el.append($('
').addClass('tile').html(
- $('
').attr('src', galaxy_config.root + 'images/loading_large_white_bg.gif')
+ $('
').attr('src', Galaxy.root + 'images/loading_large_white_bg.gif')
));
});
diff --git a/client/galaxy/scripts/viz/trackster.js b/client/galaxy/scripts/viz/trackster.js
index 7bc7ab47a6e..2c65f9aeed6 100644
--- a/client/galaxy/scripts/viz/trackster.js
+++ b/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(
'
' +
'
' +
'';
@@ -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) ); }
diff --git a/client/galaxy/scripts/viz/trackster/tracks.js b/client/galaxy/scripts/viz/trackster/tracks.js
index 935d1700242..d5318a2797d 100644
--- a/client/galaxy/scripts/viz/trackster/tracks.js
+++ b/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 = $("
").addClass("intro").appendTo(this.viewport_container);
var add_tracks_button = $("
").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,
diff --git a/client/galaxy/scripts/viz/visualization.js b/client/galaxy/scripts/viz/visualization.js
index 4c9298e1355..ad661199b17 100644
--- a/client/galaxy/scripts/viz/visualization.js
+++ b/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'
diff --git a/static/maps/galaxy-app-base.js.map b/static/maps/galaxy-app-base.js.map
index c485e32eef2..6fc2b14ac67 100644
--- a/static/maps/galaxy-app-base.js.map
+++ b/static/maps/galaxy-app-base.js.map
@@ -1 +1 @@
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diff --git a/static/maps/galaxy.library.js.map b/static/maps/galaxy.library.js.map
index af027135da5..4d087cb84b8 100644
--- a/static/maps/galaxy.library.js.map
+++ b/static/maps/galaxy.library.js.map
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diff --git a/static/maps/layout/menu.js.map b/static/maps/layout/menu.js.map
index 285743a7a04..5f44a4ca642 100644
--- a/static/maps/layout/menu.js.map
+++ b/static/maps/layout/menu.js.map
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diff --git a/static/maps/layout/scratchbook.js.map b/static/maps/layout/scratchbook.js.map
index 36a343b80bc..a585c9638a4 100644
--- a/static/maps/layout/scratchbook.js.map
+++ b/static/maps/layout/scratchbook.js.map
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diff --git a/static/maps/mvc/citation/citation-model.js.map b/static/maps/mvc/citation/citation-model.js.map
index ff4427e4345..0dcb17ca3b5 100644
--- a/static/maps/mvc/citation/citation-model.js.map
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diff --git a/static/maps/mvc/collection/collection-model.js.map b/static/maps/mvc/collection/collection-model.js.map
index 30c2e504e7d..66f67df89bc 100644
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\ No newline at end of file
diff --git a/static/maps/mvc/collection/collection-view-edit.js.map b/static/maps/mvc/collection/collection-view-edit.js.map
index 35e9a37e537..73e3c9cf801 100644
--- a/static/maps/mvc/collection/collection-view-edit.js.map
+++ b/static/maps/mvc/collection/collection-view-edit.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/collection/list-of-pairs-collection-creator.js.map b/static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
index 528abfb0b18..049018837f0 100644
--- a/static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
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\ No newline at end of file
diff --git a/static/maps/mvc/dataset/data.js.map b/static/maps/mvc/dataset/data.js.map
index 625cfb409ce..41a5a9decf8 100644
--- a/static/maps/mvc/dataset/data.js.map
+++ b/static/maps/mvc/dataset/data.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/static/maps/mvc/dataset/dataset-model.js.map b/static/maps/mvc/dataset/dataset-model.js.map
index c04170519a0..648086c8e9e 100644
--- a/static/maps/mvc/dataset/dataset-model.js.map
+++ b/static/maps/mvc/dataset/dataset-model.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/history/history-content-model.js.map b/static/maps/mvc/history/history-content-model.js.map
index ce00feb141f..005c6162eb3 100644
--- a/static/maps/mvc/history/history-content-model.js.map
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diff --git a/static/maps/mvc/history/history-contents.js.map b/static/maps/mvc/history/history-contents.js.map
index 72900e58395..1011b4e20bd 100644
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+++ b/static/maps/mvc/history/history-contents.js.map
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diff --git a/static/maps/mvc/history/history-model.js.map b/static/maps/mvc/history/history-model.js.map
index 20a79e1ebc5..bd8899088ad 100644
--- a/static/maps/mvc/history/history-model.js.map
+++ b/static/maps/mvc/history/history-model.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/static/maps/mvc/history/history-view-edit-current.js.map b/static/maps/mvc/history/history-view-edit-current.js.map
index b4fa2965a62..201d87164d7 100644
--- a/static/maps/mvc/history/history-view-edit-current.js.map
+++ b/static/maps/mvc/history/history-view-edit-current.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/history/history-view-edit.js.map b/static/maps/mvc/history/history-view-edit.js.map
index f1045f47d8e..b62ecc46623 100644
--- a/static/maps/mvc/history/history-view-edit.js.map
+++ b/static/maps/mvc/history/history-view-edit.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/history/history-view.js.map b/static/maps/mvc/history/history-view.js.map
index 2e6f49d6b9f..3af1f3f7384 100644
--- a/static/maps/mvc/history/history-view.js.map
+++ b/static/maps/mvc/history/history-view.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/history/multi-panel.js.map b/static/maps/mvc/history/multi-panel.js.map
index dfde202ca44..fe7aa5b51f8 100644
--- a/static/maps/mvc/history/multi-panel.js.map
+++ b/static/maps/mvc/history/multi-panel.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/static/maps/mvc/history/options-menu.js.map b/static/maps/mvc/history/options-menu.js.map
index 8e0bf8278f7..17707a78f2a 100644
--- a/static/maps/mvc/history/options-menu.js.map
+++ b/static/maps/mvc/history/options-menu.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/job/job-model.js.map b/static/maps/mvc/job/job-model.js.map
index 27c4fe06d99..bed0d7ba442 100644
--- a/static/maps/mvc/job/job-model.js.map
+++ b/static/maps/mvc/job/job-model.js.map
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diff --git a/static/maps/mvc/library/library-dataset-view.js.map b/static/maps/mvc/library/library-dataset-view.js.map
index 9e1bf508374..264fc9fa4ec 100644
--- a/static/maps/mvc/library/library-dataset-view.js.map
+++ b/static/maps/mvc/library/library-dataset-view.js.map
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\ No newline at end of file
diff --git a/static/maps/mvc/library/library-folder-view.js.map b/static/maps/mvc/library/library-folder-view.js.map
index 3c90e85821f..59769253184 100644
--- a/static/maps/mvc/library/library-folder-view.js.map
+++ b/static/maps/mvc/library/library-folder-view.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/library/library-foldertoolbar-view.js.map b/static/maps/mvc/library/library-foldertoolbar-view.js.map
index 1a18c654c8e..372f907f09f 100644
--- a/static/maps/mvc/library/library-foldertoolbar-view.js.map
+++ b/static/maps/mvc/library/library-foldertoolbar-view.js.map
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\ No newline at end of file
diff --git a/static/maps/mvc/library/library-library-view.js.map b/static/maps/mvc/library/library-library-view.js.map
index 869f850ca71..e9a9e6cd340 100644
--- a/static/maps/mvc/library/library-library-view.js.map
+++ b/static/maps/mvc/library/library-library-view.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/library/library-librarytoolbar-view.js.map b/static/maps/mvc/library/library-librarytoolbar-view.js.map
index 8562b1b4c24..84e52f5f8fd 100644
--- a/static/maps/mvc/library/library-librarytoolbar-view.js.map
+++ b/static/maps/mvc/library/library-librarytoolbar-view.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/library/library-model.js.map b/static/maps/mvc/library/library-model.js.map
index 798fb774bc1..0a887022d61 100644
--- a/static/maps/mvc/library/library-model.js.map
+++ b/static/maps/mvc/library/library-model.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/tag.js.map b/static/maps/mvc/tag.js.map
index 05b2d5fe7bf..fc80e507b30 100644
--- a/static/maps/mvc/tag.js.map
+++ b/static/maps/mvc/tag.js.map
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diff --git a/static/maps/mvc/tool/tools-form-workflow.js.map b/static/maps/mvc/tool/tools-form-workflow.js.map
index c49a527ec6d..4c5d409aeb8 100644
--- a/static/maps/mvc/tool/tools-form-workflow.js.map
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diff --git a/static/maps/mvc/tool/tools-jobs.js.map b/static/maps/mvc/tool/tools-jobs.js.map
index 8f94659ce2d..15e38e10f86 100644
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diff --git a/static/maps/mvc/tool/tools.js.map b/static/maps/mvc/tool/tools.js.map
index e9e36fdb63f..f0f3cbcf043 100644
--- a/static/maps/mvc/tool/tools.js.map
+++ b/static/maps/mvc/tool/tools.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/ui/ui-select-ftp.js.map b/static/maps/mvc/ui/ui-select-ftp.js.map
index 31cb7c09e4c..19b9129eba3 100644
--- a/static/maps/mvc/ui/ui-select-ftp.js.map
+++ b/static/maps/mvc/ui/ui-select-ftp.js.map
@@ -1 +1 @@
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index 8285d283879..bc5ea2f1bd4 100644
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diff --git a/static/maps/mvc/upload/upload-ftp.js.map b/static/maps/mvc/upload/upload-ftp.js.map
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diff --git a/static/maps/mvc/upload/upload-view.js.map b/static/maps/mvc/upload/upload-view.js.map
index 952a7dcf039..2914ca44958 100644
--- a/static/maps/mvc/upload/upload-view.js.map
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diff --git a/static/maps/mvc/user/user-model.js.map b/static/maps/mvc/user/user-model.js.map
index 84d742b7820..2d90517c9fa 100644
--- a/static/maps/mvc/user/user-model.js.map
+++ b/static/maps/mvc/user/user-model.js.map
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diff --git a/static/maps/mvc/visualization/visualization-model.js.map b/static/maps/mvc/visualization/visualization-model.js.map
index 64c336067cc..be38b058ef6 100644
--- a/static/maps/mvc/visualization/visualization-model.js.map
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diff --git a/static/maps/mvc/workflow/workflow-manager.js.map b/static/maps/mvc/workflow/workflow-manager.js.map
index e6dd68cff85..ad234ee72fb 100644
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diff --git a/static/maps/mvc/workflow/workflow-view-data.js.map b/static/maps/mvc/workflow/workflow-view-data.js.map
index 3be8ee94cc5..b0c7d6761c5 100644
--- a/static/maps/mvc/workflow/workflow-view-data.js.map
+++ b/static/maps/mvc/workflow/workflow-view-data.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/workflow/workflow-view.js.map b/static/maps/mvc/workflow/workflow-view.js.map
index 09c0730e1a4..5bb87dc9282 100644
--- a/static/maps/mvc/workflow/workflow-view.js.map
+++ b/static/maps/mvc/workflow/workflow-view.js.map
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diff --git a/static/maps/utils/utils.js.map b/static/maps/utils/utils.js.map
index 3264a355e0b..deb52ddab74 100644
--- a/static/maps/utils/utils.js.map
+++ b/static/maps/utils/utils.js.map
@@ -1 +1 @@
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diff --git a/static/maps/viz/circster.js.map b/static/maps/viz/circster.js.map
index c3636d5c4a7..abadf45a5f9 100644
--- a/static/maps/viz/circster.js.map
+++ b/static/maps/viz/circster.js.map
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\ No newline at end of file
diff --git a/static/maps/viz/sweepster.js.map b/static/maps/viz/sweepster.js.map
index dc608150b04..8388943bdf9 100644
--- a/static/maps/viz/sweepster.js.map
+++ b/static/maps/viz/sweepster.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/static/maps/viz/trackster.js.map b/static/maps/viz/trackster.js.map
index 94b392e6b42..1dc4c5513f1 100644
--- a/static/maps/viz/trackster.js.map
+++ b/static/maps/viz/trackster.js.map
@@ -1 +1 @@
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diff --git a/static/maps/viz/trackster/tracks.js.map b/static/maps/viz/trackster/tracks.js.map
index cf2749c2c03..8e98f38dbe0 100644
--- a/static/maps/viz/trackster/tracks.js.map
+++ b/static/maps/viz/trackster/tracks.js.map
@@ -1 +1 @@
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diff --git a/static/maps/viz/visualization.js.map b/static/maps/viz/visualization.js.map
index 72805a8b2cf..d3b661ef509 100644
--- a/static/maps/viz/visualization.js.map
+++ b/static/maps/viz/visualization.js.map
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\ No newline at end of file
diff --git a/static/scripts/bundled/analysis.bundled.js b/static/scripts/bundled/analysis.bundled.js
index fa5ca9ca5f7..ca51cf27739 100644
--- a/static/scripts/bundled/analysis.bundled.js
+++ b/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) {
- $('
').appendTo('head');
+ $('
').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],[
'
' +
@@ -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');
$popover_element.popover({
html: true,
- content: 'Please
to use this feature.',
placement: 'bottom'
}).on('shown.bs.popover', function() { // hooking on bootstrap event to automatically hide popovers after delay
setTimeout(function() {
@@ -28717,7 +28712,7 @@ webpackJsonp([0],[
else {
_.extend(frame_config, {
type: 'url',
- content: galaxy_config.root + 'datasets/' +
+ content: Galaxy.root + 'datasets/' +
dataset.id + '/display/?preview=True'
});
}
@@ -28738,7 +28733,7 @@ webpackJsonp([0],[
__webpack_require__.e/* require */(1, function(__webpack_require__) { /* WEBPACK VAR INJECTION */(function($, _) {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 = {
diff --git a/static/scripts/bundled/analysis.bundled.js.map b/static/scripts/bundled/analysis.bundled.js.map
index 5a006693cb3..f5936a8e0fb 100644
--- a/static/scripts/bundled/analysis.bundled.js.map
+++ b/static/scripts/bundled/analysis.bundled.js.map
@@ -1 +1 @@
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jQuery = require( 'jquery' ),\n $ = jQuery,\n PANEL = require( 'layout/panel' ),\n ToolPanel = require( './tool-panel' ),\n HistoryPanel = require( './history-panel' ),\n PAGE = require( 'layout/page' ),\n ToolsForm = require( 'mvc/tool/tools-form' );\n\nwindow.app = function app( options, bootstrapped ){\n Galaxy.debug( 'building app:', options, bootstrapped );\n\n // .................................................... panels and page\n var toolPanel = new ToolPanel({\n el : '#left',\n userIsAnonymous : Galaxy.user.isAnonymous(),\n require_login : options.config.require_login,\n spinner_url : options.config.spinner_url,\n search_url : options.config.search_url,\n toolbox : options.config.toolbox,\n toolbox_in_panel: options.config.toolbox_in_panel,\n stored_workflow_menu_entries : options.config.stored_workflow_menu_entries,\n }),\n centerPanel = new PANEL.CenterPanel({\n el : '#center'\n }),\n historyPanel = new HistoryPanel({\n el : '#right',\n galaxyRoot : Galaxy.root,\n userIsAnonymous : Galaxy.user.isAnonymous(),\n allow_user_dataset_purge: Galaxy.config.allow_user_dataset_purge,\n }),\n analysisPage = new PAGE.PageLayoutView( _.extend( options, {\n el : 'body',\n left : toolPanel,\n center : centerPanel,\n right : historyPanel,\n }));\n\n // .................................................... decorate the galaxy object\n // TODO: most of this is becoming unnecessary as we move to apps\n Galaxy.page = analysisPage;\n\n // add tool panel to Galaxy object\n Galaxy.toolPanel = toolPanel.tool_panel;\n Galaxy.upload = toolPanel.uploadButton;\n\n Galaxy.currHistoryPanel = historyPanel.historyView;\n Galaxy.currHistoryPanel.connectToQuotaMeter( Galaxy.quotaMeter );\n Galaxy.currHistoryPanel.listenToGalaxy( Galaxy );\n\n //HACK: move to router/App\n Galaxy.app = {\n display : function( view, target ){\n // TODO: Remove this line after select2 update\n $( '.select2-hidden-accessible' ).remove();\n centerPanel.display( view );\n },\n };\n\n // .................................................... start up\n $(function(){\n analysisPage.render();\n Galaxy.currHistoryPanel.loadCurrentHistory();\n\n // TODO: to router, remove Globals\n var params = $.extend( {}, options.config.params );\n if( params.tool_id && params.tool_id !== 'upload1' ){\n params.id = params.tool_id;\n centerPanel.display( new ToolsForm.View( params ) );\n\n } else if( params.job_id ){\n params.id = params.tool_id;\n centerPanel.display( new ToolsForm.View( params ) );\n\n } else {\n var iframeUrl = Galaxy.root;\n if( params.workflow_id ){\n iframeUrl += 'workflow/run?id=' + params.workflow_id;\n } else if( params.m_c ){\n iframeUrl += params.m_c + '/' + params.m_a;\n } else {\n iframeUrl += 'root/welcome';\n }\n centerPanel.$( '#galaxy_main' ).prop( 'src', iframeUrl );\n }\n });\n};\n\n\n\n/*****************\n ** WEBPACK FOOTER\n ** ./galaxy/scripts/apps/analysis.js\n ** module id = 0\n ** module chunks = 0\n **/","var LeftPanel = require( 'layout/panel' ).LeftPanel,\n Tools = require( 'mvc/tool/tools' ),\n Upload = require( 'mvc/upload/upload-view' );\n//TODO: localize\n\n/* Builds the tool panel on the left */\nvar ToolPanel = LeftPanel.extend({\n\n title : 'Tools',\n\n initialize: function( options ){\n LeftPanel.prototype.initialize.call( this, options );\n this.log( this + '.initialize:', options );\n this.stored_workflow_menu_entries = options.stored_workflow_menu_entries || [];\n\n // TODO: this switch doesn't belong here?\n if( options.userIsAnonymous || !options.require_login ){\n // create tool search, tool panel, and tool panel view.\n var tool_search = new Tools.ToolSearch({\n spinner_url : options.spinner_url,\n search_url : options.search_url,\n hidden : false\n });\n var tools = new Tools.ToolCollection( options.toolbox );\n this.tool_panel = new Tools.ToolPanel({\n tool_search : tool_search,\n tools : tools,\n layout : options.toolbox_in_panel\n });\n this.tool_panel_view = new Tools.ToolPanelView({ model: this.tool_panel });\n // add upload plugin\n this.uploadButton = new Upload( options );\n }\n },\n\n render : function(){\n var self = this;\n LeftPanel.prototype.render.call( self );\n self.$( '.panel-header-buttons' ).append( self.uploadButton.$el );\n\n // if there are tools, render panel and display everything\n if (self.tool_panel.get( 'layout' ).size() > 0) {\n self.tool_panel_view.render();\n //TODO: why the hide/show?\n self.$( '.toolMenu' ).show();\n }\n self.$( '.toolMenuContainer' ).prepend( self.tool_panel_view.$el );\n\n self._renderWorkflowMenu();\n\n // if a tool link has the minsizehint attribute, handle it here (gen. by hiding the tool panel)\n self.$( 'a[minsizehint]' ).click( function() {\n if ( parent.handle_minwidth_hint ) {\n parent.handle_minwidth_hint( $( self ).attr( 'minsizehint' ) );\n }\n });\n },\n\n _renderWorkflowMenu : function(){\n var self = this;\n // add internal workflow list\n self.$( '#internal-workflows' ).append( self._templateTool({\n title : 'All workflows',\n href : 'workflow/list_for_run'\n }));\n _.each( self.stored_workflow_menu_entries, function( menu_entry ){\n self.$( '#internal-workflows' ).append( self._templateTool({\n title : menu_entry.stored_workflow.name,\n href : 'workflow/run?id=' + menu_entry.encoded_stored_workflow_id\n }));\n });\n },\n\n _templateTool: function( tool ) {\n return [\n '
'\n ].join('');\n },\n\n _templateBody : function(){\n return [\n '
' +
+ '
' +
' Galaxy ' + brand_text + '' +
'' +
'