Merge branch 'release_16.07' into dev

Conflicts:
	static/scripts/bundled/analysis.bundled.js
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js
	static/scripts/bundled/libs.bundled.js.map

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

@@ -186,7 +186,7 @@ var LibraryDatasetView = Backbone.View.extend({
     this.histories.fetch({
       success: function (histories){
         if (histories.length === 0){
-          mod_toastr.warning('You have to create history first. Click this to do so.', '', {onclick: function() {window.location='/';}});
+          mod_toastr.warning('You have to create history first. Click this to do so.', '', {onclick: function() {window.location=Galaxy.root;}});
         } else {
           callback(self);
         }
@@ -233,7 +233,7 @@ var LibraryDatasetView = Backbone.View.extend({
     historyItem.save({ content : this.id, source : 'library' }, {
       success : function(){
         Galaxy.modal.hide();
-        mod_toastr.success('Dataset imported. Click this to start analyzing it.', '', {onclick: function() {window.location='/';}});
+        mod_toastr.success('Dataset imported. Click this to start analyzing it.', '', {onclick: function() {window.location=Galaxy.root;}});
       },
       error : function(model, response){
         if (typeof response.responseJSON !== "undefined"){

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

@@ -112,7 +112,7 @@ var FolderRowView = Backbone.View.extend({
           Galaxy.libraries.folderListView.collection.sortByNameAsc();
           mod_toastr.success('Dataset undeleted. Click this to see it.', '', {onclick: function() {
             var folder_id = that.model.get('folder_id');
-            window.location='#folders/' + folder_id + '/datasets/' + that.id;
+            window.location = Galaxy.root + 'library/list#folders/' + folder_id + '/datasets/' + that.id;
           }});
         },
         error : function(model, response){

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

@@ -764,11 +764,11 @@ var FolderToolbarView = Backbone.View.extend({
     var popped_item = history_item_set.pop();
     if ( typeof popped_item == "undefined" ) {
       if ( this.options.chain_call_control.failed_number === 0 ){
-        mod_toastr.success( 'Selected datasets imported into history. Click this to start analyzing it.', '', { onclick: function() { window.location='/' } } );
+        mod_toastr.success( 'Selected datasets imported into history. Click this to start analyzing it.', '', { onclick: function() { window.location=Galaxy.root } } );
       } else if ( this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number ){
         mod_toastr.error( 'There was an error and no datasets were imported into history.' );
       } else if ( this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number ){
-        mod_toastr.warning( 'Some of the datasets could not be imported into history. Click this to see what was imported.', '', { onclick: function() { window.location='/' } } );
+        mod_toastr.warning( 'Some of the datasets could not be imported into history. Click this to see what was imported.', '', { onclick: function() { window.location=Galaxy.root } } );
       }
       Galaxy.modal.hide();
       return true;

lib/galaxy/tools/__init__.py

@@ -68,7 +68,7 @@ import galaxy.jobs
 log = logging.getLogger( __name__ )
 
 HELP_UNINITIALIZED = threading.Lock()
-MODEL_TOOLS_PATH = os.path.dirname(__file__)
+MODEL_TOOLS_PATH = os.path.abspath(os.path.dirname(__file__))
 
 
 class ToolErrorLog:

lib/galaxy/tools/toolbox/base.py

@@ -565,7 +565,7 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
             if labels is not None:
                 tool.labels = labels
         except IOError:
-            log.error( "Error reading tool configuration file from path: %s." % path )
+            log.error( "Error reading tool configuration file from path: %s" % path )
         except Exception:
             log.exception( "Error reading tool from path: %s" % path )
 

templates/user/index.mako

@@ -22,9 +22,6 @@
         %else:
             <li><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller )}">${_('Manage your information')}</a></li>
             <li><a href="${h.url_for( controller='user', action='change_password' )}">${_('Change your password')}</a></li>
-            %if trans.app.config.enable_communication_server:
-                <li><a href="${h.url_for( controller='user', action='change_communication', cntrller=cntrller )}">${_('Change your communication settings')}</a></li>
-            %endif
             <li><a href="${h.url_for( controller='user', action='api_keys', cntrller=cntrller )}">${_('Manage your API keys')}</a></li>
             <li><a href="${h.url_for( controller='repository', action='manage_email_alerts', cntrller=cntrller )}">${_('Manage your email alerts')}</a></li>
             <li><a href="${h.url_for( controller='user', action='logout', logout_all=True )}" target="_top">${_('Logout')}</a> ${_('of all user sessions')}</li>