Merge branch 'release_17.09' into dev

client/galaxy/style/less/upload.less

@@ -122,12 +122,12 @@
                     .upload-text-content {
                         font-size : @font-size-small;
                         width: 100%;
-                        height: 50px;
+                        height: 80px;
                         resize: none;
                         background: inherit;
                         color: @black;
                         white-space: pre;
-                        overflow: scroll;
+                        overflow: auto;
                     }
                     .upload-text-info {
                         &:extend(.text-primary);

doc/source/releases/17.09_announce.rst

@@ -59,11 +59,11 @@ If you maintain a publicly accessible Galaxy please consider signing up for this
 Deprecation Notices
 ===================
 
-* The Galaxy Sample Tracking and External Services functionality is now considered deprecated. In future releases we will strip down the related
-  user interface and introduce configuration option to keep relevant API controllers active if desired. `Related PR <https://github.com/galaxyproject/galaxy/pull/4526>`__.
+* The Galaxy Sample Tracking and External Services functionality is now considered deprecated. In the next releases we will remove it completely. Related PRs:`#4526 <https://github.com/galaxyproject/galaxy/pull/4526>`__ `#4872 <https://github.com/galaxyproject/galaxy/pull/4872>`__ .
 * The deprecated admin-only interface for Galaxy Data Libraries is staged to be removed in the next release.
 * Workflows API: When exposing WorkflowInvocationSteps ``state`` will no longer be available.
 * The ``refresh_on_change`` attribute of a ``<param>`` tag in the tool syntax can no longer be set to a value of another parameter. Use boolean instead (e.g.``refresh_on_change="True"``). `Details <https://github.com/galaxyproject/galaxy/issues/4810>`__
+* The endpoint ``/api/configuration/toolbox`` is now deprecated and will be removed in the future. All tools are now watched for changes and this feature became obsolete.
 
 
 Release Notes

lib/galaxy/app.py

@@ -212,6 +212,7 @@ class UniverseApplication(object, config.ConfiguresGalaxyMixin):
         log.info("Galaxy app startup finished %s" % self.startup_timer)
 
     def shutdown(self):
+        self.watchers.shutdown()
         self.workflow_scheduling_manager.shutdown()
         self.job_manager.shutdown()
         self.object_store.shutdown()

lib/galaxy/webapps/galaxy/config_watchers.py

@@ -32,6 +32,12 @@ class ConfigWatchers(object):
         [self.data_manager_config_watcher.watch_file(config) for config in self.data_manager_configs]
         [self.tool_data_watcher.watch_directory(tool_data_path) for tool_data_path in self.tool_data_paths]
 
+    def shutdown(self):
+        self.tool_config_watcher.shutdown()
+        self.data_manager_config_watcher.shutdown()
+        self.tool_data_watcher.shutdown()
+        self.tool_watcher.shutdown()
+
     def update_watch_data_table_paths(self):
         if hasattr(self.tool_data_watcher, 'monitored_dirs'):
             for tool_data_table_path in self.tool_data_paths: