Merge pull request #2971 from jmchilton/galaxy-lib-import-fix

Refactor recent toolbox changes for galaxy-lib.

lib/galaxy/tools/__init__.py

@@ -24,6 +24,7 @@ from galaxy import model
 from galaxy.managers import histories
 from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper
 from galaxy import exceptions
+from galaxy.queue_worker import reload_toolbox
 from galaxy.tools.actions import DefaultToolAction
 from galaxy.tools.actions.upload import UploadToolAction
 from galaxy.tools.actions.data_source import DataSourceToolAction
@@ -103,6 +104,7 @@ class ToolBox( BaseGalaxyToolBox ):
     """
 
     def __init__( self, config_filenames, tool_root_dir, app, tool_conf_watcher=None ):
+        self._reload_count = 0
         super( ToolBox, self ).__init__(
             config_filenames=config_filenames,
             tool_root_dir=tool_root_dir,
@@ -110,6 +112,12 @@ class ToolBox( BaseGalaxyToolBox ):
             tool_conf_watcher=tool_conf_watcher
         )
 
+    def handle_reload_toolbox(self):
+        reload_toolbox(self.app)
+
+    def has_reloaded(self, other_toolbox):
+        return self._reload_count != other_toolbox._reload_count
+
     @property
     def all_requirements(self):
         reqs = [json.dumps(req, sort_keys=True) for _, tool in self.tools() for req in tool.tool_requirements]

lib/galaxy/tools/toolbox/base.py

@@ -9,7 +9,6 @@ from six import iteritems
 from six.moves.urllib.parse import urlparse
 
 from galaxy.exceptions import ObjectNotFound
-from galaxy.queue_worker import reload_toolbox
 # Next two are extra tool dependency not used by AbstractToolBox but by
 # BaseGalaxyToolBox.
 from galaxy.tools.deps import build_dependency_manager
@@ -62,7 +61,6 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
         # In-memory dictionary that defines the layout of the tool panel.
         self._tool_panel = ToolPanelElements()
         self._index = 0
-        self._reload_count = 0
         self.data_manager_tools = odict()
         self._lineage_map = LineageMap( app )
         # Sets self._integrated_tool_panel and self._integrated_tool_panel_config_has_contents
@@ -75,7 +73,7 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
         if tool_conf_watcher:
             self._tool_conf_watcher = tool_conf_watcher  # Avoids (re-)starting threads in uwsgi
         else:
-            self._tool_conf_watcher = get_tool_conf_watcher( lambda: reload_toolbox(app))
+            self._tool_conf_watcher = get_tool_conf_watcher(lambda: self.handle_reload_toolbox())
         self._filter_factory = FilterFactory( self )
         self._tool_tag_manager = tool_tag_manager( app )
         self._init_tools_from_configs( config_filenames )
@@ -84,8 +82,12 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
             self._load_tool_panel()
         self._save_integrated_tool_panel()
 
-    def has_reloaded(self, other_toolbox):
-        return self._reload_count != other_toolbox._reload_count
+    def handle_reload_toolbox(self):
+        """Extension-point for Galaxy-app specific reload logic.
+
+        This abstract representation of the toolbox shouldn't have details about
+        interacting with the rest of the Galaxy app or message queues, etc....
+        """
 
     def create_tool( self, config_file, repository_id=None, guid=None, **kwds ):
         raise NotImplementedError()