Move ToolWatcher from Toolbox to ConfigWatchers class

lib/galaxy/app.py

@@ -22,6 +22,7 @@
 from galaxy.sample_tracking import external_service_types
 from galaxy.openid.providers import OpenIDProviders
 from galaxy.tools.data_manager.manager import DataManagers
+from galaxy.tools.toolbox.cache import ToolCache
 from galaxy.jobs import metrics as job_metrics
 from galaxy.web.proxy import ProxyManager
 from galaxy.web.stack import application_stack_instance
@@ -97,6 +98,10 @@ def __init__( self, **kwargs ):
         # Initialize the job management configuration
         self.job_config = jobs.JobConfiguration(self)
 
+        # Setup a Tool Cache
+        self.tool_cache = ToolCache()
+        # Watch various config files for immediate reload
+        self.watchers = ConfigWatchers(self)
         self._configure_toolbox()
 
         # Load Data Manager
@@ -113,8 +118,6 @@ def __init__( self, **kwargs ):
         self.datatypes_registry.load_external_metadata_tool( self.toolbox )
         # Load history import/export tools.
         load_lib_tools( self.toolbox )
-        # Watch various config files for immediate reload
-        self.watchers = ConfigWatchers(self)
         # visualizations registry: associates resources with visualizations, controls how to render
         self.visualizations_registry = VisualizationsRegistry(
             self,

lib/galaxy/config.py

@@ -908,11 +908,9 @@ def _configure_toolbox( self ):
         from galaxy import tools
         from galaxy.managers.citations import CitationsManager
         from galaxy.tools.deps import containers
-        from galaxy.tools.toolbox.cache import ToolCache
         from galaxy.tools.toolbox.lineages.tool_shed import ToolVersionCache
 
         self.citations_manager = CitationsManager( self )
-        self.tool_cache = ToolCache()
         self.tool_version_cache = ToolVersionCache(self)
 
         self._toolbox_lock = threading.RLock()

lib/galaxy/tools/toolbox/base.py

@@ -33,9 +33,6 @@
 )
 from .parser import ensure_tool_conf_item, get_toolbox_parser
 from .tags import tool_tag_manager
-from .watcher import (
-    get_tool_watcher
-)
 
 log = logging.getLogger( __name__ )
 
@@ -73,7 +70,7 @@ def __init__( self, config_filenames, tool_root_dir, app ):
         # (e.g., shed_tool_conf.xml) files include the tool_path attribute within the <toolbox> tag.
         self._tool_root_dir = tool_root_dir
         self.app = app
-        self._tool_watcher = get_tool_watcher( self, app.config )
+        self._tool_watcher = self.app.watchers.tool_watcher
         self._filter_factory = FilterFactory( self )
         self._tool_tag_manager = tool_tag_manager( app )
         self._init_tools_from_configs( config_filenames )
@@ -514,10 +511,14 @@ def _load_tool_tag_set( self, item, panel_dict, integrated_panel_dict, tool_path
             path_template = item.get( "file" )
             template_kwds = self._path_template_kwds()
             path = string.Template(path_template).safe_substitute(**template_kwds)
+            concrete_path = os.path.join(tool_path, path)
+            if not os.path.exists(concrete_path):
+                # This is a lot faster than attempting to load a non-existing tool
+                raise IOError
             tool_shed_repository = None
             can_load_into_panel_dict = True
 
-            tool = self.load_tool_from_cache(os.path.join(tool_path, path))
+            tool = self.load_tool_from_cache(concrete_path)
             from_cache = tool
             if from_cache:
                 if guid and tool.id != guid:
@@ -532,9 +533,9 @@ def _load_tool_tag_set( self, item, panel_dict, integrated_panel_dict, tool_path
                     # Only load tools if the repository is not deactivated or uninstalled.
                     can_load_into_panel_dict = not tool_shed_repository.deleted
                     repository_id = self.app.security.encode_id(tool_shed_repository.id)
-                    tool = self.load_tool(os.path.join( tool_path, path ), guid=guid, repository_id=repository_id, use_cached=False)
+                    tool = self.load_tool(concrete_path, guid=guid, repository_id=repository_id, use_cached=False)
             if not tool:  # tool was not in cache and is not a tool shed tool.
-                tool = self.load_tool(os.path.join(tool_path, path), use_cached=False)
+                tool = self.load_tool(concrete_path, use_cached=False)
             if string_as_bool(item.get( 'hidden', False )):
                 tool.hidden = True
             key = 'tool_%s' % str(tool.id)
@@ -918,16 +919,6 @@ def to_dict( self, trans, in_panel=True, **kwds ):
 
         return rval
 
-    def shutdown(self):
-        exception = None
-        try:
-            self._tool_watcher.shutdown()
-        except Exception as e:
-            exception = e
-
-        if exception:
-            raise exception
-
     def _lineage_in_panel( self, panel_dict, tool=None, tool_lineage=None ):
         """ If tool with same lineage already in panel (or section) - find
         and return it. Otherwise return None.

lib/galaxy/webapps/galaxy/config_watchers.py

@@ -3,6 +3,7 @@
     reload_toolbox,
 )
 from galaxy.tools.toolbox.watcher import (
+    get_tool_watcher,
     get_tool_conf_watcher,
     get_tool_data_dir_watcher
 )
@@ -16,6 +17,7 @@ def __init__(self, app):
         self.tool_config_watcher = get_tool_conf_watcher(reload_callback=lambda: reload_toolbox(self.app), tool_cache=self.app.tool_cache)
         self.data_manager_config_watcher = get_tool_conf_watcher(reload_callback=lambda: reload_data_managers(self.app), tool_cache=self.app.tool_cache)
         self.tool_data_watcher = get_tool_data_dir_watcher(self.app.tool_data_tables, config=self.app.config)
+        self.tool_watcher = get_tool_watcher( self, app.config )
         self.start()
 
     def start(self):
@@ -26,22 +28,27 @@ def start(self):
     @property
     def data_manager_configs(self):
         data_manager_configs = []
-        data_manager_configs.append(self.app.config.data_manager_config_file)
-        if self.app.config.shed_data_manager_config_file:
+        if hasattr(self.app.config, 'data_manager_config_file'):
+            data_manager_configs.append(self.app.config.data_manager_config_file)
+        if hasattr(self.app.config, 'shed_data_manager_config_file'):
             data_manager_configs.append(self.app.config.shed_data_manager_config_file)
         return data_manager_configs
 
     @property
     def tool_data_paths(self):
         tool_data_paths = []
-        tool_data_paths.append(self.app.config.tool_data_path)
-        if self.app.config.shed_tool_data_path:
+        if hasattr(self.app.config, 'tool_data_path'):
+            tool_data_paths.append(self.app.config.tool_data_path)
+        if hasattr(self.app.config, 'shed_tool_data_path'):
             tool_data_paths.append(self.app.config.shed_tool_data_path)
         return tool_data_paths
 
     @property
     def tool_config_paths(self):
-        tool_config_paths = self.app.config.tool_configs
-        if self.app.config.migrated_tools_config not in tool_config_paths:
-            tool_config_paths.append( self.app.config.migrated_tools_config )
+        tool_config_paths = []
+        if hasattr(self.app.config, 'tool_configs'):
+            tool_config_paths = self.app.config.tool_configs
+        if hasattr(self.app.config, 'self.app.config.migrated_tools_config'):
+            if self.app.config.migrated_tools_config not in tool_config_paths:
+                tool_config_paths.append(self.app.config.migrated_tools_config)
         return tool_config_paths

test/unit/tools/test_toolbox.py

@@ -13,6 +13,7 @@
 from galaxy.tools import ToolBox
 from galaxy.tools.toolbox.lineages.tool_shed import ToolVersionCache
 from galaxy.tools.toolbox.watcher import get_tool_conf_watcher
+from galaxy.webapps.galaxy.config_watchers import ConfigWatchers
 
 from .test_toolbox_filters import mock_trans
 
@@ -62,6 +63,7 @@ def setUp( self ):
         self.app.reindex_tool_search = self.__reindex
         itp_config = os.path.join(self.test_directory, "integrated_tool_panel.xml")
         self.app.config.integrated_tool_panel_config = itp_config
+        self.app.watchers = ConfigWatchers(self.app)
         self.__toolbox = None
         self.config_files = []