diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py index 4e68b0ed759..fd6e11a3117 100644 --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -903,34 +903,25 @@ class ConfiguresGalaxyMixin: time.sleep(1) - def reload_toolbox(self): - # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file. - - tool_configs = self.config.tool_configs - if self.config.migrated_tools_config not in tool_configs: - tool_configs.append( self.config.migrated_tools_config ) - - from galaxy import tools - old_toolbox = self.toolbox - self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) - self.reindex_tool_search() - if old_toolbox: - old_toolbox.shutdown() - def _configure_toolbox( self ): + from galaxy import tools from galaxy.managers.citations import CitationsManager - self.citations_manager = CitationsManager( self ) - + 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() - self.toolbox = None - self.reload_toolbox() + # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file. + tool_configs = self.config.tool_configs + if self.config.migrated_tools_config not in tool_configs: + tool_configs.append( self.config.migrated_tools_config ) + self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) + self.reindex_tool_search() - from galaxy.tools.deps import containers galaxy_root_dir = os.path.abspath(self.config.root) file_path = os.path.abspath(getattr(self.config, "file_path")) app_info = containers.AppInfo( diff --git a/lib/galaxy/queue_worker.py b/lib/galaxy/queue_worker.py index 0ca7b928d77..8a0c9c0d564 100644 --- a/lib/galaxy/queue_worker.py +++ b/lib/galaxy/queue_worker.py @@ -226,13 +226,13 @@ class GalaxyQueueWorker(ConsumerMixin, threading.Thread): if body.get('noop', None) != self.app.config.server_name: try: f = self.task_mapping[body['task']] - log.info("Instance '%s' recieved '%s' task, executing now.", self.app.config.server_name, body['task']) + log.info("Instance '%s' received '%s' task, executing now.", self.app.config.server_name, body['task']) f(self.app, **body['kwargs']) except Exception: # this shouldn't ever throw an exception, but... log.exception("Error running control task type: %s" % body['task']) else: - log.warning("Recieved a malformed task message:\n%s" % body) + log.warning("Received a malformed task message:\n%s" % body) message.ack() def shutdown(self):