def __init__( self, **kwargs ): print >> sys.stderr, "python path is: " + ", ".join( sys.path ) self.new_installation = False # Read config file and check for errors self.config = config.Configuration( **kwargs ) self.config.check() config.configure_logging( self.config ) # Determine the database url if self.config.database_connection: db_url = self.config.database_connection else: db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database # Initialize database / check for appropriate schema version. # If this # is a new installation, we'll restrict the tool migration messaging. from galaxy.model.migrate.check import create_or_verify_database create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self ) # Alert the Galaxy admin to tools that have been moved from the distribution to the tool shed. from galaxy.tool_shed.migrate.check import verify_tools verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) # Object store manager self.object_store = build_object_store_from_config(self.config) # Setup the database engine and ORM from galaxy.model import mapping self.model = mapping.init( self.config.file_path, db_url, self.config.database_engine_options, database_query_profiling_proxy = self.config.database_query_profiling_proxy, object_store = self.object_store ) # Set up the tool sheds registry if os.path.isfile( self.config.tool_sheds_config ): self.tool_shed_registry = galaxy.tool_shed.tool_shed_registry.Registry( self.config.root, self.config.tool_sheds_config ) else: self.tool_shed_registry = None # Manage installed tool shed repositories. self.installed_repository_manager = galaxy.tool_shed.InstalledRepositoryManager( self ) # Create an empty datatypes registry. self.datatypes_registry = galaxy.datatypes.registry.Registry() # Load proprietary datatypes defined in datatypes_conf.xml files in all installed tool shed repositories. We # load proprietary datatypes before datatypes in the distribution because Galaxy's default sniffers include some # generic sniffers (eg text,xml) which catch anything, so it's impossible for proprietary sniffers to be used. # However, if there is a conflict (2 datatypes with the same extension) between a proprietary datatype and a datatype # in the Galaxy distribution, the datatype in the Galaxy distribution will take precedence. If there is a conflict # between 2 proprietary datatypes, the datatype from the repository that was installed earliest will take precedence. # This will also load proprietary datatype converters and display applications. self.installed_repository_manager.load_proprietary_datatypes() # Load the data types in the Galaxy distribution, which are defined in self.config.datatypes_config. self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) galaxy.model.set_datatypes_registry( self.datatypes_registry ) # Security helper self.security = security.SecurityHelper( id_secret=self.config.id_secret ) # Tag handler self.tag_handler = GalaxyTagHandler() # Tool data tables self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_table_config_path ) # 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 ) # Search support for tools self.toolbox_search = galaxy.tools.search.ToolBoxSearch( self.toolbox ) # If enabled, poll respective tool sheds to see if updates are available for any installed tool shed repositories. if self.config.get_bool( 'enable_tool_shed_check', False ): from tool_shed import update_manager self.update_manager = update_manager.UpdateManager( self ) # Load datatype display applications defined in local datatypes_conf.xml self.datatypes_registry.load_display_applications() # Load datatype converters defined in local datatypes_conf.xml self.datatypes_registry.load_datatype_converters( self.toolbox ) # Load external metadata tool self.datatypes_registry.load_external_metadata_tool( self.toolbox ) # Load history import/export tools. load_history_imp_exp_tools( self.toolbox ) # Load genome indexer tool. load_genome_index_tools( self.toolbox ) # Load security policy. self.security_agent = self.model.security_agent self.host_security_agent = galaxy.security.HostAgent( model=self.security_agent.model, permitted_actions=self.security_agent.permitted_actions ) # Load quota management. if self.config.enable_quotas: self.quota_agent = galaxy.quota.QuotaAgent( self.model ) else: self.quota_agent = galaxy.quota.NoQuotaAgent( self.model ) # Heartbeat and memdump for thread / heap profiling self.heartbeat = None self.memdump = None self.memory_usage = None # Container for OpenID authentication routines if self.config.enable_openid: from galaxy.web.framework import openid_manager self.openid_manager = openid_manager.OpenIDManager( self.config.openid_consumer_cache_path ) self.openid_providers = OpenIDProviders.from_file( self.config.openid_config ) else: self.openid_providers = OpenIDProviders() # Start the heartbeat process if configured and available if self.config.use_heartbeat: from galaxy.util import heartbeat if heartbeat.Heartbeat: self.heartbeat = heartbeat.Heartbeat( fname=self.config.heartbeat_log ) self.heartbeat.start() # Enable the memdump signal catcher if configured and available if self.config.use_memdump: from galaxy.util import memdump if memdump.Memdump: self.memdump = memdump.Memdump() # Transfer manager client if self.config.get_bool( 'enable_beta_job_managers', False ): from jobs import transfer_manager self.transfer_manager = transfer_manager.TransferManager( self ) # Start the job manager from jobs import manager self.job_manager = manager.JobManager( self ) # FIXME: These are exposed directly for backward compatibility self.job_queue = self.job_manager.job_queue self.job_stop_queue = self.job_manager.job_stop_queue # Initialize the external service types self.external_service_types = external_service_types.ExternalServiceTypesCollection( self.config.external_service_type_config_file, self.config.external_service_type_path, self )
def __init__(self, **kwargs): print >> sys.stderr, "python path is: " + ", ".join(sys.path) self.name = 'galaxy' self.new_installation = False # Read config file and check for errors self.config = config.Configuration(**kwargs) self.config.check() config.configure_logging(self.config) self.configure_fluent_log() self._amqp_internal_connection_obj = galaxy.queues.connection_from_config( self.config) self._configure_tool_shed_registry() self._configure_object_store(fsmon=True) # Setup the database engine and ORM config_file = kwargs.get('global_conf', {}).get('__file__', None) if config_file: log.debug('Using "galaxy.ini" config file: %s', config_file) check_migrate_tools = self.config.check_migrate_tools self._configure_models(check_migrate_databases=True, check_migrate_tools=check_migrate_tools, config_file=config_file) # Manage installed tool shed repositories. from tool_shed.galaxy_install import installed_repository_manager self.installed_repository_manager = installed_repository_manager.InstalledRepositoryManager( self) self._configure_datatypes_registry(self.installed_repository_manager) galaxy.model.set_datatypes_registry(self.datatypes_registry) # Security helper self._configure_security() # Tag handler self.tag_handler = GalaxyTagManager(self) # Dataset Collection Plugins self.dataset_collections_service = DatasetCollectionManager(self) # Tool Data Tables self._configure_tool_data_tables(from_shed_config=False) # Load dbkey / genome build manager self._configure_genome_builds(data_table_name="__dbkeys__", load_old_style=True) # Genomes self.genomes = Genomes(self) # Data providers registry. self.data_provider_registry = DataProviderRegistry() # Initialize job metrics manager, needs to be in place before # config so per-destination modifications can be made. self.job_metrics = job_metrics.JobMetrics( self.config.job_metrics_config_file, app=self) # Initialize the job management configuration self.job_config = jobs.JobConfiguration(self) self._configure_toolbox() # Load Data Manager self.data_managers = DataManagers(self) # Load the update repository manager. self.update_repository_manager = update_repository_manager.UpdateRepositoryManager( self) # Load proprietary datatype converters and display applications. self.installed_repository_manager.load_proprietary_converters_and_display_applications( ) # Load datatype display applications defined in local datatypes_conf.xml self.datatypes_registry.load_display_applications(self) # Load datatype converters defined in local datatypes_conf.xml self.datatypes_registry.load_datatype_converters(self.toolbox) # Load external metadata tool self.datatypes_registry.load_external_metadata_tool(self.toolbox) # Load history import/export tools. load_history_imp_exp_tools(self.toolbox) # visualizations registry: associates resources with visualizations, controls how to render self.visualizations_registry = VisualizationsRegistry( self, directories_setting=self.config.visualization_plugins_directory, template_cache_dir=self.config.template_cache) # Load security policy. self.security_agent = self.model.security_agent self.host_security_agent = galaxy.security.HostAgent( model=self.security_agent.model, permitted_actions=self.security_agent.permitted_actions) # Load quota management. if self.config.enable_quotas: self.quota_agent = galaxy.quota.QuotaAgent(self.model) else: self.quota_agent = galaxy.quota.NoQuotaAgent(self.model) # Heartbeat for thread profiling self.heartbeat = None # Container for OpenID authentication routines if self.config.enable_openid: from galaxy.web.framework import openid_manager self.openid_manager = openid_manager.OpenIDManager( self.config.openid_consumer_cache_path) self.openid_providers = OpenIDProviders.from_file( self.config.openid_config_file) else: self.openid_providers = OpenIDProviders() # Start the heartbeat process if configured and available if self.config.use_heartbeat: from galaxy.util import heartbeat if heartbeat.Heartbeat: self.heartbeat = heartbeat.Heartbeat( fname=self.config.heartbeat_log) self.heartbeat.daemon = True self.heartbeat.start() # Transfer manager client if self.config.get_bool('enable_beta_job_managers', False): from galaxy.jobs import transfer_manager self.transfer_manager = transfer_manager.TransferManager(self) # Start the job manager from galaxy.jobs import manager self.job_manager = manager.JobManager(self) self.job_manager.start() # FIXME: These are exposed directly for backward compatibility self.job_queue = self.job_manager.job_queue self.job_stop_queue = self.job_manager.job_stop_queue self.proxy_manager = ProxyManager(self.config) # Initialize the external service types self.external_service_types = external_service_types.ExternalServiceTypesCollection( self.config.external_service_type_config_file, self.config.external_service_type_path, self) from galaxy.workflow import scheduling_manager # Must be initialized after job_config. self.workflow_scheduling_manager = scheduling_manager.WorkflowSchedulingManager( self) self.model.engine.dispose() self.server_starttime = int(time.time()) # used for cachebusting
def __init__(self, **kwargs): if not log.handlers: # Paste didn't handle it, so we need a temporary basic log # configured. The handler added here gets dumped and replaced with # an appropriately configured logger in configure_logging below. logging.basicConfig(level=logging.DEBUG) log.debug("python path is: %s", ", ".join(sys.path)) self.name = 'galaxy' self.startup_timer = ExecutionTimer() self.new_installation = False self.application_stack = application_stack_instance() # Read config file and check for errors self.config = config.Configuration(**kwargs) self.config.check() config.configure_logging(self.config) self.configure_fluent_log() self.config.reload_sanitize_whitelist( explicit='sanitize_whitelist_file' in kwargs) self.amqp_internal_connection_obj = galaxy.queues.connection_from_config( self.config) # control_worker *can* be initialized with a queue, but here we don't # want to and we'll allow postfork to bind and start it. self.control_worker = GalaxyQueueWorker(self) self._configure_tool_shed_registry() self._configure_object_store(fsmon=True) # Setup the database engine and ORM config_file = kwargs.get('global_conf', {}).get('__file__', None) if config_file: log.debug('Using "galaxy.ini" config file: %s', config_file) check_migrate_tools = self.config.check_migrate_tools self._configure_models(check_migrate_databases=True, check_migrate_tools=check_migrate_tools, config_file=config_file) # Manage installed tool shed repositories. from tool_shed.galaxy_install import installed_repository_manager self.installed_repository_manager = installed_repository_manager.InstalledRepositoryManager( self) self._configure_datatypes_registry(self.installed_repository_manager) galaxy.model.set_datatypes_registry(self.datatypes_registry) # Security helper self._configure_security() # Tag handler self.tag_handler = GalaxyTagManager(self) # Dataset Collection Plugins self.dataset_collections_service = DatasetCollectionManager(self) # Tool Data Tables self._configure_tool_data_tables(from_shed_config=False) # Load dbkey / genome build manager self._configure_genome_builds(data_table_name="__dbkeys__", load_old_style=True) # Genomes self.genomes = Genomes(self) # Data providers registry. self.data_provider_registry = DataProviderRegistry() # Initialize job metrics manager, needs to be in place before # config so per-destination modifications can be made. self.job_metrics = job_metrics.JobMetrics( self.config.job_metrics_config_file, app=self) # Initialize the job management configuration self.job_config = jobs.JobConfiguration(self) # Setup a Tool Cache self.tool_cache = ToolCache() self.tool_shed_repository_cache = ToolShedRepositoryCache(self) # Watch various config files for immediate reload self.watchers = ConfigWatchers(self) self._configure_toolbox() # Load Data Manager self.data_managers = DataManagers(self) # Load the update repository manager. self.update_repository_manager = update_repository_manager.UpdateRepositoryManager( self) # Load proprietary datatype converters and display applications. self.installed_repository_manager.load_proprietary_converters_and_display_applications( ) # Load datatype display applications defined in local datatypes_conf.xml self.datatypes_registry.load_display_applications(self) # Load datatype converters defined in local datatypes_conf.xml self.datatypes_registry.load_datatype_converters(self.toolbox) # Load external metadata tool self.datatypes_registry.load_external_metadata_tool(self.toolbox) # Load history import/export tools. load_lib_tools(self.toolbox) # visualizations registry: associates resources with visualizations, controls how to render self.visualizations_registry = VisualizationsRegistry( self, directories_setting=self.config.visualization_plugins_directory, template_cache_dir=self.config.template_cache) # Tours registry self.tour_registry = ToursRegistry(self.config.tour_config_dir) # Webhooks registry self.webhooks_registry = WebhooksRegistry(self.config.webhooks_dirs) # Load security policy. self.security_agent = self.model.security_agent self.host_security_agent = galaxy.security.HostAgent( model=self.security_agent.model, permitted_actions=self.security_agent.permitted_actions) # Load quota management. if self.config.enable_quotas: self.quota_agent = galaxy.quota.QuotaAgent(self.model) else: self.quota_agent = galaxy.quota.NoQuotaAgent(self.model) # Heartbeat for thread profiling self.heartbeat = None # Container for OpenID authentication routines if self.config.enable_openid: from galaxy.web.framework import openid_manager self.openid_manager = openid_manager.OpenIDManager( self.config.openid_consumer_cache_path) self.openid_providers = OpenIDProviders.from_file( self.config.openid_config_file) else: self.openid_providers = OpenIDProviders() from galaxy import auth self.auth_manager = auth.AuthManager(self) # Start the heartbeat process if configured and available (wait until # postfork if using uWSGI) if self.config.use_heartbeat: if heartbeat.Heartbeat: self.heartbeat = heartbeat.Heartbeat( self.config, period=self.config.heartbeat_interval, fname=self.config.heartbeat_log) self.heartbeat.daemon = True self.application_stack.register_postfork_function( self.heartbeat.start) self.sentry_client = None if self.config.sentry_dsn: def postfork_sentry_client(): import raven self.sentry_client = raven.Client(self.config.sentry_dsn) self.application_stack.register_postfork_function( postfork_sentry_client) # Transfer manager client if self.config.get_bool('enable_beta_job_managers', False): from galaxy.jobs import transfer_manager self.transfer_manager = transfer_manager.TransferManager(self) # Start the job manager from galaxy.jobs import manager self.job_manager = manager.JobManager(self) self.job_manager.start() # FIXME: These are exposed directly for backward compatibility self.job_queue = self.job_manager.job_queue self.job_stop_queue = self.job_manager.job_stop_queue self.proxy_manager = ProxyManager(self.config) # Initialize the external service types self.external_service_types = external_service_types.ExternalServiceTypesCollection( self.config.external_service_type_config_file, self.config.external_service_type_path, self) from galaxy.workflow import scheduling_manager # Must be initialized after job_config. self.workflow_scheduling_manager = scheduling_manager.WorkflowSchedulingManager( self) # Configure handling of signals handlers = {} if self.heartbeat: handlers[signal.SIGUSR1] = self.heartbeat.dump_signal_handler self._configure_signal_handlers(handlers) self.model.engine.dispose() self.server_starttime = int(time.time()) # used for cachebusting log.info("Galaxy app startup finished %s" % self.startup_timer)