def __init__(self, **kwargs): super().__init__() self[BasicApp] = self log.debug("python path is: %s", ", ".join(sys.path)) self.name = "reports" # Read config file and check for errors self.config = config.Configuration(**kwargs) self.config.check() configure_logging(self.config) self.application_stack = application_stack_instance() # 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 # Setup the database engine and ORM self.model = galaxy.model.mapping.init( self.config.file_path, db_url, self.config.database_engine_options, create_tables=True) if not self.config.database_connection: self.targets_mysql = False else: self.targets_mysql = 'mysql' in self.config.database_connection # Security helper self.security = idencoding.IdEncodingHelper( id_secret=self.config.id_secret) self._register_singleton(idencoding.IdEncodingHelper, self.security) self._register_singleton(SharedModelMapping, self.model) # used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base. self.server_starttime = int(time.time())
def __init__(self, **kwargs): super().__init__(**kwargs) self._register_singleton(MinimalManagerApp, self) self.execution_timer_factory = self._register_singleton( ExecutionTimerFactory, ExecutionTimerFactory(self.config)) self.configure_fluent_log() self.application_stack = self._register_singleton( ApplicationStack, application_stack_instance(app=self)) # Initialize job metrics manager, needs to be in place before # config so per-destination modifications can be made. self.job_metrics = self._register_singleton( JobMetrics, JobMetrics(self.config.job_metrics_config_file, app=self)) # Initialize the job management configuration self.job_config = self._register_singleton(jobs.JobConfiguration) # Tag handler self.tag_handler = self._register_singleton(GalaxyTagHandler) self.user_manager = self._register_singleton(UserManager) self._register_singleton(GalaxySessionManager) self.hda_manager = self._register_singleton(HDAManager) self.history_manager = self._register_singleton(HistoryManager) self.job_search = self._register_singleton(JobSearch) self.dataset_collection_manager = self._register_singleton( DatasetCollectionManager) self.workflow_manager = self._register_singleton(WorkflowsManager) self.workflow_contents_manager = self._register_singleton( WorkflowContentsManager) self.library_folder_manager = self._register_singleton(FolderManager) self.library_manager = self._register_singleton(LibraryManager) self.role_manager = self._register_singleton(RoleManager) from galaxy.jobs.manager import JobManager self.job_manager = self._register_singleton(JobManager) # ConfiguredFileSources self.file_sources = self._register_singleton( ConfiguredFileSources, ConfiguredFileSources.from_app_config(self.config)) # We need the datatype registry for running certain tasks that modify HDAs, and to build the registry we need # to setup the installed repositories ... this is not ideal self._configure_tool_config_files() self.installed_repository_manager = self._register_singleton( InstalledRepositoryManager, InstalledRepositoryManager(self)) self._configure_datatypes_registry(self.installed_repository_manager) self._register_singleton(Registry, self.datatypes_registry) galaxy.model.set_datatypes_registry(self.datatypes_registry) self.sentry_client = None if self.config.sentry_dsn: def postfork_sentry_client(): import raven self.sentry_client = raven.Client( self.config.sentry_dsn, transport=raven.transport.HTTPTransport) self.application_stack.register_postfork_function( postfork_sentry_client)
def setup_heartbeat_app(app): app.config.server_name = 'test_heartbeat' app.config.attach_to_pools = False app.application_stack = stack.application_stack_instance(app=app) app.database_heartbeat = heartbeat.DatabaseHeartbeat( application_stack=app.application_stack, heartbeat_interval=0.1) yield app app.database_heartbeat.shutdown()
def __init__(self, **kwd): log.debug("python path is: %s", ", ".join(sys.path)) self.name = "tool_shed" # Read the tool_shed.ini configuration file and check for errors. self.config = config.Configuration(**kwd) self.config.check() configure_logging(self.config) self.application_stack = application_stack_instance() # Initialize the Galaxy datatypes registry. self.datatypes_registry = galaxy.datatypes.registry.Registry() self.datatypes_registry.load_datatypes(self.config.root, self.config.datatypes_config) # Initialize the Tool Shed repository_types registry. self.repository_types_registry = tool_shed.repository_types.registry.Registry() # Initialize the RepositoryGridFilterManager. self.repository_grid_filter_manager = RepositoryGridFilterManager() # Determine the Tool Shed database connection string. if self.config.database_connection: db_url = self.config.database_connection else: db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database # Initialize the Tool Shed database and check for appropriate schema version. from galaxy.webapps.tool_shed.model.migrate.check import create_or_verify_database create_or_verify_database(db_url, self.config.database_engine_options) # Set up the Tool Shed database engine and ORM. from galaxy.webapps.tool_shed.model import mapping self.model = mapping.init(self.config.file_path, db_url, self.config.database_engine_options) self.security = idencoding.IdEncodingHelper(id_secret=self.config.id_secret) # initialize the Tool Shed tag handler. self.tag_handler = CommunityTagHandler(self) # Initialize the Tool Shed tool data tables. Never pass a configuration file here # because the Tool Shed should always have an empty dictionary! self.tool_data_tables = galaxy.tools.data.ToolDataTableManager(self.config.tool_data_path) self.genome_builds = GenomeBuilds(self) from galaxy import auth self.auth_manager = auth.AuthManager(self) # Citation manager needed to load tools. from galaxy.managers.citations import CitationsManager self.citations_manager = CitationsManager(self) # The Tool Shed makes no use of a Galaxy toolbox, but this attribute is still required. self.use_tool_dependency_resolution = False self.toolbox = tools.ToolBox([], self.config.tool_path, self) # Initialize the Tool Shed security agent. self.security_agent = self.model.security_agent # The Tool Shed makes no use of a quota, but this attribute is still required. self.quota_agent = galaxy.quota.NoQuotaAgent(self.model) # Initialize the baseline Tool Shed statistics component. self.shed_counter = self.model.shed_counter # Let the Tool Shed's HgwebConfigManager know where the hgweb.config file is located. self.hgweb_config_manager = self.model.hgweb_config_manager self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir # Initialize the repository registry. self.repository_registry = tool_shed.repository_registry.Registry(self) # used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base. self.server_starttime = int(time.time()) log.debug("Tool shed hgweb.config file is: %s", self.hgweb_config_manager.hgweb_config)
def setup_queue_worker_test(app): app.some_var = 'foo' app.tasks_executed = [] server_name = "%s.%s" % (app.amqp_type, datetime.datetime.now()) app.config.server_name = server_name app.config.server_names = [server_name] app.config.attach_to_pools = False app.amqp_internal_connection_obj = connection_from_config(app.config) app.application_stack = application_stack_instance(app=app) app.database_heartbeat = DatabaseHeartbeat(application_stack=app.application_stack, heartbeat_interval=10) app.database_heartbeat.start() time.sleep(0.2) app.queue_worker = GalaxyQueueWorker(app=app, task_mapping=control_message_to_task) app.queue_worker.bind_and_start() time.sleep(0.5) return app
def test_application_stack_post_fork(monkeypatch): app = GalaxyDataTestApp() monkeypatch.setenv("SERVER_SOFTWARE", SERVER_SOFTWARE) monkeypatch.setenv("GUNICORN_WORKER_ID", "100") monkeypatch.setattr(GunicornApplicationStack, "do_post_fork", True) stack_instance = application_stack_instance(app=app, config=app.config) assert isinstance(stack_instance, GunicornApplicationStack) stack_instance.register_postfork_function( lambda: stack_instance.set_postfork_server_name(app)) assert not app.config.server_name.endswith(".100") stack_instance.late_postfork() stack_instance.late_postfork_event.set() wait_on(lambda: app.config.server_name.endswith(".100") or None, desc="server name to change", timeout=1, delta=0.1)
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' # is_webapp will be set to true when building WSGI app self.is_webapp = False self.startup_timer = ExecutionTimer() 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.execution_timer_factory = ExecutionTimerFactory(self.config) self.configure_fluent_log() # A lot of postfork initialization depends on the server name, ensure it is set immediately after forking before other postfork functions self.application_stack = application_stack_instance(app=self) self.application_stack.register_postfork_function( self.application_stack.set_postfork_server_name, self) self.config.reload_sanitize_whitelist( explicit='sanitize_whitelist_file' in kwargs) self.amqp_internal_connection_obj = galaxy.queues.connection_from_config( self.config) # queue_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.queue_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=self.config.check_migrate_databases, check_migrate_tools=check_migrate_tools, config_file=config_file) # Security helper self._configure_security() # Tag handler self.tag_handler = GalaxyTagHandler(self.model.context) self.dataset_collections_service = DatasetCollectionManager(self) self.history_manager = HistoryManager(self) self.hda_manager = HDAManager(self) self.workflow_manager = WorkflowsManager(self) self.dependency_resolvers_view = DependencyResolversView(self) self.test_data_resolver = test_data.TestDataResolver( file_dirs=self.config.tool_test_data_directories) self.library_folder_manager = FolderManager() self.library_manager = LibraryManager() self.dynamic_tool_manager = DynamicToolManager(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 error report plugins. self.error_reports = ErrorReports(self.config.error_report_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_tool_config_files() self.installed_repository_manager = InstalledRepositoryManager(self) self._configure_datatypes_registry(self.installed_repository_manager) galaxy.model.set_datatypes_registry(self.datatypes_registry) self._configure_toolbox() # Load Data Manager self.data_managers = DataManagers(self) # Load the update repository manager. self.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_path) # Tours registry self.tour_registry = ToursRegistry(self.config.tour_config_dir) # Webhooks registry self.webhooks_registry = WebhooksRegistry(self.config.webhooks_dir) # Load security policy. self.security_agent = self.model.security_agent self.host_security_agent = galaxy.model.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 from galaxy import auth self.auth_manager = auth.AuthManager(self) self.user_manager = UserManager(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.authnz_manager = None if self.config.enable_oidc: from galaxy.authnz import managers self.authnz_manager = managers.AuthnzManager( self, self.config.oidc_config, self.config.oidc_backends_config) self.sentry_client = None if self.config.sentry_dsn: def postfork_sentry_client(): import raven self.sentry_client = raven.Client( self.config.sentry_dsn, transport=raven.transport.HTTPTransport) 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.application_stack.register_postfork_function( self.job_manager.start) self.proxy_manager = ProxyManager(self.config) from galaxy.workflow import scheduling_manager # Must be initialized after job_config. self.workflow_scheduling_manager = scheduling_manager.WorkflowSchedulingManager( self) # Must be initialized after any component that might make use of stack messaging is configured. Alternatively if # it becomes more commonly needed we could create a prefork function registration method like we do with # postfork functions. self.application_stack.init_late_prefork() self.containers = {} if self.config.enable_beta_containers_interface: self.containers = build_container_interfaces( self.config.containers_config_file, containers_conf=self.config.containers_conf) self.interactivetool_manager = InteractiveToolManager(self) # Configure handling of signals handlers = {} if self.heartbeat: handlers[signal.SIGUSR1] = self.heartbeat.dump_signal_handler self._configure_signal_handlers(handlers) self.database_heartbeat = DatabaseHeartbeat( application_stack=self.application_stack) self.database_heartbeat.add_change_callback(self.watchers.change_state) self.application_stack.register_postfork_function( self.database_heartbeat.start) # Start web stack message handling self.application_stack.register_postfork_function( self.application_stack.start) self.application_stack.register_postfork_function( self.queue_worker.bind_and_start) # Delay toolbox index until after startup self.application_stack.register_postfork_function( lambda: send_local_control_task(self, 'rebuild_toolbox_search_index')) self.model.engine.dispose() # Inject url_for for components to more easily optionally depend # on url_for. self.url_for = url_for self.server_starttime = int(time.time()) # used for cachebusting log.info("Galaxy app startup finished %s" % self.startup_timer)
def __init__(self, **kwd) -> None: super().__init__() self[BasicApp] = self log.debug("python path is: %s", ", ".join(sys.path)) self.name = "tool_shed" # will be overwritten when building WSGI app self.is_webapp = False # Read the tool_shed.ini configuration file and check for errors. self.config: Any = config.Configuration(**kwd) self.config.check() configure_logging(self.config) self.application_stack = application_stack_instance() # Initialize the Galaxy datatypes registry. self.datatypes_registry = galaxy.datatypes.registry.Registry() self.datatypes_registry.load_datatypes(self.config.root, self.config.datatypes_config) # Initialize the Tool Shed repository_types registry. self.repository_types_registry = tool_shed.repository_types.registry.Registry( ) # Initialize the RepositoryGridFilterManager. self.repository_grid_filter_manager = RepositoryGridFilterManager() # Determine the Tool Shed database connection string. if self.config.database_connection: db_url = self.config.database_connection else: db_url = f"sqlite:///{self.config.database}?isolation_level=IMMEDIATE" # Initialize the Tool Shed database and check for appropriate schema version. from tool_shed.webapp.model.migrate.check import create_or_verify_database create_or_verify_database(db_url, self.config.database_engine_options) # Set up the Tool Shed database engine and ORM. from tool_shed.webapp.model import mapping model: mapping.ToolShedModelMapping = mapping.init( self.config.file_path, db_url, self.config.database_engine_options) self.model = model self.security = idencoding.IdEncodingHelper( id_secret=self.config.id_secret) self._register_singleton(idencoding.IdEncodingHelper, self.security) self._register_singleton(SharedModelMapping, model) self._register_singleton(mapping.ToolShedModelMapping, model) self._register_singleton(scoped_session, self.model.context) self._register_singleton(UserManager, UserManager) # initialize the Tool Shed tag handler. self.tag_handler = CommunityTagHandler(self) # Initialize the Tool Shed tool data tables. Never pass a configuration file here # because the Tool Shed should always have an empty dictionary! self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path) self.genome_builds = GenomeBuilds(self) self.auth_manager = self._register_singleton( auth.AuthManager, auth.AuthManager(self.config)) # Citation manager needed to load tools. self.citations_manager = self._register_singleton( CitationsManager, CitationsManager(self)) self.use_tool_dependency_resolution = False # Initialize the Tool Shed security agent. self.security_agent = model.security_agent # The Tool Shed makes no use of a quota, but this attribute is still required. self.quota_agent = self._register_singleton(QuotaAgent, NoQuotaAgent()) # Initialize the baseline Tool Shed statistics component. self.shed_counter = model.shed_counter # Let the Tool Shed's HgwebConfigManager know where the hgweb.config file is located. self.hgweb_config_manager = hgweb_config_manager self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir # Initialize the repository registry. self.repository_registry = tool_shed.repository_registry.Registry(self) # Configure Sentry client if configured self.configure_sentry_client() # used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base. self.server_starttime = int(time.time()) log.debug("Tool shed hgweb.config file is: %s", self.hgweb_config_manager.hgweb_config)
def test_application_stack_instance_factory(monkeypatch): app = GalaxyDataTestApp() monkeypatch.setenv("SERVER_SOFTWARE", SERVER_SOFTWARE) stack_instance = application_stack_instance(app=app, config=app.config) assert isinstance(stack_instance, GunicornApplicationStack) assert stack_instance.name == "Gunicorn"