Source code for galaxy.app

import collections
import errno
import logging
import os
import signal
import sys
import threading
import time
from typing import (
    Any,
    Callable,
    Dict,
    List,
    Tuple,
)

from beaker.cache import CacheManager
from beaker.util import parse_cache_config_options

import galaxy.model
import galaxy.model.security
import galaxy.queues
import galaxy.security
from galaxy import (
    auth,
    config,
    jobs,
    tools,
)
from galaxy.config_watchers import ConfigWatchers
from galaxy.datatypes.registry import Registry
from galaxy.files import ConfiguredFileSources
from galaxy.job_metrics import JobMetrics
from galaxy.jobs.manager import JobManager
from galaxy.managers.api_keys import ApiKeyManager
from galaxy.managers.citations import CitationsManager
from galaxy.managers.collections import DatasetCollectionManager
from galaxy.managers.folders import FolderManager
from galaxy.managers.hdas import HDAManager
from galaxy.managers.histories import HistoryManager
from galaxy.managers.interactivetool import InteractiveToolManager
from galaxy.managers.jobs import JobSearch
from galaxy.managers.libraries import LibraryManager
from galaxy.managers.library_datasets import LibraryDatasetsManager
from galaxy.managers.roles import RoleManager
from galaxy.managers.session import GalaxySessionManager
from galaxy.managers.tools import DynamicToolManager
from galaxy.managers.users import UserManager
from galaxy.managers.workflows import (
    WorkflowContentsManager,
    WorkflowsManager,
)
from galaxy.model import (
    custom_types,
    mapping,
)
from galaxy.model.base import SharedModelMapping
from galaxy.model.database_heartbeat import DatabaseHeartbeat
from galaxy.model.database_utils import (
    database_exists,
    is_one_database,
)
from galaxy.model.mapping import GalaxyModelMapping
from galaxy.model.migrations import verify_databases
from galaxy.model.orm.engine_factory import build_engine
from galaxy.model.scoped_session import (
    galaxy_scoped_session,
    install_model_scoped_session,
)
from galaxy.model.tags import GalaxyTagHandler
from galaxy.model.tool_shed_install import mapping as install_mapping
from galaxy.objectstore import (
    BaseObjectStore,
    build_object_store_from_config,
)
from galaxy.queue_worker import (
    GalaxyQueueWorker,
    send_local_control_task,
)
from galaxy.quota import (
    get_quota_agent,
    QuotaAgent,
)
from galaxy.schema.fields import BaseDatabaseIdField
from galaxy.security.idencoding import IdEncodingHelper
from galaxy.security.vault import (
    Vault,
    VaultFactory,
)
from galaxy.tool_shed import tool_shed_registry
from galaxy.tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
from galaxy.tool_shed.galaxy_install.update_repository_manager import UpdateRepositoryManager
from galaxy.tool_util.deps import containers
from galaxy.tool_util.deps.dependencies import AppInfo
from galaxy.tool_util.deps.views import DependencyResolversView
from galaxy.tool_util.verify.test_data import TestDataResolver
from galaxy.tools.biotools import get_galaxy_biotools_metadata_source
from galaxy.tools.cache import (
    ToolCache,
    ToolShedRepositoryCache,
)
from galaxy.tools.data import ToolDataTableManager
from galaxy.tools.data_manager.manager import DataManagers
from galaxy.tools.error_reports import ErrorReports
from galaxy.tools.search import ToolBoxSearch
from galaxy.tools.special_tools import load_lib_tools
from galaxy.tours import (
    build_tours_registry,
    ToursRegistry,
)
from galaxy.util import (
    ExecutionTimer,
    heartbeat,
    listify,
    StructuredExecutionTimer,
)
from galaxy.util.dbkeys import GenomeBuilds
from galaxy.util.task import IntervalTask
from galaxy.visualization.data_providers.registry import DataProviderRegistry
from galaxy.visualization.genomes import Genomes
from galaxy.visualization.plugins.registry import VisualizationsRegistry
from galaxy.web import (
    legacy_url_for,
    url_for,
)
from galaxy.web.framework.base import server_starttime
from galaxy.web.proxy import ProxyManager
from galaxy.web.short_term_storage import (
    ShortTermStorageAllocator,
    ShortTermStorageConfiguration,
    ShortTermStorageManager,
    ShortTermStorageMonitor,
)
from galaxy.web_stack import (
    application_stack_instance,
    ApplicationStack,
)
from galaxy.webhooks import WebhooksRegistry
from galaxy.workflow import scheduling_manager
from galaxy.workflow.trs_proxy import TrsProxy
from .di import Container
from .structured_app import (
    BasicSharedApp,
    MinimalManagerApp,
    StructuredApp,
)

log = logging.getLogger(__name__)
app = None


class HaltableContainer(Container):
    haltables: List[Tuple[str, Callable]]

    def __init__(self) -> None:
        super().__init__()
        self.haltables = []

    def shutdown(self):
        exception = None
        for what, haltable in self.haltables:
            try:
                haltable()
            except Exception as e:
                log.exception(f"Failed to shutdown {what} cleanly")
                exception = exception or e
        if exception is not None:
            raise exception


class SentryClientMixin:
    def configure_sentry_client(self):
        self.sentry_client = None
        if self.config.sentry_dsn:
            event_level = self.config.sentry_event_level.upper()
            assert event_level in [
                "DEBUG",
                "INFO",
                "WARNING",
                "ERROR",
                "CRITICAL",
            ], f"Invalid sentry event level '{self.config.sentry.event_level}'"

            import sentry_sdk
            from sentry_sdk.integrations.logging import LoggingIntegration

            sentry_logging = LoggingIntegration(
                level=logging.INFO,  # Capture info and above as breadcrumbs
                event_level=getattr(logging, event_level),  # Send errors as events
            )
            self.sentry_client = sentry_sdk.init(
                self.config.sentry_dsn,
                release=f"{self.config.version_major}.{self.config.version_minor}",
                integrations=[sentry_logging],
            )


class ConfiguresGalaxyMixin:
    """Shared code for configuring Galaxy-like app objects."""

    config: config.GalaxyAppConfiguration
    tool_cache: ToolCache
    job_config: jobs.JobConfiguration
    toolbox: tools.ToolBox
    toolbox_search: ToolBoxSearch
    container_finder: containers.ContainerFinder

    def _configure_genome_builds(self, data_table_name="__dbkeys__", load_old_style=True):
        self.genome_builds = GenomeBuilds(self, data_table_name=data_table_name, load_old_style=load_old_style)

    def wait_for_toolbox_reload(self, old_toolbox):
        timer = ExecutionTimer()
        log.debug("Waiting for toolbox reload")
        # Wait till toolbox reload has been triggered (or more than 60 seconds have passed)
        while timer.elapsed < 60:
            if self.toolbox.has_reloaded(old_toolbox):
                log.debug("Finished waiting for toolbox reload %s", timer)
                break
            time.sleep(0.1)
        else:
            log.warning("Waiting for toolbox reload timed out after 60 seconds")

    def _configure_tool_config_files(self):
        if self.config.shed_tool_config_file not in self.config.tool_configs:
            self.config.tool_configs.append(self.config.shed_tool_config_file)
        # The value of migrated_tools_config is the file reserved for containing only those tools that have been
        # eliminated from the distribution and moved to the tool shed. If migration checking is disabled, only add it if
        # it exists (since this may be an existing deployment where migrations were previously run).
        if (
            os.path.exists(self.config.migrated_tools_config)
            and self.config.migrated_tools_config not in self.config.tool_configs
        ):
            self.config.tool_configs.append(self.config.migrated_tools_config)

    def _configure_toolbox(self):
        if not isinstance(self, BasicSharedApp):
            raise Exception("Must inherit from BasicSharedApp")

        self.citations_manager = CitationsManager(self)
        self.biotools_metadata_source = get_galaxy_biotools_metadata_source(self.config)

        self.dynamic_tools_manager = DynamicToolManager(self)
        self._toolbox_lock = threading.RLock()
        self.toolbox = tools.ToolBox(self.config.tool_configs, self.config.tool_path, self)
        galaxy_root_dir = os.path.abspath(self.config.root)
        file_path = os.path.abspath(self.config.file_path)
        app_info = AppInfo(
            galaxy_root_dir=galaxy_root_dir,
            default_file_path=file_path,
            tool_data_path=self.config.tool_data_path,
            shed_tool_data_path=self.config.shed_tool_data_path,
            outputs_to_working_directory=self.config.outputs_to_working_directory,
            container_image_cache_path=self.config.container_image_cache_path,
            library_import_dir=self.config.library_import_dir,
            enable_mulled_containers=self.config.enable_mulled_containers,
            container_resolvers_config_file=self.config.container_resolvers_config_file,
            container_resolvers_config_dict=self.config.container_resolvers,
            involucro_path=self.config.involucro_path,
            involucro_auto_init=self.config.involucro_auto_init,
            mulled_channels=self.config.mulled_channels,
        )
        mulled_resolution_cache = None
        if self.config.mulled_resolution_cache_type:
            cache_opts = {
                "cache.type": self.config.mulled_resolution_cache_type,
                "cache.data_dir": self.config.mulled_resolution_cache_data_dir,
                "cache.lock_dir": self.config.mulled_resolution_cache_lock_dir,
                "cache.expire": self.config.mulled_resolution_cache_expire,
            }
            mulled_resolution_cache = CacheManager(**parse_cache_config_options(cache_opts)).get_cache(
                "mulled_resolution"
            )
        self.container_finder = containers.ContainerFinder(app_info, mulled_resolution_cache=mulled_resolution_cache)
        self._set_enabled_container_types()
        index_help = getattr(self.config, "index_tool_help", True)
        self.toolbox_search = self._register_singleton(
            ToolBoxSearch,
            ToolBoxSearch(self.toolbox, index_dir=self.config.tool_search_index_dir, index_help=index_help),
        )

    def reindex_tool_search(self):
        # Call this when tools are added or removed.
        self.toolbox_search.build_index(tool_cache=self.tool_cache, toolbox=self.toolbox)
        self.tool_cache.reset_status()

    def _set_enabled_container_types(self):
        container_types_to_destinations = collections.defaultdict(list)
        for destinations in self.job_config.destinations.values():
            for destination in destinations:
                for enabled_container_type in self.container_finder._enabled_container_types(destination.params):
                    container_types_to_destinations[enabled_container_type].append(destination)
        self.toolbox.dependency_manager.set_enabled_container_types(container_types_to_destinations)
        self.toolbox.dependency_manager.resolver_classes.update(
            self.container_finder.default_container_registry.resolver_classes
        )
        self.toolbox.dependency_manager.dependency_resolvers.extend(
            self.container_finder.default_container_registry.container_resolvers
        )

    def _configure_tool_data_tables(self, from_shed_config):
        # Initialize tool data tables using the config defined by self.config.tool_data_table_config_path.
        self.tool_data_tables = ToolDataTableManager(
            tool_data_path=self.config.tool_data_path,
            config_filename=self.config.tool_data_table_config_path,
            other_config_dict=self.config,
        )
        # Load additional entries defined by self.config.shed_tool_data_table_config into tool data tables.
        try:
            self.tool_data_tables.load_from_config_file(
                config_filename=self.config.shed_tool_data_table_config,
                tool_data_path=self.tool_data_tables.tool_data_path,
                from_shed_config=from_shed_config,
            )
        except OSError as exc:
            # Missing shed_tool_data_table_config is okay if it's the default
            if exc.errno != errno.ENOENT or self.config.is_set("shed_tool_data_table_config"):
                raise

    def _configure_datatypes_registry(
        self, installed_repository_manager=None, use_display_applications=True, use_converters=True
    ):
        # Create an empty datatypes registry.
        self.datatypes_registry = Registry(self.config)
        if installed_repository_manager and self.config.load_tool_shed_datatypes:
            # 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.
            installed_repository_manager.load_proprietary_datatypes()
        # Load the data types in the Galaxy distribution, which are defined in self.config.datatypes_config.
        datatypes_configs = self.config.datatypes_config
        for datatypes_config in listify(datatypes_configs):
            # Setting override=False would make earlier files would take
            # precedence - but then they wouldn't override tool shed
            # datatypes.
            self.datatypes_registry.load_datatypes(
                self.config.root,
                datatypes_config,
                override=True,
                use_display_applications=use_display_applications,
                use_converters=use_converters,
            )

    def _configure_object_store(self, **kwds):
        self.object_store = build_object_store_from_config(self.config, **kwds)

    def _configure_security(self):
        self.security = IdEncodingHelper(id_secret=self.config.id_secret)
        BaseDatabaseIdField.security = self.security

    def _configure_tool_shed_registry(self):
        # Set up the tool sheds registry
        if os.path.isfile(self.config.tool_sheds_config_file):
            self.tool_shed_registry = tool_shed_registry.Registry(self.config.tool_sheds_config_file)
        else:
            self.tool_shed_registry = tool_shed_registry.Registry()

    def _configure_engines(self, db_url, install_db_url, combined_install_database):
        trace_logger = getattr(self, "trace_logger", None)
        engine = build_engine(
            db_url,
            self.config.database_engine_options,
            self.config.database_query_profiling_proxy,
            trace_logger,
            self.config.slow_query_log_threshold,
            self.config.thread_local_log,
            self.config.database_log_query_counts,
        )
        install_engine = None
        if not combined_install_database:
            install_engine = build_engine(install_db_url, self.config.install_database_engine_options)
        return engine, install_engine

    def _configure_models(self, check_migrate_databases=False, config_file=None):
        """Preconditions: object_store must be set on self."""
        # TODO this block doesn't seem to belong in this method
        if getattr(self.config, "max_metadata_value_size", None):
            custom_types.MAX_METADATA_VALUE_SIZE = self.config.max_metadata_value_size

        db_url = self.config.database_connection
        install_db_url = self.config.install_database_connection
        combined_install_database = is_one_database(db_url, install_db_url)
        engine, install_engine = self._configure_engines(db_url, install_db_url, combined_install_database)

        if self.config.database_wait:
            self._wait_for_database(db_url)

        if check_migrate_databases:
            self._verify_databases(engine, install_engine, combined_install_database)

        self.model = mapping.configure_model_mapping(
            self.config.file_path,
            self.object_store,
            self.config.use_pbkdf2,
            engine,
            combined_install_database,
            self.config.thread_local_log,
        )

        if combined_install_database:
            log.info("Install database targeting Galaxy's database configuration.")  # TODO this message is ambiguous
            self.install_model = self.model
        else:
            self.install_model = install_mapping.configure_model_mapping(install_engine)
            log.info(f"Install database using its own connection {install_db_url}")

    def _verify_databases(self, engine, install_engine, combined_install_database):
        install_template, install_encoding = None, None
        if not combined_install_database:  # Otherwise these options are not used.
            install_template = getattr(self.config, "install_database_template", None)
            install_encoding = getattr(self.config, "install_database_encoding", None)

        verify_databases(
            engine,
            self.config.database_template,
            self.config.database_encoding,
            install_engine,
            install_template,
            install_encoding,
            self.config.database_auto_migrate,
        )

    def _configure_signal_handlers(self, handlers):
        for sig, handler in handlers.items():
            signal.signal(sig, handler)

    def _wait_for_database(self, url):
        attempts = self.config.database_wait_attempts
        pause = self.config.database_wait_sleep
        for i in range(1, attempts):
            try:
                database_exists(url)
                break
            except Exception:
                log.info("Waiting for database: attempt %d of %d" % (i, attempts))
                time.sleep(pause)

    @property
    def tool_dependency_dir(self):
        return self.toolbox.dependency_manager.default_base_path


class MinimalGalaxyApplication(BasicSharedApp, ConfiguresGalaxyMixin, HaltableContainer, SentryClientMixin):
    """Encapsulates the state of a minimal Galaxy application"""

    def __init__(self, fsmon=False, **kwargs) -> None:
        super().__init__()
        self.haltables = [
            ("object store", self._shutdown_object_store),
            ("database connection", self._shutdown_model),
        ]
        self._register_singleton(BasicSharedApp, self)
        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.is_webapp = False
        # Read config file and check for errors
        self.config: Any = self._register_singleton(config.Configuration, config.Configuration(**kwargs))
        self.config.check()
        self._configure_object_store(fsmon=True)
        self._register_singleton(BaseObjectStore, self.object_store)
        config_file = kwargs.get("global_conf", {}).get("__file__", None)
        if config_file:
            log.debug('Using "galaxy.ini" config file: %s', config_file)
        self._configure_models(check_migrate_databases=self.config.check_migrate_databases, config_file=config_file)
        # Security helper
        self._configure_security()
        self._register_singleton(IdEncodingHelper, self.security)
        self._register_singleton(SharedModelMapping, self.model)
        self._register_singleton(GalaxyModelMapping, self.model)
        self._register_singleton(galaxy_scoped_session, self.model.context)
        self._register_singleton(install_model_scoped_session, self.install_model.context)

    def configure_fluent_log(self):
        if self.config.fluent_log:
            from galaxy.util.custom_logging.fluent_log import FluentTraceLogger

            self.trace_logger = FluentTraceLogger("galaxy", self.config.fluent_host, self.config.fluent_port)
        else:
            self.trace_logger = None

    def _shutdown_object_store(self):
        self.object_store.shutdown()

    def _shutdown_model(self):
        self.model.engine.dispose()


class GalaxyManagerApplication(MinimalManagerApp, MinimalGalaxyApplication):
    """Extends the MinimalGalaxyApplication with most managers that are not tied to a web or job handling context."""

    def __init__(self, configure_logging=True, use_converters=True, use_display_applications=True, **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))
        if configure_logging:
            config.configure_logging(self.config, self.application_stack.facts)
        # 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)

        # Setup infrastructure for short term storage manager.
        short_term_storage_config_kwds: Dict[str, Any] = {}
        short_term_storage_config_kwds["short_term_storage_directory"] = self.config.short_term_storage_dir
        short_term_storage_default_duration = self.config.short_term_storage_default_duration
        short_term_storage_maximum_duration = self.config.short_term_storage_maximum_duration
        if short_term_storage_default_duration is not None:
            short_term_storage_config_kwds["default_storage_duration"] = short_term_storage_default_duration
        if short_term_storage_maximum_duration:
            short_term_storage_config_kwds["maximum_storage_duration"] = short_term_storage_maximum_duration

        short_term_storage_config = ShortTermStorageConfiguration(**short_term_storage_config_kwds)
        short_term_storage_manager = ShortTermStorageManager(config=short_term_storage_config)
        self._register_singleton(ShortTermStorageAllocator, short_term_storage_manager)
        self._register_singleton(ShortTermStorageMonitor, short_term_storage_manager)

        # 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.library_datasets_manager = self._register_singleton(LibraryDatasetsManager)
        self.role_manager = self._register_singleton(RoleManager)
        self.job_manager = self._register_singleton(JobManager)

        # ConfiguredFileSources
        self.file_sources = self._register_singleton(
            ConfiguredFileSources, ConfiguredFileSources.from_app_config(self.config)
        )

        self.vault = self._register_singleton(Vault, VaultFactory.from_app(self))
        # 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.
        self.quota_agent = self._register_singleton(QuotaAgent, get_quota_agent(self.config, self.model))

        # 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,
            use_converters=use_converters,
            use_display_applications=use_display_applications,
        )
        self._register_singleton(Registry, self.datatypes_registry)
        galaxy.model.set_datatypes_registry(self.datatypes_registry)
        self.configure_sentry_client()


class UniverseApplication(StructuredApp, GalaxyManagerApplication):
    """Encapsulates the state of a Universe application"""

    def __init__(self, **kwargs) -> None:
        startup_timer = ExecutionTimer()
        super().__init__(fsmon=True, **kwargs)
        self.haltables = [
            ("queue worker", self._shutdown_queue_worker),
            ("file watcher", self._shutdown_watcher),
            ("database heartbeat", self._shutdown_database_heartbeat),
            ("workflow scheduler", self._shutdown_scheduling_manager),
            ("object store", self._shutdown_object_store),
            ("job manager", self._shutdown_job_manager),
            ("application heartbeat", self._shutdown_heartbeat),
            ("repository manager", self._shutdown_repo_manager),
            ("database connection", self._shutdown_model),
            ("application stack", self._shutdown_application_stack),
        ]
        self._register_singleton(StructuredApp, self)
        # A lot of postfork initialization depends on the server name, ensure it is set immediately after forking before other postfork functions
        self.application_stack.register_postfork_function(self.application_stack.set_postfork_server_name, self)
        self.config.reload_sanitize_allowlist(explicit="sanitize_allowlist_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 = self._register_singleton(GalaxyQueueWorker, GalaxyQueueWorker(self))

        self._configure_tool_shed_registry()
        self._register_singleton(tool_shed_registry.Registry, self.tool_shed_registry)

        self.dependency_resolvers_view = self._register_singleton(
            DependencyResolversView, DependencyResolversView(self)
        )
        self.test_data_resolver = self._register_singleton(
            TestDataResolver, TestDataResolver(file_dirs=self.config.tool_test_data_directories)
        )
        self.dynamic_tool_manager = self._register_singleton(DynamicToolManager)
        self.api_keys_manager = self._register_singleton(ApiKeyManager)

        # 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 = self._register_singleton(Genomes)
        # Data providers registry.
        self.data_provider_registry = self._register_singleton(DataProviderRegistry)

        # Initialize error report plugins.
        self.error_reports = self._register_singleton(
            ErrorReports, ErrorReports(self.config.error_report_file, app=self)
        )

        # Setup a Tool Cache
        self.tool_cache = self._register_singleton(ToolCache)
        self.tool_shed_repository_cache = self._register_singleton(ToolShedRepositoryCache)
        # Watch various config files for immediate reload
        self.watchers = self._register_singleton(ConfigWatchers)
        self._configure_toolbox()
        # Load Data Manager
        self.data_managers = self._register_singleton(DataManagers)
        # Load the update repository manager.
        self.update_repository_manager = self._register_singleton(
            UpdateRepositoryManager, 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)
        # Load built-in converters
        if self.config.display_builtin_converters:
            self.toolbox.load_builtin_converters()
        self.toolbox.persist_cache(register_postfork=True)
        # visualizations registry: associates resources with visualizations, controls how to render
        self.visualizations_registry = self._register_singleton(
            VisualizationsRegistry,
            VisualizationsRegistry(
                self,
                directories_setting=self.config.visualization_plugins_directory,
                template_cache_dir=self.config.template_cache_path,
            ),
        )
        # Tours registry
        tour_registry = build_tours_registry(self.config.tour_config_dir)
        self.tour_registry = tour_registry
        self[ToursRegistry] = tour_registry  # type: ignore[misc]
        # Webhooks registry
        self.webhooks_registry = self._register_singleton(WebhooksRegistry, WebhooksRegistry(self.config.webhooks_dir))
        # Heartbeat for thread profiling
        self.heartbeat = None
        self.auth_manager = self._register_singleton(auth.AuthManager, auth.AuthManager(self.config))
        # Start the heartbeat process if configured and available
        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_file, self.config.oidc_backends_config_file
            )

        if not self.config.enable_celery_tasks and self.config.history_audit_table_prune_interval > 0:
            self.prune_history_audit_task = IntervalTask(
                func=lambda: galaxy.model.HistoryAudit.prune(self.model.session),
                name="HistoryAuditTablePruneTask",
                interval=self.config.history_audit_table_prune_interval,
                immediate_start=False,
                time_execution=True,
            )
            self.application_stack.register_postfork_function(self.prune_history_audit_task.start)
            self.haltables.append(("HistoryAuditTablePruneTask", self.prune_history_audit_task.shutdown))
        # Start the job manager
        self.application_stack.register_postfork_function(self.job_manager.start)
        self.proxy_manager = ProxyManager(self.config)

        # Must be initialized after job_config.
        self.workflow_scheduling_manager = scheduling_manager.WorkflowSchedulingManager(self)

        self.trs_proxy = self._register_singleton(TrsProxy, TrsProxy(self.config))
        # 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.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")
        )

        # Inject url_for for components to more easily optionally depend
        # on url_for.
        self.url_for = url_for
        self.legacy_url_for = legacy_url_for

        self.server_starttime = server_starttime  # used for cachebusting
        # Limit lifetime of tool shed repository cache to app startup
        self.tool_shed_repository_cache = None
        self.api_spec = None
        self.legacy_mapper = None
        log.info(f"Galaxy app startup finished {startup_timer}")

    def _shutdown_queue_worker(self):
        self.queue_worker.shutdown()

    def _shutdown_watcher(self):
        self.watchers.shutdown()

    def _shutdown_database_heartbeat(self):
        self.database_heartbeat.shutdown()

    def _shutdown_scheduling_manager(self):
        self.workflow_scheduling_manager.shutdown()

    def _shutdown_job_manager(self):
        self.job_manager.shutdown()

    def _shutdown_heartbeat(self):
        if self.heartbeat:
            self.heartbeat.shutdown()

    def _shutdown_repo_manager(self):
        self.update_repository_manager.shutdown()

    def _shutdown_application_stack(self):
        self.application_stack.shutdown()

    @property
    def is_job_handler(self) -> bool:
        return (
            self.config.track_jobs_in_database and self.job_config.is_handler
        ) or not self.config.track_jobs_in_database


class StatsdStructuredExecutionTimer(StructuredExecutionTimer):
    def __init__(self, galaxy_statsd_client, *args, **kwds):
        self.galaxy_statsd_client = galaxy_statsd_client
        super().__init__(*args, **kwds)

    def to_str(self, **kwd):
        self.galaxy_statsd_client.timing(self.timer_id, self.elapsed * 1000.0, kwd)
        return super().to_str(**kwd)


class ExecutionTimerFactory:
    def __init__(self, config):
        statsd_host = getattr(config, "statsd_host", None)
        if statsd_host:
            from galaxy.web.framework.middleware.statsd import GalaxyStatsdClient

            self.galaxy_statsd_client = GalaxyStatsdClient(
                statsd_host,
                getattr(config, "statsd_port", 8125),
                getattr(config, "statsd_prefix", "galaxy"),
                getattr(config, "statsd_influxdb", False),
                getattr(config, "statsd_mock_calls", False),
            )
        else:
            self.galaxy_statsd_client = None

    def get_timer(self, *args, **kwd):
        if self.galaxy_statsd_client:
            return StatsdStructuredExecutionTimer(self.galaxy_statsd_client, *args, **kwd)
        else:
            return StructuredExecutionTimer(*args, **kwd)