Warning

This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

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.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


[docs]class HaltableContainer(Container): haltables: List[Tuple[str, Callable]]
[docs] def __init__(self) -> None: super().__init__() self.haltables = []
[docs] 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
[docs]class SentryClientMixin:
[docs] 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}'" def postfork_sentry_client(): 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], ) self.application_stack.register_postfork_function(postfork_sentry_client)
[docs]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)
[docs] 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 _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
[docs]class MinimalGalaxyApplication(BasicSharedApp, ConfiguresGalaxyMixin, HaltableContainer, SentryClientMixin): """Encapsulates the state of a minimal Galaxy application"""
[docs] 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)
[docs] 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()
[docs]class GalaxyManagerApplication(MinimalManagerApp, MinimalGalaxyApplication): """Extends the MinimalGalaxyApplication with most managers that are not tied to a web or job handling context."""
[docs] 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.dynamic_tool_manager = self._register_singleton(DynamicToolManager) 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()
[docs]class UniverseApplication(StructuredApp, GalaxyManagerApplication): """Encapsulates the state of a Universe application"""
[docs] 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.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 = int(time.time()) # 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
[docs]class StatsdStructuredExecutionTimer(StructuredExecutionTimer):
[docs] def __init__(self, galaxy_statsd_client, *args, **kwds): self.galaxy_statsd_client = galaxy_statsd_client super().__init__(*args, **kwds)
[docs] def to_str(self, **kwd): self.galaxy_statsd_client.timing(self.timer_id, self.elapsed * 1000.0, kwd) return super().to_str(**kwd)
[docs]class ExecutionTimerFactory:
[docs] 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
[docs] def get_timer(self, *args, **kwd): if self.galaxy_statsd_client: return StatsdStructuredExecutionTimer(self.galaxy_statsd_client, *args, **kwd) else: return StructuredExecutionTimer(*args, **kwd)