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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,
Optional,
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.celery.base_task import (
GalaxyTaskBeforeStart,
GalaxyTaskBeforeStartUserRateLimitPostgres,
GalaxyTaskBeforeStartUserRateLimitStandard,
)
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.dbkeys import GenomeBuilds
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.notification import NotificationManager
from galaxy.managers.roles import RoleManager
from galaxy.managers.session import GalaxySessionManager
from galaxy.managers.tasks import (
AsyncTasksManager,
CeleryAsyncTasksManager,
)
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 (
ModelMapping,
SharedModelMapping,
)
from galaxy.model.database_heartbeat import DatabaseHeartbeat
from galaxy.model.database_utils import (
database_exists,
is_one_database,
is_postgres,
)
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 (
HasToolBox,
mapping as install_mapping,
)
from galaxy.objectstore import (
BaseObjectStore,
build_object_store_from_config,
)
from galaxy.queue_worker import (
GalaxyQueueWorker,
reload_toolbox,
send_local_control_task,
)
from galaxy.quota import (
get_quota_agent,
QuotaAgent,
)
from galaxy.schema.fields import Security
from galaxy.security.idencoding import IdEncodingHelper
from galaxy.security.vault import (
Vault,
VaultFactory,
)
from galaxy.short_term_storage import (
ShortTermStorageAllocator,
ShortTermStorageConfiguration,
ShortTermStorageManager,
ShortTermStorageMonitor,
)
from galaxy.tool_shed.cache import ToolShedRepositoryCache
from galaxy.tool_shed.galaxy_install.client import InstallationTarget
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.data import ToolDataTableManager as BaseToolDataTableManager
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
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.task import IntervalTask
from galaxy.util.tool_shed import tool_shed_registry
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 url_for
from galaxy.web.framework.base import server_starttime
from galaxy.web.proxy import ProxyManager
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 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:
config: config.GalaxyAppConfiguration
application_stack: ApplicationStack
[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}'"
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],
traces_sample_rate=self.config.sentry_traces_sample_rate,
ca_certs=self.config.sentry_ca_certs,
)
[docs]class MinimalGalaxyApplication(BasicSharedApp, HaltableContainer, SentryClientMixin, HasToolBox):
"""Encapsulates the state of a minimal Galaxy application"""
model: GalaxyModelMapping
config: config.GalaxyAppConfiguration
tool_cache: ToolCache
job_config: jobs.JobConfiguration
toolbox_search: ToolBoxSearch
container_finder: containers.ContainerFinder
install_model: ModelMapping
object_store: BaseObjectStore
[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 = self._register_singleton(config.GalaxyAppConfiguration, config.GalaxyAppConfiguration(**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)
# Load quota management.
self.quota_agent = self._register_singleton(QuotaAgent, get_quota_agent(self.config, self.model))
[docs] def configure_fluent_log(self):
if self.config.fluent_log:
from galaxy.util.custom_logging.fluent_log import FluentTraceLogger
self.trace_logger: Optional[FluentTraceLogger] = FluentTraceLogger(
"galaxy", self.config.fluent_host, self.config.fluent_port
)
else:
self.trace_logger = None
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):
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,
"cache.url": self.config.mulled_resolution_cache_url,
"cache.table_name": self.config.mulled_resolution_cache_table_name,
"cache.schema_name": self.config.mulled_resolution_cache_schema_name,
}
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),
)
@property
def toolbox(self) -> tools.ToolBox:
return self._toolbox
[docs] def reindex_tool_search(self) -> None:
# 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: BaseToolDataTableManager = 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, use_display_applications=True, use_converters=True):
# Create an empty datatypes registry.
self.datatypes_registry = Registry(self.config)
# 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)
Security.security = self.security
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) -> Optional[str]:
return self.toolbox.dependency_manager.default_base_path
def _shutdown_object_store(self):
self.object_store.shutdown()
def _shutdown_model(self):
self.model.engine.dispose()
[docs]class GalaxyManagerApplication(MinimalManagerApp, MinimalGalaxyApplication, InstallationTarget[tools.ToolBox]):
"""Extends the MinimalGalaxyApplication with most managers that are not tied to a web or job handling context."""
model: GalaxyModelMapping
[docs] def __init__(self, configure_logging=True, use_converters=True, use_display_applications=True, **kwargs):
super().__init__(**kwargs)
self._register_singleton(MinimalManagerApp, self) # type: ignore[type-abstract]
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, self.config.job_metrics, 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) # type: ignore[type-abstract]
self._register_singleton(ShortTermStorageMonitor, short_term_storage_manager) # type: ignore[type-abstract]
# 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)
self.notification_manager = self._register_singleton(NotificationManager)
self.task_manager = self._register_abstract_singleton(
AsyncTasksManager, CeleryAsyncTasksManager # type: ignore[type-abstract] # https://github.com/python/mypy/issues/4717
)
# ConfiguredFileSources
self.file_sources = self._register_singleton(
ConfiguredFileSources, ConfiguredFileSources.from_app_config(self.config)
)
self.vault = self._register_singleton(Vault, VaultFactory.from_app(self)) # type: ignore[type-abstract]
# 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
)
# 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(
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()
self._configure_tool_shed_registry()
self._register_singleton(tool_shed_registry.Registry, self.tool_shed_registry)
self._register_celery_galaxy_task_components()
def _register_celery_galaxy_task_components(self):
"""
Register subtype class instance to support implementation of a user rate limit for execution of celery tasks.
The default supertype class does not enforce a user rate limit. This is the case if the celery_user_rate_limit
config param is the default value.
"""
task_before_start: GalaxyTaskBeforeStart
if self.config.celery_user_rate_limit:
if is_postgres(self.config.database_connection): # type: ignore[arg-type]
task_before_start = GalaxyTaskBeforeStartUserRateLimitPostgres(
self.config.celery_user_rate_limit, self.model.session
)
else:
task_before_start = GalaxyTaskBeforeStartUserRateLimitStandard(
self.config.celery_user_rate_limit, self.model.session
)
else:
task_before_start = GalaxyTaskBeforeStart()
self._register_singleton(GalaxyTaskBeforeStart, task_before_start)
def _configure_tool_shed_registry(self) -> None:
# 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()
@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 UniverseApplication(StructuredApp, GalaxyManagerApplication):
"""Encapsulates the state of a Universe application"""
model: GalaxyModelMapping
[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) # type: ignore[type-abstract]
if kwargs.get("is_webapp"):
self.is_webapp = kwargs["is_webapp"]
# 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.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 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)
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[type-abstract]
# 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:
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 there is only a single external authentication provider in use
# TODO: Future work will expand on this and provide an interface for
# multiple auth providers allowing explicit authenticated association.
self.config.fixed_delegated_auth = (
len(list(self.config.oidc)) == 1 and len(list(self.auth_manager.authenticators)) == 0
)
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)
# Reload toolbox to pick up changes to toolbox made after master was ready
self.application_stack.register_postfork_function(
lambda: reload_toolbox(self, save_integrated_tool_panel=False), post_fork_only=True
)
# 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.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
self.application_stack.register_postfork_function(self.object_store.start)
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()
[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):
if statsd_host := getattr(config, "statsd_host", None):
from galaxy.web.statsd_client import GalaxyStatsdClient
self.galaxy_statsd_client: Optional[GalaxyStatsdClient] = 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)