Warning
This document is for an old release 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.workflow.scheduling_manager
import os
from functools import partial
import galaxy.workflow.schedulers
from galaxy import model
from galaxy.exceptions import HandlerAssignmentError
from galaxy.jobs.handler import ItemGrabber
from galaxy.util import plugin_config
from galaxy.util.custom_logging import get_logger
from galaxy.util.monitors import Monitors
from galaxy.util.xml_macros import load
from galaxy.web_stack.handlers import ConfiguresHandlers, HANDLER_ASSIGNMENT_METHODS
from galaxy.web_stack.message import WorkflowSchedulingMessage
log = get_logger(__name__)
DEFAULT_SCHEDULER_ID = "default" # well actually this should be called DEFAULT_DEFAULT_SCHEDULER_ID...
DEFAULT_SCHEDULER_PLUGIN_TYPE = "core"
EXCEPTION_MESSAGE_SHUTDOWN = "Exception raised while attempting to shutdown workflow scheduler."
EXCEPTION_MESSAGE_NO_SCHEDULERS = "Failed to defined workflow schedulers - no workflow schedulers defined."
EXCEPTION_MESSAGE_NO_DEFAULT_SCHEDULER = "Failed to defined workflow schedulers - no workflow scheduler found for default id '%s'."
EXCEPTION_MESSAGE_DUPLICATE_SCHEDULERS = "Failed to defined workflow schedulers - workflow scheduling plugin id '%s' duplicated."
EXCEPTION_MESSAGE_SERIALIZE = "Parallelization is not desired but handler assignment methods are non-deterministic. Set DB_PREASSIGN in workflow_schedulers_conf.xml."
[docs]class WorkflowSchedulingManager(ConfiguresHandlers):
""" A workflow scheduling manager based loosely on pattern established by
``galaxy.manager.JobManager``. Only schedules workflows on handler
processes.
"""
DEFAULT_BASE_HANDLER_POOLS = ('workflow-schedulers', 'job-handlers')
UNSUPPORTED_HANDLER_ASSIGNMENT_METHODS = {
HANDLER_ASSIGNMENT_METHODS.UWSGI_MULE_MESSAGE,
}
[docs] def __init__(self, app):
self.app = app
self.__handlers_configured = False
self.workflow_schedulers = {}
self.active_workflow_schedulers = {}
# Passive workflow schedulers won't need to be monitored I guess.
self.request_monitor = None
self.handlers = {}
self.handler_assignment_methods_configured = False
self.handler_assignment_methods = None
self.handler_max_grab = None
self.default_handler_id = None
self.__plugin_classes = self.__plugins_dict()
self.__init_schedulers()
if self._is_workflow_handler():
log.debug("Starting workflow schedulers")
self.__start_schedulers()
if self.active_workflow_schedulers:
self.__start_request_monitor()
# When assinging handlers to workflows being queued - use job_conf
# if not explicit workflow scheduling handlers have be specified or
# else use those explicit workflow scheduling handlers (on self).
if self.__handlers_configured:
self.__handlers_config = self
else:
self.__handlers_config = app.job_config
if self._is_workflow_handler():
if self.__handlers_config.use_messaging:
WorkflowSchedulingMessage().bind_default_handler(self, '_handle_message')
self.app.application_stack.register_message_handler(
self._handle_message,
name=WorkflowSchedulingMessage.target)
else:
# Process should not schedule workflows but should check for any unassigned to handlers
self.__startup_recovery()
def __startup_recovery(self):
sa_session = self.app.model.context
for invocation_id in model.WorkflowInvocation.poll_unhandled_workflow_ids(sa_session):
log.info("(%s) Handler unassigned at startup, resubmitting workflow invocation for assignment",
invocation_id)
workflow_invocation = sa_session.query(model.WorkflowInvocation).get(invocation_id)
self._assign_handler(workflow_invocation)
def _handle_setup_msg(self, workflow_invocation_id=None):
sa_session = self.app.model.context
workflow_invocation = sa_session.query(model.WorkflowInvocation).get(workflow_invocation_id)
if workflow_invocation.handler is None:
workflow_invocation.handler = self.app.config.server_name
sa_session.add(workflow_invocation)
sa_session.flush()
else:
log.warning("(%s) Handler '%s' received setup message for workflow invocation but handler '%s' is"
" already assigned, ignoring", workflow_invocation.id, self.app.config.server_name,
workflow_invocation.handler)
def _is_workflow_handler(self):
# If we have explicitly configured handlers, check them.
# Else just make sure we are a job handler.
if self.__handlers_configured:
is_handler = self.is_handler
else:
is_handler = self.app.is_job_handler
return is_handler
def _queue_callback(self, workflow_invocation):
# There isn't an in-memory queue for workflow schedulers, so if MEM_SELF is used just assign with the DB
workflow_invocation.handler = self.app.config.server_name
sa_session = self.app.model.context
sa_session.add(workflow_invocation)
sa_session.flush()
def _message_callback(self, workflow_invocation):
return WorkflowSchedulingMessage(task='setup', workflow_invocation_id=workflow_invocation.id)
def _assign_handler(self, workflow_invocation, flush=True):
# Use random-ish integer history_id to produce a consistent index to pick
# job handler with.
random_index = workflow_invocation.history.id
queue_callback = partial(self._queue_callback, workflow_invocation)
message_callback = partial(self._message_callback, workflow_invocation)
if self.app.config.parallelize_workflow_scheduling_within_histories:
random_index = None
return self.__handlers_config.assign_handler(
workflow_invocation, configured=None, index=random_index, queue_callback=queue_callback,
message_callback=message_callback, flush=flush)
[docs] def shutdown(self):
exception = None
for workflow_scheduler in self.workflow_schedulers.values():
try:
workflow_scheduler.shutdown()
except Exception as e:
exception = exception or e
log.exception(EXCEPTION_MESSAGE_SHUTDOWN)
if self.request_monitor:
try:
self.request_monitor.shutdown()
except Exception as e:
exception = exception or e
log.exception("Failed to shutdown workflow request monitor.")
if exception:
raise exception
[docs] def queue(self, workflow_invocation, request_params, flush=True):
workflow_invocation.state = model.WorkflowInvocation.states.NEW
workflow_invocation.scheduler = request_params.get("scheduler", None) or self.default_scheduler_id
sa_session = self.app.model.context
sa_session.add(workflow_invocation)
# Assign handler
try:
self._assign_handler(workflow_invocation, flush=flush)
except HandlerAssignmentError:
raise RuntimeError(f"Unable to set a handler for workflow invocation '{workflow_invocation.id}'")
return workflow_invocation
def __start_schedulers(self):
for workflow_scheduler in self.workflow_schedulers.values():
workflow_scheduler.startup(self.app)
def __plugins_dict(self):
return plugin_config.plugins_dict(galaxy.workflow.schedulers, 'plugin_type')
@property
def __stack_has_pool(self):
# TODO: In the future it should be possible to map workflows to handlers based on workflow params. When that
# happens, we'll need to defer pool checks until execution time.
return any(map(self.app.application_stack.has_pool, self.DEFAULT_BASE_HANDLER_POOLS))
def __init_schedulers(self):
config_file = self.app.config.workflow_schedulers_config_file
use_default_scheduler = False
if not config_file or (not os.path.exists(config_file) and not self.app.config.is_set('workflow_schedulers_config_file')):
log.info("No workflow schedulers plugin config file defined, using default scheduler.")
use_default_scheduler = True
elif not os.path.exists(config_file):
log.info(f"Cannot find workflow schedulers plugin config file '{config_file}', using default scheduler.")
use_default_scheduler = True
if use_default_scheduler:
self.__init_default_scheduler()
else:
self.DEFAULT_BASE_HANDLER_POOLS = ('workflow-schedulers',)
plugins_element = load(config_file).getroot()
self.__init_schedulers_for_element(plugins_element)
if not self.__handlers_configured and self.__stack_has_pool:
# Stack has a pool for us so override inherited config and use the pool
self.__init_handlers()
self.__handlers_configured = True
elif use_default_scheduler:
self._set_default_handler_assignment_methods()
def __init_default_scheduler(self):
self.default_scheduler_id = DEFAULT_SCHEDULER_ID
self.__init_plugin(DEFAULT_SCHEDULER_PLUGIN_TYPE)
def __init_schedulers_for_element(self, plugins_element):
plugins_kwds = dict(plugins_element.items())
self.default_scheduler_id = plugins_kwds.get('default', DEFAULT_SCHEDULER_ID)
for config_element in plugins_element:
config_element_tag = config_element.tag
if config_element_tag == "handlers":
self.__init_handlers(config_element)
# Determine the default handler(s)
self.default_handler_id = self._get_default(
self.app.config, config_element, list(self.handlers.keys()), required=False)
else:
plugin_type = config_element_tag
plugin_element = config_element
# Configuring a scheduling plugin...
plugin_kwds = dict(plugin_element.items())
workflow_scheduler_id = plugin_kwds.get('id', None)
self.__init_plugin(plugin_type, workflow_scheduler_id, **plugin_kwds)
if not self.workflow_schedulers:
raise Exception(EXCEPTION_MESSAGE_NO_SCHEDULERS)
if self.default_scheduler_id not in self.workflow_schedulers:
raise Exception(EXCEPTION_MESSAGE_NO_DEFAULT_SCHEDULER % self.default_scheduler_id)
if self.app.config.parallelize_workflow_scheduling_within_histories \
and not self.deterministic_handler_assignment:
if self.__handlers_configured:
# There's an explicit configuration, the admin should fix it.
raise Exception(EXCEPTION_MESSAGE_SERIALIZE)
else:
log.warning(EXCEPTION_MESSAGE_SERIALIZE)
def __init_handlers(self, config_element=None):
assert not self.__handlers_configured
handling_config_dict = ConfiguresHandlers.xml_to_dict(self.app.config, config_element)
self._init_handler_assignment_methods(handling_config_dict)
self._init_handlers(handling_config_dict)
if not self.handler_assignment_methods_configured:
self._set_default_handler_assignment_methods()
else:
self.app.application_stack.init_job_handling(self)
log.info("Workflow scheduling handler assignment method(s): %s", ', '.join(self.handler_assignment_methods))
for tag, handlers in [(t, h) for t, h in self.handlers.items() if isinstance(h, list)]:
log.info("Tag [%s] handlers: %s", tag, ', '.join(handlers))
self.__handlers_configured = True
def __init_plugin(self, plugin_type, workflow_scheduler_id=None, **kwds):
workflow_scheduler_id = workflow_scheduler_id or self.default_scheduler_id
if workflow_scheduler_id in self.workflow_schedulers:
raise Exception(EXCEPTION_MESSAGE_DUPLICATE_SCHEDULERS % workflow_scheduler_id)
workflow_scheduler = self.__plugin_classes[plugin_type](**kwds)
self.workflow_schedulers[workflow_scheduler_id] = workflow_scheduler
if isinstance(workflow_scheduler, galaxy.workflow.schedulers.ActiveWorkflowSchedulingPlugin):
self.active_workflow_schedulers[workflow_scheduler_id] = workflow_scheduler
def __start_request_monitor(self):
self.request_monitor = WorkflowRequestMonitor(self.app, self)
self.app.application_stack.register_postfork_function(self.request_monitor.start)
[docs]class WorkflowRequestMonitor(Monitors):
[docs] def __init__(self, app, workflow_scheduling_manager):
self.app = app
self.workflow_scheduling_manager = workflow_scheduling_manager
self._init_monitor_thread(name="WorkflowRequestMonitor.monitor_thread", target=self.__monitor, config=app.config)
self.invocation_grabber = None
self_handler_tags = set(self.app.job_config.self_handler_tags)
self_handler_tags.add(self.workflow_scheduling_manager.default_handler_id)
handler_assignment_method = ItemGrabber.get_grabbable_handler_assignment_method(self.workflow_scheduling_manager.handler_assignment_methods)
if handler_assignment_method:
self.invocation_grabber = ItemGrabber(
app=app,
grab_type='WorkflowInvocation',
handler_assignment_method=handler_assignment_method,
max_grab=self.workflow_scheduling_manager.handler_max_grab,
self_handler_tags=self_handler_tags,
handler_tags=self_handler_tags,
)
def __monitor(self):
to_monitor = self.workflow_scheduling_manager.active_workflow_schedulers
while self.monitor_running:
try:
if self.invocation_grabber:
self.invocation_grabber.grab_unhandled_items()
monitor_step_timer = self.app.execution_timer_factory.get_timer(
'internal.galaxy.workflows.scheduling_manager.monitor_step',
'Workflow scheduling manager monitor step complete.'
)
for workflow_scheduler_id, workflow_scheduler in to_monitor.items():
if not self.monitor_running:
return
self.__schedule(workflow_scheduler_id, workflow_scheduler)
log.trace(monitor_step_timer.to_str())
except Exception:
log.exception('An exception occured scheduling while scheduling workflows')
self._monitor_sleep(1)
def __schedule(self, workflow_scheduler_id, workflow_scheduler):
invocation_ids = self.__active_invocation_ids(workflow_scheduler_id)
for invocation_id in invocation_ids:
log.debug("Attempting to schedule workflow invocation [%s]", invocation_id)
self.__attempt_schedule(invocation_id, workflow_scheduler)
if not self.monitor_running:
return
def __attempt_schedule(self, invocation_id, workflow_scheduler):
sa_session = self.app.model.context
workflow_invocation = sa_session.query(model.WorkflowInvocation).get(invocation_id)
try:
if not workflow_invocation or not workflow_invocation.active:
return False
# This ensures we're only ever working on the 'first' active
# workflow invocation in a given history, to force sequential
# activation.
if self.app.config.history_local_serial_workflow_scheduling:
for i in workflow_invocation.history.workflow_invocations:
if i.active and i.id < workflow_invocation.id:
return False
workflow_scheduler.schedule(workflow_invocation)
log.debug("Workflow invocation [%s] scheduled", workflow_invocation.id)
except Exception:
# TODO: eventually fail this - or fail it right away?
log.exception("Exception raised while attempting to schedule workflow request.")
return False
finally:
sa_session.expunge_all()
# A workflow was obtained and scheduled...
return True
def __active_invocation_ids(self, scheduler_id):
sa_session = self.app.model.context
handler = self.app.config.server_name
return model.WorkflowInvocation.poll_active_workflow_ids(
sa_session,
scheduler=scheduler_id,
handler=handler,
)