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.web_stack.handlers

"""Utilities for dealing with the Galaxy 'handler' process pattern.

A 'handler' is a named Python process running the Galaxy application responsible
for some activity such as queuing up jobs or scheduling workflows.
from __future__ import absolute_import

import logging
import os
import random
from collections import namedtuple

from sqlalchemy.orm import object_session

from galaxy.exceptions import HandlerAssignmentError
from galaxy.util import (

log = logging.getLogger(__name__)

_handler_assignment_methods = (
HANDLER_ASSIGNMENT_METHODS = namedtuple('JOB_HANDLER_ASSIGNMENT_METHODS', _handler_assignment_methods)(
    *[x.lower().replace('_', '-') for x in _handler_assignment_methods]

[docs]class HandlerAssignmentSkip(Exception): """Exception for handler assignment methods to raise if the next method should be tried. """ pass
[docs] def add_handler(self, handler_id, tags): if handler_id not in self.handlers: self.handlers[handler_id] = (handler_id,) for tag in tags: if tag in self.handlers and handler_id not in self.handlers[tag]: self.handlers[tag].append(handler_id) else: self.handlers[tag] = [handler_id]
[docs] @staticmethod def xml_to_dict(config, config_element): handling_config_dict = {} processes = {} handling_config_dict["processes"] = processes # Parse handlers if config_element is not None: for handler in ConfiguresHandlers._findall_with_required(config_element, 'handler'): handler_id = handler.get('id') if handler_id in processes: log.error("Handler '%s' overlaps handler with the same name, ignoring", handler_id) else: log.debug("Read definition for handler '%s'", handler_id) plugins = [] for plugin in ConfiguresHandlers._findall_with_required(handler, 'plugin', ['id']): plugins.append(plugin.get("id")) tags = [x.strip() for x in handler.get('tags', ConfiguresHandlers.DEFAULT_HANDLER_TAG).split(',')] handler_def = {"tags": tags} if plugins: handler_def["plugins"] = plugins processes[handler_id] = handler_def default_handler = ConfiguresHandlers.get_xml_default(config, config_element) if default_handler: handling_config_dict["default"] = default_handler assign = listify(config_element.attrib.get('assign_with', []), do_strip=True) if len(assign) > 0: handling_config_dict["assign"] = assign max_grab_str = config_element.attrib.get('max_grab', None) if max_grab_str: handling_config_dict["max_grab"] = int(max_grab_str) return handling_config_dict
def _init_handlers(self, handling_config_dict=None): handling_config_dict = handling_config_dict or {} for handler_id, process in handling_config_dict.get("processes", {}).items(): process = process or {} if handler_id in self.handlers: log.error("Handler '%s' overlaps handler with the same name, ignoring", handler_id) else: log.debug("Read definition for handler '%s'", handler_id) self._parse_handler(handler_id, process) self.add_handler(handler_id, process.get("tags") or [self.DEFAULT_HANDLER_TAG]) self.default_handler_id = self._ensure_default_set(handling_config_dict.get("default"), list(self.handlers.keys()), required=False) def _init_handler_assignment_methods(self, handling_config_dict=None): handling_config_dict = handling_config_dict or {} self.__is_handler = None # This is set by the stack job handler init code self.pool_for_tag = {} self._handler_assignment_method_methods = { HANDLER_ASSIGNMENT_METHODS.MEM_SELF: self._assign_mem_self_handler, HANDLER_ASSIGNMENT_METHODS.DB_SELF: self._assign_db_self_handler, HANDLER_ASSIGNMENT_METHODS.DB_PREASSIGN: self._assign_db_preassign_handler, HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION: self._assign_db_tag, HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED: self._assign_db_tag, HANDLER_ASSIGNMENT_METHODS.UWSGI_MULE_MESSAGE: self._assign_uwsgi_mule_message_handler, } if handling_config_dict: for method in handling_config_dict.get("assign", []): method = method.lower() assert method in HANDLER_ASSIGNMENT_METHODS, \ "Invalid job handler assignment method '%s', must be one of: %s" % ( method, ', '.join(HANDLER_ASSIGNMENT_METHODS)) try: self.handler_assignment_methods.append(method) except AttributeError: self.handler_assignment_methods_configured = True self.handler_assignment_methods = [method] if self.handler_assignment_methods == [HANDLER_ASSIGNMENT_METHODS.MEM_SELF]: self.app.config.track_jobs_in_database = False self.handler_max_grab = handling_config_dict.get('max_grab', self.handler_max_grab) if self.handler_max_grab is not None: self.handler_max_grab = int(self.handler_max_grab) def _set_default_handler_assignment_methods(self): if not self.handler_assignment_methods_configured: if not self.app.config.track_jobs_in_database and \ HANDLER_ASSIGNMENT_METHODS.MEM_SELF not in self.UNSUPPORTED_HANDLER_ASSIGNMENT_METHODS: # DEPRECATED: You should just set mem_self as the only method if you want this log.warning("The `track_jobs_in_database` option is deprecated, please set `%s` as the job" " handler assignment method in the job handler configuration", HANDLER_ASSIGNMENT_METHODS.MEM_SELF) self.handler_assignment_methods = [HANDLER_ASSIGNMENT_METHODS.MEM_SELF] elif not self.handlers: # No handlers defined, default is for processes to handle the jobs they create self.handler_assignment_methods = [HANDLER_ASSIGNMENT_METHODS.DB_SELF] else: # Handlers are defined, default is the value if the default attribute, or any untagged handler if # default attribute is unset self.handler_assignment_methods = [HANDLER_ASSIGNMENT_METHODS.DB_PREASSIGN] # If the stack has handler pools it can override these defaults self.app.application_stack.init_job_handling(self) log.info("%s: No job handler assignment method is set, defaulting to '%s', set the `assign_with` attribute" " on <handlers> to override the default", self.__class__.__name__, self.handler_assignment_methods[0]) def _parse_handler(self, handler_id, handler_def): pass
[docs] @staticmethod def get_xml_default(config, parent): rval = parent.get('default') if 'default_from_environ' in parent.attrib: environ_var = parent.attrib['default_from_environ'] rval = os.environ.get(environ_var, rval) elif 'default_from_config' in parent.attrib: config_val = parent.attrib['default_from_config'] rval = config.config_dict.get(config_val, rval) return rval
def _get_default(self, config, parent, names, auto=False, required=True): """ Returns the default attribute set in a parent tag like <handlers> or <destinations>, or return the ID of the child, if there is no explicit default and only one child. :param parent: Object representing a tag that may or may not have a 'default' attribute. :type parent: ``xml.etree.ElementTree.Element`` :param names: The list of destination or handler IDs or tags that were loaded. :type names: list of str :param auto: Automatically set a default if there is no default in the parent tag and there is only one child. :type auto: bool :param required: Require a default to be set or determined automatically, else raise Exception :type required: bool :returns: str -- id or tag representing the default. """ rval = ConfiguresHandlers.get_xml_default(config, parent) return self._ensure_default_set(rval, names, auto=auto, required=required) def _ensure_default_set(self, rval, names, auto=False, required=True): if rval is not None: # If the parent element has a 'default' attribute, use the id or tag in that attribute if required and rval not in names: raise Exception("default attribute '%s' does not match a defined id or tag in a child element" % (rval)) log.debug("default set to child with id or tag '%s'" % (rval)) elif auto and len(names) == 1: log.info("Setting default to child with id '%s'" % (names[0])) rval = names[0] elif required: raise Exception("No default specified, please specify a valid id or tag with the 'default' attribute") return rval @staticmethod def _findall_with_required(parent, match, attribs=None): """Like ``xml.etree.ElementTree.Element.findall()``, except only returns children that have the specified attribs. :param parent: Parent element in which to find. :type parent: ``xml.etree.ElementTree.Element`` :param match: Name of child elements to find. :type match: str :param attribs: List of required attributes in children elements. :type attribs: list of str :returns: list of ``xml.etree.ElementTree.Element`` """ rval = [] if attribs is None: attribs = ('id',) for elem in parent.findall(match): for attrib in attribs: if attrib not in elem.attrib: log.warning("required '%s' attribute is missing from <%s> element" % (attrib, match)) break else: rval.append(elem) return rval @property def use_messaging(self): # The job manager uses this to determine whether the messaging job queue should be used return HANDLER_ASSIGNMENT_METHODS.UWSGI_MULE_MESSAGE in self.handler_assignment_methods @property def deterministic_handler_assignment(self): return self.handler_assignment_methods and any( filter(lambda x: x in ( HANDLER_ASSIGNMENT_METHODS.UWSGI_MULE_MESSAGE, HANDLER_ASSIGNMENT_METHODS.DB_PREASSIGN, ), self.handler_assignment_methods)) def _get_is_handler(self): """Indicate whether the current server is configured as a handler. :return: bool """ if self.__is_handler is not None: return self.__is_handler if (HANDLER_ASSIGNMENT_METHODS.DB_SELF in self.handler_assignment_methods or HANDLER_ASSIGNMENT_METHODS.MEM_SELF in self.handler_assignment_methods): return True for collection in self.handlers.values(): if self.app.config.server_name in collection: return True return False def _set_is_handler(self, value): self.__is_handler = value is_handler = property(_get_is_handler, _set_is_handler) def _get_single_item(self, collection, index=None): """Given a collection of handlers or destinations, return one item from the collection at random. """ # Done like this to avoid random under the assumption it's faster to avoid it if len(collection) == 1: return collection[0] elif index is None: return random.choice(collection) else: return collection[index % len(collection)] @property def handler_tags(self): """Get an iteratable of all configured handler tags. """ return filter(lambda k: isinstance(self.handlers[k], list), self.handlers.keys()) @property def self_handler_tags(self): """Get an iterable of the current process's configured handler tags. """ return filter(lambda k: self.app.config.server_name in self.handlers[k], self.handler_tags) # If these get to be any more complex we should probably modularize them, or at least move to a separate class def _assign_handler_direct(self, obj, configured): """Directly assign a handler if the object has been preconfigured to a known single static handler. :param obj: Same as :method:`ConfiguresHandlers.assign_handler()`. :param configured: Same as :method:`ConfiguresHandlers.assign_handler()`. :returns: str -- A valid handler ID, or False if no handler was assigned. """ if self.app.config.track_jobs_in_database and configured: try: handlers = self.handlers[configured] except KeyError: handlers = None if handlers == (configured,): obj.set_handler(configured) _timed_flush_obj(obj) return configured return False def _assign_mem_self_handler(self, obj, method, configured, queue_callback=None, **kwargs): """Assign object to this handler using this process's in-memory queue. This method ignores all handler configuration. :param obj: Same as :method:`ConfiguresHandlers.assign_handler()`. :param method: Same as :method:`ConfiguresHandlers._assign_db_preassign_handler()`. :param configured: Ignored. :param queue_callback: Callback to be executed when the job should be queued (i.e. a callback to the handler's ``put()`` method). No arguments are passed. :type queue_callback: callable :returns: str -- This process's server name (handler ID). """ assert queue_callback is not None, \ "Cannot perform '%s' handler assignment: `queue_callback` is None" % HANDLER_ASSIGNMENT_METHODS.MEM_SELF if configured: log.warning("(%s) Ignoring handler assignment to '%s' because configured handler assignment method" " '' overrides per-tool handler assignment", obj.log_str(), HANDLER_ASSIGNMENT_METHODS.MEM_SELF, configured) _timed_flush_obj(obj) queue_callback() return self.app.config.server_name def _assign_db_self_handler(self, obj, method, configured, **kwargs): """Assign object to this process by setting its ``handler`` column in the database to this process. This only occurs if there is not an explicitly configured handler assignment for the object. Otherwise, it is passed to the DB_PREASSIGN method for assignment. :param obj: Same as :method:`ConfiguresHandlers.assign_handler()`. :param method: Same as :method:`ConfiguresHandlers._assign_db_preassign_handler()`. :param configured: Same as :method:`ConfiguresHandlers.assign_handler()`. :returns: str -- The assigned handler ID. """ if configured: return self._handler_assignment_method_methods[HANDLER_ASSIGNMENT_METHODS.DB_PREASSIGN]( obj, method, configured, **kwargs ) obj.set_handler(self.app.config.server_name) _timed_flush_obj(obj) return self.app.config.server_name def _assign_db_preassign_handler(self, obj, method, configured, index=None, **kwargs): """Assign object to a handler by setting its ``handler`` column in the database to a handler selected at random from the known handlers in the appropriate tag. Given a handler ID or tag, return a handler matching it, of those handlers that are statically configured in the job configuration, or known via preconfigured pools. :param obj: Same as :method:`ConfiguresHandlers.assign_handler()`. :param method: Assignment method currently being checked. :type method: Value in :data:`HANDLER_ASSIGNMENT_METHODS`. :param configured: Same as :method:`ConfiguresHandlers.assign_handler()`. :param index: Generate "consistent" "random" handlers with this index if specified. :type index: int :raises KeyError: if the configured or default handler is not a known handler ID or tag. :returns: str -- A valid job handler ID. """ handler = configured if handler is None: handler = self.default_handler_id or self.DEFAULT_HANDLER_TAG # Get a random handler ID from the possible handlers. If the admin has configured a tool with a handler tag that # does not exist, or if there are no default handlers and configured is None, this will raise KeyError to # assign_handler, which should log it, try the next method (if any), and if no other methods succeed, raise # HandlerAssigmentError. handler_id = self._get_single_item(self.handlers[handler], index=index) if handler != handler_id: log.debug("(%s) Selected handler '%s' by random choice from handler tag '%s'", obj.log_str(), handler_id, handler) obj.set_handler(handler_id) _timed_flush_obj(obj) return handler_id def _assign_db_tag(self, obj, method, configured, **kwargs): """Assign object to a handler by setting its ``handler`` column in the database to either the configured handler ID or tag, or to the default tag (or ``_default_``) :param obj: Same as :method:`ConfiguresHandlers.assign_handler()`. :param method: Same as :method:`ConfiguresHandlers._assign_db_preassign_handler()`. :param configured: Same as :method:`ConfiguresHandlers.assign_handler()`. :returns: str -- The assigned handler pool. """ handler = configured if handler is None: handler = self.default_handler_id or self.DEFAULT_HANDLER_TAG obj.set_handler(handler) _timed_flush_obj(obj) return handler def _assign_uwsgi_mule_message_handler(self, obj, method, configured, message_callback=None, **kwargs): """Assign object to a handler by sending a setup message to the appropriate handler pool (farm), where a handler (mule) will receive the message and assign itself. :param obj: Same as :method:`ConfiguresHandlers.assign_handler()`. :param method: Same as :method:`ConfiguresHandlers._assign_db_preassign_handler()`. :param configured: Same as :method:`ConfiguresHandlers.assign_handler()`. :param queue_callback: Callback returning a setup message to be sent via the stack messaging interface's ``send_message()`` method. No arguments are passed. :type queue_callback: callable :raises HandlerAssignmentSkip: if the configured or default handler is not a known handler pool (farm) :returns: str -- The assigned handler pool. """ assert message_callback is not None, \ "Cannot perform '%s' handler assignment: `message_callback` is None" \ % HANDLER_ASSIGNMENT_METHODS.UWSGI_MULE_MESSAGE tag = configured or self.DEFAULT_HANDLER_TAG pool = self.pool_for_tag.get(tag) if pool is None: log.debug("(%s) No handler pool (uWSGI farm) for '%s' found", obj.log_str(), tag) raise HandlerAssignmentSkip() else: _timed_flush_obj(obj) message = message_callback() self.app.application_stack.send_message(pool, message) return pool
[docs] def assign_handler(self, obj, configured=None, **kwargs): """Set a job handler, flush obj Called assignment methods should raise :exception:`HandlerAssignmentSkip` to indicate that the next method should be tried. :param obj: Object to assign a handler to (must be a model object with ``handler`` attribute and ``log_str`` callable). :type obj: instance of :class:`galaxy.model.Job` or other model object with a ``set_handler()`` method. :param configured: Preconfigured handler (ID, tag, or None) for the given object. :type configured: str or None. :returns: bool -- True on successful assignment, False otherwise. """ # It's a bit awkward that the method that actually hands off job execution is in the JobConfiguration, but # that's currently the best place for it. It's worth noting that this method is also part of the # WorkflowSchedulingManager, which acts like a combined JobConfiguration and JobManager. Combining those two # classes would probably be reasonable (and would remove the need for the queue callback). if self._assign_handler_direct(obj, configured): log.info("(%s) Skipped handler assignment logic due to explicit configuration to a single handler: %s", obj.log_str(), configured) return True for method in self.handler_assignment_methods: try: handler = self._handler_assignment_method_methods[method]( obj, method, configured=configured, **kwargs) log.info("(%s) Handler '%s' assigned using '%s' assignment method", obj.log_str(), handler, method) return handler except HandlerAssignmentSkip: log.debug("(%s) Handler assignment method '%s' did not assign a handler, trying next method", obj.log_str(), method) except Exception: log.exception("Caught exception in handler assignment method: %s", method) else: # Ideally we could just expunge the object from the SA session here, but in most cases, some of its related # objects have already been created, so instead we'll just have to fail it. log.error("(%s) Failed to select handler", obj.log_str()) raise HandlerAssignmentError("Job handler assignment failed.", obj=obj)
def _timed_flush_obj(obj): obj_flush_timer = ExecutionTimer() sa_session = object_session(obj) sa_session.flush() log.info("Flushed transaction for %s %s" % (obj.log_str(), obj_flush_timer))