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Source code for galaxy.web_stack
"""Web application stack operations
"""
from __future__ import absolute_import
import inspect
import json
import logging
import os
# The uwsgi module is automatically injected by the parent uwsgi process and only exists that way. If anything works,
# this is a uwsgi-managed process.
try:
import uwsgi
except ImportError:
uwsgi = None
import yaml
from six import string_types
from galaxy.util import unicodify
from galaxy.util.facts import get_facts
from galaxy.util.path import has_ext
from galaxy.util.properties import nice_config_parser
from .handlers import HANDLER_ASSIGNMENT_METHODS
from .message import ApplicationStackMessage, ApplicationStackMessageDispatcher
from .transport import ApplicationStackTransport, UWSGIFarmMessageTransport
log = logging.getLogger(__name__)
[docs]class UWSGILogFilter(logging.Filter):
[docs] def filter(self, record):
record.worker_id = uwsgi.worker_id()
record.mule_id = uwsgi.mule_id()
return True
[docs]class ApplicationStack(object):
name = None
prohibited_middleware = frozenset()
transport_class = ApplicationStackTransport
log_filter_class = ApplicationStackLogFilter
log_format = '%(name)s %(levelname)s %(asctime)s %(message)s'
# TODO: this belongs in the pool configuration
server_name_template = '{server_name}'
default_app_name = 'main'
[docs] @classmethod
def get_app_kwds(cls, config_section, app_name=None, for_paste_app=False):
return {}
[docs] def __init__(self, app=None, config=None):
self.app = app
self.config = config or (app and app.config)
self.running = False
if app:
log.debug("%s initialized", self.__class__.__name__)
def _set_default_job_handler_assignment_methods(self, job_config, base_pool):
"""Override in subclasses to set default job handler assignment methods if not explicitly configured by the administrator.
Called once per job_config.
"""
pass
def _init_job_handler_assignment_methods(self, job_config, base_pool):
if not job_config.handler_assignment_methods_configured:
self._set_default_job_handler_assignment_methods(job_config, base_pool)
def _init_job_handler_subpools(self, job_config, base_pool):
"""Set up members of "subpools" ("base_pool.*") as handlers (including the base pool itself, if it exists).
"""
for pool_name in self.configured_pools:
if pool_name == base_pool:
tag = job_config.DEFAULT_HANDLER_TAG
elif pool_name.startswith(base_pool + '.'):
tag = pool_name.replace(base_pool + '.', '', 1)
else:
continue
# Pools are hierarchical (so that you can have e.g. workflow schedulers use the job handlers pool if no
# workflow schedulers pool exists), so if a pool for a given tag has already been found higher in the
# hierarchy, don't add members from a pool lower in the hierarchy.
if tag not in job_config.pool_for_tag:
if self.in_pool(pool_name):
job_config.is_handler = True
for handler in self.pool_members(pool_name):
job_config.add_handler(handler, [tag])
job_config.pool_for_tag[tag] = pool_name
[docs] def init_job_handling(self, job_config):
"""Automatically add pools as handlers if they are named per predefined names and there is not an explicit
job handler assignment configuration.
Also automatically set the preferred assignment method if pool handlers are found and an assignment method is
not explicitly configured by the administrator.
"""
stack_assignment_methods_configured = False
for base_pool in job_config.DEFAULT_BASE_HANDLER_POOLS:
if self.has_base_pool(base_pool):
if not stack_assignment_methods_configured:
self._init_job_handler_assignment_methods(job_config, base_pool)
stack_assignment_methods_configured = True
self._init_job_handler_subpools(job_config, base_pool)
[docs] def log_startup(self):
log.info("Galaxy server instance '%s' is running" % self.config.server_name)
[docs] def allowed_middleware(self, middleware):
if hasattr(middleware, '__name__'):
middleware = middleware.__name__
return middleware not in self.prohibited_middleware
@property
def pool_name(self):
# TODO: ideally jobs would be mappable to handlers by pool name
return None
@property
def configured_pools(self):
return {}
[docs] def has_base_pool(self, pool_name):
return self.has_pool(pool_name) or any([pool.startswith(pool_name + '.') for pool in self.configured_pools])
@property
def facts(self):
facts = get_facts(config=self.config)
facts.update({'pool_name': self.pool_name})
return facts
[docs] def set_postfork_server_name(self, app):
app.config.server_name = self.server_name_template.format(**self.facts)
log.debug('server_name set to: %s', app.config.server_name)
[docs]class MessageApplicationStack(ApplicationStack):
[docs] def __init__(self, app=None, config=None):
super(MessageApplicationStack, self).__init__(app=app, config=config)
self.use_messaging = False
self.dispatcher = ApplicationStackMessageDispatcher()
self.transport = self.transport_class(app, stack=self, dispatcher=self.dispatcher)
[docs] def start(self):
super(MessageApplicationStack, self).start()
if self.use_messaging and not self.running:
self.transport.start()
self.running = True
[docs] def register_message_handler(self, func, name=None):
self.dispatcher.register_func(func, name)
self.transport.start_if_needed()
[docs] def deregister_message_handler(self, func=None, name=None):
self.dispatcher.deregister_func(func, name)
self.transport.stop_if_unneeded()
[docs] def send_message(self, dest, msg=None, target=None, params=None, **kwargs):
assert msg is not None or target is not None, "Either 'msg' or 'target' parameters must be set"
if not msg:
msg = ApplicationStackMessage(
target=target,
params=params,
**kwargs
)
self.transport.send_message(msg.encode(), dest)
[docs] def shutdown(self):
if self.use_messaging and self.running:
log.info('Application stack interface shutting down')
self.transport.shutdown()
self.running = False
[docs]class UWSGIApplicationStack(MessageApplicationStack):
"""Interface to the uWSGI application stack. Supports running additional webless Galaxy workers as mules. Mules
must be farmed to be communicable via uWSGI mule messaging, unfarmed mules are not supported.
Note that mules will use this as their stack class even though they start with the "webless" loading point.
"""
name = 'uWSGI'
prohibited_middleware = frozenset([
'wrap_in_static',
'EvalException',
])
transport_class = UWSGIFarmMessageTransport
log_filter_class = UWSGILogFilter
log_format = '%(name)s %(levelname)s %(asctime)s [p:%(process)s,w:%(worker_id)s,m:%(mule_id)s] [%(threadName)s] %(message)s'
server_name_template = '{server_name}.{pool_name}.{instance_id}'
postfork_functions = []
localhost_addrs = ('127.0.0.1', '[::1]')
bind_all_addrs = ('', '0.0.0.0', '[::]')
@staticmethod
def _get_config_file(confs, loader, section):
"""uWSGI allows config merging, in which case the corresponding config file option will be a list.
"""
conf = None
if isinstance(confs, list):
gconfs = [_ for _ in confs if os.path.exists(_) and section in loader(open(_))]
if len(gconfs) == 1:
conf = gconfs[0]
elif len(gconfs) == 0:
log.warning('Could not locate a config file containing a Galaxy config from: %s',
', '.join(confs))
else:
log.warning('Multiple config files contain Galaxy configs, merging is not supported: %s',
', '.join(gconfs))
else:
conf = confs
return conf
@staticmethod
def _socket_opt_to_str(opt, val):
try:
opt = unicodify(opt)
val = unicodify(val)
if val.startswith('='):
val = unicodify(uwsgi.opt.get('shared-socket', [])[int(val.split('=')[1])])
proto = opt if opt != 'socket' else 'uwsgi'
if proto == 'uwsgi' and ':' not in val:
return 'uwsgi://' + val
else:
proto = proto + '://'
host, port = val.rsplit(':', 1)
port = ':' + port.split(',', 1)[0]
if host in UWSGIApplicationStack.bind_all_addrs:
host = UWSGIApplicationStack.localhost_addrs[0]
return proto + host + port
except (IndexError, AttributeError):
return '%s %s' % (opt, val)
@staticmethod
def _socket_opts():
for opt in ('https', 'http', 'socket'):
if opt in uwsgi.opt:
val = uwsgi.opt[opt]
if isinstance(val, list):
for v in val:
yield (opt, v)
else:
yield (opt, val)
@staticmethod
def _serving_on():
for opt, val in UWSGIApplicationStack._socket_opts():
yield UWSGIApplicationStack._socket_opt_to_str(opt, val)
[docs] @classmethod
def get_app_kwds(cls, config_section, app_name=None):
kwds = {
'config_file': None,
'config_section': config_section,
}
uwsgi_opt = uwsgi.opt
config_file = None
# check for --set galaxy_config_file=<path>, this overrides whatever config file uWSGI was loaded with (which
# may not actually include a Galaxy config)
if uwsgi_opt.get("galaxy_config_file"):
config_file = uwsgi_opt.get("galaxy_config_file")
# check for --yaml or --json uWSGI config options next
if config_file is None:
config_file = (UWSGIApplicationStack._get_config_file(uwsgi_opt.get("yaml"), yaml.safe_load, config_section)
or UWSGIApplicationStack._get_config_file(uwsgi_opt.get("json"), json.load, config_section))
# --ini and --ini-paste don't behave the same way, but this method will only be called by mules if the main
# application was loaded with --ini-paste, so we can make some assumptions, most notably, uWSGI does not have
# any way to set the app name when loading with paste.deploy:loadapp(), so hardcoding the alternate section
# name to `app:main` is fine.
has_ini_config = config_file is None and uwsgi_opt.get("ini") or uwsgi_opt.get("ini-paste")
has_ini_config = has_ini_config or (config_file and has_ext(config_file, "ini", aliases=True, ignore="sample"))
if has_ini_config:
config_file = config_file or uwsgi_opt.get("ini") or uwsgi_opt.get("ini-paste")
parser = nice_config_parser(config_file)
if not parser.has_section(config_section) and parser.has_section('app:main'):
kwds['config_section'] = 'app:main'
kwds['config_file'] = unicodify(config_file)
return kwds
[docs] @classmethod
def register_postfork_function(cls, f, *args, **kwargs):
if uwsgi.mule_id() == 0:
cls.postfork_functions.append((f, args, kwargs))
else:
# mules are forked from the master and run the master's postfork functions immediately before the forked
# process is replaced. that is prevented in the _do_uwsgi_postfork function, and because programmed mules
# are standalone non-forking processes, they should run postfork functions immediately
f(*args, **kwargs)
[docs] def __init__(self, app=None, config=None):
self._farms_dict = None
self._mules_list = None
self._farm_server_names_dict = None
# If there's more than one farm *and* more than one farm will be using farm messaging, additional locks need to
# be configured by the admin. This allows us to keep track of how many such farms are configured.
self._lock_farms = set()
super(UWSGIApplicationStack, self).__init__(app=app, config=config)
def _set_default_job_handler_assignment_methods(self, job_config, base_pool):
# Disable DB_SELF if a valid farm (pool) is configured. Use mule messaging unless the job_config doesn't allow
# it (e.g. workflow scheduling manager), in which case, use DB_PREASSIGN.
#
# TODO MULTIPOOL: if there is no default in any base_pool (and no job_config.default_handler_id) then don't
# remove DB_SELF
conf_class_name = job_config.__class__.__name__
remove_methods = [HANDLER_ASSIGNMENT_METHODS.DB_SELF]
if (HANDLER_ASSIGNMENT_METHODS.UWSGI_MULE_MESSAGE not in job_config.UNSUPPORTED_HANDLER_ASSIGNMENT_METHODS):
add_method = HANDLER_ASSIGNMENT_METHODS.UWSGI_MULE_MESSAGE
else:
add_method = HANDLER_ASSIGNMENT_METHODS.DB_PREASSIGN
remove_methods.append(HANDLER_ASSIGNMENT_METHODS.UWSGI_MULE_MESSAGE)
log.debug("%s: No job handler assignment methods were configured but a uWSGI farm named '%s' exists,"
" automatically enabling the '%s' assignment method", conf_class_name, base_pool, add_method)
for m in remove_methods:
try:
job_config.handler_assignment_methods.remove(m)
log.debug("%s: Removed '%s' from handler assignment methods due to use of mules", conf_class_name, m)
except ValueError:
pass
if add_method not in job_config.handler_assignment_methods:
job_config.handler_assignment_methods.insert(0, add_method)
log.debug("%s: handler assignment methods updated to: %s", conf_class_name,
', '.join(job_config.handler_assignment_methods))
def _init_job_handler_assignment_methods(self, job_config, base_pool):
super(UWSGIApplicationStack, self)._init_job_handler_assignment_methods(job_config, base_pool)
# Determine if stack messaging should be enabled
if HANDLER_ASSIGNMENT_METHODS.UWSGI_MULE_MESSAGE in job_config.handler_assignment_methods:
self.use_messaging = True
def _init_job_handler_subpools(self, job_config, base_pool):
super(UWSGIApplicationStack, self)._init_job_handler_subpools(job_config, base_pool)
# Count the required number of uWSGI locks
if job_config.use_messaging:
for pool_name in self.configured_pools:
if (pool_name == base_pool or pool_name.startswith(base_pool + '.')):
self._lock_farms.add(pool_name)
@property
def _configured_mules(self):
if self._mules_list is None:
self._mules_list = _uwsgi_configured_mules()
return self._mules_list
@property
def _is_mule(self):
return uwsgi.mule_id() > 0
@property
def configured_pools(self):
if self._farms_dict is None:
self._farms_dict = {}
farms = uwsgi.opt.get('farm', [])
farms = farms if isinstance(farms, list) else [farms]
for farm in farms:
farm = unicodify(farm)
name, mules = farm.split(':', 1)
self._farms_dict[name] = [int(m) for m in mules.split(',')]
return self._farms_dict
@property
def _farms(self):
farms = []
for farm, mules in self.configured_pools.items():
if uwsgi.mule_id() in mules:
farms.append(farm)
return farms
def _mule_index_in_farm(self, farm_name, mule_id=None):
mule_id = mule_id or uwsgi.mule_id()
try:
mules = self.configured_pools[farm_name]
return mules.index(mule_id)
except (KeyError, ValueError):
return -1
@property
def _farm_name(self):
# TODO: to allow mules to be in multiple farms you'll need to start here
try:
return self._farms[0]
except IndexError:
return None
@property
def _farm_server_names(self):
if self._farm_server_names_dict is None:
self._farm_server_names_dict = {}
for farm_name, mules in self.configured_pools.items():
server_names = []
facts = self.facts
for mule in mules:
facts.update({
'pool_name': farm_name,
'server_id': mule,
'instance_id': self._mule_index_in_farm(farm_name, mule) + 1,
})
server_names.append(self.server_name_template.format(**facts))
self._farm_server_names_dict[farm_name] = server_names
return self._farm_server_names_dict
@property
def instance_id(self):
if not self._is_mule:
instance_id = uwsgi.worker_id()
elif self._farm_name:
return self._mule_index_in_farm(self._farm_name) + 1
else:
instance_id = uwsgi.mule_id()
return instance_id
[docs] def log_startup(self):
msg = ["Galaxy server instance '%s' is running" % self.config.server_name]
# Log the next messages when the first worker finishes starting. This
# may not be the first to finish (so Galaxy could be serving already),
# but it's a good approximation and gives the correct root_pid below
# when there is no master process.
if not self._is_mule and self.instance_id == 1:
# We use the same text printed by Paste to not break scripts
# grepping for this line. Here root_pid is the same that gets
# written to file when using the --pidfile option of uwsgi
root_pid = uwsgi.masterpid() or os.getpid()
msg.append('Starting server in PID %d.' % root_pid)
for s in UWSGIApplicationStack._serving_on():
msg.append('serving on ' + s)
if len(msg) == 1:
msg.append('serving on unknown URL')
log.info('\n'.join(msg))
[docs] def start(self):
# Does a generalized `is_worker` attribute make sense? Hard to say w/o other stack paradigms.
if self._is_mule and self._farm_name:
# used by main.py to send a shutdown message on termination
os.environ['_GALAXY_UWSGI_FARM_NAMES'] = ','.join(self._farms)
super(UWSGIApplicationStack, self).start()
[docs] def in_pool(self, pool_name):
if not self._is_mule:
return False
else:
return pool_name in self._farms
@property
def facts(self):
facts = super(UWSGIApplicationStack, self).facts
if not self._is_mule:
facts.update({
'pool_name': 'web',
'server_id': uwsgi.worker_id(),
})
else:
facts.update({
'pool_name': self._farm_name,
'server_id': uwsgi.mule_id(),
})
facts['instance_id'] = self.instance_id
return facts
[docs]class WeblessApplicationStack(ApplicationStack):
name = 'Webless'
def _set_default_job_handler_assignment_methods(self, job_config, base_pool):
# We will only get here if --attach-to-pool has been set so it is safe to assume that this handler is dynamic
# and that we want to use one of the DB serialization methods.
#
# Disable DB_SELF if a valid pool is configured. Use DB "SKIP LOCKED" if the DB engine supports it, transaction
# isolation if it doesn't, or DB_PREASSIGN if the job_config doesn't allow either.
conf_class_name = job_config.__class__.__name__
remove_methods = [HANDLER_ASSIGNMENT_METHODS.DB_SELF]
dialect = self.app.model.session.bind.dialect
if ((dialect.name == 'postgresql' and dialect.server_version_info >= (9, 5))
or (dialect.name == 'mysql' and dialect.server_version_info >= (8, 0, 1))):
add_method = HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED
else:
add_method = HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION
if add_method in job_config.UNSUPPORTED_HANDLER_ASSIGNMENT_METHODS:
remove_methods.append(add_method)
add_method = HANDLER_ASSIGNMENT_METHODS.DB_PREASSIGN
log.debug("%s: No job handler assignment methods were configured but this server is configured to attach to the"
" '%s' pool, automatically enabling the '%s' assignment method", conf_class_name, base_pool, add_method)
for m in remove_methods:
try:
job_config.handler_assignment_methods.remove(m)
log.debug("%s: Removed '%s' from handler assignment methods due to use of mules", conf_class_name, m)
except ValueError:
pass
if add_method not in job_config.handler_assignment_methods:
job_config.handler_assignment_methods.insert(0, add_method)
log.debug("%s: handler assignment methods updated to: %s", conf_class_name,
', '.join(job_config.handler_assignment_methods))
[docs] def __init__(self, app=None, config=None):
super(WeblessApplicationStack, self).__init__(app=app, config=config)
if self.app and self.config and self.config.attach_to_pools:
log.debug("Will attach to pool(s): %s", ', '.join(self.config.attach_to_pools))
@property
def configured_pools(self):
return {p: self.config.server_name for p in self.config.attach_to_pools}
[docs] def pool_members(self, pool_name):
return (self.config.server_name,) if self.in_pool(pool_name) else None
[docs]def application_stack_class():
"""Returns the correct ApplicationStack class for the stack under which
this Galaxy process is running.
"""
if uwsgi is not None and hasattr(uwsgi, 'numproc'):
return UWSGIApplicationStack
else:
# cleverer ideas welcome
for frame in inspect.stack():
if frame[1].endswith(os.path.join('pastescript', 'loadwsgi.py')):
return PasteApplicationStack
return WeblessApplicationStack
[docs]def application_stack_instance(app=None, config=None):
stack_class = application_stack_class()
return stack_class(app=app, config=config)
[docs]def application_stack_log_formatter():
return logging.Formatter(fmt=application_stack_class().log_format)
[docs]def register_postfork_function(f, *args, **kwargs):
application_stack_class().register_postfork_function(f, *args, **kwargs)
[docs]def get_app_kwds(config_section, app_name=None):
return application_stack_class().get_app_kwds(config_section, app_name=app_name)
def _uwsgi_configured_mules():
mules = uwsgi.opt.get('mule', [])
return [mules] if isinstance(mules, string_types) or mules is True else mules
def _do_uwsgi_postfork():
for i, mule in enumerate(_uwsgi_configured_mules()):
if mule is not True and i + 1 == uwsgi.mule_id():
# mules will inherit the postfork function list and call them immediately upon fork, but programmed mules
# should not do that (they will call the postfork functions in-place as they start up after exec())
UWSGIApplicationStack.postfork_functions = [(_mule_fixup, (), {})]
for f, args, kwargs in [t for t in UWSGIApplicationStack.postfork_functions]:
log.debug('Calling postfork function: %s', f)
f(*args, **kwargs)
def _mule_fixup():
from six.moves.urllib.request import install_opener
install_opener(None)
if uwsgi:
uwsgi.post_fork_hook = _do_uwsgi_postfork