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galaxy.web_stack package

Web application stack operations

class galaxy.web_stack.ApplicationStackLogFilter(name='')

Bases: logging.Filter

filter(record)

class galaxy.web_stack.UWSGILogFilter(name='')

Bases: logging.Filter

filter(record)

class galaxy.web_stack.ApplicationStack(app=None, config=None)

Bases: object

name = None

prohibited_middleware = frozenset()

transport_class

alias of galaxy.web_stack.transport.ApplicationStackTransport

log_filter_class

alias of ApplicationStackLogFilter

log_format = '%(name)s %(levelname)s %(asctime)s %(message)s'

server_name_template = '{server_name}'

default_app_name = 'main'

classmethod log_filter()

classmethod get_app_kwds(config_section, app_name=None, for_paste_app=False)

classmethod register_postfork_function(f, *args, **kwargs)

__init__(app=None, config=None)

init_job_handling(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.

init_late_prefork()

log_startup()

start()

allowed_middleware(middleware)

workers()

pool_name

configured_pools

has_base_pool(pool_name)

has_pool(pool_name)

in_pool(pool_name)

pool_members(pool_name)

facts

set_postfork_server_name(app)

register_message_handler(func, name=None)

deregister_message_handler(func=None, name=None)

send_message(dest, msg=None, target=None, params=None, **kwargs)

shutdown()

class galaxy.web_stack.MessageApplicationStack(app=None, config=None)

Bases: galaxy.web_stack.ApplicationStack

__init__(app=None, config=None)

init_late_prefork()

start()

register_message_handler(func, name=None)

deregister_message_handler(func=None, name=None)

send_message(dest, msg=None, target=None, params=None, **kwargs)

shutdown()

class galaxy.web_stack.UWSGIApplicationStack(app=None, config=None)

Bases: galaxy.web_stack.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

alias of galaxy.web_stack.transport.UWSGIFarmMessageTransport

log_filter_class

alias of 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', '[::]')

classmethod get_app_kwds(config_section, app_name=None)

classmethod register_postfork_function(f, *args, **kwargs)

__init__(app=None, config=None)

configured_pools

instance_id

log_startup()

start()

in_pool(pool_name)

pool_members(pool_name)

workers()

facts

shutdown()

class galaxy.web_stack.PasteApplicationStack(app=None, config=None)

Bases: galaxy.web_stack.ApplicationStack

name = 'Python Paste'

class galaxy.web_stack.WeblessApplicationStack(app=None, config=None)

Bases: galaxy.web_stack.ApplicationStack

name = 'Webless'

__init__(app=None, config=None)

configured_pools

in_pool(pool_name)

pool_members(pool_name)

galaxy.web_stack.application_stack_class()

Returns the correct ApplicationStack class for the stack under which this Galaxy process is running.

galaxy.web_stack.application_stack_instance(app=None, config=None)

galaxy.web_stack.application_stack_log_filter()

galaxy.web_stack.application_stack_log_formatter()

galaxy.web_stack.register_postfork_function(f, *args, **kwargs)

galaxy.web_stack.get_app_kwds(config_section, app_name=None)

galaxy.web_stack.get_stack_facts(config=None)

Submodules

galaxy.web_stack.handlers module

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.

exception galaxy.web_stack.handlers.HandlerAssignmentSkip

Bases: Exception

Exception for handler assignment methods to raise if the next method should be tried.

class galaxy.web_stack.handlers.ConfiguresHandlers

Bases: object

DEFAULT_HANDLER_TAG = '_default_'

DEFAULT_BASE_HANDLER_POOLS = ()

UNSUPPORTED_HANDLER_ASSIGNMENT_METHODS = ()

add_handler(handler_id, tags)

static xml_to_dict(config, config_element)

static get_xml_default(config, parent)

use_messaging

deterministic_handler_assignment

is_handler

Indicate whether the current server is configured as a handler.

Returns:bool

handler_tags

Get an iterable of all configured handler tags.

self_handler_tags

Get an iterable of the current process’s configured handler tags.

assign_handler(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.

Parameters:

• obj (instance of galaxy.model.Job or other model object with a set_handler() method.) – Object to assign a handler to (must be a model object with handler attribute and log_str callable).
• configured (str or None.) – Preconfigured handler (ID, tag, or None) for the given object.

Returns:

bool – True on successful assignment, False otherwise.

galaxy.web_stack.message module

Web Application Stack worker messaging

class galaxy.web_stack.message.ApplicationStackMessageDispatcher

Bases: object

__init__()

register_func(func, name=None)

deregister_func(func=None, name=None)

handler_count

dispatch(msg_str)

class galaxy.web_stack.message.ApplicationStackMessage(target=None, **kwargs)

Bases: dict

default_handler = None

__init__(target=None, **kwargs)

validate()

encode()

bind_default_handler(obj, name)

Bind the default handler method to obj as attribute name.

This could also be implemented as a mixin class.

target

set_target

class galaxy.web_stack.message.ParamMessage(target=None, params=None, **kwargs)

Bases: galaxy.web_stack.message.ApplicationStackMessage

__init__(target=None, params=None, **kwargs)

validate()

params

set_params

class galaxy.web_stack.message.TaskMessage(target=None, params=None, **kwargs)

Bases: galaxy.web_stack.message.ParamMessage

static default_handler(msg)

Can be bound to an instance of any class that has message handling methods named like _handle_{task}_method

task

class galaxy.web_stack.message.JobHandlerMessage(target=None, params=None, **kwargs)

Bases: galaxy.web_stack.message.TaskMessage

target = 'job_handler'

class galaxy.web_stack.message.WorkflowSchedulingMessage(target=None, params=None, **kwargs)

Bases: galaxy.web_stack.message.TaskMessage

target = 'workflow_scheduling'

galaxy.web_stack.message.decode(msg_str)

galaxy.web_stack.transport module

Web application stack operations

class galaxy.web_stack.transport.ApplicationStackTransport(app, stack, dispatcher=None)

Bases: object

SHUTDOWN_MSG = '__SHUTDOWN__'

__init__(app, stack, dispatcher=None)

Pre-fork initialization.

init_late_prefork()

start_if_needed()

stop_if_unneeded()

start()

Post-fork initialization.

send_message(msg, dest)

shutdown()

class galaxy.web_stack.transport.UWSGIFarmMessageTransport(app, stack, dispatcher=None)

Bases: galaxy.web_stack.transport.ApplicationStackTransport

Communication via uWSGI Mule Farm messages. Communication is unidirectional (workers -> mules).

init_late_prefork()

__init__(app, stack, dispatcher=None)

start()

Post-fork initialization.

This is mainly done here for the future possibility that we’ll be able to run mules post-fork without exec()ing. In a programmed mule it could be done at __init__ time.

shutdown()

send_message(msg, dest)