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galaxy package

Galaxy root package – this is a namespace package.

Subpackages

Submodules

galaxy.app module

class galaxy.app.UniverseApplication(**kwargs)[source]

Bases: galaxy.config.ConfiguresGalaxyMixin

Encapsulates the state of a Universe application

__init__(**kwargs)[source]
shutdown()[source]
configure_fluent_log()[source]
is_job_handler

galaxy.config module

Universe configuration builder.

galaxy.config.LOGGING_CONFIG_DEFAULT = {'filters': {'stack': {'()': 'galaxy.web.stack.application_stack_log_filter'}}, 'formatters': {'stack': {'()': 'galaxy.web.stack.application_stack_log_formatter'}}, 'handlers': {'console': {'filters': ['stack'], 'formatter': 'stack', 'class': 'logging.StreamHandler', 'stream': 'ext://sys.stderr', 'level': 'DEBUG'}}, 'loggers': {'paste.httpserver.ThreadPool': {'qualname': 'paste.httpserver.ThreadPool', 'level': 'WARN'}, 'routes.middleware': {'qualname': 'routes.middleware', 'level': 'WARN'}, 'galaxy': {'qualname': 'galaxy', 'level': 'DEBUG', 'propagate': 0, 'handlers': ['console']}}, 'root': {'level': 'INFO', 'handlers': ['console']}, 'version': 1}

Default value for logging configuration, passed to logging.config.dictConfig()

galaxy.config.resolve_path(path, root)[source]

If ‘path’ is relative make absolute by prepending ‘root’

galaxy.config.find_path(kwargs, var, root)[source]

Find a configuration path that may exist at different defaults.

galaxy.config.find_root(kwargs)[source]
class galaxy.config.Configuration(**kwargs)[source]

Bases: object

deprecated_options = ('database_file',)
__init__(**kwargs)[source]
sentry_dsn_public

Sentry URL with private key removed for use in client side scripts, sentry server will need to be configured to accept events

reload_sanitize_whitelist(explicit=True)[source]
get(key, default)[source]
get_bool(key, default)[source]
ensure_tempdir()[source]
check()[source]
is_admin_user(user)[source]

Determine if the provided user is listed in admin_users.

NOTE: This is temporary, admin users will likely be specified in the
database in the future.
resolve_path(path)[source]

Resolve a path relative to Galaxy’s root.

guess_galaxy_port()[source]
galaxy.config.parse_dependency_options(kwargs, root, dependency_resolvers_config_file)[source]
galaxy.config.get_database_engine_options(kwargs, model_prefix='')[source]

Allow options for the SQLAlchemy database engine to be passed by using the prefix “database_engine_option”.

galaxy.config.get_database_url(config)[source]
galaxy.config.init_models_from_config(config, map_install_models=False, object_store=None, trace_logger=None)[source]
galaxy.config.configure_logging(config)[source]

Allow some basic logging configuration to be read from ini file.

This should be able to consume either a galaxy.config.Configuration object or a simple dictionary of configuration variables.

class galaxy.config.ConfiguresGalaxyMixin[source]

Bases: object

Shared code for configuring Galaxy-like app objects.

wait_for_toolbox_reload(old_toolbox)[source]

galaxy.main module

Entry point for starting Galaxy without starting as part of a web server.

Example Usage: Start a job/workflow handler without a web server and with a given name using.

galaxy-main –server-name handler0

Start as a daemon with (requires daemonized - install with ‘pip install daemonize’):

galaxy-main -d –daemon-log-file=handler0-daemon.log –pid-file handler0.pid –server-name handler0

In daemon mode logging of Galaxy (as opposed to this script) is configured via a loggers section in Galaxy’s ini file - this can be overridden with sensible defaults logging to a single file with the following:

galaxy-main -d –server-name handler0 –daemon-log-file=handler0-daemon.log –pid-file handler0.pid –log-file handler0.log

This can also be used to start Galaxy as a uWSGI mule, e.g. for job handling:

uwsgi … –py-call-osafterfork –mule=lib/galaxy/main.py –mule=lib/galaxy/main.py –farm=job-handlers:1,2

The –py-call-osafterfork allows for proper shutdown on SIGTERM/SIGINT.

galaxy.main.load_galaxy_app(config_builder, config_env=False, log=None, **kwds)[source]
galaxy.main.handle_signal(signum, frame)[source]
galaxy.main.register_signals()[source]
galaxy.main.app_loop(args, log)[source]
galaxy.main.absolute_config_path(path, galaxy_root)[source]
galaxy.main.find_config(supplied_config, galaxy_root)[source]
class galaxy.main.GalaxyConfigBuilder(args=None, **kwds)[source]

Bases: object

Generate paste-like configuration from supplied command-line arguments.

__init__(args=None, **kwds)[source]
classmethod populate_options(arg_parser)[source]
config_is_ini
app_kwds()[source]
global_conf()[source]
setup_logging()[source]
galaxy.main.main()[source]

galaxy.queue_worker module

Galaxy control queue and worker. This is used to handle ‘app’ control like reloading the toolbox, etc., across multiple processes.

galaxy.queue_worker.send_local_control_task(app, task, kwargs={})[source]

This sends a message to the process-local control worker, which is useful for one-time asynchronous tasks like recalculating user disk usage.

galaxy.queue_worker.send_control_task(app, task, noop_self=False, kwargs={})[source]

This sends a control task out to all processes, useful for things like reloading a data table, which needs to happen individually in all processes.

galaxy.queue_worker.create_panel_section(app, **kwargs)[source]

Updates in memory toolbox dictionary.

galaxy.queue_worker.reload_tool(app, **kwargs)[source]
galaxy.queue_worker.reload_toolbox(app, **kwargs)[source]
galaxy.queue_worker.reload_data_managers(app, **kwargs)[source]
galaxy.queue_worker.reload_display_application(app, **kwargs)[source]
galaxy.queue_worker.reload_sanitize_whitelist(app)[source]
galaxy.queue_worker.recalculate_user_disk_usage(app, **kwargs)[source]
galaxy.queue_worker.reload_tool_data_tables(app, **kwargs)[source]
galaxy.queue_worker.rebuild_toolbox_search_index(app, **kwargs)[source]
galaxy.queue_worker.reload_job_rules(app, **kwargs)[source]
galaxy.queue_worker.admin_job_lock(app, **kwargs)[source]
class galaxy.queue_worker.GalaxyQueueWorker(app, queue=None, task_mapping={'admin_job_lock': <function admin_job_lock at 0x7fc9907569b0>, 'create_panel_section': <function create_panel_section at 0x7fc990756488>, 'rebuild_toolbox_search_index': <function rebuild_toolbox_search_index at 0x7fc9907568c0>, 'recalculate_user_disk_usage': <function recalculate_user_disk_usage at 0x7fc9907567d0>, 'reload_data_managers': <function reload_data_managers at 0x7fc990756668>, 'reload_display_application': <function reload_display_application at 0x7fc9907566e0>, 'reload_job_rules': <function reload_job_rules at 0x7fc990756938>, 'reload_sanitize_whitelist': <function reload_sanitize_whitelist at 0x7fc990756758>, 'reload_tool': <function reload_tool at 0x7fc990756500>, 'reload_tool_data_tables': <function reload_tool_data_tables at 0x7fc990756848>, 'reload_toolbox': <function reload_toolbox at 0x7fc990756578>}, connection=None)[source]

Bases: kombu.mixins.ConsumerMixin, threading.Thread

This is a flexible worker for galaxy’s queues. Each process, web or handler, will have one of these used for dispatching so called ‘control’ tasks.

__init__(app, queue=None, task_mapping={'admin_job_lock': <function admin_job_lock at 0x7fc9907569b0>, 'create_panel_section': <function create_panel_section at 0x7fc990756488>, 'rebuild_toolbox_search_index': <function rebuild_toolbox_search_index at 0x7fc9907568c0>, 'recalculate_user_disk_usage': <function recalculate_user_disk_usage at 0x7fc9907567d0>, 'reload_data_managers': <function reload_data_managers at 0x7fc990756668>, 'reload_display_application': <function reload_display_application at 0x7fc9907566e0>, 'reload_job_rules': <function reload_job_rules at 0x7fc990756938>, 'reload_sanitize_whitelist': <function reload_sanitize_whitelist at 0x7fc990756758>, 'reload_tool': <function reload_tool at 0x7fc990756500>, 'reload_tool_data_tables': <function reload_tool_data_tables at 0x7fc990756848>, 'reload_toolbox': <function reload_toolbox at 0x7fc990756578>}, connection=None)[source]
bind_and_start()[source]
get_consumers(Consumer, channel)[source]
process_task(body, message)[source]
shutdown()[source]

galaxy.queues module

All message queues used by Galaxy

galaxy.queues.all_control_queues_for_declare(config, application_stack)[source]

For in-memory routing (used by sqlalchemy-based transports), we need to be able to build the entire routing table in producers.

Refactor later to actually persist this somewhere instead of building it repeatedly.

galaxy.queues.control_queue_from_config(config)[source]

Returns a Queue instance with the correct name and routing key for this galaxy process’s config

galaxy.queues.connection_from_config(config)[source]

galaxy.version module