Warning

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.

galaxy.config package

Universe configuration builder.

galaxy.config.LOGGING_CONFIG_DEFAULT = {'disable_existing_loggers': False, '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'}, 'amqp': {'qualname': 'amqp', 'level': 'INFO'}}, 'root': {'level': 'DEBUG', 'handlers': ['console']}, 'version': 1}

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

galaxy.config.find_root(kwargs)[source]
class galaxy.config.BaseAppConfiguration[source]

Bases: object

class galaxy.config.GalaxyAppConfiguration(**kwargs)[source]

Bases: galaxy.config.BaseAppConfiguration

deprecated_options = ('database_file', 'track_jobs_in_database')
default_config_file_name = 'galaxy.yml'
__init__(**kwargs)[source]
update_reloadable_property(key, value)[source]
admin_users
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

parse_config_file_options(kwargs)[source]

Backwards compatibility for config files moved to the config/ dir.

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.

galaxy.config.Configuration

alias of galaxy.config.GalaxyAppConfiguration

galaxy.config.reload_config_options(current_config, path=None)[source]

Reload modified reloadable config options

galaxy.config.get_reloadable_config_options()[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]
tool_dependency_dir

Submodules

galaxy.config.script module

galaxy.config.script.main(argv=None)[source]