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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': {'class': 'logging.StreamHandler', 'filters': ['stack'], 'formatter': 'stack', 'level': 'DEBUG', 'stream': 'ext://sys.stderr'}}, 'loggers': {'amqp': {'level': 'INFO', 'qualname': 'amqp'}, 'paste.httpserver.ThreadPool': {'level': 'WARN', 'qualname': 'paste.httpserver.ThreadPool'}, 'routes.middleware': {'level': 'WARN', 'qualname': 'routes.middleware'}}, 'root': {'handlers': ['console'], 'level': 'DEBUG'}, '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'
deprecated_dirs = {'config_dir': 'config', 'data_dir': 'database'}
__init__(**kwargs)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

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=None)[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_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]