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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', 'formatter': 'stack', 'level': 'DEBUG', 'stream': 'ext://sys.stderr', 'filters': ['stack']}}, 'loggers': {'paste.httpserver.ThreadPool': {'level': 'WARN', 'qualname': 'paste.httpserver.ThreadPool'}, 'routes.middleware': {'level': 'WARN', 'qualname': 'routes.middleware'}, 'amqp': {'level': 'INFO', 'qualname': 'amqp'}}, 'root': {'handlers': ['console'], 'level': 'DEBUG'}, 'version': 1}

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

galaxy.config.find_root(kwargs)

class galaxy.config.BaseAppConfiguration

Bases: object

class galaxy.config.GalaxyAppConfiguration(**kwargs)

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)

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)

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

reload_sanitize_whitelist(explicit=True)

get(key, default=None)

get_bool(key, default)

ensure_tempdir()

check()

is_admin_user(user)

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)

Resolve a path relative to Galaxy’s root.

galaxy.config.Configuration

alias of galaxy.config.GalaxyAppConfiguration

galaxy.config.reload_config_options(current_config)

Reload modified reloadable config options

galaxy.config.get_database_engine_options(kwargs, model_prefix='')

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

galaxy.config.get_database_url(config)

galaxy.config.init_models_from_config(config, map_install_models=False, object_store=None, trace_logger=None)

galaxy.config.configure_logging(config)

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

Bases: object

Shared code for configuring Galaxy-like app objects.

wait_for_toolbox_reload(old_toolbox)

reindex_tool_search()

tool_dependency_dir

Submodules

galaxy.config.script module

galaxy.config.script.main(argv=None)