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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'}, 'dogpile': {'level': 'WARN', 'qualname': 'dogpile'}, '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(**kwargs)[source]

Bases: object

renamed_options = None
deprecated_dirs = None
__init__(**kwargs)[source]

Initialize self. See help(type(self)) for accurate signature.

resolve_path(path)[source]

Resolve a path relative to Galaxy’s root.

class galaxy.config.CommonConfigurationMixin[source]

Bases: object

Shared configuration settings code for Galaxy and ToolShed.

property admin_users
is_admin_user(user)[source]

Determine if the provided user is listed in admin_users.

property 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

get_bool(key, default)[source]
get(key, default=None)[source]
class galaxy.config.GalaxyAppConfiguration(**kwargs)[source]

Bases: galaxy.config.BaseAppConfiguration, galaxy.config.CommonConfigurationMixin

deprecated_options = ('database_file', 'track_jobs_in_database', 'blacklist_file', 'whitelist_file', 'sanitize_whitelist_file', 'user_library_import_symlink_whitelist', 'fetch_url_whitelist')
renamed_options = {'blacklist_file': 'email_domain_blocklist_file', 'fetch_url_whitelist': 'fetch_url_allowlist', 'sanitize_whitelist_file': 'sanitize_allowlist_file', 'user_library_import_symlink_whitelist': 'user_library_import_symlink_allowlist', 'whitelist_file': 'email_domain_allowlist_file'}
default_config_file_name = 'galaxy.yml'
deprecated_dirs = {'config_dir': 'config', 'data_dir': 'database'}
__init__(**kwargs)[source]

Initialize self. See help(type(self)) for accurate signature.

parse_config_file_options(kwargs)[source]

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

reload_sanitize_allowlist(explicit=True)[source]
ensure_tempdir()[source]
check()[source]
galaxy.config.Configuration

alias of galaxy.config.GalaxyAppConfiguration

galaxy.config.reload_config_options(current_config)[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]
property tool_dependency_dir

Submodules

galaxy.config.config_manage module

class galaxy.config.config_manage.App(config_paths, default_port, expected_app_factories, destination, schema_path, uwsgi_module)

Bases: tuple

property app_name
property config_paths

Alias for field number 0

property default_port

Alias for field number 1

property destination

Alias for field number 3

property expected_app_factories

Alias for field number 2

property sample_destination
property schema
property schema_path

Alias for field number 4

property uwsgi_module

Alias for field number 5

class galaxy.config.config_manage.OptionValue(name, value, option)

Bases: tuple

property name

Alias for field number 0

property option

Alias for field number 2

property value

Alias for field number 1

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

Entry point for conversion process.

class galaxy.config.config_manage.PrefixFilter(name, prefix)[source]

Bases: object

__init__(name, prefix)[source]

Initialize self. See help(type(self)) for accurate signature.

class galaxy.config.config_manage.GzipFilter(name)[source]

Bases: object

__init__(name)[source]

Initialize self. See help(type(self)) for accurate signature.

galaxy.config.schema module

class galaxy.config.schema.Schema(mapping)[source]

Bases: object

__init__(mapping)[source]

Initialize self. See help(type(self)) for accurate signature.

get_app_option(name)[source]
class galaxy.config.schema.AppSchema(schema_path, app_name)[source]

Bases: galaxy.config.schema.Schema

__init__(schema_path, app_name)[source]

Initialize self. See help(type(self)) for accurate signature.

property defaults
property paths_to_resolve
property reloadable_options
validate_path_resolution_graph()[source]

This method is for tests only: we SHOULD validate the schema’s path resolution graph as part of automated testing; but we should NOT validate it at runtime.

galaxy.config.script module

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