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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'}, 'botocore': {'level': 'INFO', 'qualname': 'botocore'}, 'paste.httpserver.ThreadPool': {'level': 'WARN', 'qualname': 'paste.httpserver.ThreadPool'}, 'routes.middleware': {'level': 'WARN', 'qualname': 'routes.middleware'}, 'sqlalchemy_json.track': {'level': 'WARN', 'qualname': 'sqlalchemy_json.track'}, 'urllib3.connectionpool': {'level': 'WARN', 'qualname': 'urllib3.connectionpool'}}, '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(**kwargs)

Bases: object

renamed_options: Optional[Dict[str, str]] = None

deprecated_dirs: Dict[str, str] = {}

paths_to_check_against_root: Set[str] = {}

add_sample_file_to_defaults: Set[str] = {}

listify_options: Set[str] = {}

__init__(**kwargs)

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

is_set(key)

Check if a configuration option has been explicitly set.

resolve_path(path)

Resolve a path relative to Galaxy’s root.

class galaxy.config.CommonConfigurationMixin

Bases: object

Shared configuration settings code for Galaxy and ToolShed.

property admin_users

is_admin_user(user)

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)

get(key, default=None)

class galaxy.config.GalaxyAppConfiguration(**kwargs)

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: Optional[Dict[str, str]] = {'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: Dict[str, str] = {'config_dir': 'config', 'data_dir': 'database'}

paths_to_check_against_root: Set[str] = {'auth_config_file', 'build_sites_config_file', 'containers_config_file', 'data_manager_config_file', 'datatypes_config_file', 'dependency_resolvers_config_file', 'error_report_file', 'file_path', 'job_config_file', 'job_metrics_config_file', 'job_resource_params_file', 'local_conda_mapping_file', 'markdown_export_css', 'markdown_export_css_invocation_reports', 'markdown_export_css_pages', 'migrated_tools_config', 'modules_mapping_files', 'object_store_config_file', 'oidc_backends_config_file', 'oidc_config_file', 'shed_data_manager_config_file', 'shed_tool_config_file', 'shed_tool_data_table_config', 'tool_config_file', 'tool_data_table_config_path', 'tool_destinations_config_file', 'tool_sheds_config_file', 'user_preferences_extra_conf_path', 'workflow_resource_params_file', 'workflow_schedulers_config_file'}

add_sample_file_to_defaults: Set[str] = {'build_sites_config_file', 'datatypes_config_file', 'job_metrics_config_file', 'tool_config_file', 'tool_data_table_config_path'}

listify_options: Set[str] = {'tool_config_file', 'tool_data_table_config_path'}

__init__(**kwargs)

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

reload_sanitize_allowlist(explicit=True)

ensure_tempdir()

check()

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()

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 config_paths

Alias for field number 0

property default_port

Alias for field number 1

property expected_app_factories

Alias for field number 2

property destination

Alias for field number 3

property schema_path

Alias for field number 4

property uwsgi_module

Alias for field number 5

property app_name

property sample_destination

property schema

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

Bases: tuple

property name

Alias for field number 0

property value

Alias for field number 1

property option

Alias for field number 2

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

Entry point for conversion process.

class galaxy.config.config_manage.PrefixFilter(name, prefix)

Bases: object

__init__(name, prefix)

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

class galaxy.config.config_manage.GzipFilter(name)

Bases: object

__init__(name)

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

galaxy.config.schema module

class galaxy.config.schema.Schema(mapping)

Bases: object

__init__(mapping)

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

get_app_option(name)

class galaxy.config.schema.AppSchema(schema_path, app_name)

Bases: galaxy.config.schema.Schema

__init__(schema_path, app_name)

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

property defaults

property paths_to_resolve

property reloadable_options

validate_path_resolution_graph()

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)