Warning
This document is for an old release 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: Dict[str, Any] = {'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'}, 'gunicorn.access': {'handlers': ['console'], 'level': 'INFO', 'propagate': False, 'qualname': 'gunicorn.access'}, '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.configure_logging(config, facts=None)[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.
- galaxy.config.expand_pretty_datetime_format(value)[source]¶
>>> expand_pretty_datetime_format("%H:%M:%S %Z") '%H:%M:%S %Z' >>> locale_format = expand_pretty_datetime_format("$locale (UTC)") >>> import locale >>> expected_format = '%s (UTC)' % locale.nl_langinfo(locale.D_T_FMT) >>> locale_format == expected_format True >>> expand_pretty_datetime_format("$iso8601") '%Y-%m-%d %H:%M:%S'
- class galaxy.config.CommonConfigurationMixin[source]¶
Bases:
object
Shared configuration settings code for Galaxy and ToolShed.
- property 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
- class galaxy.config.GalaxyAppConfiguration(**kwargs)[source]¶
Bases:
BaseAppConfiguration
,CommonConfigurationMixin
- deprecated_options = ('database_file', 'track_jobs_in_database', 'blacklist_file', 'whitelist_file', 'sanitize_whitelist_file', 'user_library_import_symlink_whitelist', 'fetch_url_whitelist', 'containers_resolvers_config_file')¶
- renamed_options: Optional[Dict[str, str]] = {'blacklist_file': 'email_domain_blocklist_file', 'containers_resolvers_config_file': 'container_resolvers_config_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'¶
- paths_to_check_against_root: Set[str] = {'auth_config_file', 'build_sites_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'}¶
- galaxy.config.Configuration¶
alias of
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”.
Submodules¶
galaxy.config.config_manage module¶
- class galaxy.config.config_manage.App(config_paths, default_port, expected_app_factories, destination, schema_path)[source]¶
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 app_name¶
- property sample_destination¶
- property schema¶
- class galaxy.config.config_manage.OptionValue(name, value, option)[source]¶
Bases:
tuple
- property name¶
Alias for field number 0
- property value¶
Alias for field number 1
- property option¶
Alias for field number 2