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'}, '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)

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.find_root(kwargs)

galaxy.config.expand_pretty_datetime_format(value)

>>> 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.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] = {}

object_store_store_by: str

__init__(**kwargs)

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.

sentry_dsn: str

config_dict: Dict[str, str]

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', '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'

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'}

database_connection: str

tool_path: str

tool_data_path: str

builds_file_path: str

len_file_path: str

integrated_tool_panel_config: str

toolbox_filter_base_modules: List[str]

tool_filters: List[str]

tool_label_filters: List[str]

tool_section_filters: List[str]

user_tool_filters: List[str]

user_tool_section_filters: List[str]

user_tool_label_filters: List[str]

password_expiration_period: datetime.timedelta

shed_tool_data_path: str

hours_between_check: int

galaxy_data_manager_data_path: str

use_remote_user: bool

cluster_files_directory: str

preserve_python_environment: str

email_from: str

workflow_resource_params_mapper: str

sanitize_allowlist_file: str

allowed_origin_hostnames: List[str]

trust_jupyter_notebook_conversion: bool

user_library_import_symlink_allowlist: List[str]

user_library_import_dir_auto_creation: bool

container_resolvers_config_file: str

tool_dependency_dir: Optional[str]

involucro_path: str

mulled_channels: List[str]

nginx_upload_store: str

tus_upload_store: str

pretty_datetime_format: str

visualization_plugins_directory: str

galaxy_infrastructure_url: str

__init__(**kwargs)

config_value_for_host(config_option, host)

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”.

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)

class galaxy.config.config_manage.GzipFilter(name)

Bases: object

__init__(name)

galaxy.config.schema module

class galaxy.config.schema.Schema(mapping)

Bases: object

__init__(mapping)

get_app_option(name)

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

Bases: galaxy.config.schema.Schema

__init__(schema_path, app_name)

property defaults

property paths_to_resolve

property reloadable_options

property per_host_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)