Warning

This document is for an in-development version 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'}, 'celery.utils.functional': {'level': 'INFO', 'qualname': 'celery.utils.functional'}, 'gunicorn.access': {'handlers': ['console'], 'level': 'INFO', 'propagate': False, 'qualname': 'gunicorn.access'}, 'paste.httpserver.ThreadPool': {'level': 'WARN', 'qualname': 'paste.httpserver.ThreadPool'}, 'py.warnings': {'level': 'ERROR', 'qualname': 'py.warnings'}, 'routes.middleware': {'level': 'WARN', 'qualname': 'routes.middleware'}, 'sqlalchemy_json.track': {'level': 'WARN', 'qualname': 'sqlalchemy_json.track'}, 'urllib3.connectionpool': {'level': 'WARN', 'qualname': 'urllib3.connectionpool'}, 'watchdog.observers.inotify_buffer': {'level': 'INFO', 'qualname': 'watchdog.observers.inotify_buffer'}}, 'root': {'handlers': ['console'], 'level': 'DEBUG'}, 'version': 1}: Default value for logging configuration, passed to logging.config.dictConfig()

galaxy.config.DEPENDENT_CONFIG_DEFAULTS: Dict[str, str] = {'biotools_service_cache_url': 'database_connection', 'citation_cache_url': 'database_connection', 'mulled_resolution_cache_url': 'database_connection'}: Config parameters whose default is the value of another config parameter This should be moved to a .yml config file.

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.find_root(kwargs) → str[source]

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.BaseAppConfiguration(**kwargs)[source]

Bases: object

renamed_options: Dict[str, str] | None = 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

shed_tools_dir: str

__init__(**kwargs)[source]

is_set(key)[source]: Check if a configuration option has been explicitly set.

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.

sentry_dsn: str

config_dict: Dict[str, str]

property admin_users

is_admin_user(user: User | None) → bool[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: BaseAppConfiguration, CommonConfigurationMixin

renamed_options: Dict[str, str] | None = {'activation_email': 'email_from', 'blacklist_file': 'email_domain_blocklist_file', 'containers_resolvers_config_file': 'container_resolvers_config_file', 'fetch_url_whitelist': 'fetch_url_allowlist', 'ga4gh_service_organization_name': 'organization_name', 'ga4gh_service_organization_url': 'organization_url', 'sanitize_whitelist_file': 'sanitize_allowlist_file', 'user_library_import_symlink_whitelist': 'user_library_import_symlink_allowlist', 'whitelist_file': 'email_domain_allowlist_file'}

deprecated_options = ['blacklist_file', 'whitelist_file', 'sanitize_whitelist_file', 'user_library_import_symlink_whitelist', 'fetch_url_whitelist', 'containers_resolvers_config_file', 'activation_email', 'ga4gh_service_organization_name', 'ga4gh_service_organization_url', 'database_file', 'track_jobs_in_database']

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', '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', 'themes_config_file', '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', 'tool_config_file', 'tool_data_table_config_path'}

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

allowed_origin_hostnames: List[str]

builds_file_path: str

container_resolvers_config_file: str

database_connection: str

drmaa_external_runjob_script: str

email_from: str | None

enable_tool_shed_check: bool

file_source_temp_dir: str

galaxy_data_manager_data_path: str

galaxy_infrastructure_url: str

hours_between_check: int

integrated_tool_panel_config: str

involucro_path: str

len_file_path: str

manage_dependency_relationships: bool

monitor_thread_join_timeout: int

mulled_channels: List[str]

new_file_path: str

nginx_upload_store: str

password_expiration_period: timedelta

preserve_python_environment: str

pretty_datetime_format: str

sanitize_allowlist_file: str

shed_tool_data_path: str

themes: Dict[str, Dict[str, str]]

themes_by_host: Dict[str, Dict[str, Dict[str, str]]]

tool_data_path: str

tool_dependency_dir: str | None

tool_filters: List[str]

tool_label_filters: List[str]

tool_path: str

tool_section_filters: List[str]

toolbox_filter_base_modules: List[str]

track_jobs_in_database: bool

trust_jupyter_notebook_conversion: bool

tus_upload_store: str

use_remote_user: bool

user_library_import_dir_auto_creation: bool

user_library_import_symlink_allowlist: List[str]

user_tool_filters: List[str]

user_tool_label_filters: List[str]

user_tool_section_filters: List[str]

visualization_plugins_directory: str

workflow_resource_params_mapper: str

__init__(**kwargs)[source]

config_value_for_host(config_option, host)[source]

reload_sanitize_allowlist(explicit=True)[source]

ensure_tempdir()[source]

check()[source]

is_fetch_with_celery_enabled()[source]: True iff celery is enabled and celery_conf[“task_routes”][“galaxy.fetch_data”] != DISABLED_FLAG.

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

config_paths: List[str]: Alias for field number 0

default_port: str: Alias for field number 1

expected_app_factories: List[str]: Alias for field number 2

destination: str: Alias for field number 3

schema_path: Traversable: Alias for field number 4

property app_name: str

property sample_destination: str

property schema: AppSchema

class galaxy.config.config_manage.OptionValue(name, value, option)[source]

Bases: tuple

name: str: Alias for field number 0

value: Any: Alias for field number 1

option: Dict[str, Any]: Alias for field number 2

galaxy.config.config_manage.main(argv: List[str] | None = None) → None[source]: Entry point for conversion process.

galaxy.config.schema module

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

Bases: object

__init__(mapping)[source]

get_app_option(name)[source]

class galaxy.config.schema.AppSchema(schema_path: Traversable, app_name: str)[source]

Bases: Schema

__init__(schema_path: Traversable, app_name: str)[source]

property defaults

property paths_to_resolve

property reloadable_options

property per_host_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]