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galaxy.config package¶
Universe configuration builder.
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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()
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class
galaxy.config.
CommonConfigurationMixin
[source]¶ Bases:
object
Shared configuration settings code for Galaxy and ToolShed.
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property
admin_users
¶
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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
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property
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class
galaxy.config.
GalaxyAppConfiguration
(**kwargs)[source]¶ Bases:
galaxy.config.BaseAppConfiguration
,galaxy.config.CommonConfigurationMixin
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deprecated_options
= ('database_file', 'track_jobs_in_database', 'blacklist_file', 'whitelist_file', 'sanitize_whitelist_file', 'user_library_import_symlink_whitelist', 'fetch_url_whitelist')¶
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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'}¶
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default_config_file_name
= 'galaxy.yml'¶
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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'}¶
-
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galaxy.config.
Configuration
¶ alias of
galaxy.config.GalaxyAppConfiguration
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galaxy.config.
reload_config_options
(current_config)[source]¶ Reload modified reloadable config options.
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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”.
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galaxy.config.
init_models_from_config
(config, map_install_models=False, object_store=None, trace_logger=None)[source]¶
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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.
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class
galaxy.config.
ConfiguresGalaxyMixin
[source]¶ Bases:
object
Shared code for configuring Galaxy-like app objects.
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property
tool_dependency_dir
¶
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property
Submodules¶
galaxy.config.config_manage module¶
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class
galaxy.config.config_manage.
App
(config_paths, default_port, expected_app_factories, destination, schema_path, uwsgi_module)[source]¶ Bases:
tuple
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property
config_paths
¶ Alias for field number 0
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property
default_port
¶ Alias for field number 1
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property
expected_app_factories
¶ Alias for field number 2
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property
destination
¶ Alias for field number 3
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property
schema_path
¶ Alias for field number 4
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property
uwsgi_module
¶ Alias for field number 5
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property
app_name
¶
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property
sample_destination
¶
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property
schema
¶
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property
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class
galaxy.config.config_manage.
OptionValue
(name, value, option)[source]¶ Bases:
tuple
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property
name
¶ Alias for field number 0
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property
value
¶ Alias for field number 1
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property
option
¶ Alias for field number 2
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property