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tool_shed.webapp package

The Galaxy Tool Shed application.

tool_shed.webapp.url_for(*args, **kwargs) → str

Tries to resolve the URL using the routes module.

This only works in a WSGI app so a deprecation message is returned when running an ASGI app.

tool_shed.webapp.expose(func)[source]: Decorator: mark a function as ‘exposed’ and thus web accessible

Subpackages

Submodules

tool_shed.webapp.app module

class tool_shed.webapp.app.UniverseApplication(**kwd)[source]

Bases: ToolShedApp, SentryClientMixin, HaltableContainer

Encapsulates the state of a Universe application

__init__(**kwd) → None[source]

property tool_data_tables: ToolDataTableManager

property genome_builds: GenomeBuilds

tool_shed.webapp.buildapp module

Provides factory methods to assemble the Galaxy web application

class tool_shed.webapp.buildapp.ToolShedGalaxyWebTransaction(environ: dict[str, Any], app: BasicSharedApp, webapp: WebApplication, session_cookie: str | None = None)[source]

Bases: GalaxyWebTransaction

property repositories_hostname: str

get_or_create_default_history()[source]: Gets or creates a default history and associates it with the current session.

class tool_shed.webapp.buildapp.CommunityWebApplication(galaxy_app: MinimalApp, session_cookie: str = 'galaxysession', name: str | None = None)[source]

Bases: WebApplication

injection_aware: bool = True

transaction_chooser(environ, galaxy_app: BasicSharedApp, session_cookie: str)[source]

tool_shed.webapp.buildapp.add_ui_controllers(webapp, app)[source]: Search for controllers in the ‘galaxy.webapps.controllers’ module and add them to the webapp.

tool_shed.webapp.buildapp.app_factory(*args, **kwargs)[source]: Return a wsgi application serving the root object

tool_shed.webapp.buildapp.app_pair(global_conf, load_app_kwds=None, **kwargs)[source]: Return a wsgi application serving the root object

tool_shed.webapp.buildapp.wrap_in_middleware(app, global_conf, application_stack, **local_conf)[source]: Based on the configuration wrap app in a set of common and useful middleware.

tool_shed.webapp.config module

Universe configuration builder.

class tool_shed.webapp.config.ToolShedAppConfiguration(**kwargs)[source]

Bases: BaseAppConfiguration, CommonConfigurationMixin

default_config_file_name = 'tool_shed.yml'

add_sample_file_to_defaults: set[str] = {'datatypes_config_file'}

__init__(**kwargs)[source]

property shed_tool_data_path

check()[source]

tool_shed.webapp.config.Configuration: alias of ToolShedAppConfiguration

tool_shed.webapp.fast_app module

tool_shed.webapp.fast_app.add_request_id_middleware(app: FastAPI)[source]

tool_shed.webapp.fast_app.get_openapi_schema() → dict[str, Any][source]: Dumps openAPI schema without starting a full app and webserver.

tool_shed.webapp.fast_app.initialize_fast_app(gx_webapp, tool_shed_app)[source]

tool_shed.webapp.fast_factory module

Module containing factory class for building uvicorn app for the Galaxy Tool Shed.

Information on uvicorn, its various settings, and how to invoke it can be found at https://www.uvicorn.org/.

The Galaxy Tool Shed can be launched with uvicorn using the following invocation:

uvicorn --app-dir lib --factory tool_shed.webapp.fast_factory:factory

Use the environment variable TOOL_SHED_CONFIG_FILE to specify a Tool Shed configuration file.

TOOL_SHED_CONFIG_FILE=config/tool_shed.yml uvicorn --app-dir lib --factory tool_shed.webapp.fast_factory:factory

Note

Information on additional ways to configure uvicorn can be found at https://www.uvicorn.org/.

Gunicorn is a server with more complex management options.

This factory function can be executed as a uvicorn worker managed with gunicorn with the following command-line.

gunicorn 'tool_shed.webapp.fast_factory:factory()' --env TOOL_SHED_CONFIG_FILE=config/tool_shed.yml --pythonpath lib -w 4 -k uvicorn.workers.UvicornWorker --config lib/galaxy/web_stack/gunicorn_config.py

tool_shed.webapp.fast_factory.factory()[source]