galaxy.webapps.reports package

The Galaxy Reports application.

galaxy.webapps.reports.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.

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

Subpackages

Submodules

galaxy.webapps.reports.app module

class galaxy.webapps.reports.app.UniverseApplication(**kwargs)[source]

Bases: BasicSharedApp

Encapsulates the state of a Universe application

__init__(**kwargs)[source]

shutdown()[source]

galaxy.webapps.reports.buildapp module

Provides factory methods to assemble the Galaxy web application

class galaxy.webapps.reports.buildapp.ReportsWebApplication(galaxy_app: MinimalApp, session_cookie: str = 'galaxysession', name: str | None = None)[source]: Bases: WebApplication

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

galaxy.webapps.reports.buildapp.app_factory(global_conf, load_app_kwds=None, **kwargs)[source]: Return a wsgi application serving the root object

galaxy.webapps.reports.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.

galaxy.webapps.reports.config module

Universe configuration builder.

galaxy.webapps.reports.config.resolve_path(path, root)[source]: If ‘path’ is relative make absolute by prepending ‘root’

exception galaxy.webapps.reports.config.ConfigurationError[source]: Bases: Exception

class galaxy.webapps.reports.config.Configuration(**kwargs)[source]

Bases: object

__init__(**kwargs)[source]

get(key, default=None)[source]

check()[source]

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

galaxy.webapps.reports.config.get_database_engine_options(kwargs)[source]: Allow options for the SQLAlchemy database engine to be passed by using the prefix “database_engine_option”.

galaxy.webapps.reports.fast_app module

galaxy.webapps.reports.fast_app.initialize_fast_app(gx_webapp)[source]

galaxy.webapps.reports.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 galaxy.webapps.reports.fast_factory:factory

Use the environment variable GALAXY_REPORTS_CONFIG to specify a Galaxy Reports configuration file.

GALAXY_REPORTS_CONFIG=config/reports.yml uvicorn --app-dir lib --factory galaxy.webapps.reports.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 'galaxy.webapps.reports.fast_factory:factory()' --env GALAXY_REPORTS_CONFIG=config/reports.yml --pythonpath lib -w 4 -k uvicorn.workers.UvicornWorker

galaxy.webapps.reports.fast_factory.factory()[source]