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.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]¶

Parameters:: container – Optional container if provided the existing definitions will be copied

:param log_undefined_deps indicates if a log message should be emmited when an undefined dep is loaded

name: str¶

config: Any¶

application_stack: ApplicationStack¶

model: SharedModelMapping¶

security: IdEncodingHelper¶

shutdown()[source]¶

datatypes_registry: Registry¶

auth_manager: AuthManager¶

security_agent: Any¶

quota_agent: QuotaAgent¶

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: Optional[str] = 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]¶