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Source code for galaxy.webapps.reports.buildapp

Provides factory methods to assemble the Galaxy web application
import atexit
import logging
import os
from inspect import isclass

from paste import httpexceptions

import galaxy.model
import galaxy.model.mapping
import galaxy.webapps.base.webapp
from galaxy.util import asbool
from galaxy.util.properties import load_app_properties
from galaxy.web.framework.middleware.error import ErrorMiddleware
from galaxy.web.framework.middleware.request_id import RequestIDMiddleware
from galaxy.web.framework.middleware.xforwardedhost import XForwardedHostMiddleware
from galaxy.webapps.base.webapp import build_url_map
from galaxy.webapps.util import wrap_if_allowed

log = logging.getLogger(__name__)

[docs]class ReportsWebApplication(galaxy.webapps.base.webapp.WebApplication): pass
[docs]def add_ui_controllers(webapp, app): """ Search for controllers in the 'galaxy.webapps.controllers' module and add them to the webapp. """ import galaxy.webapps.reports.controllers from galaxy.webapps.base.controller import BaseUIController controller_dir = galaxy.webapps.reports.controllers.__path__[0] for fname in os.listdir(controller_dir): if not fname.startswith("_") and fname.endswith(".py"): name = fname[:-3] module_name = f"galaxy.webapps.reports.controllers.{name}" module = __import__(module_name) for comp in module_name.split(".")[1:]: module = getattr(module, comp) # Look for a controller inside the modules for key in dir(module): T = getattr(module, key) if isclass(T) and T is not BaseUIController and issubclass(T, BaseUIController): webapp.add_ui_controller(name, T(app))
[docs]def app_factory(global_conf, load_app_kwds=None, **kwargs): """Return a wsgi application serving the root object""" # Create the Galaxy application unless passed in load_app_kwds = load_app_kwds or {} kwargs = load_app_properties(kwds=kwargs, **load_app_kwds) if "app" in kwargs: app = kwargs.pop("app") else: from galaxy.webapps.reports.app import UniverseApplication app = UniverseApplication(global_conf=global_conf, **kwargs) atexit.register(app.shutdown) # Create the universe WSGI application webapp = ReportsWebApplication(app, session_cookie="galaxyreportssession", name="reports") add_ui_controllers(webapp, app) # These two routes handle our simple needs at the moment webapp.add_route("/{controller}/{action}", controller="root", action="index") webapp.add_route("/{action}", controller="root", action="index") webapp.finalize_config() # Wrap the webapp in some useful middleware if kwargs.get("middleware", True): webapp = wrap_in_middleware(webapp, global_conf, app.application_stack, **kwargs) if asbool(kwargs.get("static_enabled", True)): webapp = wrap_if_allowed(webapp, app.application_stack, build_url_map, args=(global_conf,), kwargs=kwargs) return webapp
[docs]def wrap_in_middleware(app, global_conf, application_stack, **local_conf): """Based on the configuration wrap `app` in a set of common and useful middleware.""" stack = application_stack # Merge the global and local configurations conf = global_conf.copy() conf.update(local_conf) # First put into place httpexceptions, which must be most closely # wrapped around the application (it can interact poorly with # other middleware): app = wrap_if_allowed(app, stack, httpexceptions.make_middleware, name="paste.httpexceptions", args=(conf,)) # Error middleware app = wrap_if_allowed(app, stack, ErrorMiddleware, args=(conf,)) # Transaction logging (apache access.log style) if asbool(conf.get("use_translogger", True)): from paste.translogger import TransLogger app = wrap_if_allowed(app, stack, TransLogger) # X-Forwarded-Host handling app = wrap_if_allowed(app, stack, XForwardedHostMiddleware) # Request ID handling app = wrap_if_allowed(app, stack, RequestIDMiddleware) return app