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Source code for galaxy.webapps.reports.buildapp

"""
Provides factory methods to assemble the Galaxy web application
"""

import logging
import atexit
import os

from inspect import isclass

from paste import httpexceptions

from galaxy.util import asbool
from galaxy.webapps.util import (
    MiddlewareWrapUnsupported,
    build_template_error_formatters,
    wrap_if_allowed,
    wrap_if_allowed_or_fail
)
import galaxy.model
import galaxy.model.mapping
import galaxy.web.framework.webapp
from galaxy.util.properties import load_app_properties

log = logging.getLogger(__name__)


[docs]class ReportsWebApplication(galaxy.web.framework.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. """ from galaxy.web.base.controller import BaseUIController import galaxy.webapps.reports.controllers 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 = "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={}, **kwargs): """Return a wsgi application serving the root object""" # Create the Galaxy application unless passed in 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, wrap_in_static, args=(global_conf,), kwargs=kwargs) # Close any pooled database connections before forking try: galaxy.model.mapping.metadata.bind.dispose() except: log.exception("Unable to dispose of pooled galaxy model database connections.") # Return 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) debug = asbool(conf.get('debug', False)) # 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,)) # The recursive middleware allows for including requests in other # requests or forwarding of requests, all on the server side. if asbool(conf.get('use_recursive', True)): from paste import recursive app = wrap_if_allowed(app, stack, recursive.RecursiveMiddleware, args=(conf,)) # Various debug middleware that can only be turned on if the debug # flag is set, either because they are insecure or greatly hurt # performance if debug: # Middleware to check for WSGI compliance if asbool(conf.get('use_lint', True)): from paste import lint app = wrap_if_allowed(app, stack, lint.make_middleware, name='paste.lint', args=(conf,)) # Middleware to run the python profiler on each request if asbool(conf.get('use_profile', False)): import profile app = wrap_if_allowed(app, stack, profile.ProfileMiddleware, args=(conf,)) # Middleware that intercepts print statements and shows them on the # returned page if asbool(conf.get('use_printdebug', True)): from paste.debug import prints app = wrap_if_allowed(app, stack, prints.PrintDebugMiddleware, args=(conf,)) if debug and asbool(conf.get('use_interactive', False)): # Interactive exception debugging, scary dangerous if publicly # accessible, if not enabled we'll use the regular error printing # middleware. try: from weberror import evalexception app = wrap_if_allowed_or_fail(app, stack, evalexception.EvalException, args=(conf,), kwargs=dict(templating_formatters=build_template_error_formatters())) except MiddlewareWrapUnsupported as exc: log.warning(str(exc)) import galaxy.web.framework.middleware.error app = wrap_if_allowed(app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,)) else: # Not in interactive debug mode, just use the regular error middleware import galaxy.web.framework.middleware.error app = wrap_if_allowed(app, stack, galaxy.web.framework.middleware.error.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 from galaxy.web.framework.middleware.xforwardedhost import XForwardedHostMiddleware app = wrap_if_allowed(app, stack, XForwardedHostMiddleware) return app
[docs]def wrap_in_static(app, global_conf, **local_conf): urlmap, _ = galaxy.web.framework.webapp.build_url_map(app, global_conf, local_conf) return urlmap
[docs]def uwsgi_app(): return galaxy.web.framework.webapp.build_native_uwsgi_app(app_factory, "reports")