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Source code for galaxy.webapps.tool_shed.buildapp

Provides factory methods to assemble the Galaxy web application
import atexit
import logging
import os
import routes

from six.moves.urllib.parse import parse_qs
from inspect import isclass
from paste import httpexceptions
from galaxy.util import asbool

import galaxy.webapps.tool_shed.model
import galaxy.webapps.tool_shed.model.mapping
import galaxy.web.framework.webapp
from galaxy.webapps.util import (
from galaxy import util
from galaxy.util.properties import load_app_properties
from routes.middleware import RoutesMiddleware

log = logging.getLogger( __name__ )

[docs]class CommunityWebApplication( 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.tool_shed.controllers controller_dir = galaxy.webapps.tool_shed.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.tool_shed.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, **kwargs ): """Return a wsgi application serving the root object""" # Create the Galaxy tool shed application unless passed in kwargs = load_app_properties( kwds=kwargs, config_prefix='TOOL_SHED_CONFIG_' ) if 'app' in kwargs: app = kwargs.pop( 'app' ) else: try: from galaxy.webapps.tool_shed.app import UniverseApplication app = UniverseApplication( global_conf=global_conf, **kwargs ) except: import traceback import sys traceback.print_exc() sys.exit( 1 ) atexit.register( app.shutdown ) # Create the universe WSGI application webapp = CommunityWebApplication( app, session_cookie='galaxycommunitysession', name="tool_shed" ) add_ui_controllers( webapp, app ) webapp.add_route( '/view/{owner}', controller='repository', action='sharable_owner' ) webapp.add_route( '/view/{owner}/{name}', controller='repository', action='sharable_repository' ) webapp.add_route( '/view/{owner}/{name}/{changeset_revision}', controller='repository', action='sharable_repository_revision' ) # Handle displaying tool help images and README file images for tools contained in repositories. webapp.add_route( '/repository/static/images/{repository_id}/{image_file:.+?}', controller='repository', action='display_image_in_repository', repository_id=None, image_file=None ) webapp.add_route( '/{controller}/{action}', action='index' ) webapp.add_route( '/{action}', controller='repository', action='index' ) # Enable 'hg clone' functionality on repos by letting hgwebapp handle the request webapp.add_route( '/repos/*path_info', controller='hg', action='handle_request', path_info='/' ) # Add the web API. # A good resource for RESTful services - http://routes.readthedocs.org/en/latest/restful.html webapp.add_api_controllers( 'galaxy.webapps.tool_shed.api', app ) webapp.mapper.connect( 'api_key_retrieval', '/api/authenticate/baseauth/', controller='authenticate', action='get_tool_shed_api_key', conditions=dict( method=[ "GET" ] ) ) webapp.mapper.connect( 'group', '/api/groups/', controller='groups', action='index', conditions=dict( method=[ "GET" ] ) ) webapp.mapper.connect( 'group', '/api/groups/', controller='groups', action='create', conditions=dict( method=[ "POST" ] ) ) webapp.mapper.connect( 'group', '/api/groups/{encoded_id}', controller='groups', action='show', conditions=dict( method=[ "GET" ] ) ) webapp.mapper.resource( 'category', 'categories', controller='categories', name_prefix='category_', path_prefix='/api', parent_resources=dict( member_name='category', collection_name='categories' ) ) webapp.mapper.connect( 'repositories_in_category', '/api/categories/{category_id}/repositories', controller='categories', action='get_repositories', conditions=dict( method=[ "GET" ] ) ) webapp.mapper.connect( 'show_updates_for_repository', '/api/repositories/updates', controller='repositories', action='updates', conditions=dict( method=[ "GET" ] ) ) webapp.mapper.resource( 'repository', 'repositories', controller='repositories', collection={ 'add_repository_registry_entry': 'POST', 'get_repository_revision_install_info': 'GET', 'get_ordered_installable_revisions': 'GET', 'get_installable_revisions': 'GET', 'remove_repository_registry_entry': 'POST', 'repository_ids_for_setting_metadata': 'GET', 'reset_metadata_on_repositories': 'POST', 'reset_metadata_on_repository': 'POST' }, name_prefix='repository_', path_prefix='/api', new={ 'import_capsule': 'POST' }, parent_resources=dict( member_name='repository', collection_name='repositories' ) ) webapp.mapper.resource( 'repository_revision', 'repository_revisions', member={ 'repository_dependencies': 'GET', 'export': 'POST' }, controller='repository_revisions', name_prefix='repository_revision_', path_prefix='/api', parent_resources=dict( member_name='repository_revision', collection_name='repository_revisions' ) ) webapp.mapper.resource( 'user', 'users', controller='users', name_prefix='user_', path_prefix='/api', parent_resources=dict( member_name='user', collection_name='users' ) ) webapp.mapper.connect( 'update_repository', '/api/repositories/{id}', controller='repositories', action='update', conditions=dict( method=[ "PATCH", "PUT" ] ) ) webapp.mapper.connect( 'repository_create_changeset_revision', '/api/repositories/{id}/changeset_revision', controller='repositories', action='create_changeset_revision', conditions=dict( method=[ "POST" ] ) ) webapp.mapper.connect( 'repository_get_metadata', '/api/repositories/{id}/metadata', controller='repositories', action='metadata', conditions=dict( method=[ "GET" ] ) ) webapp.mapper.connect( 'repository_show_tools', '/api/repositories/{id}/{changeset}/show_tools', controller='repositories', action='show_tools', conditions=dict( method=[ "GET" ] ) ) webapp.mapper.connect( 'create_repository', '/api/repositories', controller='repositories', action='create', conditions=dict( method=[ "POST" ] ) ) webapp.mapper.connect( 'tools', '/api/tools', controller='tools', action='index', conditions=dict( method=[ "GET" ] ) ) webapp.mapper.connect( "version", "/api/version", controller="configuration", action="version", conditions=dict( method=[ "GET" ] ) ) 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.webapps.tool_shed.model.mapping.metadata.bind.dispose() except: log.exception("Unable to dispose of pooled tool_shed 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,) ) # Create a separate mapper for redirects to prevent conflicts. redirect_mapper = routes.Mapper() redirect_mapper = _map_redirects( redirect_mapper ) # Load the Routes middleware which we use for redirecting app = wrap_if_allowed( app, stack, RoutesMiddleware, args=(redirect_mapper,) ) # If we're using remote_user authentication, add middleware that # protects Galaxy from improperly configured authentication in the # upstream server if asbool(conf.get( 'use_remote_user', False )): from galaxy.webapps.tool_shed.framework.middleware.remoteuser import RemoteUser app = wrap_if_allowed( app, stack, RemoteUser, kwargs=dict( maildomain=conf.get('remote_user_maildomain', None), display_servers=util.listify( conf.get('display_servers', '')), admin_users=conf.get('admin_users', '').split(','), remote_user_header=conf.get('remote_user_header', 'HTTP_REMOTE_USER'), remote_user_secret_header=conf.get('remote_user_secret', None), normalize_remote_user_email=conf.get('normalize_remote_user_email', False)) ) # 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,) ) 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 ) # If sentry logging is enabled, log here before propogating up to # the error middleware # TODO sentry config is duplicated between tool_shed/galaxy, refactor this. sentry_dsn = conf.get( 'sentry_dsn', None ) if sentry_dsn: from galaxy.web.framework.middleware.sentry import Sentry app = wrap_if_allowed( app, stack, Sentry, args=(sentry_dsn,) ) # X-Forwarded-Host handling from galaxy.web.framework.middleware.xforwardedhost import XForwardedHostMiddleware app = wrap_if_allowed( app, stack, XForwardedHostMiddleware ) # Various debug middleware that can only be turned on if the debug # flag is set, either because they are insecure or greatly hurt # performance. The print debug middleware needs to be loaded last, # since there is a quirk in its behavior that breaks some (but not # all) subsequent middlewares. 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,) ) 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
def _map_redirects( mapper ): """ Add redirect to the Routes mapper and forward the received query string. Subsequently when the redirect is triggered in Routes middleware the request will not even reach the webapp. """ def forward_qs(environ, result): qs_dict = parse_qs(environ['QUERY_STRING']) for qs in qs_dict: result[ qs ] = qs_dict[ qs ] return True mapper.redirect( "/repository/status_for_installed_repository", "/api/repositories/updates/", _redirect_code="301 Moved Permanently", conditions=dict( function=forward_qs ) ) return mapper