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Source code for tool_shed.webapp.buildapp
"""
Provides factory methods to assemble the Galaxy web application
"""
import atexit
import logging
import os
from inspect import isclass
from urllib.parse import parse_qs
import routes
from paste import httpexceptions
from routes.middleware import RoutesMiddleware
import galaxy.webapps.base.webapp
import tool_shed.webapp.model
import tool_shed.webapp.model.mapping
from galaxy import util
from galaxy.util import asbool
from galaxy.util.properties import load_app_properties
from galaxy.webapps.util import wrap_if_allowed
log = logging.getLogger(__name__)
[docs]def add_ui_controllers(webapp, app):
"""
Search for controllers in the 'galaxy.webapps.controllers' module and add
them to the webapp.
"""
from galaxy.webapps.base.controller import BaseUIController
import tool_shed.webapp.controllers
controller_dir = tool_shed.webapp.controllers.__path__[0]
for fname in os.listdir(controller_dir):
if not fname.startswith("_") and fname.endswith(".py"):
name = fname[:-3]
module_name = "tool_shed.webapp.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 tool shed application unless passed in
load_app_kwds = load_app_kwds or {}
kwargs = load_app_properties(
kwds=kwargs,
config_prefix='TOOL_SHED_CONFIG_',
**load_app_kwds
)
if 'app' in kwargs:
app = kwargs.pop('app')
else:
try:
from tool_shed.webapp.app import UniverseApplication
app = UniverseApplication(global_conf=global_conf, **kwargs)
except Exception:
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 - https://routes.readthedocs.io/en/latest/restful.html
webapp.add_api_controllers('tool_shed.webapp.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',
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('json',
'/api/tools/json',
controller='tools',
action='json',
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:
tool_shed.webapp.model.mapping.metadata.bind.dispose()
except Exception:
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 tool_shed.webapp.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,))
# 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.
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)):
from paste.debug import profile
app = wrap_if_allowed(app, stack, profile.ProfileMiddleware, args=(conf,))
# Error middleware
import galaxy.web.framework.middleware.error
app = wrap_if_allowed(app, stack, galaxy.web.framework.middleware.error.ErrorMiddleware, args=(conf,))
return app
[docs]def wrap_in_static(app, global_conf, **local_conf):
urlmap, _ = galaxy.webapps.base.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
[docs]def uwsgi_app():
return galaxy.webapps.base.webapp.build_native_uwsgi_app(app_factory, "tool_shed")