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
from galaxy import util
from galaxy.structured_app import BasicSharedApp
from galaxy.util import asbool
from galaxy.util.properties import load_app_properties
from galaxy.web import url_for
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,
    GalaxyWebTransaction,
)
from galaxy.webapps.util import wrap_if_allowed

SHED_API_VERSION = os.environ.get("TOOL_SHED_API_VERSION", "v1")

log = logging.getLogger(__name__)


[docs]class ToolShedGalaxyWebTransaction(GalaxyWebTransaction): @property def repositories_hostname(self) -> str: return url_for("/", qualified=True).rstrip("/")
[docs] def get_or_create_default_history(self): # tool shed has no concept of histories raise NotImplementedError
[docs]class CommunityWebApplication(galaxy.webapps.base.webapp.WebApplication): injection_aware: bool = True
[docs] def transaction_chooser(self, environ, galaxy_app: BasicSharedApp, session_cookie: str): return ToolShedGalaxyWebTransaction(environ, galaxy_app, self, session_cookie)
[docs]def add_ui_controllers(webapp, app): """ Search for controllers in the 'galaxy.webapps.controllers' module and add them to the webapp. """ import tool_shed.webapp.controllers from galaxy.webapps.base.controller import BaseUIController 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 = f"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(*args, **kwargs): """ Return a wsgi application serving the root object """ return app_pair(*args, **kwargs)[0]
[docs]def app_pair(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") import tool_shed.webapp.app tool_shed.webapp.app.app = app else: try: import tool_shed.webapp.app app = tool_shed.webapp.app.UniverseApplication(global_conf=global_conf, **kwargs) tool_shed.webapp.app.app = app except Exception: import sys import traceback 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 if SHED_API_VERSION == "v1": 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", "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/build_search_index", controller="tools", action="build_search_index", conditions=dict(method=["PUT"]), ) 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, build_url_map, args=(global_conf,), kwargs=kwargs) return webapp, app
[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,)) # 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), ), ) # 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) # Error middleware app = wrap_if_allowed(app, stack, ErrorMiddleware, args=(conf,)) return app
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