Warning

This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.authnz.custos_authnz

import base64
import hashlib
import logging
import os
from datetime import datetime, timedelta

import jwt
import requests
from oauthlib.common import generate_nonce
from requests_oauthlib import OAuth2Session
from six.moves.urllib.parse import quote

from galaxy import exceptions
from galaxy import util
from galaxy.model import CustosAuthnzToken, User
from ..authnz import IdentityProvider

log = logging.getLogger(__name__)
STATE_COOKIE_NAME = 'galaxy-oidc-state'
NONCE_COOKIE_NAME = 'galaxy-oidc-nonce'
KEYCLOAK_BACKENDS = {'custos', 'cilogon', 'keycloak'}


[docs]class CustosAuthnz(IdentityProvider):
[docs] def __init__(self, provider, oidc_config, oidc_backend_config, idphint=None): provider = provider.lower() self.config = {'provider': provider} self.config['verify_ssl'] = oidc_config['VERIFY_SSL'] self.config['url'] = oidc_backend_config['url'] self.config['client_id'] = oidc_backend_config['client_id'] self.config['client_secret'] = oidc_backend_config['client_secret'] self.config['redirect_uri'] = oidc_backend_config['redirect_uri'] self.config['ca_bundle'] = oidc_backend_config.get('ca_bundle', None) self.config['extra_params'] = { 'kc_idp_hint': oidc_backend_config.get('idphint', 'oidc' if self.config['provider'] in ['custos', 'keycloak'] else 'cilogon') } if provider == 'cilogon': self._load_config_for_cilogon() elif provider == 'custos': self._load_config_for_custos() elif provider == 'keycloak': self._load_config_for_keycloak()
[docs] def authenticate(self, trans, idphint=None): base_authorize_url = self.config['authorization_endpoint'] scopes = ['openid', 'email', 'profile'] if self.config['provider'] in ['custos', 'cilogon']: scopes.append('org.cilogon.userinfo') oauth2_session = self._create_oauth2_session(scope=scopes) nonce = generate_nonce() nonce_hash = self._hash_nonce(nonce) extra_params = {"nonce": nonce_hash} if idphint is not None: extra_params['idphint'] = idphint if "extra_params" in self.config: extra_params.update(self.config['extra_params']) authorization_url, state = oauth2_session.authorization_url( base_authorize_url, **extra_params) trans.set_cookie(value=state, name=STATE_COOKIE_NAME) trans.set_cookie(value=nonce, name=NONCE_COOKIE_NAME) return authorization_url
[docs] def callback(self, state_token, authz_code, trans, login_redirect_url): # Take state value to validate from token. OAuth2Session.fetch_token # will validate that the state query parameter value on the URL matches # this value. state_cookie = trans.get_cookie(name=STATE_COOKIE_NAME) oauth2_session = self._create_oauth2_session(state=state_cookie) token = self._fetch_token(oauth2_session, trans) access_token = token['access_token'] id_token = token['id_token'] refresh_token = token['refresh_token'] if 'refresh_token' in token else None expiration_time = datetime.now() + timedelta(seconds=token.get('expires_in', 3600)) refresh_expiration_time = (datetime.now() + timedelta(seconds=token['refresh_expires_in'])) if 'refresh_expires_in' in token else None # Get nonce from token['id_token'] and validate. 'nonce' in the # id_token is a hash of the nonce stored in the NONCE_COOKIE_NAME # cookie. id_token_decoded = jwt.decode(id_token, verify=False) nonce_hash = id_token_decoded['nonce'] self._validate_nonce(trans, nonce_hash) # Get userinfo and lookup/create Galaxy user record if id_token_decoded.get('email', None): userinfo = id_token_decoded else: userinfo = self._get_userinfo(oauth2_session) email = userinfo['email'] # Check if username if already taken username = userinfo.get('preferred_username', self._generate_username(trans, email)) user_id = userinfo['sub'] # Create or update custos_authnz_token record custos_authnz_token = self._get_custos_authnz_token(trans.sa_session, user_id, self.config['provider']) if custos_authnz_token is None: user = trans.user if not user: existing_user = trans.sa_session.query(User).filter_by(email=email).first() if existing_user: # If there is only a single external authentication # provider in use, trust the user provided and # automatically associate. # TODO: Future work will expand on this and provide an # interface for when there are multiple auth providers # allowing explicit authenticated association. if (trans.app.config.enable_oidc and len(trans.app.config.oidc) == 1 and len(trans.app.auth_manager.authenticators) == 0): user = existing_user else: message = "There already exists a user with email %s. To associate this external login, you must first be logged in as that existing account." % email log.exception(message) raise exceptions.AuthenticationFailed(message) else: user = trans.app.user_manager.create(email=email, username=username) if trans.app.config.user_activation_on: trans.app.user_manager.send_activation_email(trans, email, username) custos_authnz_token = CustosAuthnzToken(user=user, external_user_id=user_id, provider=self.config['provider'], access_token=access_token, id_token=id_token, refresh_token=refresh_token, expiration_time=expiration_time, refresh_expiration_time=refresh_expiration_time) else: custos_authnz_token.access_token = access_token custos_authnz_token.id_token = id_token custos_authnz_token.refresh_token = refresh_token custos_authnz_token.expiration_time = expiration_time custos_authnz_token.refresh_expiration_time = refresh_expiration_time trans.sa_session.add(custos_authnz_token) trans.sa_session.flush() return login_redirect_url, custos_authnz_token.user
[docs] def disconnect(self, provider, trans, email=None, disconnect_redirect_url=None): try: user = trans.user index = 0 # Find CustosAuthnzToken record for this provider (should only be one) provider_tokens = [token for token in user.custos_auth if token.provider == self.config["provider"]] if len(provider_tokens) == 0: raise Exception("User is not associated with provider {}".format(self.config["provider"])) if len(provider_tokens) > 1: for idx, token in enumerate(provider_tokens): id_token_decoded = jwt.decode(token.id_token, verify=False) if (id_token_decoded['email'] == email): index = idx trans.sa_session.delete(provider_tokens[index]) trans.sa_session.flush() return True, "", disconnect_redirect_url except Exception as e: return False, "Failed to disconnect provider {}: {}".format(provider, util.unicodify(e)), None
[docs] def logout(self, trans, post_logout_redirect_url=None): try: redirect_url = self.config['end_session_endpoint'] if post_logout_redirect_url is not None: redirect_url += "?redirect_uri={}".format(quote(post_logout_redirect_url)) return redirect_url except Exception as e: log.error("Failed to generate logout redirect_url", exc_info=e) return None
def _create_oauth2_session(self, state=None, scope=None): client_id = self.config['client_id'] redirect_uri = self.config['redirect_uri'] if (redirect_uri.startswith('http://localhost') and os.environ.get("OAUTHLIB_INSECURE_TRANSPORT", None) != "1"): log.warning("Setting OAUTHLIB_INSECURE_TRANSPORT to '1' to allow plain HTTP (non-SSL) callback") os.environ['OAUTHLIB_INSECURE_TRANSPORT'] = "1" session = OAuth2Session(client_id, scope=scope, redirect_uri=redirect_uri, state=state) session.verify = self._get_verify_param() return session def _fetch_token(self, oauth2_session, trans): if self.config.get('iam_client_secret'): # Custos uses the Keycloak client secret to get the token client_secret = self.config['iam_client_secret'] else: client_secret = self.config['client_secret'] token_endpoint = self.config['token_endpoint'] clientIdAndSec = self.config['client_id'] + ":" + self.config['client_secret'] # for custos return oauth2_session.fetch_token( token_endpoint, client_secret=client_secret, authorization_response=trans.request.url, headers={"Authorization": "Basic %s" % util.unicodify(base64.b64encode(util.smart_str(clientIdAndSec)))}, # for custos verify=self._get_verify_param()) def _get_userinfo(self, oauth2_session): userinfo_endpoint = self.config['userinfo_endpoint'] return oauth2_session.get(userinfo_endpoint, verify=self._get_verify_param()).json() def _get_custos_authnz_token(self, sa_session, user_id, provider): return sa_session.query(CustosAuthnzToken).filter_by( external_user_id=user_id, provider=provider).one_or_none() def _hash_nonce(self, nonce): return hashlib.sha256(util.smart_str(nonce)).hexdigest() def _validate_nonce(self, trans, nonce_hash): nonce_cookie = trans.get_cookie(name=NONCE_COOKIE_NAME) # Delete the nonce cookie trans.set_cookie('', name=NONCE_COOKIE_NAME, age=-1) nonce_cookie_hash = self._hash_nonce(nonce_cookie) if nonce_hash != nonce_cookie_hash: raise Exception("Nonce mismatch!") def _load_config_for_cilogon(self): # Set cilogon endpoints self.config['authorization_endpoint'] = "https://cilogon.org/authorize" self.config['token_endpoint'] = "https://cilogon.org/oauth2/token" self.config['userinfo_endpoint'] = "https://cilogon.org/oauth2/userinfo" def _load_config_for_custos(self): self.config['well_known_oidc_config_uri'] = self._get_well_known_uri_from_url(self.config['provider']) self.config['credential_url'] = '/'.join([self.config['url'].rstrip('/'), 'credentials']) self._get_custos_credentials() # Set custos endpoints clientIdAndSec = self.config['client_id'] + ":" + self.config['client_secret'] eps = requests.get(self.config['well_known_oidc_config_uri'], headers={"Authorization": "Basic %s" % util.unicodify(base64.b64encode(util.smart_str(clientIdAndSec)))}, verify=False, params={'client_id': self.config['client_id']}) well_known_oidc_config = eps.json() self._load_well_known_oidc_config(well_known_oidc_config) def _load_config_for_keycloak(self): self.config['well_known_oidc_config_uri'] = self._get_well_known_uri_from_url(self.config['provider']) well_known_oidc_config = self._fetch_well_known_oidc_config(self.config['well_known_oidc_config_uri']) self._load_well_known_oidc_config(well_known_oidc_config) def _get_custos_credentials(self): clientIdAndSec = self.config['client_id'] + ":" + self.config['client_secret'] creds = requests.get(self.config['credential_url'], headers={"Authorization": "Basic %s" % util.unicodify(base64.b64encode(util.smart_str(clientIdAndSec)))}, verify=False, params={'client_id': self.config['client_id']}) credentials = creds.json() self.config['iam_client_secret'] = credentials['iam_client_secret'] def _get_well_known_uri_from_url(self, provider): # TODO: Look up this URL from a Python library if provider in ['custos', 'keycloak']: base_url = self.config["url"] # Remove potential trailing slash to avoid "//realms" base_url = base_url if base_url[-1] != "/" else base_url[:-1] return "{}/.well-known/openid-configuration".format(base_url) else: raise Exception("Unknown Custos provider name: {}".format(provider)) def _fetch_well_known_oidc_config(self, well_known_uri): try: return requests.get(well_known_uri, verify=self._get_verify_param()).json() except Exception: log.error("Failed to load well-known OIDC config URI: {}".format(well_known_uri)) raise def _load_well_known_oidc_config(self, well_known_oidc_config): self.config['authorization_endpoint'] = well_known_oidc_config['authorization_endpoint'] self.config['token_endpoint'] = well_known_oidc_config['token_endpoint'] self.config['userinfo_endpoint'] = well_known_oidc_config['userinfo_endpoint'] self.config['end_session_endpoint'] = well_known_oidc_config['end_session_endpoint'] def _get_verify_param(self): """Return 'ca_bundle' if 'verify_ssl' is true and 'ca_bundle' is configured.""" # in requests_oauthlib, the verify param can either be a boolean or a CA bundle path if self.config['ca_bundle'] is not None and self.config['verify_ssl']: return self.config['ca_bundle'] else: return self.config['verify_ssl'] def _generate_username(self, trans, email): temp_username = email.split('@')[0] # username created from username portion of email count = 0 if (trans.sa_session.query(trans.app.model.User).filter_by(username=temp_username).first()): # if username already exists in database, append integer and iterate until unique username found while (trans.sa_session.query(trans.app.model.User).filter_by(username=(temp_username + str(count))).first()): count += 1 else: return temp_username return temp_username + str(count)