diff --git a/lib/galaxy/authnz/custos_authnz.py b/lib/galaxy/authnz/custos_authnz.py index a28553b113e..56903c2aed4 100644 --- a/lib/galaxy/authnz/custos_authnz.py +++ b/lib/galaxy/authnz/custos_authnz.py @@ -90,6 +90,7 @@ class CustosAuthnz(IdentityProvider): else: userinfo = self._get_userinfo(oauth2_session) email = userinfo['email'] + username = userinfo.get('preferred_username', self._generate_username(trans, email)) user_id = userinfo['sub'] # Create or update custos_authnz_token record @@ -113,9 +114,13 @@ class CustosAuthnz(IdentityProvider): message = f"There already exists a user with email {email}. To associate this external login, you must first be logged in as that existing account." log.exception(message) raise exceptions.AuthenticationFailed(message) - else: + elif self.config['provider'] == 'custos': login_redirect_url = f"{login_redirect_url}root/login?confirm=true&custos_token={json.dumps(token)}" return login_redirect_url, None + 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, @@ -133,7 +138,7 @@ class CustosAuthnz(IdentityProvider): 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 + return "/", custos_authnz_token.user def create_user(self, token, trans, login_redirect_url): token_dict = json.loads(token) @@ -309,7 +314,7 @@ class CustosAuthnz(IdentityProvider): 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'] + self.config['end_session_endpoint'] = well_known_oidc_config.get('end_session_endpoint') def _get_verify_param(self): """Return 'ca_bundle' if 'verify_ssl' is true and 'ca_bundle' is configured.""" diff --git a/lib/galaxy/tool_util/deps/container_classes.py b/lib/galaxy/tool_util/deps/container_classes.py index 30e2364d853..8eec47ae62a 100644 --- a/lib/galaxy/tool_util/deps/container_classes.py +++ b/lib/galaxy/tool_util/deps/container_classes.py @@ -117,6 +117,10 @@ def preprocess_volumes(volumes_raw_str, container_type): ro for Singularity iff no subdirectories are rw (Singularity does not allow ro parent directories with rw subdirectories). + >>> preprocess_volumes(None, DOCKER_CONTAINER_TYPE) + [] + >>> preprocess_volumes("", DOCKER_CONTAINER_TYPE) + [] >>> preprocess_volumes("/a/b", DOCKER_CONTAINER_TYPE) ['/a/b:rw'] >>> preprocess_volumes("/a/b:ro,/a/b/c:rw", DOCKER_CONTAINER_TYPE) @@ -131,6 +135,9 @@ def preprocess_volumes(volumes_raw_str, container_type): ['/a/b', '/a/b/c'] """ + if not volumes_raw_str: + return [] + volumes_raw_strs = [v.strip() for v in volumes_raw_str.split(",")] volumes = [] rw_paths = [] diff --git a/test/unit/authnz/test_custos_authnz.py b/test/unit/authnz/test_custos_authnz.py index e42deef9e86..7b8c33cded5 100644 --- a/test/unit/authnz/test_custos_authnz.py +++ b/test/unit/authnz/test_custos_authnz.py @@ -322,7 +322,7 @@ class CustosAuthnzTestCase(unittest.TestCase): self.assertTrue(self._create_oauth2_session_called) self.assertTrue(self._fetch_token_called) self.assertTrue(self._get_userinfo_called) - self.assertEqual(login_redirect_url, "http://localhost:8000/") + self.assertEqual(login_redirect_url, "/") self.assertIsNotNone(user) def test_callback_nonce_validation_with_bad_nonce(self):