Merge remote-tracking branch 'upstream/release_21.05' into dev

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."""

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 = []

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):