Merge 8d6e69b into 2fb0647

.secrets.baseline

@@ -181,8 +181,7 @@
         "filename": "fence/resources/google/utils.py",
         "hashed_secret": "1348b145fa1a555461c1b790a2f66614781091e9",
         "is_verified": false,
-        "line_number": 125,
-        "is_secret": false
+        "line_number": 127
       }
     ],
     "fence/utils.py": [
@@ -209,16 +208,14 @@
         "filename": "tests/conftest.py",
         "hashed_secret": "1348b145fa1a555461c1b790a2f66614781091e9",
         "is_verified": false,
-        "line_number": 1362,
-        "is_secret": false
+        "line_number": 1472
       },
       {
         "type": "Base64 High Entropy String",
         "filename": "tests/conftest.py",
         "hashed_secret": "227dea087477346785aefd575f91dd13ab86c108",
         "is_verified": false,
-        "line_number": 1385,
-        "is_secret": false
+        "line_number": 1495
       }
     ],
     "tests/credentials/google/test_credentials.py": [
@@ -273,8 +270,7 @@
         "filename": "tests/ras/test_ras.py",
         "hashed_secret": "d9db6fe5c14dc55edd34115cdf3958845ac30882",
         "is_verified": false,
-        "line_number": 105,
-        "is_secret": false
+        "line_number": 120
       }
     ],
     "tests/test-fence-config.yaml": [
@@ -288,5 +284,5 @@
       }
     ]
   },
-  "generated_at": "2022-01-03T05:29:40Z"
+  "generated_at": "2021-12-20T23:13:45Z"
 }

bin/fence_create.py

@@ -18,6 +18,7 @@
     delete_client_action,
     delete_users,
     delete_expired_google_access,
+    cleanup_expired_ga4gh_information,
     google_init,
     list_client_action,
     link_external_bucket,
@@ -34,7 +35,7 @@
     force_update_google_link,
     migrate_database,
     google_list_authz_groups,
-    update_user_visas,
+    access_token_polling_job,
 )
 from fence.settings import CONFIG_SEARCH_FOLDERS
 
@@ -149,6 +150,7 @@ def parse_arguments():
     subparsers.add_parser("expired-service-account-delete")
     subparsers.add_parser("bucket-access-group-verify")
     subparsers.add_parser("delete-expired-google-access")
+    subparsers.add_parser("cleanup-expired-ga4gh-information")
 
     hmac_create = subparsers.add_parser("hmac-create")
     hmac_create.add_argument("yaml-input")
@@ -407,9 +409,6 @@ def main():
     STORAGE_CREDENTIALS = os.environ.get("STORAGE_CREDENTIALS") or config.get(
         "STORAGE_CREDENTIALS"
     )
-    usersync = config.get("USERSYNC", {})
-    sync_from_visas = usersync.get("sync_from_visas", False)
-    fallback_to_dbgap_sftp = usersync.get("fallback_to_dbgap_sftp", False)
 
     arborist = None
     if args.arborist:
@@ -463,6 +462,8 @@ def main():
         verify_bucket_access_group(DB)
     elif args.action == "delete-expired-google-access":
         delete_expired_google_access(DB)
+    elif args.action == "cleanup-expired-ga4gh-information":
+        cleanup_expired_ga4gh_information(DB)
     elif args.action == "sync":
         sync_users(
             dbGaP,
@@ -474,8 +475,6 @@ def main():
             sync_from_local_yaml_file=args.yaml,
             folder=args.folder,
             arborist=arborist,
-            sync_from_visas=sync_from_visas,
-            fallback_to_dbgap_sftp=fallback_to_dbgap_sftp,
         )
     elif args.action == "dbgap-download-access-files":
         download_dbgap_files(
@@ -576,7 +575,7 @@ def main():
     elif args.action == "migrate":
         migrate_database(DB)
     elif args.action == "update-visas":
-        update_user_visas(
+        access_token_polling_job(
             DB,
             chunk_size=args.chunk_size,
             concurrency=args.concurrency,

fence/auth.py

@@ -114,6 +114,7 @@ def set_flask_session_values(user):
 
         if id_from_idp:
             user.id_from_idp = id_from_idp
+            # TODO: update iss_sub mapping table?
 
     # setup idp connection for new user (or existing user w/o it setup)
     idp = (