Merge b8fab61 into 8bdb967

fence/sync/sync_users.py

@@ -1,45 +1,44 @@
+import collections
+import copy
+import datetime
 import glob
-import jwt
+import hashlib
 import os
 import re
 import subprocess as sp
-import yaml
-import copy
-import datetime
 import uuid
-import collections
-import hashlib
-
-from contextlib import contextmanager
 from collections import defaultdict
+from contextlib import contextmanager
 from csv import DictReader
 from io import StringIO
 from stat import S_ISDIR
 
+import jwt
 import paramiko
+import yaml
 from cdislogging import get_logger
-from email_validator import validate_email, EmailNotValidError
+from email_validator import EmailNotValidError, validate_email
 from gen3authz.client.arborist.errors import ArboristError
 from gen3users.validation import validate_user_yaml
 from paramiko.proxy import ProxyCommand
-from sqlalchemy.exc import IntegrityError
 from sqlalchemy import func
+from sqlalchemy.exc import IntegrityError
 from userdatamodel.driver import SQLAlchemyDriver
 
 from fence.config import config
 from fence.models import (
     AccessPrivilege,
     AuthorizationProvider,
+    Client,
+    IdentityProvider,
     Project,
     Tag,
     User,
-    query_for_user,
-    Client,
-    IdentityProvider,
     get_project_to_authz_mapping,
+    query_for_user,
 )
-from fence.resources.storage import StorageManager
 from fence.resources.google.access_utils import bulk_update_google_groups
+from fence.resources.storage import StorageManager
 from fence.sync import utils
 from fence.sync.passport_sync.ras_sync import RASVisa
 
@@ -370,7 +369,7 @@ def _match_pattern(filepath, id_patterns, encrypted=True):
         Returns:
             bool: whether the pattern matches
         """
-        id_patterns.append("authentication_file_phs(\d{6}).(csv|txt)")
+        id_patterns.append("authentication_file_phs(\\\d{6}).(csv|txt)")
         for pattern in id_patterns:
             pattern = r"{}".format(pattern)
             if encrypted:

tests/dbgap_sync/test_user_sync.py

@@ -91,7 +91,7 @@ def test_sync(
     )
     monkeypatch.setattr(syncer, "parse_consent_code", parse_consent_code_config)
     monkeypatch.setitem(
-        syncer.dbGaP[2], "allow_non_dbGaP_whitelist", allow_non_dbgap_whitelist
+        syncer.dbGaP[1], "allow_non_dbGaP_whitelist", allow_non_dbgap_whitelist
     )
 
     syncer.sync()
@@ -717,7 +717,7 @@ def mock_merge(dbgap_servers, sess):
 
     # this function will be called once for each sftp server
     # the test config file has 3 dbgap sftp servers
-    assert syncer._process_dbgap_files.call_count == 3
+    assert syncer._process_dbgap_files.call_count == 2
 
 
 def setup_ras_sync_testing(