Resolve main conflicts (#556)

populationgenomics · Sep 25, 2023 · d2f5ca8 · d2f5ca8
1 parent 6d1f9f1
commit d2f5ca8
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Showing 6 changed files with 64 additions and 70 deletions.
diff --git a/metamist/audit/audithelper.py b/metamist/audit/audithelper.py
@@ -1,7 +1,6 @@
 # pylint: disable=no-member
 import csv
 import logging
-import os
 from collections import defaultdict
 from typing import Any
 
@@ -14,9 +13,6 @@
 class AuditHelper(CloudHelper):
     """General helper class for bucket auditing"""
 
-    #
-    EXCLUDED_SGS = os.getenv('SM_AUDIT_HELPER_EXCLUDED_SGS', '').split(',')
-
     @staticmethod
     def get_gcs_bucket_subdirs_to_search(paths: list[str]) -> defaultdict[str, list]:
         """

diff --git a/scripts/find_sequence_files_to_delete.py b/scripts/find_sequence_files_to_delete.py
@@ -34,7 +34,9 @@
 projapi = ProjectApi()
 
 # TODO: fetch this from metamist
-CPG_SEQUENCING_GROUP_IDS_TO_SKIP = {}
+CPG_SEQUENCING_GROUP_IDS_TO_SKIP: set[str] = set(
+    sg for sg in os.getenv('CPG_SEQUENCING_GROUP_IDS_TO_SKIP', '').split(',') if sg
+)
 
 
 def get_bucket_name_from_path(path_input):

diff --git a/scripts/sync_seqr.py b/scripts/sync_seqr.py
@@ -55,7 +55,7 @@
     ),
 }
 
-SGS_TO_IGNORE = {}
+SGS_TO_IGNORE: set[str] = set()
 BASE, SEQR_AUDIENCE = ENVS[ENVIRONMENT]
 
 url_individuals_sync = '/api/project/sa/{projectGuid}/individuals/sync'