Resolve main conflicts (#556)

populationgenomics · Sep 28, 2023 · f5aacdb · f5aacdb
1 parent 034b837
commit f5aacdb
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Showing 6 changed files with 69 additions and 68 deletions.
diff --git a/metamist/audit/audithelper.py b/metamist/audit/audithelper.py
@@ -14,8 +14,11 @@
 class AuditHelper(CloudHelper):
     """General helper class for bucket auditing"""
 
-    #
-    EXCLUDED_SGS = os.getenv('SM_AUDIT_HELPER_EXCLUDED_SGS', '').split(',')
+    EXCLUDED_SGS: set[str] = set(
+        sg for sg in
+        os.getenv('SM_AUDIT_EXCLUDED_SGS', '').split(',')
+        if sg
+    )
 
     @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'