script for processing the metadata of the ESR samples; moved delete_entries_on_arvados script in scripts directory

1 files changed, 0 insertions, 34 deletions

diff --git a/workflows/pangenome-generate/delete_entries_on_arvados.py b/workflows/pangenome-generate/delete_entries_on_arvados.py
deleted file mode 100644
index d281456..0000000
--- a/workflows/pangenome-generate/delete_entries_on_arvados.py
+++ /dev/null
@@ -1,34 +0,0 @@
-import sys
-import arvados
-import arvados.collection
-
-from datetime import datetime
-
-date_time_str = '2020-08-20'
-date_time_obj = datetime.strptime(date_time_str, '%Y-%m-%d')
-
-api = arvados.api()
-keepclient = arvados.keep.KeepClient(api_client=api)
-
-validated = arvados.util.list_all(api.collections().list, filters=[
-    ["owner_uuid", "=", sys.argv[1]],
-#    ["properties.status", "=", "validated"]
-])
-
-# validated.sort(key=lambda v: v["portable_data_hash"])
-
-num_sample_deleted = 0
-for item in validated:
-    sequence_label = item['properties']["sequence_label"]
-
-    # The SRA samples start with SRR or ERR
-    if not sequence_label.startswith('SRR') and not sequence_label.startswith('ERR'):
-        created_at_obj = datetime.strptime(item["created_at"], '%Y-%m-%dT%H:%M:%S.%fZ')
-        # print(item, created_at_obj)
-
-        if created_at_obj < date_time_obj:
-            api.collections().delete(uuid=item['current_version_uuid']).execute()
-            num_sample_deleted += 1
-            print(sequence_label)
-
-print('num_sample_deleted: {}'.format(num_sample_deleted))