blob: d281456edfc88c2f861e5adb905567be7fdafe5f (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
|
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))
|
