From 7c12e4976337a063301be260cb3954bf4303f5e0 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Sat, 26 Sep 2020 12:12:17 +0200
Subject: script for processing the metadata of the ESR samples; moved
 delete_entries_on_arvados script in scripts directory

---
 .../delete_entries_on_arvados.py                   | 34 ----------------------
 1 file changed, 34 deletions(-)
 delete mode 100644 workflows/pangenome-generate/delete_entries_on_arvados.py

(limited to 'workflows/pangenome-generate')

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))
-- 
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