From 992f18e1274d7604074f4098e3ba5ddf478e17bf Mon Sep 17 00:00:00 2001
From: "Uehara.Keizo" <keizou.bos@gmail.com>
Date: Thu, 23 Dec 2021 01:32:16 +0000
Subject: [PATCH] Disable cleanup thread of cloud objectstore in
 set_metadata.py

Apply the following fixes for s3.py to cloud.py
Be more explcit about starting cache monitor thread 494c15cb9d622c3c75bbcf72b880ee386cbe01f5
Disable cleanup thread in set_metadata.py 6a56f3a5deb51dd1fafa8c588f32b14e67d10245
Fix S3 object store shutdown 7a63fd1db202a9993c09cb6f10c0615dc8dc5c99
---
 lib/galaxy/objectstore/cloud.py           | 29 ++++++++++++++++-------
 test/unit/objectstore/test_objectstore.py |  2 ++
 2 files changed, 23 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/objectstore/cloud.py b/lib/galaxy/objectstore/cloud.py
index 9b19a4fcc5b..867d1cba89d 100644
--- a/lib/galaxy/objectstore/cloud.py
+++ b/lib/galaxy/objectstore/cloud.py
@@ -57,7 +57,8 @@ class CloudConfigMixin:
             "cache": {
                 "size": self.cache_size,
                 "path": self.staging_path,
-            }
+            },
+            'enable_cache_monitor': False,
         }
 
 
@@ -76,6 +77,7 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
         bucket_dict = config_dict['bucket']
         connection_dict = config_dict.get('connection', {})
         cache_dict = config_dict['cache']
+        self.enable_cache_monitor = config_dict.get('enable_cache_monitor', True)
 
         self.provider = config_dict["provider"]
         self.credentials = config_dict["auth"]
@@ -100,8 +102,17 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
 
         self.conn = self._get_connection(self.provider, self.credentials)
         self.bucket = self._get_bucket(self.bucket_name)
+        self.start_cache_monitor()
+        # Test if 'axel' is available for parallel download and pull the key into cache
+        try:
+            subprocess.call('axel')
+            self.use_axel = True
+        except OSError:
+            self.use_axel = False
+
+    def start_cache_monitor(self):
         # Clean cache only if value is set in galaxy.ini
-        if self.cache_size != -1:
+        if self.cache_size != -1 and self.enable_cache_monitor:
             # Convert GBs to bytes for comparison
             self.cache_size = self.cache_size * 1073741824
             # Helper for interruptable sleep
@@ -109,12 +120,6 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
             self.cache_monitor_thread = threading.Thread(target=self.__cache_monitor)
             self.cache_monitor_thread.start()
             log.info("Cache cleaner manager started")
-        # Test if 'axel' is available for parallel download and pull the key into cache
-        try:
-            subprocess.call('axel')
-            self.use_axel = True
-        except OSError:
-            self.use_axel = False
 
     @staticmethod
     def _get_connection(provider, credentials):
@@ -710,3 +715,11 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
 
     def _get_store_usage_percent(self):
         return 0.0
+
+    def shutdown(self):
+        self.running = False
+        thread = getattr(self, 'cache_monitor_thread', None)
+        if thread:
+            log.debug("Shutting down thread")
+            self.sleeper.wake()
+            thread.join(5)
diff --git a/test/unit/objectstore/test_objectstore.py b/test/unit/objectstore/test_objectstore.py
index 25a3ad20bf0..83e5306a257 100644
--- a/test/unit/objectstore/test_objectstore.py
+++ b/test/unit/objectstore/test_objectstore.py
@@ -723,6 +723,8 @@ def test_config_parse_cloud():
             _assert_key_has_value(cache_dict, "size", 1000.0)
             _assert_key_has_value(cache_dict, "path", "database/object_store_cache")
 
+            _assert_key_has_value(as_dict, "enable_cache_monitor", False)
+
             extra_dirs = as_dict["extra_dirs"]
             assert len(extra_dirs) == 2