Merge pull request galaxyproject#19594 from sanjaysrikakulam/cleanup_…

…jwd_periodic_task

Add failed jobs working directory cleanup as a celery periodic task

doc/source/admin/galaxy_options.rst

@@ -5747,4 +5747,41 @@
 :Type: int
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``enable_failed_jobs_working_directory_cleanup``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Enables the cleanup of failed Galaxy job's working directories.
+    Runs in a Celery task.
+:Default: ``false``
+:Type: bool
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``failed_jobs_working_directory_cleanup_days``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    The number of days to keep failed Galaxy job's working directories
+    before attempting to delete them if
+    enable_failed_jobs_working_directory_cleanup is ``true``. Runs in
+    a Celery task.
+:Default: ``5``
+:Type: int
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``failed_jobs_working_directory_cleanup_interval``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    The interval in seconds between attempts to delete all failed
+    Galaxy job's working directories from the filesystem (every 24
+    hours by default) if enable_failed_jobs_working_directory_cleanup
+    is ``true``. Runs in a Celery task.
+:Default: ``86400``
+:Type: int
+
+
 

lib/galaxy/celery/__init__.py

@@ -246,6 +246,9 @@ def schedule_task(task, interval):
     if config.object_store_cache_monitor_driver in ["auto", "celery"]:
         schedule_task("clean_object_store_caches", config.object_store_cache_monitor_interval)
 
+    if config.enable_failed_jobs_working_directory_cleanup:
+        schedule_task("cleanup_jwds", config.failed_jobs_working_directory_cleanup_interval)
+
     if beat_schedule:
         celery_app.conf.beat_schedule = beat_schedule
 

lib/galaxy/celery/tasks.py

@@ -508,7 +508,7 @@ def dispatch_pending_notifications(notification_manager: NotificationManager):
 
 
 @galaxy_task(action="clean up job working directories")
-def cleanup_jwds(sa_session: galaxy_scoped_session, object_store: BaseObjectStore, days: int = 5):
+def cleanup_jwds(sa_session: galaxy_scoped_session, object_store: BaseObjectStore, config: GalaxyAppConfiguration):
     """Cleanup job working directories for failed jobs that are older than X days"""
 
     def get_failed_jobs():
@@ -530,6 +530,7 @@ def delete_jwd(job):
             log.error(f"Error deleting job working directory: {path} : {e.strerror}")
 
     failed_jobs = get_failed_jobs()
+    days = config.failed_jobs_working_directory_cleanup_days
 
     if not failed_jobs:
         log.info("No failed jobs found within the last %s days", days)

lib/galaxy/config/sample/galaxy.yml.sample

@@ -1,21 +1,21 @@
 # Galaxy is configured by default to be usable in a single-user development
 # environment.  To tune the application for a multi-user production
 # environment, see the documentation at:
-# 
+#
 #  https://docs.galaxyproject.org/en/master/admin/production.html
-# 
+#
 # Throughout this sample configuration file, except where stated otherwise,
 # uncommented values override the default if left unset, whereas commented
 # values are set to the default value.  Relative paths are relative to the root
 # Galaxy directory.
-# 
+#
 # Examples of many of these options are explained in more detail in the Galaxy
 # Community Hub.
-# 
+#
 #   https://galaxyproject.org/admin/config
-# 
+#
 # Config hackers are encouraged to check there before asking for help.
-# 
+#
 # Configuration for Gravity process manager.
 # ``uwsgi:`` section will be ignored if Galaxy is started via Gravity commands (e.g ``./run.sh``, ``galaxy`` or ``galaxyctl``).
 gravity:
@@ -3067,3 +3067,19 @@ galaxy:
   # affects s3fs file sources.
   #file_source_listings_expiry_time: 60
 
+  # Enables the cleanup of failed Galaxy job's working directories. Runs
+  # in a Celery task.
+  #enable_failed_jobs_working_directory_cleanup: false
+
+  # The number of days to keep failed Galaxy job's working directories
+  # before attempting to delete them if
+  # enable_failed_jobs_working_directory_cleanup is ``true``. Runs in a
+  # Celery task.
+  #failed_jobs_working_directory_cleanup_days: 5
+
+  # The interval in seconds between attempts to delete all failed Galaxy
+  # job's working directories from the filesystem (every 24 hours by
+  # default) if enable_failed_jobs_working_directory_cleanup is
+  # ``true``. Runs in a Celery task.
+  #failed_jobs_working_directory_cleanup_interval: 86400
+

lib/galaxy/config/schemas/config_schema.yml

@@ -4240,3 +4240,24 @@ mapping:
           Number of seconds before file source content listings are refreshed. Shorter times will result in more
           queries while browsing a file sources. Longer times will result in fewer requests to file sources but
           outdated contents might be displayed to the user. Currently only affects s3fs file sources.
+
+      enable_failed_jobs_working_directory_cleanup:
+        type: bool
+        default: false
+        required: false
+        desc: |
+          Enables the cleanup of failed Galaxy job's working directories. Runs in a Celery task.
+
+      failed_jobs_working_directory_cleanup_days:
+        type: int
+        required: false
+        default: 5
+        desc: |
+          The number of days to keep failed Galaxy job's working directories before attempting to delete them if enable_failed_jobs_working_directory_cleanup is ``true``. Runs in a Celery task.
+
+      failed_jobs_working_directory_cleanup_interval:
+        type: int
+        required: false
+        default: 86400
+        desc: |
+          The interval in seconds between attempts to delete all failed Galaxy job's working directories from the filesystem (every 24 hours by default) if enable_failed_jobs_working_directory_cleanup is ``true``. Runs in a Celery task.