Hi folks,
Has someone seen this behaviour? I'm trying to do a once-over maintenance cleanup of our galaxy installs. The galaxy account is getting emailed nightly with an error which is happening when it gets to delete_datasets.sh cron task, basically:
AttributeError: 'NoneType' object has no attribute 'dataset_id'
1) Now I found this thread: http://dev.list.galaxyproject.org/Error-when-running-cleanup-datasets-py-td4... - and implemented that solution which removed some of the preceding log error info, but this related error remains:
sh ... /production2/galaxy-dist/scripts/cleanup_datasets/delete_datasets.sh
Traceback (most recent call last): File "./scripts/cleanup_datasets/cleanup_datasets.py", line 524, in <module> if __name__ == "__main__": main() File "./scripts/cleanup_datasets/cleanup_datasets.py", line 126, in main delete_datasets( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 301, in delete_datasets dataset_ids.append( ldda.dataset_id ) AttributeError: 'NoneType' object has no attribute 'dataset_id'
In the delete_datasets.log it shows that this is last log line before error occurs:
######### Processing LibraryDataset id: 14201
2) So to recap, in step 1 I found:
galaxydb_prod2=> select * from library_dataset where library_dataset_dataset_association_id is null; id | library_dataset_dataset_association_id | folder_id | order_id | create_time | update_time | name | info | deleted | purged -------+----------------------------------------+-----------+----------+----------------------------+----------------------------+---------------+------+---------+-------- 14201 | | 544 | 18 | 2012-11-01 17:26:23.877817 | 2012-11-01 17:26:35.787611 | NC_006625.fna | | f | f (1 row)
And so I ran the recommended query, "update library_dataset set folder_id = null where id=14201;" and that seemed to have a positive effect.
For what its worth,
galaxydb_prod2=> select * from library_dataset_dataset_association where id = 14201 galaxydb_prod2-> ; id | library_dataset_id | dataset_id | create_time | update_time | copied_from_history_dataset_association_id | copied_from_library_dataset_dataset_association_id | name | info | blurb | peek | extension | metadata | parent_id | designation | deleted | visible | user_id | message | state | tool_version -------+--------------------+------------+----------------------------+--------------------------+--------------------------------------------+----------------------------------------------------+---------------+------+-------+------+-----------+------------------+-----------+-------------+---------+---------+---------+---------+-------+-------------- 14201 | 14201 | 14706 | 2012-11-01 17:26:28.593081 | 2012-11-01 17:26:30.8649 | | | NC_006625.fna | | | | auto | {"dbkey": ["?"]} | | | f | t | 1 | | | (1 row)
The last thing I'd say is that this 'NC_006625.fna' item doesn't show up in the website front-end's sole Data Library list of folders and sub-items, nor does it show in the deleted list. It seems orphaned but I'd rather someone had confident advice on this one. My novice attempt at surgery would probably lead to lots of blood on the table.
Help much appreciated!
Damion