Dataset deletion / database update after user purge

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Dataset deletion / database update after user purge

Nicolas Lapalu
Hi Galaxy team,


We performed a database and datasets purge of our Galaxy server. We
decided to delete and purge few user accounts. We supposed that the
purge of a user would trigger cascade deletions in database. So we used
the web interface to delete and to purge these accounts. Then we
launched cleanup_dataset.py in several ways:

python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d
1 -1 -r > cleanup_1.log
python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d
1 -2 -r > cleanup_2.log
python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d
1 -3 -r > cleanup_3.log
python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d
1 -5 -r > cleanup_5.log
python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d
1 -4 -r > cleanup_4.log
python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d
1 -6 -r > cleanup_6.log


After a simple control, I can see that some datasets belonging to (and
only to) purged user accounts are still present with a status : deleted
= t and purged = f. Moreover, some datasets (not shared with other users
or linked to a library) have the status deleted = f and purged = f. When
I look at the history status associated with the dataset, I can obtain
deleted = t and purged = f. So, the purge of a user account don't change
the status of his histories and datasets.
Do you thing that I can change the history status 'deleted = f to
deleted = t, and purged = f to purged = t' for all purged users ? I
expect that the cleanup script launches the cascade purge !


below the sql command:

// all datasets belonging to at least one purged user (shared or not)
select D.id as "dataset id",U.email, D.deleted as "dataset deleted",
D.purged as "dataset purged" , H.deleted as "history deleted" ,H.purged
as "history purged" from galaxy_user U,history H
,history_dataset_association A, dataset D where A.dataset_id=D.id and
H.id=A.history_id and U.id=H.user_id and D.id in (select D.id from
galaxy_user U,history H ,history_dataset_association A, dataset D where
A.dataset_id=D.id and H.id=A.history_id and U.id=H.user_id and U.deleted
= 't' and U.purged = 't') order by D.id;
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