Hi Nate,
I checked and there are 3 rows of dataset 301 in the history_dataset_association table (none in library_dataset_dataset_association):
dataset_id create_time update_time deleted 301 2/14/14 18:49 3/25/14 20:27 TRUE 301 3/6/14 15:48 3/25/14 18:41 TRUE 301 3/6/14 20:11 3/6/14 20:11 FALSE
The one with the most recent create_time has its deleted status set to false. The other 2, older ones are true.
I would have guessed that the most recent create_time instance is still false due being created within 30 days, but the second most recent is only 5 hours older and is set to true. Perhaps that instance was deleted by its user. That would cause its deleted status to become true, correct?
I assume that if I were to wait until all 3 instances' create_times are past 30 days, my process will work, as admin_cleanup_datasets.py will set all 3 instances to false.
Perchance, is there any setting on admin_cleanup_datasets.py that would cause it to judge datasets by their physical file's timestamp instead?
---------------------------------------------- Ravi Sanka ICS – Sr. Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 ----------------------------------------------
From: Nate Coraor <nate@bx.psu.edumailto:nate@bx.psu.edu> Date: Friday, March 28, 2014 1:56 PM To: Ravi Sanka <rsanka@jcvi.orgmailto:rsanka@jcvi.org> Cc: Carl Eberhard <carlfeberhard@gmail.commailto:carlfeberhard@gmail.com>, Peter Cock <p.j.a.cock@googlemail.commailto:p.j.a.cock@googlemail.com>, "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu> Subject: [CONTENT] Re: Re: [galaxy-dev] Re: Re: Unable to remove old datasets
Hi Ravi,
Can you check whether any other history_dataset_association or library_dataset_dataset_association rows exist which reference the dataset_id that you are attempting to remove?
When you run admin_cleanup_datasets.py, it'll set history_dataset_association.deleted = true. After that is done, you need to run cleanup_datasets.py with the `-6 -d 0` option to mark dataset.deleted = true, followed by `-3 -d 0 -r ` to remove the dataset file from disk and set dataset.purged = true. Note that the latter two operations will not do anything until *all* associated history_dataset_association and library_dataset_dataset_association rows are set to deleted = true.
--nate
On Fri, Mar 28, 2014 at 1:52 PM, Sanka, Ravi <rsanka@jcvi.orgmailto:rsanka@jcvi.org> wrote: Hi Nate,
I checked the dataset's entry in history_dataset_association, and the value in field "deleted" is true.
But if this does not enable the cleanup scripts to remove the dataset from disk, then how can I accomplish that? As an admin, my intention is to completely remove datasets that are past a certain age from Galaxy, including all instances of the dataset that may exist, regardless of whether or not the various users who own said instances have deleted them from their histories.
Can this be done with admin_cleanup_datasets.py? If so, how?
---------------------------------------------- Ravi Sanka ICS – Sr. Bioinformatics Engineer J. Craig Venter Institute 301-795-7743tel:301-795-7743 ----------------------------------------------
From: Nate Coraor <nate@bx.psu.edumailto:nate@bx.psu.edu> Date: Friday, March 28, 2014 9:59 AM To: Ravi Sanka <rsanka@jcvi.orgmailto:rsanka@jcvi.org> Cc: Carl Eberhard <carlfeberhard@gmail.commailto:carlfeberhard@gmail.com>, Peter Cock <p.j.a.cock@googlemail.commailto:p.j.a.cock@googlemail.com>, "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu> Subject: [CONTENT] Re: [galaxy-dev] Re: Re: Unable to remove old datasets
Hi Ravi,
If you take a look at the dataset's entry in the history_dataset_association table, is that marked deleted? admin_cleanup_datasets.py only marks history_dataset_association rows deleted, not datasets.
Running the cleanup_datasets.py flow with -d 0 should have then caused the dataset to be deleted and purged, but this may not be the case if there is more than one instance of the dataset you are trying to purge (either another copy in a history somewhere, or in a library).
--nate
On Tue, Mar 25, 2014 at 5:12 PM, Sanka, Ravi <rsanka@jcvi.orgmailto:rsanka@jcvi.org> wrote: I have now been able to successfully remove datasets from disk. After deleting the dataset or history from the front-end interface (as the user), I then run the cleanup scripts as admin:
python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 0 -1 $@ >> ./scripts/cleanup_datasets/delete_userless_histories.log python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 0 -2 -r $@ >> ./scripts/cleanup_datasets/purge_histories.log python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 0 -3 -r $@ >> ./scripts/cleanup_datasets/purge_datasets.log python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 0 -5 -r $@ >> ./scripts/cleanup_datasets/purge_folders.log python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 0 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 0 -6 -r $@ >> ./scripts/cleanup_datasets/delete_datasets.log
However, my final goal is to have a process that can remove old datasets from disk regardless of whether or not the users have deleted them at the front-end (and then automate said process via cronjob). This will be essentially in a situation where users are likely to leave datasets unattended and accumulating disk space.
I found the following Galaxy thread:
http://dev.list.galaxyproject.org/Re-Improving-Administrative-Data-Clean-Up-...
And am trying to use the script it mentions:
python ./scripts/cleanup_datasets/admin_cleanup_datasets.py universe_wsgi.ini -d 30 --smtp <smtp server> --fromaddr rsanka@jcvi.orgmailto:rsanka@jcvi.org
I chose –d 30 to remove all datasets older than 30 days, which currently only targets one dataset. The resulting stdout indicates success:
""""""""""""""""""""""""""""""""""""" # 2014-03-25 16:27:47 - Handling stuff older than 30 days Marked HistoryDatasetAssociation id 301 as deleted
From: rsanka@jcvi.orgmailto:rsanka@jcvi.org To: isingh@jcvi.orgmailto:isingh@jcvi.org Subject: Galaxy Server Cleanup - 1 datasets DELETED ---------- Galaxy Server Cleanup --------------------- The following datasets you own on Galaxy are older than 30 days and have been DELETED:
"Small.fastq" in history "Unnamed history"
You may be able to undelete them by logging into Galaxy, navigating to the appropriate history, selecting "Include Deleted Datasets" from the history options menu, and clicking on the link to undelete each dataset that you want to keep. You can then download the datasets. Thank you for your understanding and cooporation in this necessary cleanup in order to keep the Galaxy resource available. Please don't hesitate to contact us if you have any questions.
-- Galaxy Administrators
Marked 1 dataset instances as deleted """""""""""""""""""""""""""""""""""""
But when I check the database, the status of dataset 301 is unchanged (ok-false-false-true).
I then run the same cleanup_datasets.py routine from above (but with –d 30), but dataset 301 is still present. I tried a second time, this time using –d 0, but still no deletion (which is not surprising since the dataset's deleted status is still false).
If I run admin_cleanup_datasets.py again with the same parameters, the stdout says no datasets matched the criteria, so it seems to remember it's previous execution, but it's NOT actually updating the database.
What am I doing wrong?
---------------------------------------------- Ravi Sanka ICS – Sr. Bioinformatics Engineer J. Craig Venter Institute 301-795-7743tel:301-795-7743 ----------------------------------------------
From: Carl Eberhard <carlfeberhard@gmail.commailto:carlfeberhard@gmail.com> Date: Tuesday, March 18, 2014 2:09 PM To: Peter Cock <p.j.a.cock@googlemail.commailto:p.j.a.cock@googlemail.com> Cc: Ravi Sanka <rsanka@jcvi.orgmailto:rsanka@jcvi.org>, "galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu> Subject: [CONTENT] Re: [galaxy-dev] Re: Unable to remove old datasets
The cleanup scripts enforce a sort of "lifetime" for the datasets.
The first time they're run, they may mark a dataset as deleted and also reset the update time and you'll have to wait N days for the next stage of the lifetime.
The next time they're run, or if a dataset has already been marked as deleted, the actual file removal happens and purged is set to true (if it wasn't already).
You can manually pass in '-d 0' to force removal of datasets recently marked as deleted.
The purge scripts do not check 'allow_user_dataset_purge', of course.
On Tue, Mar 18, 2014 at 11:50 AM, Carl Eberhard <carlfeberhard@gmail.commailto:carlfeberhard@gmail.com> wrote: I believe it's a (BAD) silent failure mode in the server code.
If I understand correctly, the purge request isn't coughing an error when it gets to the 'allow_user_dataset_purge' check and instead is silently marking (or re-marking) the datasets as deleted.
I would rather it fail with a 403 error if purge is explicitly requested.
That said, it of course would be better to remove the purge operation based on the configuration then to show an error after we've found you can't do the operation. The same holds true for the 'permanently remove this dataset' link in deleted datasets.
I'll see if I can find out the answer to your question on the cleanup scripts.
On Tue, Mar 18, 2014 at 10:49 AM, Peter Cock <p.j.a.cock@googlemail.commailto:p.j.a.cock@googlemail.com> wrote: On Tue, Mar 18, 2014 at 2:14 PM, Carl Eberhard <carlfeberhard@gmail.commailto:carlfeberhard@gmail.com> wrote:
Thanks, Ravi & Peter
I've added a card to get the allow_user_dataset_purge options into the client and to better show the viable options to the user: https://trello.com/c/RCPZ9zMF
Thanks Carl - so this was a user interface bug, showing the user non-functional permanent delete (purge) options. That's clearer now.
In this situation can the user just 'delete', and wait N days for the cleanup scripts to actually purge the files and free the space? (It seems N=10 in scripts/cleanup/purge_*.sh at least, elsewhere like the underlying Python script the default looks like N=60).
Regards,
Peter
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