Hi Ravi,

I believe admin_cleanup_datasets.py only works on database times. The rest
of your assumptions are likely correct, although without looking at more
details of the database I can't confirm.

--nate


On Fri, Mar 28, 2014 at 5:12 PM, Sanka, Ravi <rsa...@jcvi.org> wrote:

> 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 <n...@bx.psu.edu>
> Date: Friday, March 28, 2014 1:56 PM
>
> To: Ravi Sanka <rsa...@jcvi.org>
> Cc: Carl Eberhard <carlfeberh...@gmail.com>, Peter Cock <
> p.j.a.c...@googlemail.com>, "galaxy-dev@lists.bx.psu.edu" <
> 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 <rsa...@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
>> 301-795-7743
>> ----------------------------------------------
>>
>> From: Nate Coraor <n...@bx.psu.edu>
>> Date: Friday, March 28, 2014 9:59 AM
>> To: Ravi Sanka <rsa...@jcvi.org>
>> Cc: Carl Eberhard <carlfeberh...@gmail.com>, Peter Cock <
>> p.j.a.c...@googlemail.com>, "galaxy-dev@lists.bx.psu.edu" <
>> 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 <rsa...@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-pgcleanup-py-vs-cleanup-datasets-py-td4659330.html
>>>
>>> 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 rsa...@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: rsa...@jcvi.org
>>> To: isi...@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
>>> 301-795-7743
>>> ----------------------------------------------
>>>
>>> From: Carl Eberhard <carlfeberh...@gmail.com>
>>> Date: Tuesday, March 18, 2014 2:09 PM
>>> To: Peter Cock <p.j.a.c...@googlemail.com>
>>> Cc: Ravi Sanka <rsa...@jcvi.org>, "galaxy-dev@lists.bx.psu.edu" <
>>> 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 <carlfeberh...@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.c...@googlemail.com
>>>> > wrote:
>>>>
>>>>> On Tue, Mar 18, 2014 at 2:14 PM, Carl Eberhard <
>>>>> carlfeberh...@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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>>
>>
>
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