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 >>>>> >>>> >>>> >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> >> >
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