Re: [galaxy-dev] [CONTENT] Re: Re: Re: Re: Unable to remove old datasets
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
Re: [galaxy-dev] [CONTENT] Re: Re: Re: Re: Unable to remove old datasets
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 15:483/25/14 18:41 TRUE 301 3/6/14 20:113/6/14 20:11FALSE 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.edumailto:n...@bx.psu.edu Date: Friday, March 28, 2014 1:56 PM To: Ravi Sanka rsa...@jcvi.orgmailto:rsa...@jcvi.org Cc: Carl Eberhard carlfeberh...@gmail.commailto:carlfeberh...@gmail.com, Peter Cock p.j.a.c...@googlemail.commailto:p.j.a.c...@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 rsa...@jcvi.orgmailto: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 301-795-7743tel:301-795-7743 -- From: Nate Coraor n...@bx.psu.edumailto:n...@bx.psu.edu Date: Friday, March 28, 2014 9:59 AM To: Ravi Sanka rsa...@jcvi.orgmailto:rsa...@jcvi.org Cc: Carl Eberhard carlfeberh...@gmail.commailto:carlfeberh...@gmail.com, Peter Cock p.j.a.c...@googlemail.commailto:p.j.a.c...@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 rsa...@jcvi.orgmailto: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
