On Mar 22, 2013, at 4:57 PM, Lance Parsons wrote: > Nate Coraor wrote: >> >> On Mar 22, 2013, at 11:56 AM, Lance Parsons wrote: >> >>> I have been running a Galaxy server for our sequencing researchers for a >>> while now and it's become increasingly successful. The biggest resource >>> challenge for us has been, and continues to be disk space. As such, I'd >>> like to implement some additional cleanup scripts. I thought I run a few >>> questions by this list before I got too far into things. >>> >>> In general, I'm wondering how to implement updates/additions to the cleanup >>> system that will be in line with the direction that the Galaxy project is >>> headed. The pgcleanup.py script is the newest piece of code in this area >>> (and even adds cleanup of exported histories, which are absent from the >>> older cleanup scripts). Also, the pgcleanup.py script uses a >>> "cleanup_event" table that I don't believe is used by the older >>> cleanup_datasets.py script. However, the new pgcleanup.py script only works >>> for Postgres, and worse, only for version 9.1+. I run my system on RedHat >>> (CentOS) and thus we use version 8.4 of Postgres. Are there plans to >>> support other databases or older versions of Postgres? >> >> Hi Lance, >> >> pgcleanup.py makes extensive use of Writable CTEs, so there is not really a >> way to port it to older versions. For 8.4 or MySQL, you can still use the >> older cleanup_datasets.py. > After looking at it a bit more, I see what you mean. Are there plans to > implement and additional cleanup scripts for non-postgres 9.1 users? Just > curious so I don't reinvent the wheel, I'd be happy to help with existing > efforts.
No, there aren't any plans as long as the alternative (cleanup_datasets.py) still works for other versions. >>> I'd like to implement a script to delete (set the deleted flag) for certain >>> datasets (e.g. raw data imported from our archive, for old, inactive users, >>> etc.). I'm wondering if it would make sense to try and extend pgcleanup.py >>> or cleanup_datasets.py. Or perhaps it would be best to just implement a >>> separate script, though that seems like I'd have to re-implement a lot of >>> boilerplate code for configuration reading, connections, logging, etc. >>> Any tips on generally acceptable (supported) procedures for marking a >>> dataset as deleted? >> >> You could probably reuse a lot of the code from either of the cleanup >> scripts for this. > Right. It seems to make sense to me to focus on the cleanup_datasets.py > since that will work for everyone. I would like to essentially mimic the > user deleting a dataset. I'd then email them to let them know that some old > data had been marked for deletion and let the rest of the scripts proceed as > normal, cleaning that up if they don't undelete it. > > It looks like I would want to mark the HistoryDatasetAssociations as deleted? > Is that correct? Would I need to do anything else to simulate the user > deleting the dataset? That's correct. --nate > > Thanks for the help, > Lance >> Thanks, >> --nate >> > > -- > Lance Parsons - Scientific Programmer > 134 Carl C. Icahn Laboratory > Lewis-Sigler Institute for Integrative Genomics > Princeton University > ___________________________________________________________ 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/
