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.

> 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.

Thanks,
--nate

> 
> Of course, I'll make any of the enhancements available (and would be happy to 
> submit pull requests if there is interest).
> 
> -- 
> Lance Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
> 
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