On Jan 31, 2012, at 11:25 AM, Kip Bodi wrote:

> Hi Nate,
> 
> For those of us who might be having some storage issues and need to purge 
> datasets, is there a field(s) we can manually update in the database to get 
> past this issue for the time being?  I'll definitely make some backups first…

Hi Kip,

Here are the necessary changes to fix this.  You can either pull up to this 
changeset from galaxy-central or just copy over the cleanup_datasets.py script:

https://bitbucket.org/galaxy/galaxy-central/changeset/115068e367b3

--nate

> 
> Cheers,
> 
> Kip
> 
> On Mon, Jan 30, 2012 at 12:50 PM, Nate Coraor <n...@bx.psu.edu> wrote:
> On Jan 25, 2012, at 10:37 AM, Leandro Hermida wrote:
> 
> > Hello,
> >
> > In the latest galaxy-dist version when running the system cleanup commands 
> > in the documented order I get an error when running the purge_datasets.sh 
> > script:
> >
> > sh delete_userless_histories.sh
> > sh purge_histories.sh
> > sh purge_libraries.sh
> > sh purge_folders.sh
> > sh delete_datasets.sh
> > sh purge_datasets.sh
> > Traceback (most recent call last):
> >  File "./scripts/cleanup_datasets/cleanup_datasets.py", line 518, in 
> > <module>
> >    if __name__ == "__main__": main()
> >  File "./scripts/cleanup_datasets/cleanup_datasets.py", line 116, in main
> >    purge_datasets( app, cutoff_time, options.remove_from_disk, info_only = 
> > options.info_only, force_retry = options.force_retry )
> >  File "./scripts/cleanup_datasets/cleanup_datasets.py", line 353, in 
> > purge_datasets
> >    _purge_dataset( app, dataset, remove_from_disk, info_only = info_only )
> >  File "./scripts/cleanup_datasets/cleanup_datasets.py", line 478, in 
> > _purge_dataset
> >    print "Error attempting to purge data file: ", dataset.file_name, " 
> > error: ", str( exc )
> >  File 
> > "/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/lib/galaxy/model/__init__.py",
> >  line 651, in get_file_name
> >    assert self.object_store is not None, "Object Store has not been 
> > initialized for dataset %s" % self.id
> > AssertionError: Object Store has not been initialized for dataset 58
> >
> > What could be going wrong?
> 
> Hi Leandro,
> 
> This is a bug that cropped up when we added the object store backend to 
> Galaxy.  I'm working on a fix which should be available in the next release 
> of Galaxy.  Sorry for the inconvenience.
> 
> Thanks,
> --nate
> 
> >
> > regards,
> > Leandro
> > ___________________________________________________________
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> 
> 
> ___________________________________________________________
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> 
> 
> -- 
> Kip Lord Bodi
> Tufts University School of Medicine
> 136 Harrison Avenue, South Cove 803
> Boston, MA 02118
> 617-636-3763
> kip.b...@tufts.edu
> www.tucf.org | genomics.med.tufts.edu


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