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...

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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-- 
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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