On Nov 8, 2012, at 8:55 PM, Liisa Koski wrote:
> Hi Nate,
> I'm back to trying to figure this out again as I am running out of disk
> space. I added the bit of code you suggested below, but I don't think it
> helped, I'm not so familiar with python.
>
> I'm now running Galaxy Reports and it tells me that I have 7479 datasets that
> were deleted but have not yet been purged.
>
> I get the error below when I run cleanup_datasets.py with both the -5 and -4
> flag
>
> Marking as deleted: LibraryDatasetDatasetAssociation id 6907 (for dataset id
> 51991)
> Deleting dataset id 51991
> Deleting library dataset id 7225
> Traceback (most recent call last):
> File "scripts/cleanup_datasets/cleanup_datasets.py", line 526, in <module>
> if __name__ == "__main__": main()
> File "scripts/cleanup_datasets/cleanup_datasets.py", line 124, in main
> purge_folders( 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 247, in
> purge_folders
> _purge_folder( folder, app, remove_from_disk, info_only = info_only )
> File "scripts/cleanup_datasets/cleanup_datasets.py", line 499, in
> _purge_folder
> _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only )
> File "scripts/cleanup_datasets/cleanup_datasets.py", line 499, in
> _purge_folder
> _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only )
> File "scripts/cleanup_datasets/cleanup_datasets.py", line 497, in
> _purge_folder
> _purge_dataset_instance( ldda, app, remove_from_disk, info_only =
> info_only ) #mark a DatasetInstance as deleted, clear associated files, and
> mark the Dataset as deleted if it is deletable
> File "scripts/cleanup_datasets/cleanup_datasets.py", line 373, in
> _purge_dataset_instance
> log.debug( '%s %s has None dataset' % ( type( dataset_instance ),
> dataset_instance.id ) )
> AttributeError: 'NoneType' object has no attribute 'id'
Ah, I was looking at the wrong level. You have a library_dataset without an
associated library_dataset_dataset_association. The following SQL should
return it and any others:
select id from library_dataset where library_dataset_dataset_association_id
is null
Although the output indicates that the offending library_dataset id should be
7225. The easiest way to solve this problem is probably to orphan the broken
library dataset, e.g.:
update library_dataset set folder_id = null where id=7225;
--nate
>
> Thanks in advance for your help,
> Liisa
>
>
>
>
>
> From: Nate Coraor <n...@bx.psu.edu>
> To: Liisa Koski <liisa.ko...@basf.com>
> Cc: galaxy-dev@lists.bx.psu.edu
> Date: 02/10/2012 10:50 AM
> Subject: Re: [galaxy-dev] Error when running cleanup_datasets.py
>
>
>
> On Oct 2, 2012, at 10:44 AM, Liisa Koski wrote:
>
> > Hi Nate,
> > That select statement does not return anything :(
>
> Could you add a bit of debugging to the script to see what the id is of the
> dataset_instance that has a None dataset?
>
> if dataset_instance is None:
> log.debug( '%s %s has None dataset' % ( type( dataset_instance ),
> dataset_instance.id ) )
>
> Thanks,
> --nate
>
> >
> > Thanks,
> > Liisa
> >
> >
> >
> >
> >
> > From: Nate Coraor <n...@bx.psu.edu>
> > To: Liisa Koski <liisa.ko...@basf.com>
> > Cc: galaxy-dev@lists.bx.psu.edu
> > Date: 01/10/2012 01:01 PM
> > Subject: Re: [galaxy-dev] Error when running cleanup_datasets.py
> >
> >
> >
> > On Sep 24, 2012, at 10:41 AM, Liisa Koski wrote:
> >
> > > Hello,
> > > I am trying to run the cleanup scripts on my local installation but get
> > > stuck when trying to run the following:
> > >
> > > ./scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 10 -5
> > > -r
> > >
> > > Deleting library dataset id 7225
> > > Traceback (most recent call last):
> > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 524, in
> > > <module>
> > > if __name__ == "__main__": main()
> > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 124, in
> > > main
> > > purge_folders( 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 247, in
> > > purge_folders
> > > _purge_folder( folder, app, remove_from_disk, info_only = info_only )
> > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 497, in
> > > _purge_folder
> > > _purge_folder( sub_folder, app, remove_from_disk, info_only =
> > > info_only )
> > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 497, in
> > > _purge_folder
> > > _purge_folder( sub_folder, app, remove_from_disk, info_only =
> > > info_only )
> > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 495, in
> > > _purge_folder
> > > _purge_dataset_instance( ldda, app, remove_from_disk, info_only =
> > > info_only ) #mark a DatasetInstance as deleted, clear associated files,
> > > and mark the Dataset as deleted if it is deletable
> > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 376, in
> > > _purge_dataset_instance
> > > ( dataset_instance.__class__.__name__, dataset_instance.id,
> > > dataset_instance.dataset.id )
> > > AttributeError: 'NoneType' object has no attribute 'id'
> >
> > Hi Liisa,
> >
> > It'd appear that you have a library_dataset_dataset_association in your
> > dataset that lacks an associated dataset. Does 'select id from
> > library_dataset_dataset_association where dataset_id is null' in your
> > database return anything?
> >
> > --nate
> >
> > >
> > >
> > > Any help would be much appreciated.
> > >
> > > Thanks,
> > > Liisa
> > > ___________________________________________________________
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> >
> >
>
>
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