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'

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 
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
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> >  http://lists.bx.psu.edu/
> 
> 


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