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 <nate@bx.psu.edu>
To:
Liisa Koski <liisa.koski@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 <nate@bx.psu.edu>
> To: Liisa Koski <liisa.koski@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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>