That did it! Thanks Nate!



From:   Nate Coraor <n...@bx.psu.edu>
To:     Liisa Koski <liisa.ko...@basf.com>
Cc:     galaxy-dev@lists.bx.psu.edu
Date:   12/11/2012 12:13 PM
Subject:        Re: [galaxy-dev] Error when running cleanup_datasets.py



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


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