Error when running cleanup_datasets.py
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' Any help would be much appreciated. Thanks, Liisa
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" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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
Hi Nate, That select statement does not return anything :( 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: main
purge_folders( app, cutoff_time, options.remove_from_disk, info_only
File "./scripts/cleanup_datasets/cleanup_datasets.py", line 247, in
= options.info_only, force_retry = options.force_retry ) 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" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (2)
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Liisa Koski -
Nate Coraor