Hi Nate,
For those of us who might be having some storage issues and need to purge datasets, is there a field(s) we can manually update in the database to get past this issue for the time being? I'll definitely make some backups first...
Cheers,
Kip
On Mon, Jan 30, 2012 at 12:50 PM, Nate Coraor nate@bx.psu.edu wrote:
On Jan 25, 2012, at 10:37 AM, Leandro Hermida wrote:
Hello,
In the latest galaxy-dist version when running the system cleanup
commands in the documented order I get an error when running the purge_datasets.sh script:
sh delete_userless_histories.sh sh purge_histories.sh sh purge_libraries.sh sh purge_folders.sh sh delete_datasets.sh sh purge_datasets.sh Traceback (most recent call last): File "./scripts/cleanup_datasets/cleanup_datasets.py", line 518, in
<module> > if __name__ == "__main__": main() > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 116, in main > purge_datasets( 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 353, in purge_datasets > _purge_dataset( app, dataset, remove_from_disk, info_only = info_only ) > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 478, in _purge_dataset > print "Error attempting to purge data file: ", dataset.file_name, " error: ", str( exc ) > File "/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/lib/galaxy/model/__init__.py", line 651, in get_file_name > assert self.object_store is not None, "Object Store has not been initialized for dataset %s" % self.id > AssertionError: Object Store has not been initialized for dataset 58 > > What could be going wrong?
Hi Leandro,
This is a bug that cropped up when we added the object store backend to Galaxy. I'm working on a fix which should be available in the next release of Galaxy. Sorry for the inconvenience.
Thanks, --nate
regards, Leandro ___________________________________________________________ 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:
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On Jan 31, 2012, at 11:25 AM, Kip Bodi wrote:
Hi Nate,
For those of us who might be having some storage issues and need to purge datasets, is there a field(s) we can manually update in the database to get past this issue for the time being? I'll definitely make some backups first…
Hi Kip,
Here are the necessary changes to fix this. You can either pull up to this changeset from galaxy-central or just copy over the cleanup_datasets.py script:
https://bitbucket.org/galaxy/galaxy-central/changeset/115068e367b3
--nate
Cheers,
Kip
On Mon, Jan 30, 2012 at 12:50 PM, Nate Coraor nate@bx.psu.edu wrote: On Jan 25, 2012, at 10:37 AM, Leandro Hermida wrote:
Hello,
In the latest galaxy-dist version when running the system cleanup commands in the documented order I get an error when running the purge_datasets.sh script:
sh delete_userless_histories.sh sh purge_histories.sh sh purge_libraries.sh sh purge_folders.sh sh delete_datasets.sh sh purge_datasets.sh Traceback (most recent call last): File "./scripts/cleanup_datasets/cleanup_datasets.py", line 518, in <module> if __name__ == "__main__": main() File "./scripts/cleanup_datasets/cleanup_datasets.py", line 116, in main purge_datasets( 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 353, in purge_datasets _purge_dataset( app, dataset, remove_from_disk, info_only = info_only ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 478, in _purge_dataset print "Error attempting to purge data file: ", dataset.file_name, " error: ", str( exc ) File "/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/lib/galaxy/model/__init__.py", line 651, in get_file_name assert self.object_store is not None, "Object Store has not been initialized for dataset %s" % self.id AssertionError: Object Store has not been initialized for dataset 58
What could be going wrong?
Hi Leandro,
This is a bug that cropped up when we added the object store backend to Galaxy. I'm working on a fix which should be available in the next release of Galaxy. Sorry for the inconvenience.
Thanks, --nate
regards, Leandro ___________________________________________________________ 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:
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:
-- Kip Lord Bodi Tufts University School of Medicine 136 Harrison Avenue, South Cove 803 Boston, MA 02118 617-636-3763 kip.bodi@tufts.edu www.tucf.org | genomics.med.tufts.edu
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