purge and delete data
From the interface my libraries are flagged purged as expected ... but on the disk I still have the files ! how can I remove these files from
Dear Galaxy developers, I just started to configure and use Galaxy, and I don't really understand how we can delete/purge data from the disk. I delete several dataset or libraries from the admin interface and then run the script/cleanup_datasets scripts as explained in https://bitbucket.org/galaxy/galaxy-central/wiki/Config/PurgeHistoriesAndDat... (with the -d0 option) the disk ? Another question, the purged libraries are still available through the advanced search - deleted, how can I completely remove these libraries from Galaxy ? Thanks for your help, Regards, Nicolas -- Nicolas Servant Equipe Bioinformatique Institut Curie 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE Email: Nicolas.Servant@curie.fr Tel: 01 56 24 69 85 http://bioinfo.curie.fr/
Hello Nicolas, On Mar 16, 2011, at 1:23 PM, Nicolas Servant wrote:
Dear Galaxy developers,
I just started to configure and use Galaxy, and I don't really understand how we can delete/purge data from the disk. I delete several dataset or libraries from the admin interface and then run the script/cleanup_datasets scripts as explained in https://bitbucket.org/galaxy/galaxy-central/wiki/Config/PurgeHistoriesAndDat... (with the -d0 option)
In order for a file to be removed from disk ( purged ), no undeleted items can point to it, where "items" refers to both data library items and any user's history items. A library item ( i.e., library dataset ) points to a disk file via a LibraryDatasetDatasetAssociation object, and a history item ( the boxes in a history ) points to the file via a HistoryDatasetAssociation. So in order for a file to be removed, all library dataset "items" that point to it must be deleted as well as all history items. Clicking the "X" in the history item will mark it as deleted.
From the interface my libraries are flagged purged as expected ... but on the disk I still have the files ! how can I remove these files from the disk ? Another question, the purged libraries are still available through the advanced search - deleted, how can I completely remove these libraries from Galaxy ?
These database records are never deleted from the database, just either marked as "deleted" or "purged". However, data libraries and data library items ( folders, library datasets )marked as "purged" are not displayed in the UI.
Thanks for your help, Regards,
Nicolas
-- Nicolas Servant Equipe Bioinformatique Institut Curie 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE
Email: Nicolas.Servant@curie.fr Tel: 01 56 24 69 85 http://bioinfo.curie.fr/
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Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
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