Galaxy dataset deletion

Data deletion

Managing library datasets is a bit complex, so here is a scenario that hopefully provides clarification. The complexities of handling library datasets is mostly contained in the delete_datasets() method in cleanup_datasets.py script.

Assume we have 1 library dataset with: LibraryDatasetDatasetAssociation -> LibraryDataset and Dataset. At this point, we have the following database column values:

   LibraryDatasetDatasetAssociation deleted: False
   LibraryDataset deleted: False, purged: False
   Dataset deleted: False purged: False

1. A user deletes the assumed dataset above from a data library via a UI menu option. This action results in the following database column values (changes from previous step marked with *):

   LibraryDatasetDatasetAssociation deleted: False
   LibraryDataset deleted: True*, purged: False
   Dataset deleted: False, purged: False
   

2. After the number of days configured for the delete_datasets() method (option -6 below) have passed, execution of the delete_datasets() method results in the following database column values (changes from previous step marked with *):

   LibraryDatasetDatasetAssociation deleted: True*
   LibraryDataset deleted: True, purged: True*
   Dataset deleted: True*, purged: False
   

3. After the number of days configured for the purge_datasets() method (option -3 below) have passed, execution of the purge_datasets() method results in the following database column values (changes from previous step marked with *):

   LibraryDatasetDatasetAssociation deleted: True
   LibraryDataset deleted: True, purged: True
   Dataset deleted: True, purged: True* (dataset file removed from disk if -r flag is used)

This scenario is about as simple as it gets.

Keep in mind that a Dataset object can have many HistoryDatasetAssociations and many LibraryDatasetDatasetAssociations, and a LibraryDataset can have many LibraryDatasetDatasetAssociations.

Another way of stating it is: LibraryDatasetDatasetAssociation objects map LibraryDataset objects to Dataset objects, and Dataset objects may be mapped to History objects via HistoryDatasetAssociation objects.

References

• The source code: cleanup_datasets.py.
• Galaxy mailing list.