I believe I may have found the bug...

Line 258 of cleanup_datasets.py is the query for library_dataset_ids when "force_retry" is set. While it correctly eliminates the the app.model.LibraryDataset.table.c.purged == False from the where clause, it incorrectly eliminates the app.model.LibraryDataset.table.c.deleted == True.


My suggested fix would be to correct that query by adding app.model.LibraryDataset.table.c.deleted == True to the where clause.

Cleaning up users databases might be a bit trickier, but I think you could find the affected library datasets by the following query:

select * from library_dataset where deleted=f and purged=t;

With those, I would think setting purged to f and then setting deleted = f for the associated library_dataset_dataset_association records.

Lance

Nate Coraor wrote:
Lance Parsons wrote:
Good catch, that does indeed seem to be the issue.  And it only
seems to happen with my older data libraries.

I didn't see a bug report for this, but I'd be happy to file one
and/or take a stab at a fix if someone can point me in the right
direction in the code.

Any community offers to debug/fix are always happily welcomed. =)

My reply to Alex:

See line 1925 in lib/galaxy/web/controllers/library_common.py.  Try
adding a bit of debugging to find out if hda.deleted == True when the
copied HistoryDatasetAssociation is created, and whether the source
LibraryDatasetDatasetAssociation is itself deleted (which should be the
only way the resulting hda could be deleted).

I'll add that a key to figuring this out is probably is determining
what's different about these older library items and the newer ones that
don't exhibit the problem (if this is also true in your environment as
it is in his).

If no answers turn up in a few days, then we can open an issue for it in
Bitbucket.

--nate

Lance

Nate Coraor wrote:
Lance Parsons wrote:
I'm running a local instance of Galaxy that has been working quite
well.  However, I've recently run into a problem when importing
datasets from a data library into a history.  The Size on Disk of
the history grows by the size of the imported dataset, however, the
new dataset is not visible (and the number of datasets does not
change in the saved histories view).

Any thoughts on what might be going on here?  Thanks.
Hey Lance,

No real ideas, but Alex Bossers just posted up saying that old library
datasets are importing into his histories as deleted.  Could you check
and see if this is the case in your instance as well?

Thanks,
--nate

--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University


--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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