Lance,

Do you use the administrative deletion script you wrote? That would
probably cause d.deleted and not hda.purged.

d.deleted isn't for queries, it's sort of a deletion buffer. After all hda
w/ hda.dataset_id = d.id are hda.purged, the next cleanup step is to mark
d.deleted. Then after d.deleted, it's marked d.purged and the file(s) are
actually removed from disk. It's a bit of a failsafe so that datasets can
be intercepted if unintentionally deleted.

--nate

On Fri, Dec 2, 2016 at 12:39 PM, Lance Parsons <lpars...@princeton.edu>
wrote:

> Thanks Nate, that makes sense. However it seems I still have an issue:
>
> ```
> select count(d.id)
>     from dataset d
>     join history_dataset_association hda on d.id = hda.dataset_id
>     where d.deleted = 't' and hda.purged = 'f';
>  count
> -------
>  67464
> (1 row)
> ```
>
> Perhaps I'll need to write some script to check each of these to see if
> the data does, indeed, exist, and then set the flag appropriately... Hrmm.
>
> Does anyone know what the `dataset.deleted` flag is used for? Is that just
> supposed to be set when all `hda.purged` are `t`. Sort of like a shortcut
> for queries?
>
> - Lance
>
> Nate Coraor <n...@bx.psu.edu>
> December 2, 2016 at 11:15 AM
> Lance,
>
> usegalaxy.org has 4,652,912 such datasets. The cause here is that
> deleting an entire history does not mark the HDAs deleted (so that if you
> view a deleted history you can see what datasets were deleted and which
> were not at the time of deletion). There is a separate hda.purged column
> that indicates that an HDA is no longer user-recoverable by the user. I
> have 699 datasets that are d.deleted but not hda.purged, this number should
> be 0.
>
> --nate
>
>
> Lance Parsons <lpars...@princeton.edu>
> November 30, 2016 at 2:20 PM
> I've run into issues over the past year where some jobs would occasionally
> fail to start (stuck in a `new` state). I tracked them down to a situataion
> where `dataset.deleted` is set to `t` yet the 
> `history_dataset_association.deleted`
> is `f`. Simply setting `dataset.deleted` to `f` in those instances resolved
> the issue and the jobs ran. The datasets have all still been on disk.
>
> Since this is a pretty annoying situation, I thought I'd check to see if
> there are other datasets with this problem. Shockingly, I found many
> thousands of such datasets:
>
> ```
> select count(d.id)
>     from dataset d
>     join history_dataset_association hda on d.id = hda.dataset_id
>     where d.deleted = 't' and hda.deleted = 'f';
>  count
> -------
>  76977
> (1 row)
> ```
>
> I'm hesitant to update so many rows in my database so I thought I'd put
> this out there for comment. What do others see when running the above
> query? Has anyone run into this or a similar issue? Thanks.
>
>
> --
> Lance Parsons - Scientific Programmer
> Carl C. Icahn Laboratory - Room 136
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
>
>
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