Hey Pieter, sure.  The sqlite database is in sqlite3 format, so you'll need
to use 'sqlite3 database/universe.sqlite' to access it.

The following should work:

sqlite3 database/universe.sqlite '.dump migrate_tmp' > temporary_backup.sql
sqlite3 database/universe.sqlite 'drop table migrate_tmp;'

And, once that's done, verify that everything works as expected and that
whatever table is in temporary_backup.sql actually did get migrated.

-Dannon


On Tue, Apr 22, 2014 at 8:41 AM, Lukasse, Pieter <pieter.luka...@wur.nl>wrote:

>  Hi Dannon,
>
>
>
> I’m facing the same problem now. Could you help me with the steps to
> delete the migrate_tmp table manually? I’m trying to use sqlite from
> command line but get the following error:
>
>
>
> Unable to open database "universe.sqlite": file is encrypted or is not a
> database
>
>
>
> Thanks and regards,
>
>
>
> Pieter.
>
>
>
> *From:* galaxy-dev-boun...@lists.bx.psu.edu [mailto:
> galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Dannon Baker
> *Sent:* dinsdag 18 februari 2014 14:40
> *To:* Peter Cock
> *Cc:* Galaxy Dev
> *Subject:* Re: [galaxy-dev] (OperationalError) no such column:
> history_dataset_association.extended_metadata_id
>
>
>
> On Tue, Feb 18, 2014 at 8:30 AM, Peter Cock <p.j.a.c...@googlemail.com>
> wrote:
>
> This fixed the history_dataset_association.extended_metadata_id
> error - so is the most likely explanation a failed schema update?
> Might a stale migration_tmp table have been to blame?
>
>
>
> Yes, I've seen this before when I've killed (or otherwise crashed) a
> migration in process; migrate_tmp doesn't get automatically cleaned up --
> and, to allow for recovery, probably shouldn't.    Any idea what may have
> caused it in your case?For a development database I've most commonly just
> deleted the migrate_tmp table manually and rerun the migration.  It's worth
> noting that *only* sqlite can have this problem, due to the way migrations
> work.
>
>
>
> -Dannon
>
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