Ok, great, glad that worked for you.  And, thanks for the heads up on the actual table name :)

-Dannon


On Tue, Apr 22, 2014 at 9:14 AM, Lukasse, Pieter <pieter.lukasse@wur.nl> wrote:

Hi Dannon,

 

Thanks, this helped.

 

Just for the record: I did find a small typo in my mail and in your script : should be migration_tmp instead of migrate_tmp    ;)

 

Best regards,

 

Pieter.

 

From: Dannon Baker [mailto:dannon.baker@gmail.com]
Sent: dinsdag 22 april 2014 14:59
To: Lukasse, Pieter
Cc: Peter Cock; Galaxy Dev


Subject: Re: [galaxy-dev] (OperationalError) no such column: history_dataset_association.extended_metadata_id

 

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.lukasse@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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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.cock@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