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,


From: Dannon Baker [mailto:dannon.ba...@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: 

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.


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

Thanks and regards,


 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: 

On Tue, Feb 18, 2014 at 8:30 AM, Peter Cock 
<p.j.a.c...@googlemail.com<mailto: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.


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