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.luka...@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.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: > 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.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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