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 >
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/