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<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 database Thanks and regards, Pieter. From: galaxy-dev-boun...@lists.bx.psu.edu<mailto:galaxy-dev-boun...@lists.bx.psu.edu> [mailto: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<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. -Dannon
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