Hi Peter, Galaxy starts, but any operation that involves changes in the database seems to fail.
One "solution" I found was to move to the default branch (hg update default) instead of the "stable" one...there the problem seems to be fixed somehow. However, then I get another error when trying to create a new history because the attribute "genome_build" in the payload is "null" and, according to the error, it should be a string. Details: source annotation deleted false genome_build null id cc4287507a7e4aae model_class History name test1235 nice_size 0 bytes published false purged false state new state_details discarded 0 empty 0 error 0 failed_metadata 0 new 0 ok 0 paused 0 queued 0 running 0 setting_metadata 0 upload 0 state_ids discarded empty error failed_metadata new ok paused queued running setting_metadata upload tags url /api/histories/cc4287507a7e4aae user username pieterlukasse quota_percent null total_disk_usage 36654268543 nice_total_disk_usage 34.1 GB email pieter.luka...@wur.nl<mailto:pieter.luka...@wur.nl> model_class User id f2db41e1fa331b3e diskSize 0 xhr readyState 4 responseText { "error": "genome_build must be a string: " } responseJSON error genome_build must be a string: status 400 statusText Bad Request responseHeaders Date Wed, 18 Dec 2013 13:43:26 GMT cache-control max-age=0,no-cache,no-store Server PasteWSGIServer/0.5 Python/2.7.5+ Connection close content-type application/json options validate true parse true emulateHTTP false emulateJSON false Disabling this specific validation in /home/lukas007/galaxy-dist/lib/galaxy/webapps/galaxy/api/histories.py (by disabling I mean just putting a dummy string value in "genome_build") will restore the "normal" Galaxy functionality and all seems to be working fine now...until I hit something that depends on this "genome_build" parameter of course... Is this a known issue? If not, hereby ;) Regards, Pieter. -----Original Message----- From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: woensdag 18 december 2013 17:36 To: Lukasse, Pieter Cc: Galaxy Dev Subject: Re: New Galaxy won't start, SQLite (OperationalError) database is locked On Wed, Dec 18, 2013 at 12:51 PM, Lukasse, Pieter <pieter.luka...@wur.nl<mailto:pieter.luka...@wur.nl>> wrote: > Hi Peter, > > I know that ;) Still I am curious about the possible solution. Any ideas? > > Regards, > > Pieter. Could you clarify the nature of the problem - is it failing to even start as in the situation I reported at the start of this thread, or an intermittent problem? Note that while generally stable I have had problems with my development machine with heavy SQLite DB access, e.g. a large multi-part job being split creating many child jobs in quick succession. Peter
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