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

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

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.lukasse@wur.nl

model_class	User
id	f2db41e1fa331b3e

diskSize

xhr

readyState

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.cock@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.lukasse@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