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.lukasse@wur.nl<mailto:pieter.lukasse@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.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<mailto: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