Re: [galaxy-dev] New Galaxy won't start, SQLite (OperationalError) database is locked
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.nlmailto: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.nlmailto: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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Re: [galaxy-dev] New Galaxy won't start, SQLite (OperationalError) database is locked
Hi Peter, Thanks for reporting this. I am now facing the same error, but I don't get it For example: normally it appears when I try to change something in the DB (e.g. adding a new history), but then suddenly I managed to create one new history itemand now it is occurring again. It seems to be a transient locked state, so every now and then the lock is released somehow. Anyway, are there any ideas on what could be a real solution to this problem? This is the second Galaxy server I upgrade which now is stuck after the upgrade...any help is appreciated! Thanks and regards, Pieter. -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Peter Cock Sent: donderdag 31 oktober 2013 11:54 To: Galaxy Dev Subject: [galaxy-dev] New Galaxy won't start, SQLite (OperationalError) database is locked Hello all, While attempting a fresh Galaxy install from both galaxy-central and galaxy-dist, I ran into a problem initialising the default SQLite database (database/universe.sqlite), $ hg clone https://bitbucket.org/galaxy/galaxy-dist ... $ cd galaxy-dist $ ./run.sh ... galaxy.model.migrate.check DEBUG 2013-10-31 10:28:26,143 pysqlite=2 egg successfully loaded for sqlite dialect Traceback (most recent call last): ... OperationalError: (OperationalError) database is locked u'PRAGMA table_info(dataset)' () After some puzzlement, I realised this was down to the file system - I was trying this under my home directory mounted via a distributed file system (gluster I think). Repeating the experiment under /tmp on a local hard disk worked :) (I'm posting this message for future reference; hopefully Google and/or mailing list searches will help anyone else facing this error) Regards, Peter ___ 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/ ___ 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/
Re: [galaxy-dev] New Galaxy won't start, SQLite (OperationalError) database is locked
Hi Pieter, Using SQLite is NOT recommended for a production Galaxy, it is only really used for development and testing (having the whole database as one file on disk without worrying about creating a proper database, user accounts etc is nice). Peter On Wednesday, December 18, 2013, Lukasse, Pieter wrote: Hi Peter, Thanks for reporting this. I am now facing the same error, but I don't get it For example: normally it appears when I try to change something in the DB (e.g. adding a new history), but then suddenly I managed to create one new history itemand now it is occurring again. It seems to be a transient locked state, so every now and then the lock is released somehow. Anyway, are there any ideas on what could be a real solution to this problem? This is the second Galaxy server I upgrade which now is stuck after the upgrade...any help is appreciated! Thanks and regards, Pieter. -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu javascript:; [mailto: galaxy-dev-boun...@lists.bx.psu.edu javascript:;] On Behalf Of Peter Cock Sent: donderdag 31 oktober 2013 11:54 To: Galaxy Dev Subject: [galaxy-dev] New Galaxy won't start, SQLite (OperationalError) database is locked Hello all, While attempting a fresh Galaxy install from both galaxy-central and galaxy-dist, I ran into a problem initialising the default SQLite database (database/universe.sqlite), $ hg clone https://bitbucket.org/galaxy/galaxy-dist ... $ cd galaxy-dist $ ./run.sh ... galaxy.model.migrate.check DEBUG 2013-10-31 10:28:26,143 pysqlite=2 egg successfully loaded for sqlite dialect Traceback (most recent call last): ... OperationalError: (OperationalError) database is locked u'PRAGMA table_info(dataset)' () After some puzzlement, I realised this was down to the file system - I was trying this under my home directory mounted via a distributed file system (gluster I think). Repeating the experiment under /tmp on a local hard disk worked :) (I'm posting this message for future reference; hopefully Google and/or mailing list searches will help anyone else facing this error) Regards, Peter ___ 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/ ___ 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/
Re: [galaxy-dev] New Galaxy won't start, SQLite (OperationalError) database is locked
Hi Peter, I know that ;) Still I am curious about the possible solution. Any ideas? Regards, Pieter. From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: woensdag 18 december 2013 13:31 To: Lukasse, Pieter Cc: Galaxy Dev Subject: Re: New Galaxy won't start, SQLite (OperationalError) database is locked Hi Pieter, Using SQLite is NOT recommended for a production Galaxy, it is only really used for development and testing (having the whole database as one file on disk without worrying about creating a proper database, user accounts etc is nice). Peter On Wednesday, December 18, 2013, Lukasse, Pieter wrote: Hi Peter, Thanks for reporting this. I am now facing the same error, but I don't get it For example: normally it appears when I try to change something in the DB (e.g. adding a new history), but then suddenly I managed to create one new history itemand now it is occurring again. It seems to be a transient locked state, so every now and then the lock is released somehow. Anyway, are there any ideas on what could be a real solution to this problem? This is the second Galaxy server I upgrade which now is stuck after the upgrade...any help is appreciated! Thanks and regards, Pieter. -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edujavascript:; [mailto:galaxy-dev-boun...@lists.bx.psu.edujavascript:;] On Behalf Of Peter Cock Sent: donderdag 31 oktober 2013 11:54 To: Galaxy Dev Subject: [galaxy-dev] New Galaxy won't start, SQLite (OperationalError) database is locked Hello all, While attempting a fresh Galaxy install from both galaxy-central and galaxy-dist, I ran into a problem initialising the default SQLite database (database/universe.sqlite), $ hg clone https://bitbucket.org/galaxy/galaxy-dist ... $ cd galaxy-dist $ ./run.sh ... galaxy.model.migrate.check DEBUG 2013-10-31 10:28:26,143 pysqlite=2 egg successfully loaded for sqlite dialect Traceback (most recent call last): ... OperationalError: (OperationalError) database is locked u'PRAGMA table_info(dataset)' () After some puzzlement, I realised this was down to the file system - I was trying this under my home directory mounted via a distributed file system (gluster I think). Repeating the experiment under /tmp on a local hard disk worked :) (I'm posting this message for future reference; hopefully Google and/or mailing list searches will help anyone else facing this error) Regards, Peter ___ 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/ ___ 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/
Re: [galaxy-dev] 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 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 ___ 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/
