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 item....and 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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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/

Hi Peter,

I know that ;) Still I am curious about the possible solution. Any ideas?

Regards,

Pieter.

From: Peter Cock [mailto:p.j.a.cock@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 item....and 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-bounces@lists.bx.psu.edujavascript:; [mailto:galaxy-dev-bounces@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/

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.nlmailto: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.nlmailto: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