UTF8 problem with database "An error occured when getting updates from the server"
Dear all, I have just changed my galaxy database encoding in utf8 to avoid error of loading histories. It works fine. But when I run a new job after this change, the bad characters re-appear in my output and the error "An error occured when getting updates from the server" re-appear too. When I've changed my galaxy database envoding, I've modified the /etc/mysql/my.cnf file and replace all of the bad charcater in the previous database before re-install it. Any idea of a change I omit ? Thanks. Julie
Hi Julie, We ran into some encoding issues last month when working on a new Galaxy server with MySQL, and decided to switch to PostgreSQL instead - and so far that has been fine: http://dev.list.galaxyproject.org/MySQL-amp-ToolShed-installs-latin-1-codec-... The closest match I could find in the mailing list archive was from December 2013 when actually running tools: http://dev.list.galaxyproject.org/error-with-unicode-output-td4662783.html In that thread John Chilton talked about changing the default encoding, and later make this easier to do by adding the environment variable $GALAXY_DEFAULT_ENCODING with a default for UTF8: https://github.com/galaxyproject/galaxy/commit/f14111d4927691e176342e044e3f9... DEFAULT_ENCODING = os.environ.get('GALAXY_DEFAULT_ENCODING', 'utf-8') https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/util/__init__.py... John can perhaps give more information on what to try, and if your MySQL database should have an encoding set? We took the pragmatic route and went for PostgreSQL as this is more tested than MySQL (e.g. http://usegalaxy.org). Peter On Mon, May 9, 2016 at 2:39 PM, julie dubois <dubjulie@gmail.com> wrote:
Dear all, I have just changed my galaxy database encoding in utf8 to avoid error of loading histories. It works fine. But when I run a new job after this change, the bad characters re-appear in my output and the error "An error occured when getting updates from the server" re-appear too.
When I've changed my galaxy database envoding, I've modified the /etc/mysql/my.cnf file and replace all of the bad charcater in the previous database before re-install it.
Any idea of a change I omit ?
Thanks.
Julie ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Dear Peter, Thanks for your answer. In my case, all of modifications, you've pointed in your answer, are already present in my galaxy instance. And as I said, I've modify the encoding default parameter in /etc/my.cnf for MySQL and I've changed all bad character in my galaxy database. It worked, but with a new run of job which have generated special character, galaxy bugs while the special characters are well encoded in the new galaxy database (e.g no bad character mis-encoded). So I don't understand why the content of the concerned history disappears and this message appears again : "An error occured when getting updates from the server". I'll test the adding of "?charset=utf8" in my connection string in universe.ini as soon as I can restart Galaxy. Thanks. Julie 2016-05-09 16:33 GMT+02:00 Peter Cock <p.j.a.cock@googlemail.com>:
Hi Julie,
We ran into some encoding issues last month when working on a new Galaxy server with MySQL, and decided to switch to PostgreSQL instead - and so far that has been fine:
http://dev.list.galaxyproject.org/MySQL-amp-ToolShed-installs-latin-1-codec-...
The closest match I could find in the mailing list archive was from December 2013 when actually running tools:
http://dev.list.galaxyproject.org/error-with-unicode-output-td4662783.html
In that thread John Chilton talked about changing the default encoding, and later make this easier to do by adding the environment variable $GALAXY_DEFAULT_ENCODING with a default for UTF8:
https://github.com/galaxyproject/galaxy/commit/f14111d4927691e176342e044e3f9...
DEFAULT_ENCODING = os.environ.get('GALAXY_DEFAULT_ENCODING', 'utf-8')
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/util/__init__.py...
John can perhaps give more information on what to try, and if your MySQL database should have an encoding set?
We took the pragmatic route and went for PostgreSQL as this is more tested than MySQL (e.g. http://usegalaxy.org).
Peter
On Mon, May 9, 2016 at 2:39 PM, julie dubois <dubjulie@gmail.com> wrote:
Dear all, I have just changed my galaxy database encoding in utf8 to avoid error of loading histories. It works fine. But when I run a new job after this change, the bad characters re-appear in my output and the error "An error occured when getting updates from the server" re-appear too.
When I've changed my galaxy database envoding, I've modified the /etc/mysql/my.cnf file and replace all of the bad charcater in the previous database before re-install it.
Any idea of a change I omit ?
Thanks.
Julie ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (2)
-
julie dubois -
Peter Cock