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.c...@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-can-t-encode-character-td4669251.html
>
> 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/f14111d4927691e176342e044e3f91593cb1eb61
>
> DEFAULT_ENCODING = os.environ.get('GALAXY_DEFAULT_ENCODING', 'utf-8')
>
> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/util/__init__.py#L62
>
> 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 <dubju...@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
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