UTF8 problem with database "An error occured when getting updates from the server"

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UTF8 problem with database "An error occured when getting updates from the server"

juliech
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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Re: UTF8 problem with database "An error occured when getting updates from the server"

Peter Cock
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 <[hidden email]> 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/
___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: UTF8 problem with database "An error occured when getting updates from the server"

juliech
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 <[hidden email]>:

> 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 <[hidden email]> 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/
___________________________________________________________
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/