I tried different combinations ...
The
DEFAULT_ENCODING = 'latin-1'
in
lib/galaxy/util/__init__.py
is what worked!
some background information:
Yes, we also use a MySQL database.
All encodings (server, R/Bioconductor, used editors, ... ) are UTF-8.
The changeset
Adding ?charset=utf8 to the connection string worked!
However, there is one really weird side effect that probably has nothing to do
with utf8. The tool creates two pdf files and one zip file as output. For the
two pdf files, the expansion of the dataset in the history bar shows 'Image in
Okay all, Christian followed up off list and mentioned that his
columns had not been UTF-8 encoded.
So I think the best thing to do is use Postgres, but if you have to
use MySQL make sure columns are UTF-8 encoded with the newest Galaxy
and add ?charset=utf8 to your database connection string. I
I have installed the ngsplot galaxy tool from http://code.google.com/p/ngsplot.
This tool creates a set of three pdf files. In older versions of Galaxy, the
tool ran correctly with no problems. A recent update broke the tool. The job
runs but is unable to finish. Here is the error
Hi David, hi all!
I have a similar/the same issue in another setting...
galaxy/galaxy_dist/lib/galaxy/jobs/runners/local.py, line 116, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
[...]
David, Christian,
Very sorry about this - this is probably related to fixing some other
errors -
http://dev.list.galaxyproject.org/Unicode-in-tool-stderr-crashing-galaxy-tt4661749.html#a4661750.
I will try to look into this.
Christian - what database are targeting? Is it MySQL as well?
David -
Actually, can you verify that this commit
https://bitbucket.org/galaxy/galaxy-central/commits/e786022dc67ed918050bd81b9ac679ac958e4f75
is in your distribution and if it is try changing:
DEFAULT_ENCODING = 'utf-8'
in lib/galaxy/util.py to
DEFAULT_ENCODING = 'latin-1'
If that works then - I can
My version is 11216:c458a0fe1ba8. Does this cover the commit?
On Dec 5, 2013, at 12:32 PM, John Chilton wrote:
Actually, can you verify that this commit
https://bitbucket.org/galaxy/galaxy-central/commits/e786022dc67ed918050bd81b9ac679ac958e4f75
is in your distribution and if it is try
Looks to yes...
% hg contains -c c458a0fe1ba8 e786022dc67ed918050bd81b9ac679ac958e4f75
lookup for revision 'e786022dc67ed918050bd81b9ac679ac958e4f75' yields
changeset 10953:e786022dc67e
true
You could also verify lib/galaxy/jobs/__init__.py contains the import
from galaxy.util import unicodify.
Right, nevermind, 'hg log' listed that changeset 10953:e786022dc67e.
Changing DEFAULT_ENCODING to 'latin-1' in lib/galaxy/util/__init__.py worked.
Do I need to alter ALL the MySQL tables to UTF-8, or just a selection of
tables? Will future updates explicitly create new tables with
Fantastic!
For this particular problem - I guess you don't strictly need to
modify more than just job and maybe task tables. I suspect at some
point there will be a non-latin-1 job parameter or history name or
username, etc... that will result in a similar problem though - so if
you could just
John,
I stopped galaxy, then ran ALTER DATABASE galaxydb DEFAULT CHARACTER SET =
'utf8', then ran ALTER TABLE `[table]` DEFAULT CHARACTER SET = 'utf8' on all
the tables in galaxydb. After starting up galaxy and rerunning the jobs (using
the unaltered version of lib/galaxy/util/__init__.py),
Hmmm... can you try adding ?charset=utf8 to your database connection
string - that may fix the problem?
If not - is there a way to tell if the actual columns have changed.
Some comments on stackoverflow make it sound like the commands you
listed will only affect new columns.
Can you try the
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