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 make it all UTF-8 that would probably be ideal.
-John
On Thu, Dec 5, 2013 at 12:01 PM, David Hoover hooverdm@helix.nih.gov wrote:
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 CHARSET=utf-8, or do I need to reconfigure MySQL to have a new default?
-- David
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/e786022dc67ed918050bd81b... 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 create a database_encoding_default option in universe_wsgi.ini and let you switch it to latin-1 instead of needing to patch Galaxy. Otherwise, setting the MySQL tables to be UTF-8 is probably the better approach - though again - backup and test before applying that change in production.
Hope this helps, -John
On Thu, Dec 5, 2013 at 11:17 AM, John Chilton chilton@msi.umn.edu wrote:
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-tt4.... I will try to look into this.
Christian - what database are targeting? Is it MySQL as well?
David - do you have a test setup you can hack on? I wonder if this would go away if you converted your tables to UTF-8.
http://stackoverflow.com/questions/6115612/how-to-convert-an-entire-mysql-da...
That is not my official recommendation though - I need to do some more research first.
-John
On Thu, Dec 5, 2013 at 11:04 AM, Christian Hundsrucker christian.hundsrucker@fmi.ch wrote:
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 ) [...]
galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py", line 485, in _emit_update_statements [...]
UnicodeEncodeError: 'latin-1' codec can't encode character u'\u2018' in position 134: ordinal not in range(256)
I am integrating a set of R/Bioconductor modules into our local Galaxy instance. To do so, I use the discard_stderr_wrapper.sh. It worked fine until the recent update* As the error appears upon any R-output (via print, cat or error channel), I just set the option "-v" for the cat command in the discard_stderr_wrapper.sh:
cat $TMPFILE >&2 => cat -v $TMPFILE >&2
as a temporary workaround. No idea if this is applicable in your case?!
Cheers, Christian
changeset: 11219:5c789ab4144a branch: stable tag: tip
On 05.12.2013 17:29, David Hoover wrote:
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 reported:
Traceback (most recent call last): File "/spin1/users/galaxy/galaxy/lib/galaxy/jobs/runners/local.py", line 116, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/spin1/users/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 1015, in finish self.sa_session.flush() File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/scoping.py", line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 1718, in flush self._flush(objects) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 1789, in _flush flush_context.execute() File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 331, in execute rec.execute(self) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 475, in execute uow File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 59, in save_obj mapper, table, update) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 485, in _emit_update_statements execute(statement, params) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1449, in execute params) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1584, in _execute_clauseelement compiled_sql, distilled_params File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1691, in _execute_context context) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line 331, in do_execute cursor.execute(statement, parameters) File "build/bdist.linux-x86_64/egg/MySQLdb/cursors.py", line 158, in execute query = query % db.literal(args) File "build/bdist.linux-x86_64/egg/MySQLdb/connections.py", line 265, in literal return self.escape(o, self.encoders) File "build/bdist.linux-x86_64/egg/MySQLdb/connections.py", line 203, in unicode_literal return db.literal(u.encode(unicode_literal.charset)) UnicodeEncodeError: 'latin-1' codec can't encode character u'\ufffd' in position 11: ordinal not in range(256)
There is a set of files created in the job_working_directory that start with 'metadata_', some of which contain the unicode.
Is there anything I can do to fix this?
David Hoover Helix Systems Staff
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