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/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 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 <chil...@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-tt4661749.html#a4661750. >> 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-database-characterset-and-collation-to-utf-8 >> >> 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.hundsruc...@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 >>> >>> >>> >>> ___________________________________________________________ >>> 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: >>> http://lists.bx.psu.edu/ >>> >>> 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: >>> http://lists.bx.psu.edu/ >>> >>> 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: > http://lists.bx.psu.edu/ > > 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
