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 CONVERT TO CHARACTER SET. ALTER TABLE tbl_name CONVERT TO CHARACTER SET utf8 COLLATE utf8_general_ci; I don't think the problem is sqlalchemy right - this works for postgres and sqlite I believe - it is either that MySQL cannot store UTF-8 data in that column or there is a problem in the mysql connector. It is not clear to me where the problem is based on your stack trace and explanation. I would be happy to work around a limitation in the mysql connector by adding a config option to Galaxy if I were certain that there was a bug in the mysql connector. -John On Thu, Dec 5, 2013 at 12:55 PM, David Hoover <hoove...@helix.nih.gov> wrote: > 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), the job failed > with the same error. > > Can I configure the sqlalchemy connection to use utf8? Or must I reconfigure > the entire server to use utf8? > > --David > > On Dec 5, 2013, at 1:32 PM, John Chilton wrote: > >> 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 <hoove...@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/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/
