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)

cat $TMPFILE >&2
=>
cat -v $TMPFILE >&2

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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