Hi;

I'm getting an error when comparing two datasets (two tabular files) with "Join, substract and group" (Error pasted bellow). If I execute joinWrapper.py manually I don't get the error, and also it doesn't happen if I use the Galaxy version changeset 5743:720455407d1c. Any clues? Any help would be much appreciated, I need this for a paper I'm writting and deadline is too close :-)


Regards

Traceback (most recent call last):
File "/home/megana/galaxy-dist-Erick/lib/galaxy/jobs/runners/local.py", line 125, in run_job
    job_wrapper.finish( stdout, stderr )
File "/home/megana/galaxy-dist-Erick/lib/galaxy/jobs/__init__.py", line 607, in finish
    self.sa_session.flush()
File "/home/megana/galaxy-dist-Erick/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py", line 127, in do
    return getattr(self.registry(), name)(*args, **kwargs)
File "/home/megana/galaxy-dist-Erick/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1356, in flush
    self._flush(objects)
File "/home/megana/galaxy-dist-Erick/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1434, in _flush
    flush_context.execute()
File "/home/megana/galaxy-dist-Erick/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 261, in execute
    UOWExecutor().execute(self, tasks)
File "/home/megana/galaxy-dist-Erick/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 753, in execute
    self.execute_save_steps(trans, task)
File "/home/megana/galaxy-dist-Erick/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 773, in execute_save_steps
    self.execute_cyclical_dependencies(trans, task, False)
File "/home/megana/galaxy-dist-Erick/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 789, in execute_cyclical_dependencies
    self.execute(trans, [t], isdelete)
File "/home/megana/galaxy-dist-Erick/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 753, in execute
    self.execute_save_steps(trans, task)
File "/home/megana/galaxy-dist-Erick/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 768, in execute_save_steps
    self.save_objects(trans, task)
File "/home/megana/galaxy-dist-Erick/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 759, in save_objects
    task.mapper._save_obj(task.polymorphic_tosave_objects, trans)
File "/home/megana/galaxy-dist-Erick/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1413, in _save_obj
    c = connection.execute(statement.values(value_params), params)
File "/home/megana/galaxy-dist-Erick/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute
    return Connection.executors[c](self, object, multiparams, params)
File "/home/megana/galaxy-dist-Erick/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement
    return self.__execute_context(context)
File "/home/megana/galaxy-dist-Erick/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File "/home/megana/galaxy-dist-Erick/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute
    self._handle_dbapi_exception(e, statement, parameters, cursor, context)
File "/home/megana/galaxy-dist-Erick/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 931, in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) ProgrammingError: (ProgrammingError) You must not use 8-bit bytestrings unless you use a text_factory that can interpret 8-bit bytestrings (like text_factory = str). It is highly recommended that you instead just switch your application to Unicode strings. u'UPDATE history_dataset_association SET update_time=?, info=?, blurb=?, peek=? WHERE history_dataset_association.id = ?' ['2012-03-22 16:23:45.441156', 'join (GNU coreutils) 7.4\nCopyright \xc2\xa9 2009 Free Software Foundation, Inc.\nLicencia GPLv3+: GNU GPL versi\xc3\xb3n 3 o superior .\nEsto es software libre: es libre de cambiarlo y redistribuirlo.\nNO HAY NINGUNA GARANT\xc3\x8dA, en la me', 'empty', 'no peek', 330]


--
Mikel Egaña Aranguren, PhD
http://mikeleganaaranguren.com

Marie Curie post-doc at Ontology Engineering Group, UPM
http://www.oeg-upm.net/

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