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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