Hi,
I am new to Galaxy and have not found a solution on dev-list to this 8-bit
bytestrings error.
That occurs on my local installation but not on Galaxy main server.
Cheers
Dataset generation errors
*Dataset 22: Neighbor Joining Tree on data 20*
The Galaxy framework encountered the following error while attempting to
run the tool: Traceback (most recent call last): File
"/data/APPLIS/GALAXY/galaxy-dist/lib/galaxy/jobs/runners/local.py", line
123, in run_job job_wrapper.finish( stdout, stderr ) File
"/data/APPLIS/GALAXY/galaxy-dist/lib/galaxy/jobs/__init__.py", line 573,
in finish self.sa_session.flush() File
"/data/APPLIS/GALAXY/galaxy-dist/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
"/data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py",
line 1356, in flush self._flush(objects) File
"/data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py",
line 1434, in _flush flush_context.execute() File
"/data/APPLIS/GALAXY/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py",
line 261, in execute UOWExecutor().execute(self, tasks) File
"/data/APPLIS/GALAXY/galaxy-dist/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
"/data/APPLIS/GALAXY/galaxy-dist/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
"/data/APPLIS/GALAXY/galaxy-dist/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
"/data/APPLIS/GALAXY/galaxy-dist/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
"/data/APPLIS/GALAXY/galaxy-dist/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
"/data/APPLIS/GALAXY/galaxy-dist/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
"/data/APPLIS/GALAXY/galaxy-dist/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
"/data/APPLIS/GALAXY/galaxy-dist/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
"/data/APPLIS/GALAXY/galaxy-dist/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
"/data/APPLIS/GALAXY/galaxy-dist/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
"/data/APPLIS/GALAXY/galaxy-dist/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
"/data/APPLIS/GALAXY/galaxy-dist/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 = ?' ['2012-09-04 06:23:08.928377',
'Single Alignment Analyses\nsh:
/data/APPLIS/GALAXY/galaxy-dist/tool-data/HYPHY/HYPHY: Aucun fichier ou
r\xc3\xa9pertoire de ce type\n', 'error', 'no peek', 55]
--
Gauthier Jean-Pierre.
Bio-informatique.
INRA. UMR IGEPP.
Domaine de la Motte. BP. 35327.
35653 LE RHEU CEDEX.
tel : 33(0)2.23.48.51.68
fax : 33(0)2.23.48.51.50
mail : jean-pierre.gauth...@rennes.inra.fr
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