Hi Weilong,
Could you please send me the file you are using? I think it is related to http://code.djangoproject.com/changeset/8276 and would like to try the fix on your dataset.
Thanks,
Kanwei
On Dec 21, 2009, at 2:12 AM, guoweilong wrote:
Hi,
I'm a PhD student in Tsinghua University, Beijing. I set up a local Galaxy, and import a bed file. I want to sort all the rows by the the second column' value, "start position" ,in ascending order. It failed when executed in my local version, however, it's OK to run on the Galaxy's public site. The system is Ubuntu 9.10,and the python version is 2.6.4. The bed file is about 150,000 lines.
Is it the problem of database or other? I am not using any external database for the local galaxy.
Best, Weilong Guo
The error message is as follow.
Traceback (most recent call last): File "/home/guoweilong/GWL-galaxy/galaxy_gwl/lib/galaxy/jobs/runners/local.py", line 122, in run_job job_wrapper.finish( stdout, stderr ) File "/home/guoweilong/GWL-galaxy/galaxy_gwl/lib/galaxy/jobs/__init__.py", line 569, in finish self.sa_session.flush() File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/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/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1356, in flush self._flush(objects) File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/! sqlalchemy/orm/session.py", line 1434, in _flush flush_context.execute() File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 261, in execute UOWExecutor().execute(self, tasks) File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/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/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/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/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/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/guoweilong/GWL-galaxy/ga! laxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sq lalchemy/orm/unitofwork.py", line 753, in execute self.execute_save_steps(trans, task) File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/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/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/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/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/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/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparam! s, params) File "/home/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/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/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/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/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/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/guoweilong/GWL-galaxy/galaxy_gwl/eggs/py2.6-noplatform/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, conne! ction_invalidated=is_disconnect) ProgrammingError: (ProgrammingErro r) 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 = ?' ['2009-12-21 02:41:54.450928', 'sort: \xe5\xa4\x9a\xe5\xad\x97\xe7\xac\xa6\xe6\xa0\x87\xe7\xad\xbe\xe2\x80\x9c$\t\xe2\x80\x9d\n', 'error', 'no peek', 7]
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