Hi;
I have developed a Perl tool that generates a tabular file with 3 columns. I need to compare it with another tabular file (Gene Ontology Annotation file) and I use "Join, substract, group", "Compare two datasets". When I try to do so, I get the error pasted bellow. I assume my perl code is generating the file with the wrong encoding, but I have tried to generate the file in UTF8 to no avail. Any clues? Thanks
Traceback (most recent call last): File "/home/megana/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 125, in run_job job_wrapper.finish( stdout, stderr ) File "/home/megana/galaxy-dist/lib/galaxy/jobs/__init__.py", line 658, in finish self.sa_session.flush() File "/home/megana/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 "/home/megana/galaxy-dist/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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=?, tool_version=?, metadata=? WHERE history_dataset_association.id = ?' ['2012-03-16 15:20:29.158287', 'join (GNU coreutils) 7.4\nCopyright \xc2\xa9 2009 Free Software Foundation, Inc.\nLicencia GPLv3+: GNU GPL versi\xc3\xb3n 3 o superior http://gnu.org/licenses/gpl.html.\nEsto es software libre: es libre de cambiarlo y redistribuirlo.\nNO HAY NINGUNA GARANT\xc3\x8dA, en la me', '5,547 lines', u'UniProtKB\tB5B2P3\tNFATC2\t\tGO:0001816\tGO_REF:0000019\tIEA\tEnsembl:ENSMUSP00000074198\tP\tNuclear factor of activated T-cells c2 isoform IB-IIL-deltaXa\tB5B2P3_HUMAN|NFATC2|hCG_2018585|IPI00297845\tprotein\ttaxon:9606\t20110709\tENSEMBL\n\nUniProtKB\tE7DVW4\tFABP4\t\tGO:0001816\tGO_REF:0000019\tIEA\tEnsembl:ENSMUSP00000029041\tP\tFatty acid binding protein 4, adipocyte\tE7DVW4_HUMAN|FABP4|IPI00215746\tprotein\ttaxon:9606\t20110709\tENSEMBL\n\nUniProtKB\tE9PHR7\tNFAT5\t\tGO:0001816\tGO_REF:0000019\tIEA\tEnsembl:ENSMUSP00000127784\tP\tUncharacterized protein\tE9PHR7_HUMAN|NFAT5|IPI00514115\tprotein\ttaxon:9606\t20110709\tENSEMBL\n\nUniProtKB\tE9PJN7\tZCCHC11\t\tGO:0001816\tGO_REF:0000019\tIEA\tEnsembl:ENSMUSP00000044836\tP\tUncharacterized protein\tE9PJN7_HUMAN|ZCCHC11|IPI00985026\tprotein\ttaxon:9606\t20110709\tENSEMBL\n\nUniProtKB\tE9PQS7\tZCCHC11\t\tGO:0001816\tGO_REF:0000019\tIEA\tEnsembl:ENSMUSP00000044836\tP\tUncharacterized protein\tE9PQS7_HUMAN|ZCCHC11|IPI00975697\tprotein\ttaxon:9606\t20110709\tENSEMBL\n\nUniProtKB\tP01730\tCD4\t\tGO:0001816\tGO_REF:0000019\tIEA\tEnsembl:ENSMUSP00000024044\tP\tT-cell surface glycoprotein CD4\tCD4_HUMAN|CD4|IPI00003983|B2R737|D3DUS5|Q4ZGK2|Q5U066|Q9UDE5\tprotein\ttaxon:9606\t20110709\tENSEMBL\n', '', <read-only buffer for 0x7ad9210, size -1, offset 0 at 0x7f7054536770>, 118]