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]

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

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

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to