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/