Hi Galaxy-team,
I'm running Galaxy on my local system, but recently get an coding error.
The database I'm using is postgresql, I also modified part of the code,
hope that will not make things complex.
Looks like the tool generate a pdf file, and a geek of the file contains
some binary code which is failed to store into the database.
Below is the error message. Appreciate for suggestions.
galaxy.jobs.runners.local ERROR 2012-10-30 10:47:28,855 Job wrapper finish
method failed
Traceback (most recent call last):
File "/data/CistromeAP/lib/galaxy/jobs/runners/local.py", line 133, in
run_job
job_wrapper.finish( stdout, stderr )
File "/data/CistromeAP/lib/galaxy/jobs/__init__.py", line 454, in finish
tool=self.tool, stdout=stdout, stderr=stderr )
File "/data/CistromeAP/lib/galaxy/tools/__init__.py", line 2207, in
call_hook
return code( *args, **kwargs )
File "./tools/expression/norm_code.py", line 103, in exec_after_process
app.model.context.flush()
File
"/data/CistromeAP/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/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py",
line 1356, in flush
self._flush(objects)
File
"/data/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py",
line 1434, in _flush
flush_context.execute()
File
"/data/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py",
line 261, in execute
UOWExecutor().execute(self, tasks)
File
"/data/CistromeAP/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/CistromeAP/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/CistromeAP/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/CistromeAP/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/CistromeAP/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/CistromeAP/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/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py",
line 1424, in _save_obj
c = connection.execute(statement.values(value_params), params)
File
"/data/CistromeAP/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/CistromeAP/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/CistromeAP/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/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
line 952, in _cursor_execute
self._handle_dbapi_exception(e, statement, parameters, cursor, context)
File
"/data/CistromeAP/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py",
line 933, in _handle_dbapi_exception
raise exc.DBAPIError.instance(statement, parameters, e,
connection_invalidated=is_disconnect)
DataError: ('E', 'r', 'r', 'o', 'r', ' ', 'i', 'n', ' ', "'", 'G', 'e',
'n', 'e', ' ', 'e', 'x', 'p', 'r', 'e', 's', 's', 'i', 'o', 'n', ' ', 'i',
'n', 'd', 'e', 'x', "'", ' ', 'h', 'o', 'o', 'k', ' ', "'", 'e', 'x', 'e',
'c', '_', 'a', 'f', 't', 'e', 'r', '_', 'p', 'r', 'o', 'c', 'e', 's', 's',
"'", ',', ' ', 'o', 'r', 'i', 'g', 'i', 'n', 'a', 'l', ' ', 'm', 'e', 's',
's', 'a', 'g', 'e', ':', ' ', '(', 'D', 'a', 't', 'a', 'E', 'r', 'r', 'o',
'r', ')', ' ', 'i', 'n', 'v', 'a', 'l', 'i', 'd', ' ', 'b', 'y', 't', 'e',
' ', 's', 'e', 'q', 'u', 'e', 'n', 'c', 'e', ' ', 'f', 'o', 'r', ' ', 'e',
'n', 'c', 'o', 'd', 'i', 'n', 'g', ' ', '"', 'U', 'T', 'F', '8', '"', ':',
' ', '0', 'x', '8', '1', '\n', 'H', 'I', 'N', 'T', ':', ' ', ' ', 'T', 'h',
'i', 's', ' ', 'e', 'r', 'r', 'o', 'r', ' ', 'c', 'a', 'n', ' ', 'a', 'l',
's', 'o', ' ', 'h', 'a', 'p', 'p', 'e', 'n', ' ', 'i', 'f', ' ', 't', 'h',
'e', ' ', 'b', 'y', 't', 'e', ' ', 's', 'e', 'q', 'u', 'e', 'n', 'c', 'e',
' ', 'd', 'o', 'e', 's', ' ', 'n', 'o', 't', ' ', 'm', 'a', 't', 'c', 'h',
' ', 't', 'h', 'e', ' ', 'e', 'n', 'c', 'o', 'd', 'i', 'n', 'g', ' ', 'e',
'x', 'p', 'e', 'c', 't', 'e', 'd', ' ', 'b', 'y', ' ', 't', 'h', 'e', ' ',
's', 'e', 'r', 'v', 'e', 'r', ',', ' ', 'w', 'h', 'i', 'c', 'h', ' ', 'i',
's', ' ', 'c', 'o', 'n', 't', 'r', 'o', 'l', 'l', 'e', 'd', ' ', 'b', 'y',
' ', '"', 'c', 'l', 'i', 'e', 'n', 't', '_', 'e', 'n', 'c', 'o', 'd', 'i',
'n', 'g', '"', '.', '\n') 'INSERT INTO history_dataset_association (id,
history_id, dataset_id, create_time, update_time, state,
copied_from_history_dataset_association_id,
copied_from_library_dataset_dataset_association_id, hid, name, info, blurb,
peek, tool_version, extension, metadata, parent_id, designation, deleted,
purged, visible) VALUES (%(id)s, %(history_id)s, %(dataset_id)s,
%(create_time)s, %(update_time)s, %(_state)s,
%(copied_from_history_dataset_association_id)s,
%(copied_from_library_dataset_dataset_association_id)s, %(hid)s, %(name)s,
%(info)s, %(blurb)s, %(peek)s, %(tool_version)s, %(extension)s,
%(_metadata)s, %(parent_id)s, %(designation)s, %(deleted)s, %(purged)s,
%(visible)s)' {'info': 'makeAffyBatch, Normalized_rma_Raw_Plots.pdf',
'peek': "%PDF-1.4\n%\x81\xe2\x81\xe3\x81\xcf\x81\xd3\\r\n1 0
obj\n<<\n/CreationDate (D:20121030103557)\n/ModDate
(D:20121030103557)\n/Title (R Graphics Output)\n/Producer (R
2.15.1)\n/Creator (R)\n>>\nendobj\n2 0 obj\n<< /Type /Catalog /Pages 3 0 R
>>\nendobj\n7 0 obj\n<< /Type /Page /Parent 3 0 R /Contents 8 0 R
/Resources 4 0 R >>\nendobj\n8 0 obj\n<<\n/Length 990 /Filter
/FlateDecode\n>>\nstream\nx\x9c\xa5W\xcb\x8eT9\x0c\xdd\xe7+\xbc\xec^\x10\x928\xcf--\x06\xa9\x05HP%\xb1@,\x80\x194B]\xbc\x1a\t>\x1f'vr\x1f}\x9b\xaaRon\xe9D\xc7'\xceI\xe2\xb8,\\\x83\x85\xcf\xf0]\xbd\x82\xef`\x8d\xd71\x83\xf3Nc\x06o\xbdN\x0e0Y\x1d\x1c\xfc\xf8\x0f\xde\xc0\x17\xf5\xf8\xf6\xf5\xb3'p\xb5SF\x1bc`\xfe\xdd]\xbdTN\xbb\x00\xbf\xd4\xdbw`\xe0_e\xe0Z\x91\xba\xb2\x95\x00/\x94uQ{\x0f\xe8H\x18\xe1\x006%\x1d\x07\xbe\x81\xaa\x9aZ<4!$\xc4J\xb6*\x05\xa7\x8d\x07\x97\x8a\xb6\xb6F3",
'update_time': datetime.datetime(2012, 10, 30, 14, 36, 51, 684), 'name':
'Normalized_rma_Raw_Plots.pdf', 'extension': 'pdf', 'tool_version': None,
'deleted': False, 'history_id': None,
'copied_from_library_dataset_dataset_association_id': None, '_state': None,
'designation': None, 'purged': False, 'parent_id': None, 'create_time':
datetime.datetime(2012, 10, 30, 14, 36, 51, 587), 'hid': None, '_metadata':
<psycopg2._psycopg.Binary object at 0x49231b8>, 'visible': True,
'dataset_id': 727L, 'id': 739L, 'blurb': None,
'copied_from_history_dataset_association_id': None}
--
best，
Jian Ma,
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