Hi David, hi all!
I have a similar/the same issue in another setting...
galaxy/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 116, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
[...]
galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py",
line 485, in _emit_update_statements
[...]
UnicodeEncodeError: 'latin-1' codec can't encode character u'\u2018' in
position 134: ordinal not in range(256)
I am integrating a set of R/Bioconductor modules into our local Galaxy
instance.
To do so, I use the discard_stderr_wrapper.sh
<https://bitbucket.org/ro6ert/galaxy-central-hbc/src/966e4a5fe4bc/tools/scde_pathprint/discard_stderr_wrapper.sh?at=default>.
It worked fine until the recent update*
As the error appears upon any R-output (via print, cat or error
channel), I just set the option "-v" for the cat command in the
discard_stderr_wrapper.sh:
cat$TMPFILE >&2
=>
cat*-v* $TMPFILE >&2
as a temporary workaround.
No idea if this is applicable in your case?!
Cheers,
Christian
*
changeset: 11219:5c789ab4144a
branch: stable
tag: tip
On 05.12.2013 17:29, David Hoover wrote:
I have installed the ngsplot galaxy tool from http://code.google.com/p/ngsplot.
This tool creates a set of three pdf files. In older versions of Galaxy, the
tool ran correctly with no problems. A recent update broke the tool. The job
runs but is unable to finish. Here is the error reported:
Traceback (most recent call last):
File "/spin1/users/galaxy/galaxy/lib/galaxy/jobs/runners/local.py", line
116, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/spin1/users/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 1015, in
finish
self.sa_session.flush()
File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/scoping.py", line 114, in
do
return getattr(self.registry(), name)(*args, **kwargs)
File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 1718, in
flush
self._flush(objects)
File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 1789, in
_flush
flush_context.execute()
File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 331,
in execute
rec.execute(self)
File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 475,
in execute
uow
File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 59,
in save_obj
mapper, table, update)
File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 485,
in _emit_update_statements
execute(statement, params)
File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1449, in
execute
params)
File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1584, in
_execute_clauseelement
compiled_sql, distilled_params
File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1691, in
_execute_context
context)
File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line 331,
in do_execute
cursor.execute(statement, parameters)
File "build/bdist.linux-x86_64/egg/MySQLdb/cursors.py", line 158, in execute
query = query % db.literal(args)
File "build/bdist.linux-x86_64/egg/MySQLdb/connections.py", line 265, in
literal
return self.escape(o, self.encoders)
File "build/bdist.linux-x86_64/egg/MySQLdb/connections.py", line 203, in
unicode_literal
return db.literal(u.encode(unicode_literal.charset))
UnicodeEncodeError: 'latin-1' codec can't encode character u'\ufffd' in
position 11: ordinal not in range(256)
There is a set of files created in the job_working_directory that start with
'metadata_', some of which contain the unicode.
Is there anything I can do to fix this?
David Hoover
Helix Systems Staff
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