Question: UnicodeEncodeError: 'latin-1' codec can't encode character u'\u2018' in position 534: ordinal not in range(256)
0
gravatar for yychangsd
2.0 years ago by
yychangsd30
yychangsd30 wrote:

My local galaxy instance is connected with mysql.

When I run a job I get an error:

Traceback (most recent call last):

File "/home/oasis/data/galaxy-new/lib/galaxy/jobs/runners/local.py", line 128, in queue_job job_wrapper.finish( stdout, stderr, exit_code )

File "/home/oasis/data/galaxy-new/lib/galaxy/jobs/__init__.py", line 1278, in finish self.sa_session.flush()

File "/home/oasis/data/galaxy-new/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/scoping.py", line 150, in do return getattr(self.registry(), name)(args, *kwargs)

File "/home/oasis/data/galaxy-new/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2004, in flush self._flush(objects)

File "/home/oasis/data/galaxy-new/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2122, in _flush transaction.rollback(_capture_exception=True)

File "/home/oasis/data/galaxy-new/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 60, in __exit__ compat.reraise(exc_type, exc_value, exc_tb)

File "/home/oasis/data/galaxy-new/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2086, in _flush flush_context.execute()

File "/home/oasis/data/galaxy-new/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 373, in execute rec.execute(self)

File "/home/oasis/data/galaxy-new/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 532, in execute uow

File "/home/oasis/data/galaxy-new/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 170, in save_obj mapper, table, update)

File "/home/oasis/data/galaxy-new/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 692, in _emit_update_statements execute(statement, multiparams)

File "/home/oasis/data/galaxy-new/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 914, in execute return meth(self, multiparams, params)

File "/home/oasis/data/galaxy-new/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params)

File "/home/oasis/data/galaxy-new/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1010, in _execute_clauseelement compiled_sql, distilled_params

File "/home/oasis/data/galaxy-new/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1146, in _execute_context context)

File "/home/oasis/data/galaxy-new/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1344, in _handle_dbapi_exception util.reraise(*exc_info)

File "/home/oasis/data/galaxy-new/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1139, in _execute_context context)

File "/home/oasis/data/galaxy-new/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 450, in do_execute cursor.execute(statement, parameters)

File "/home/oasis/data/galaxy-new/.venv/local/lib/python2.7/site-packages/MySQLdb/cursors.py", line 187, in execute query = query % tuple([db.literal(item) for item in args])

File "/home/oasis/data/galaxy-new/.venv/local/lib/python2.7/site-packages/MySQLdb/connections.py", line 278, in literal return self.escape(o, self.encoders)

File "/home/oasis/data/galaxy-new/.venv/local/lib/python2.7/site-packages/MySQLdb/connections.py", line 208, in unicode_literal return db.literal(u.encode(unicode_literal.charset))

UnicodeEncodeError: 'latin-1' codec can't encode character u'\u2018' in position 534: ordinal not in range(256)

I guess it may be caused by mysql ..

Any suggestions would be greatly appreciated..

Thanks...

error admin jobs local unicode • 1.2k views
ADD COMMENTlink written 2.0 years ago by yychangsd30
1
gravatar for Devon Ryan
2.0 years ago by
Devon Ryan1.9k
Germany
Devon Ryan1.9k wrote:

I had an error somewhat like this with postgresql about a year ago. The fix was to convert the database to use the unicode codec. Having said that, since this is happening with the local job runner I wonder if you just have a funky character in job_conf.xml.

ADD COMMENTlink written 2.0 years ago by Devon Ryan1.9k

Thanks for your comments.

Actually I used this to convert my galaxy_db in mysql: mysql> ALTER DATABASE galaxy_db CHARACTER SET utf8 COLLATE utf8_unicode_ci; Query OK, 1 row affected (0.01 sec)

And I also checked job_conf.xml. It seems fine.

But I still get this error...

ADD REPLYlink written 2.0 years ago by yychangsd30
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