Hi Todd,

just to be sure, you are running know postgresql as Galaxy database, or?

These locking error is only known from sqlite as far as I know. Can you
double check to database backend.

Thanks,
Bjoern

> Hi All,
> We have been having issues with workflows generating intermittent
> errors using sqlite. We recently converted to postgresql  9.3 in an
> attempt to resolve the issue as suggested in prior posts. Despite
> switching to postgresql we continue to have these errors. Does anyone
> have any additional suggestions that may resolve this issue?
> 
>  
> 
> Thanks,
> 
>  
> 
> Todd
> 
>  
> 
> Traceback (most recent call last):
> 
>   File "/opt/paml/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
> line 122, in prepare_job
> 
>     job_wrapper.runner_command_line =
> self.build_command_line( job_wrapper,
> include_metadata=include_metadata,
> include_work_dir_outputs=include_work_dir_outputs )
> 
>   File "/opt/paml/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
> line 172, in build_command_line
> 
>     work_dir_outputs = self.get_work_dir_outputs( job_wrapper )
> 
>   File "/opt/paml/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
> line 222, in get_work_dir_outputs
> 
>     for dataset in dataset_assoc.dataset.dataset.history_associations
> + dataset_assoc.dataset.dataset.library_associations:
> 
>   File
> "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py",
>  line 168, in __get__
> 
>     return self.impl.get(instance_state(instance),dict_)
> 
>   File
> "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py",
>  line 453, in get
> 
>     value = self.callable_(state, passive)
> 
>   File
> "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py",
>  line 508, in _load_for_state
> 
>     return self._emit_lazyload(session, state, ident_key)
> 
>   File
> "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py",
>  line 574, in _emit_lazyload
> 
>     result = q.all()
> 
>   File
> "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
>  line 2115, in all
> 
>     return list(self)
> 
>   File
> "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
>  line 2227, in __iter__
> 
>     return self._execute_and_instances(context)
> 
>   File
> "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
>  line 2242, in _execute_and_instances
> 
>     result = conn.execute(querycontext.statement, self._params)
> 
>   File
> "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
>  line 1449, in execute
> 
>     params)
> 
>   File
> "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
>  line 1584, in _execute_clauseelement
> 
>     compiled_sql, distilled_params
> 
>   File
> "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
>  line 1698, in _execute_context
> 
>     context)
> 
>   File
> "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
>  line 1691, in _execute_context
> 
>     context)
> 
>   File
> "/opt/paml/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
>  line 331, in do_execute
> 
>     cursor.execute(statement, parameters)
> 
> 
> OperationalError: (OperationalError) database is locked u'SELECT
> library_dataset_dataset_association.id AS
> library_dataset_dataset_association_id,
> 
>  
> 
>  
> 
> 
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