[galaxy-dev] Error after migrating to latest changeset

12 Jul 2011

      Good Morning,

I am getting a big problem with our production server when I upgrade to the latest change set (it was quite out of date). I have attached quite a long paster output to try and show whats going on,

Our galaxy instance no longer seems to run jobs at all, they are not allocated a job runner and the following is given in the paster log

I look forwards to your assistance.

Thanks

Michael.
======

galaxy.datatypes.registry DEBUG 2011-07-12 11:46:50,433 Loaded indexer: INDEXER_Interval_0
galaxy.jobs.runners.local INFO 2011-07-12 11:46:50,436 starting workers
galaxy.jobs.runners.local DEBUG 2011-07-12 11:46:50,437 5 workers ready
galaxy.jobs DEBUG 2011-07-12 11:46:50,438 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner
galaxy.jobs.runners.drmaa DEBUG 2011-07-12 11:46:50,483 10 workers ready
galaxy.jobs DEBUG 2011-07-12 11:46:50,483 Loaded job runner: galaxy.jobs.runners.drmaa:DRMAAJobRunner
galaxy.jobs INFO 2011-07-12 11:46:50,484 job manager started
galaxy.jobs DEBUG 2011-07-12 11:46:50,861 no runner: 4400 is still in new state, adding to the jobs queue
galaxy.jobs DEBUG 2011-07-12 11:46:50,862 no runner: 4401 is still in new state, adding to the jobs queue
galaxy.jobs DEBUG 2011-07-12 11:46:50,862 no runner: 4403 is still in new state, adding to the jobs queue
galaxy.jobs DEBUG 2011-07-12 11:46:50,862 no runner: 4404 is still in new state, adding to the jobs queue
galaxy.jobs INFO 2011-07-12 11:46:50,869 job stopper started
galaxy.sample_tracking.external_service_types DEBUG 2011-07-12 11:46:50,872 Loaded external_service_type: Simple unknown sequencer 1.0.0
galaxy.sample_tracking.external_service_types DEBUG 2011-07-12 11:46:50,875 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0
galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,895 Enabling 'admin' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,898 Enabling 'async' controller, class: ASync
galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,915 Enabling 'dataset' controller, class: DatasetInterface
galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,917 Enabling 'error' controller, class: Error
galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,920 Enabling 'forms' controller, class: Forms
galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,924 Enabling 'history' controller, class: HistoryController
galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,942 Enabling 'library' controller, class: Library
galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,946 Enabling 'library_admin' controller, class: LibraryAdmin
galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,947 Enabling 'library_common' controller, class: LibraryCommon
galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,949 Enabling 'mobile' controller, class: Mobile
galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,952 Enabling 'page' controller, class: PageController
galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,958 Enabling 'requests' controller, class: Requests
galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,996 Enabling 'requests_admin' controller, class: RequestsAdmin
galaxy.web.framework.base DEBUG 2011-07-12 11:46:50,997 Enabling 'requests_common' controller, class: RequestsCommon
galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,000 Enabling 'root' controller, class: RootController
galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,002 Enabling 'tag' controller, class: TagsController
galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,004 Enabling 'tool_runner' controller, class: ToolRunner
galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,013 Enabling 'tracks' controller, class: TracksController
galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,016 Enabling 'ucsc_proxy' controller, class: UCSCProxy
galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,019 Enabling 'user' controller, class: User
galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,022 Enabling 'visualization' controller, class: VisualizationController
galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,107 Enabling 'workflow' controller, class: WorkflowController
galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,110 Enabling 'external_service' controller, class: ExternalService
galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,112 Enabling 'external_services' controller, class: ExternalServiceController
galaxy.web.framework.base DEBUG 2011-07-12 11:46:51,115 Enabling 'request_type' controller, class: RequestType
galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,146 Enabling 'httpexceptions' middleware
galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,148 Enabling 'recursive' middleware
galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,169 Enabling 'error' middleware
galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,173 Enabling 'trans logger' middleware
galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,173 Enabling 'config' middleware
galaxy.web.buildapp DEBUG 2011-07-12 11:46:51,174 Enabling 'x-forwarded-host' middleware

Starting server in PID 3738.
serving on http://127.0.0.1:8080
sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:00,942 Error closing cursor: current transaction is aborted, commands ignored until end of transaction block

galaxy.jobs ERROR 2011-07-12 11:47:00,942 failure running job 4400
Traceback (most recent call last):
  File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 187, in __monitor_step
    job_state = self.__check_if_ready_to_run( job )
  File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 232, in __check_if_ready_to_run
    for dataset_assoc in job.input_datasets + job.input_library_datasets:
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__
    return self.impl.get(instance_state(instance), instance_dict(instance))
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get
    value = callable_()
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__
    result = q.all()
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all
    return list(self)
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__
    return self._execute_and_instances(context)
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances
    result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none())
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute
    clause, params or {})
  File "/home/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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) relation "job_to_input_library_dataset" does not exist
 'SELECT job_to_input_library_dataset.id AS job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS job_to_input_library_dataset_job_id, job_to_input_library_dataset.ldda_id AS job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name AS job_to_input_library_dataset_name, library_dataset_dataset_association_1.id AS library_dataset_dataset_association_1_id, library_dataset_dataset_association_1.library_dataset_id AS library_dataset_dataset_association_1_library_dataset_id, library_dataset_dataset_association_1.dataset_id AS library_dataset_dataset_association_1_dataset_id, library_dataset_dataset_association_1.create_time AS library_dataset_dataset_association_1_create_time, library_dataset_dataset_association_1.update_time AS library_dataset_dataset_association_1_update_time, library_dataset_dataset_association_1.state AS library_dataset_dataset_association_1_state, library_dataset_dataset_association_1.copied_from_history_dataset_association_id AS library_dataset_dataset_association_1_copied_from_history_1, library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id AS library_dataset_dataset_association_1_copied_from_library_2, library_dataset_dataset_association_1.name AS library_dataset_dataset_association_1_name, library_dataset_dataset_association_1.info AS library_dataset_dataset_association_1_info, library_dataset_dataset_association_1.blurb AS library_dataset_dataset_association_1_blurb, library_dataset_dataset_association_1.peek AS library_dataset_dataset_association_1_peek, library_dataset_dataset_association_1.extension AS library_dataset_dataset_association_1_extension, library_dataset_dataset_association_1.metadata AS library_dataset_dataset_association_1_metadata, library_dataset_dataset_association_1.parent_id AS library_dataset_dataset_association_1_parent_id, library_dataset_dataset_association_1.designation AS library_dataset_dataset_association_1_designation, library_dataset_dataset_association_1.deleted AS library_dataset_dataset_association_1_deleted, library_dataset_dataset_association_1.visible AS library_dataset_dataset_association_1_visible, library_dataset_dataset_association_1.user_id AS library_dataset_dataset_association_1_user_id, library_dataset_dataset_association_1.message AS library_dataset_dataset_association_1_message \nFROM job_to_input_library_dataset LEFT OUTER JOIN library_dataset_dataset_association AS library_dataset_dataset_association_1 ON library_dataset_dataset_association_1.id = job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = job_to_input_library_dataset.job_id' {'param_1': 4400}
sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:00,978 Error closing cursor: current transaction is aborted, commands ignored until end of transaction block

galaxy.jobs ERROR 2011-07-12 11:47:00,979 failure running job 4401
Traceback (most recent call last):
  File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 187, in __monitor_step
    job_state = self.__check_if_ready_to_run( job )
  File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 232, in __check_if_ready_to_run
    for dataset_assoc in job.input_datasets + job.input_library_datasets:
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__
    return self.impl.get(instance_state(instance), instance_dict(instance))
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get
    value = callable_()
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__
    result = q.all()
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all
    return list(self)
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__
    return self._execute_and_instances(context)
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances
    result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none())
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute
    clause, params or {})
  File "/home/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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) relation "job_to_input_library_dataset" does not exist
 'SELECT job_to_input_library_dataset.id AS job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS job_to_input_library_dataset_job_id, job_to_input_library_dataset.ldda_id AS job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name AS job_to_input_library_dataset_name, library_dataset_dataset_association_1.id AS library_dataset_dataset_association_1_id, library_dataset_dataset_association_1.library_dataset_id AS library_dataset_dataset_association_1_library_dataset_id, library_dataset_dataset_association_1.dataset_id AS library_dataset_dataset_association_1_dataset_id, library_dataset_dataset_association_1.create_time AS library_dataset_dataset_association_1_create_time, library_dataset_dataset_association_1.update_time AS library_dataset_dataset_association_1_update_time, library_dataset_dataset_association_1.state AS library_dataset_dataset_association_1_state, library_dataset_dataset_association_1.copied_from_history_dataset_association_id AS library_dataset_dataset_association_1_copied_from_history_1, library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id AS library_dataset_dataset_association_1_copied_from_library_2, library_dataset_dataset_association_1.name AS library_dataset_dataset_association_1_name, library_dataset_dataset_association_1.info AS library_dataset_dataset_association_1_info, library_dataset_dataset_association_1.blurb AS library_dataset_dataset_association_1_blurb, library_dataset_dataset_association_1.peek AS library_dataset_dataset_association_1_peek, library_dataset_dataset_association_1.extension AS library_dataset_dataset_association_1_extension, library_dataset_dataset_association_1.metadata AS library_dataset_dataset_association_1_metadata, library_dataset_dataset_association_1.parent_id AS library_dataset_dataset_association_1_parent_id, library_dataset_dataset_association_1.designation AS library_dataset_dataset_association_1_designation, library_dataset_dataset_association_1.deleted AS library_dataset_dataset_association_1_deleted, library_dataset_dataset_association_1.visible AS library_dataset_dataset_association_1_visible, library_dataset_dataset_association_1.user_id AS library_dataset_dataset_association_1_user_id, library_dataset_dataset_association_1.message AS library_dataset_dataset_association_1_message \nFROM job_to_input_library_dataset LEFT OUTER JOIN library_dataset_dataset_association AS library_dataset_dataset_association_1 ON library_dataset_dataset_association_1.id = job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = job_to_input_library_dataset.job_id' {'param_1': 4401}
sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:00,999 Error closing cursor: current transaction is aborted, commands ignored until end of transaction block

galaxy.jobs ERROR 2011-07-12 11:47:00,999 failure running job 4403
Traceback (most recent call last):
  File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 187, in __monitor_step
    job_state = self.__check_if_ready_to_run( job )
  File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 232, in __check_if_ready_to_run
    for dataset_assoc in job.input_datasets + job.input_library_datasets:
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__
    return self.impl.get(instance_state(instance), instance_dict(instance))
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get
    value = callable_()
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__
    result = q.all()
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all
    return list(self)
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__
    return self._execute_and_instances(context)
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances
    result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none())
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute
    clause, params or {})
  File "/home/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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) relation "job_to_input_library_dataset" does not exist
 'SELECT job_to_input_library_dataset.id AS job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS job_to_input_library_dataset_job_id, job_to_input_library_dataset.ldda_id AS job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name AS job_to_input_library_dataset_name, library_dataset_dataset_association_1.id AS library_dataset_dataset_association_1_id, library_dataset_dataset_association_1.library_dataset_id AS library_dataset_dataset_association_1_library_dataset_id, library_dataset_dataset_association_1.dataset_id AS library_dataset_dataset_association_1_dataset_id, library_dataset_dataset_association_1.create_time AS library_dataset_dataset_association_1_create_time, library_dataset_dataset_association_1.update_time AS library_dataset_dataset_association_1_update_time, library_dataset_dataset_association_1.state AS library_dataset_dataset_association_1_state, library_dataset_dataset_association_1.copied_from_history_dataset_association_id AS library_dataset_dataset_association_1_copied_from_history_1, library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id AS library_dataset_dataset_association_1_copied_from_library_2, library_dataset_dataset_association_1.name AS library_dataset_dataset_association_1_name, library_dataset_dataset_association_1.info AS library_dataset_dataset_association_1_info, library_dataset_dataset_association_1.blurb AS library_dataset_dataset_association_1_blurb, library_dataset_dataset_association_1.peek AS library_dataset_dataset_association_1_peek, library_dataset_dataset_association_1.extension AS library_dataset_dataset_association_1_extension, library_dataset_dataset_association_1.metadata AS library_dataset_dataset_association_1_metadata, library_dataset_dataset_association_1.parent_id AS library_dataset_dataset_association_1_parent_id, library_dataset_dataset_association_1.designation AS library_dataset_dataset_association_1_designation, library_dataset_dataset_association_1.deleted AS library_dataset_dataset_association_1_deleted, library_dataset_dataset_association_1.visible AS library_dataset_dataset_association_1_visible, library_dataset_dataset_association_1.user_id AS library_dataset_dataset_association_1_user_id, library_dataset_dataset_association_1.message AS library_dataset_dataset_association_1_message \nFROM job_to_input_library_dataset LEFT OUTER JOIN library_dataset_dataset_association AS library_dataset_dataset_association_1 ON library_dataset_dataset_association_1.id = job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = job_to_input_library_dataset.job_id' {'param_1': 4403}
sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:01,027 Error closing cursor: current transaction is aborted, commands ignored until end of transaction block

galaxy.jobs ERROR 2011-07-12 11:47:01,028 failure running job 4404
Traceback (most recent call last):
  File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 187, in __monitor_step
    job_state = self.__check_if_ready_to_run( job )
  File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 232, in __check_if_ready_to_run
    for dataset_assoc in job.input_datasets + job.input_library_datasets:
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__
    return self.impl.get(instance_state(instance), instance_dict(instance))
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get
    value = callable_()
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__
    result = q.all()
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all
    return list(self)
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__
    return self._execute_and_instances(context)
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances
    result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none())
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute
    clause, params or {})
  File "/home/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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) relation "job_to_input_library_dataset" does not exist
 'SELECT job_to_input_library_dataset.id AS job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS job_to_input_library_dataset_job_id, job_to_input_library_dataset.ldda_id AS job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name AS job_to_input_library_dataset_name, library_dataset_dataset_association_1.id AS library_dataset_dataset_association_1_id, library_dataset_dataset_association_1.library_dataset_id AS library_dataset_dataset_association_1_library_dataset_id, library_dataset_dataset_association_1.dataset_id AS library_dataset_dataset_association_1_dataset_id, library_dataset_dataset_association_1.create_time AS library_dataset_dataset_association_1_create_time, library_dataset_dataset_association_1.update_time AS library_dataset_dataset_association_1_update_time, library_dataset_dataset_association_1.state AS library_dataset_dataset_association_1_state, library_dataset_dataset_association_1.copied_from_history_dataset_association_id AS library_dataset_dataset_association_1_copied_from_history_1, library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id AS library_dataset_dataset_association_1_copied_from_library_2, library_dataset_dataset_association_1.name AS library_dataset_dataset_association_1_name, library_dataset_dataset_association_1.info AS library_dataset_dataset_association_1_info, library_dataset_dataset_association_1.blurb AS library_dataset_dataset_association_1_blurb, library_dataset_dataset_association_1.peek AS library_dataset_dataset_association_1_peek, library_dataset_dataset_association_1.extension AS library_dataset_dataset_association_1_extension, library_dataset_dataset_association_1.metadata AS library_dataset_dataset_association_1_metadata, library_dataset_dataset_association_1.parent_id AS library_dataset_dataset_association_1_parent_id, library_dataset_dataset_association_1.designation AS library_dataset_dataset_association_1_designation, library_dataset_dataset_association_1.deleted AS library_dataset_dataset_association_1_deleted, library_dataset_dataset_association_1.visible AS library_dataset_dataset_association_1_visible, library_dataset_dataset_association_1.user_id AS library_dataset_dataset_association_1_user_id, library_dataset_dataset_association_1.message AS library_dataset_dataset_association_1_message \nFROM job_to_input_library_dataset LEFT OUTER JOIN library_dataset_dataset_association AS library_dataset_dataset_association_1 ON library_dataset_dataset_association_1.id = job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = job_to_input_library_dataset.job_id' {'param_1': 4404}
149.155.218.28 - - [12/Jul/2011:11:47:31 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_8; en-us) AppleWebKit/533.21.1 (KHTML, like Gecko) Version/5.0.5 Safari/533.21.1"
149.155.221.116 - - [12/Jul/2011:11:47:33 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-GB; rv:1.9.2.19) Gecko/20110707 Firefox/3.6.19"
149.155.221.194 - - [12/Jul/2011:11:47:33 +0100] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0"
149.155.221.194 - - [12/Jul/2011:11:47:33 +0100] "GET /history HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0"
149.155.221.194 - - [12/Jul/2011:11:47:33 +0100] "GET /root/tool_menu HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0"
149.155.218.28 - - [12/Jul/2011:11:47:35 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_8; en-us) AppleWebKit/533.21.1 (KHTML, like Gecko) Version/5.0.5 Safari/533.21.1"
149.155.221.116 - - [12/Jul/2011:11:47:37 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-GB; rv:1.9.2.19) Gecko/20110707 Firefox/3.6.19"
149.155.221.194 - - [12/Jul/2011:11:47:36 +0100] "GET /tool_runner/rerun?id=6014 HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0"
149.155.221.194 - - [12/Jul/2011:11:47:38 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0"
149.155.218.28 - - [12/Jul/2011:11:47:39 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_8; en-us) AppleWebKit/533.21.1 (KHTML, like Gecko) Version/5.0.5 Safari/533.21.1"
149.155.221.194 - - [12/Jul/2011:11:47:39 +0100] "POST /tool_runner/index HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/tool_runner/rerun?id=6014" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0"
sqlalchemy.pool.QueuePool.0x...b590 WARNING 2011-07-12 11:47:40,371 Error closing cursor: current transaction is aborted, commands ignored until end of transaction block

galaxy.jobs ERROR 2011-07-12 11:47:40,372 failure running job 4405
Traceback (most recent call last):
  File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 187, in __monitor_step
    job_state = self.__check_if_ready_to_run( job )
  File "/home/home/galaxy/software/galaxy-ceneral/lib/galaxy/jobs/__init__.py", line 232, in __check_if_ready_to_run
    for dataset_assoc in job.input_datasets + job.input_library_datasets:
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 158, in __get__
    return self.impl.get(instance_state(instance), instance_dict(instance))
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get
    value = callable_()
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/strategies.py", line 587, in __call__
    result = q.all()
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all
    return list(self)
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__
    return self._execute_and_instances(context)
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances
    result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none())
  File "/home/home/galaxy/software/galaxy-ceneral/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute
    clause, params or {})
  File "/home/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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/home/galaxy/software/galaxy-ceneral/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) relation "job_to_input_library_dataset" does not exist
 'SELECT job_to_input_library_dataset.id AS job_to_input_library_dataset_id, job_to_input_library_dataset.job_id AS job_to_input_library_dataset_job_id, job_to_input_library_dataset.ldda_id AS job_to_input_library_dataset_ldda_id, job_to_input_library_dataset.name AS job_to_input_library_dataset_name, library_dataset_dataset_association_1.id AS library_dataset_dataset_association_1_id, library_dataset_dataset_association_1.library_dataset_id AS library_dataset_dataset_association_1_library_dataset_id, library_dataset_dataset_association_1.dataset_id AS library_dataset_dataset_association_1_dataset_id, library_dataset_dataset_association_1.create_time AS library_dataset_dataset_association_1_create_time, library_dataset_dataset_association_1.update_time AS library_dataset_dataset_association_1_update_time, library_dataset_dataset_association_1.state AS library_dataset_dataset_association_1_state, library_dataset_dataset_association_1.copied_from_history_dataset_association_id AS library_dataset_dataset_association_1_copied_from_history_1, library_dataset_dataset_association_1.copied_from_library_dataset_dataset_association_id AS library_dataset_dataset_association_1_copied_from_library_2, library_dataset_dataset_association_1.name AS library_dataset_dataset_association_1_name, library_dataset_dataset_association_1.info AS library_dataset_dataset_association_1_info, library_dataset_dataset_association_1.blurb AS library_dataset_dataset_association_1_blurb, library_dataset_dataset_association_1.peek AS library_dataset_dataset_association_1_peek, library_dataset_dataset_association_1.extension AS library_dataset_dataset_association_1_extension, library_dataset_dataset_association_1.metadata AS library_dataset_dataset_association_1_metadata, library_dataset_dataset_association_1.parent_id AS library_dataset_dataset_association_1_parent_id, library_dataset_dataset_association_1.designation AS library_dataset_dataset_association_1_designation, library_dataset_dataset_association_1.deleted AS library_dataset_dataset_association_1_deleted, library_dataset_dataset_association_1.visible AS library_dataset_dataset_association_1_visible, library_dataset_dataset_association_1.user_id AS library_dataset_dataset_association_1_user_id, library_dataset_dataset_association_1.message AS library_dataset_dataset_association_1_message \nFROM job_to_input_library_dataset LEFT OUTER JOIN library_dataset_dataset_association AS library_dataset_dataset_association_1 ON library_dataset_dataset_association_1.id = job_to_input_library_dataset.ldda_id \nWHERE %(param_1)s = job_to_input_library_dataset.job_id' {'param_1': 4405}
149.155.221.194 - - [12/Jul/2011:11:47:40 +0100] "GET /user/get_most_recently_used_tool_async HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/root/tool_menu" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0"
149.155.221.194 - - [12/Jul/2011:11:47:40 +0100] "GET /history HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/tool_runner/index" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0"
149.155.221.116 - - [12/Jul/2011:11:47:41 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-GB; rv:1.9.2.19) Gecko/20110707 Firefox/3.6.19"
149.155.221.194 - - [12/Jul/2011:11:47:42 +0100] "GET /root/delete_async?id=6014 HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:5.0) Gecko/20100101 Firefox/5.0"
149.155.218.28 - - [12/Jul/2011:11:47:43 +0100] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy.tsl.ac.uk/history" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_8; en-us) AppleWebKit/533.21.1 (KHTML, like Gecko) Version/5.0.5 Safari/533.21.1"

[galaxy-dev] Error after migrating to latest changeset

michael burrell (TSL)