michael burrell (TSL) wrote: > 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 latest change set (it was quite out of date).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.
Hi Michael, Sorry for the delay in response. Did you ever find a solution to your problem, or are you still experiencing it? Thanks, --nate > > 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, libr! ar! > y_dataset_dataset_association_1.deleted AS library_dataset_dat! > aset_ass > ociation_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, libr! ar! > y_dataset_dataset_association_1.deleted AS library_dataset_dat! > aset_ass > ociation_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, libr! ar! > y_dataset_dataset_association_1.deleted AS library_dataset_dat! > aset_ass > ociation_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, libr! ar! > y_dataset_dataset_association_1.deleted AS library_dataset_dat! > aset_ass > ociation_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, libr! ar! > y_dataset_dataset_association_1.deleted AS library_dataset_dat! > aset_ass > ociation_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" > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
