Re: [galaxy-dev] Error after migrating to latest changeset
michael burrell (TSL) wrote:
Good Morning Nate,
Thanks for the response, I was not able to find a work around for this so we redeployed a fresh version of galaxy. Any ideas what could have caused this issue ?
It looks like a database migration had failed but still incremented the database version. If you still have the database we could double check, although it may not be possible to determine how it happened regardless. --nate
Thanks
Michael.
On 16/08/2011 20:05, "Nate Coraor" <nate@bx.psu.edu> wrote:
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I am getting a big problem with our production server when I upgrade to the latest change set (it was quite out of date).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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_associa tion_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, librar! 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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_associa tion_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, librar! 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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_associa tion_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, librar! 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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_associa tion_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, librar! 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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_r649 8-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_associa tion_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, librar! 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"
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Nate Coraor