error and question from using galaxy kickstart
Hi Folks, So I managed to ran through the ansible. What I did was to remove certain steps. For example, I don't need slurm-drmaa and docker, then I skipped the update cache. After these minor changes, it finished successfully(?) with an error message it ignored. Then I tried to access the UI, but nothing worked. I pasted it below for your reference. If anyone has seen this before, please help. :-) Sorry for the beginner question, so once the ansible playbook ran through...seems the galaxy and the postgresql etc were started. How do I start/stop them manually? Do I have to run the playbook every time I want to run galaxy or only after I modify the playbook? Also, if I don't look at the log, I don't even know that the UI is at 127.0.0.1:4001. Is there any documentation for this? Thanks, Rui error message: galaxy.web.stack INFO 2018-10-12 19:41:53,874 [p:102477,w:1,m:0] [MainThread] Galaxy server instance 'main.web.1' is running Starting server in PID 101567. serving on uwsgi://127.0.0.1:4001 galaxy.jobs.handler ERROR 2018-10-12 19:42:48,487 [p:102477,w:1,m:0] [JobHandlerQueue.monitor_thread] Exception in monitor_step Traceback (most recent call last): File "lib/galaxy/jobs/handler.py", line 213, in __monitor self.__monitor_step() File "lib/galaxy/jobs/handler.py", line 272, in __monitor_step .order_by(model.Job.id).all() File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2737, in all return list(self) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2889, in __iter__ return self._execute_and_instances(context) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2912, in _execute_and_instances result = conn.execute(querycontext.statement, self._params) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute return meth(self, multiparams, params) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 269, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1060, in _execute_clauseelement compiled_sql, distilled_params File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context context) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception exc_info File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause reraise(type(exception), exception, tb=exc_tb, cause=cause) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context context) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute cursor.execute(statement, parameters) OperationalError: (psycopg2.OperationalError) server closed the connection unexpectedly This probably means the server terminated abnormally before or while processing the request. [SQL: 'SELECT EXISTS (SELECT history_dataset_association.id, history_dataset_association.history_id, history_dataset_association.dataset_id, history_dataset_association.create_time, history_dataset_association.update_time, history_dataset_association.state, history_dataset_association.copied_from_history_dataset_association_id, history_dataset_association.copied_from_library_dataset_dataset_association_id, history_dataset_association.name, history_dataset_association.info, history_dataset_association.blurb, history_dataset_association.peek, history_dataset_association.tool_version, history_dataset_association.extension, history_dataset_association.metadata, history_dataset_association.parent_id, history_dataset_association.designation, history_dataset_association.deleted, history_dataset_association.visible, history_dataset_association.extended_metadata_id, history_dataset_association.version, history_dataset_association.hid, history_dataset_association.purged, history_dataset_association.hidden_beneath_collection_instance_id \nFROM history_dataset_association, job_to_output_dataset \nWHERE job.id = job_to_output_dataset.job_id AND history_dataset_association.id = job_to_output_dataset.dataset_id AND history_dataset_association.deleted = true) AS anon_1, EXISTS (SELECT history_dataset_collection_association.id \nFROM history_dataset_collection_association, job_to_output_dataset_collection \nWHERE job.id = job_to_output_dataset_collection.job_id AND history_dataset_collection_association.id = job_to_output_dataset_collection.dataset_collection_id AND history_dataset_collection_association.deleted = true) AS anon_2, job.id AS job_id, job.create_time AS job_create_time, job.update_time AS job_update_time, job.history_id AS job_history_id, job.library_folder_id AS job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS job_tool_version, job.state AS job_state, job.info AS job_info, job.copied_from_job_id AS job_copied_from_job_id, job.command_line AS job_command_line, job.dependencies AS job_dependencies, job.param_filename AS job_param_filename, job.runner_name AS job_runner_name_1, job.stdout AS job_stdout, job.stderr AS job_stderr, job.exit_code AS job_exit_code, job.traceback AS job_traceback, job.session_id AS job_session_id, job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name, job.job_runner_external_id AS job_job_runner_external_id, job.destination_id AS job_destination_id, job.destination_params AS job_destination_params, job.object_store_id AS job_object_store_id, job.imported AS job_imported, job.params AS job_params, job.handler AS job_handler \nFROM job \nWHERE job.state = %(state_1)s AND job.handler = %(handler_1)s AND job.id NOT IN (SELECT job.id \nFROM job JOIN job_to_input_dataset ON job.id = job_to_input_dataset.job_id JOIN history_dataset_association ON history_dataset_association.id = job_to_input_dataset.dataset_id JOIN dataset ON dataset.id = history_dataset_association.dataset_id \nWHERE job.state = %(state_2)s AND (history_dataset_association.state = %(_state_1)s OR history_dataset_association.deleted = true OR dataset.state != %(state_3)s OR dataset.deleted = true)) AND job.id NOT IN (SELECT job.id \nFROM job JOIN job_to_input_library_dataset ON job.id = job_to_input_library_dataset.job_id JOIN library_dataset_dataset_association ON library_dataset_dataset_association.id = job_to_input_library_dataset.ldda_id JOIN dataset ON dataset.id = library_dataset_dataset_association.dataset_id \nWHERE job.state = %(state_4)s AND (library_dataset_dataset_association.state IS NOT NULL OR library_dataset_dataset_association.deleted = true OR dataset.state != %(state_5)s OR dataset.deleted = true)) ORDER BY job.id'] [parameters: {'state_3': 'ok', 'handler_1': 'main.web.1', 'state_1': 'new', '_state_1': 'failed_metadata', 'state_2': 'new', 'state_5': 'ok', 'state_4': 'new'}] (Background on this error at: http://sqlalche.me/e/e3q8) galaxy.jobs.handler ERROR 2018-10-12 19:42:48,488 [p:102478,w:2,m:0] [JobHandlerQueue.monitor_thread] Exception in monitor_step Traceback (most recent call last): File "lib/galaxy/jobs/handler.py", line 213, in __monitor self.__monitor_step() File "lib/galaxy/jobs/handler.py", line 272, in __monitor_step .order_by(model.Job.id).all() File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2737, in all return list(self) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2889, in __iter__ return self._execute_and_instances(context) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2912, in _execute_and_instances result = conn.execute(querycontext.statement, self._params) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute return meth(self, multiparams, params) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 269, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1060, in _execute_clauseelement compiled_sql, distilled_params File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context context) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception exc_info File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause reraise(type(exception), exception, tb=exc_tb, cause=cause) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context context) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute cursor.execute(statement, parameters) OperationalError: (psycopg2.OperationalError) server closed the connection unexpectedly This probably means the server terminated abnormally before or while processing the request. [SQL: 'SELECT EXISTS (SELECT history_dataset_association.id, history_dataset_association.history_id, history_dataset_association.dataset_id, history_dataset_association.create_time, history_dataset_association.update_time, history_dataset_association.state, history_dataset_association.copied_from_history_dataset_association_id, history_dataset_association.copied_from_library_dataset_dataset_association_id, history_dataset_association.name, history_dataset_association.info, history_dataset_association.blurb, history_dataset_association.peek, history_dataset_association.tool_version, history_dataset_association.extension, history_dataset_association.metadata, history_dataset_association.parent_id, history_dataset_association.designation, history_dataset_association.deleted, history_dataset_association.visible, history_dataset_association.extended_metadata_id, history_dataset_association.version, history_dataset_association.hid, history_dataset_association.purged, history_dataset_association.hidden_beneath_collection_instance_id \nFROM history_dataset_association, job_to_output_dataset \nWHERE job.id = job_to_output_dataset.job_id AND history_dataset_association.id = job_to_output_dataset.dataset_id AND history_dataset_association.deleted = true) AS anon_1, EXISTS (SELECT history_dataset_collection_association.id \nFROM history_dataset_collection_association, job_to_output_dataset_collection \nWHERE job.id = job_to_output_dataset_collection.job_id AND history_dataset_collection_association.id = job_to_output_dataset_collection.dataset_collection_id AND history_dataset_collection_association.deleted = true) AS anon_2, job.id AS job_id, job.create_time AS job_create_time, job.update_time AS job_update_time, job.history_id AS job_history_id, job.library_folder_id AS job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS job_tool_version, job.state AS job_state, job.info AS job_info, job.copied_from_job_id AS job_copied_from_job_id, job.command_line AS job_command_line, job.dependencies AS job_dependencies, job.param_filename AS job_param_filename, job.runner_name AS job_runner_name_1, job.stdout AS job_stdout, job.stderr AS job_stderr, job.exit_code AS job_exit_code, job.traceback AS job_traceback, job.session_id AS job_session_id, job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name, job.job_runner_external_id AS job_job_runner_external_id, job.destination_id AS job_destination_id, job.destination_params AS job_destination_params, job.object_store_id AS job_object_store_id, job.imported AS job_imported, job.params AS job_params, job.handler AS job_handler \nFROM job \nWHERE job.state = %(state_1)s AND job.handler = %(handler_1)s AND job.id NOT IN (SELECT job.id \nFROM job JOIN job_to_input_dataset ON job.id = job_to_input_dataset.job_id JOIN history_dataset_association ON history_dataset_association.id = job_to_input_dataset.dataset_id JOIN dataset ON dataset.id = history_dataset_association.dataset_id \nWHERE job.state = %(state_2)s AND (history_dataset_association.state = %(_state_1)s OR history_dataset_association.deleted = true OR dataset.state != %(state_3)s OR dataset.deleted = true)) AND job.id NOT IN (SELECT job.id \nFROM job JOIN job_to_input_library_dataset ON job.id = job_to_input_library_dataset.job_id JOIN library_dataset_dataset_association ON library_dataset_dataset_association.id = job_to_input_library_dataset.ldda_id JOIN dataset ON dataset.id = library_dataset_dataset_association.dataset_id \nWHERE job.state = %(state_4)s AND (library_dataset_dataset_association.state IS NOT NULL OR library_dataset_dataset_association.deleted = true OR dataset.state != %(state_5)s OR dataset.deleted = true)) ORDER BY job.id'] [parameters: {'state_3': 'ok', 'handler_1': 'main.web.2', 'state_1': 'new', '_state_1': 'failed_metadata', 'state_2': 'new', 'state_5': 'ok', 'state_4': 'new'}] (Background on this error at: http://sqlalche.me/e/e3q8)
Never mind folks, it was that I had an older version of nginx running with a different config file. After I added the upload module and restarted it, now I could simply go to the UI by just specifying the host name. But...how do I stop/start this still remains unclear. please help if you could. :-) I see that I have so many python processes and postgresql processes: bioinfo+ 101567 101415 0 19:41 ? 00:00:04 /media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/bin/python2 /media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/bin/uwsgi --virtualenv /media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv --ini-paste /media/libraryfiles/bioinfoadmin/bioinfoadmin/config/galaxy.ini --logdate --thunder-lock --master --processes 2 --threads 2 --logto /media/libraryfiles/bioinfoadmin/bioinfoadmin/uwsgi.log --socket 127.0.0.1:4001 --pythonpath lib --stats 127.0.0.1:9191 -b 16384 bioinfo+ 101568 101415 1 19:41 ? 00:01:38 /media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/bin/python ./lib/galaxy/main.py -c /media/libraryfiles/bioinfoadmin/bioinfoadmin/config/galaxy.ini --server-name=handler0 --log-file=/media/libraryfiles/bioinfoadmin/bioinfoadmin/handler0.log bioinfo+ 101569 101415 1 19:41 ? 00:01:37 /media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/bin/python ./lib/galaxy/main.py -c /media/libraryfiles/bioinfoadmin/bioinfoadmin/config/galaxy.ini --server-name=handler1 --log-file=/media/libraryfiles/bioinfoadmin/bioinfoadmin/handler1.log bioinfo+ 101570 101415 1 19:41 ? 00:01:38 /media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/bin/python ./lib/galaxy/main.py -c /media/libraryfiles/bioinfoadmin/bioinfoadmin/config/galaxy.ini --server-name=handler2 --log-file=/media/libraryfiles/bioinfoadmin/bioinfoadmin/handler2.log bioinfo+ 101571 101415 1 19:41 ? 00:01:38 /media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/bin/python ./lib/galaxy/main.py -c /media/libraryfiles/bioinfoadmin/bioinfoadmin/config/galaxy.ini --server-name=handler3 --log-file=/media/libraryfiles/bioinfoadmin/bioinfoadmin/handler3.log bioinfo+ 102477 101567 1 19:41 ? 00:01:39 /media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/bin/python2 /media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/bin/uwsgi --virtualenv /media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv --ini-paste /media/libraryfiles/bioinfoadmin/bioinfoadmin/config/galaxy.ini --logdate --thunder-lock --master --processes 2 --threads 2 --logto /media/libraryfiles/bioinfoadmin/bioinfoadmin/uwsgi.log --socket 127.0.0.1:4001 --pythonpath lib --stats 127.0.0.1:9191 -b 16384 bioinfo+ 102478 101567 1 19:41 ? 00:01:39 /media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/bin/python2 /media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/bin/uwsgi --virtualenv /media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv --ini-paste /media/libraryfiles/bioinfoadmin/bioinfoadmin/config/galaxy.ini --logdate --thunder-lock --master --processes 2 --threads 2 --logto /media/libraryfiles/bioinfoadmin/bioinfoadmin/uwsgi.log --socket 127.0.0.1:4001 --pythonpath lib --stats 127.0.0.1:9191 -b 16384 $ ps -ef | grep -i post postgres 102744 1 0 19:41 ? 00:00:00 /usr/lib/postgresql/10/bin/postgres -D /var/lib/postgresql/10/main -c config_file=/etc/postgresql/10/main/postgresql.conf postgres 102747 102744 0 19:41 ? 00:00:00 postgres: 10/main: checkpointer process postgres 102748 102744 0 19:41 ? 00:00:00 postgres: 10/main: writer process postgres 102749 102744 0 19:41 ? 00:00:00 postgres: 10/main: wal writer process postgres 102750 102744 0 19:41 ? 00:00:00 postgres: 10/main: autovacuum launcher process postgres 102751 102744 0 19:41 ? 00:00:00 postgres: 10/main: stats collector process postgres 102752 102744 0 19:41 ? 00:00:00 postgres: 10/main: bgworker: logical replication launcher postgres 103679 101415 0 19:42 ? 00:00:00 /usr/lib/postgresql/9.5/bin/postmaster -D /var/lib/postgresql/9.5/main -c config_file=/etc/postgresql/9.5/main/postgresql.conf postgres 103689 103679 0 19:42 ? 00:00:00 postgres: checkpointer process postgres 103690 103679 0 19:42 ? 00:00:00 postgres: writer process postgres 103691 103679 0 19:42 ? 00:00:00 postgres: wal writer process postgres 103692 103679 0 19:42 ? 00:00:00 postgres: autovacuum launcher process postgres 103693 103679 0 19:42 ? 00:00:01 postgres: stats collector process postgres 103694 103679 0 19:42 ? 00:00:04 postgres: bioinfoadmin galaxy 127.0.0.1(36144) idle postgres 103695 103679 0 19:42 ? 00:00:04 postgres: bioinfoadmin galaxy 127.0.0.1(36146) idle postgres 103696 103679 0 19:42 ? 00:00:04 postgres: bioinfoadmin galaxy 127.0.0.1(36148) idle postgres 103697 103679 0 19:42 ? 00:00:04 postgres: bioinfoadmin galaxy 127.0.0.1(36150) idle postgres 103698 103679 0 19:42 ? 00:00:11 postgres: bioinfoadmin galaxy 127.0.0.1(36152) idle postgres 103699 103679 0 19:42 ? 00:00:11 postgres: bioinfoadmin galaxy 127.0.0.1(36154) idle postgres 103700 103679 0 19:42 ? 00:00:12 postgres: bioinfoadmin galaxy 127.0.0.1(36156) idle postgres 103701 103679 0 19:42 ? 00:00:12 postgres: bioinfoadmin galaxy 127.0.0.1(36158) idle postgres 103702 103679 0 19:42 ? 00:00:12 postgres: bioinfoadmin galaxy 127.0.0.1(36160) idle postgres 103703 103679 0 19:42 ? 00:00:11 postgres: bioinfoadmin galaxy 127.0.0.1(36162) idle postgres 103704 103679 0 19:42 ? 00:00:11 postgres: bioinfoadmin galaxy 127.0.0.1(36164) idle postgres 103705 103679 0 19:42 ? 00:00:11 postgres: bioinfoadmin galaxy 127.0.0.1(36166) idle postgres 103706 103679 0 19:42 ? 00:00:11 postgres: bioinfoadmin galaxy 127.0.0.1(36168) idle postgres 103707 103679 0 19:42 ? 00:00:11 postgres: bioinfoadmin galaxy 127.0.0.1(36170) idle postgres 103708 103679 0 19:42 ? 00:00:11 postgres: bioinfoadmin galaxy 127.0.0.1(36172) idle postgres 103709 103679 0 19:42 ? 00:00:11 postgres: bioinfoadmin galaxy 127.0.0.1(36174) idle postgres 103710 103679 0 19:42 ? 00:00:04 postgres: bioinfoadmin galaxy 127.0.0.1(36176) idle postgres 103711 103679 0 19:42 ? 00:00:04 postgres: bioinfoadmin galaxy 127.0.0.1(36178) idle Is there a script to do the work? Thanks, Rui On Fri, Oct 12, 2018 at 8:10 PM Rui Wang <ruiwang.sz@gmail.com> wrote:
Hi Folks,
So I managed to ran through the ansible. What I did was to remove certain steps. For example, I don't need slurm-drmaa and docker, then I skipped the update cache. After these minor changes, it finished successfully(?) with an error message it ignored. Then I tried to access the UI, but nothing worked. I pasted it below for your reference. If anyone has seen this before, please help. :-)
Sorry for the beginner question, so once the ansible playbook ran through...seems the galaxy and the postgresql etc were started. How do I start/stop them manually? Do I have to run the playbook every time I want to run galaxy or only after I modify the playbook? Also, if I don't look at the log, I don't even know that the UI is at 127.0.0.1:4001. Is there any documentation for this?
Thanks, Rui
error message:
galaxy.web.stack INFO 2018-10-12 19:41:53,874 [p:102477,w:1,m:0] [MainThread] Galaxy server instance 'main.web.1' is running Starting server in PID 101567. serving on uwsgi://127.0.0.1:4001 galaxy.jobs.handler ERROR 2018-10-12 19:42:48,487 [p:102477,w:1,m:0] [JobHandlerQueue.monitor_thread] Exception in monitor_step Traceback (most recent call last): File "lib/galaxy/jobs/handler.py", line 213, in __monitor self.__monitor_step() File "lib/galaxy/jobs/handler.py", line 272, in __monitor_step .order_by(model.Job.id).all() File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2737, in all return list(self) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2889, in __iter__ return self._execute_and_instances(context) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2912, in _execute_and_instances result = conn.execute(querycontext.statement, self._params) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute return meth(self, multiparams, params) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 269, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1060, in _execute_clauseelement compiled_sql, distilled_params File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context context) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception exc_info File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause reraise(type(exception), exception, tb=exc_tb, cause=cause) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context context) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute cursor.execute(statement, parameters) OperationalError: (psycopg2.OperationalError) server closed the connection unexpectedly This probably means the server terminated abnormally before or while processing the request. [SQL: 'SELECT EXISTS (SELECT history_dataset_association.id, history_dataset_association.history_id, history_dataset_association.dataset_id, history_dataset_association.create_time, history_dataset_association.update_time, history_dataset_association.state, history_dataset_association.copied_from_history_dataset_association_id, history_dataset_association.copied_from_library_dataset_dataset_association_id, history_dataset_association.name, history_dataset_association.info, history_dataset_association.blurb, history_dataset_association.peek, history_dataset_association.tool_version, history_dataset_association.extension, history_dataset_association.metadata, history_dataset_association.parent_id, history_dataset_association.designation, history_dataset_association.deleted, history_dataset_association.visible, history_dataset_association.extended_metadata_id, history_dataset_association.version, history_dataset_association.hid, history_dataset_association.purged, history_dataset_association.hidden_beneath_collection_instance_id \nFROM history_dataset_association, job_to_output_dataset \nWHERE job.id = job_to_output_dataset.job_id AND history_dataset_association.id = job_to_output_dataset.dataset_id AND history_dataset_association.deleted = true) AS anon_1, EXISTS (SELECT history_dataset_collection_association.id \nFROM history_dataset_collection_association, job_to_output_dataset_collection \nWHERE job.id = job_to_output_dataset_collection.job_id AND history_dataset_collection_association.id = job_to_output_dataset_collection.dataset_collection_id AND history_dataset_collection_association.deleted = true) AS anon_2, job.id AS job_id, job.create_time AS job_create_time, job.update_time AS job_update_time, job.history_id AS job_history_id, job.library_folder_id AS job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS job_tool_version, job.state AS job_state, job.info AS job_info, job.copied_from_job_id AS job_copied_from_job_id, job.command_line AS job_command_line, job.dependencies AS job_dependencies, job.param_filename AS job_param_filename, job.runner_name AS job_runner_name_1, job.stdout AS job_stdout, job.stderr AS job_stderr, job.exit_code AS job_exit_code, job.traceback AS job_traceback, job.session_id AS job_session_id, job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name, job.job_runner_external_id AS job_job_runner_external_id, job.destination_id AS job_destination_id, job.destination_params AS job_destination_params, job.object_store_id AS job_object_store_id, job.imported AS job_imported, job.params AS job_params, job.handler AS job_handler \nFROM job \nWHERE job.state = %(state_1)s AND job.handler = %(handler_1)s AND job.id NOT IN (SELECT job.id \nFROM job JOIN job_to_input_dataset ON job.id = job_to_input_dataset.job_id JOIN history_dataset_association ON history_dataset_association.id = job_to_input_dataset.dataset_id JOIN dataset ON dataset.id = history_dataset_association.dataset_id \nWHERE job.state = %(state_2)s AND (history_dataset_association.state = %(_state_1)s OR history_dataset_association.deleted = true OR dataset.state != %(state_3)s OR dataset.deleted = true)) AND job.id NOT IN (SELECT job.id \nFROM job JOIN job_to_input_library_dataset ON job.id = job_to_input_library_dataset.job_id JOIN library_dataset_dataset_association ON library_dataset_dataset_association.id = job_to_input_library_dataset.ldda_id JOIN dataset ON dataset.id = library_dataset_dataset_association.dataset_id \nWHERE job.state = %(state_4)s AND (library_dataset_dataset_association.state IS NOT NULL OR library_dataset_dataset_association.deleted = true OR dataset.state != %(state_5)s OR dataset.deleted = true)) ORDER BY job.id'] [parameters: {'state_3': 'ok', 'handler_1': 'main.web.1', 'state_1': 'new', '_state_1': 'failed_metadata', 'state_2': 'new', 'state_5': 'ok', 'state_4': 'new'}] (Background on this error at: http://sqlalche.me/e/e3q8) galaxy.jobs.handler ERROR 2018-10-12 19:42:48,488 [p:102478,w:2,m:0] [JobHandlerQueue.monitor_thread] Exception in monitor_step Traceback (most recent call last): File "lib/galaxy/jobs/handler.py", line 213, in __monitor self.__monitor_step() File "lib/galaxy/jobs/handler.py", line 272, in __monitor_step .order_by(model.Job.id).all() File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2737, in all return list(self) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2889, in __iter__ return self._execute_and_instances(context) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2912, in _execute_and_instances result = conn.execute(querycontext.statement, self._params) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute return meth(self, multiparams, params) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 269, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1060, in _execute_clauseelement compiled_sql, distilled_params File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context context) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception exc_info File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause reraise(type(exception), exception, tb=exc_tb, cause=cause) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context context) File "/media/libraryfiles/bioinfoadmin/bioinfoadmin/.venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute cursor.execute(statement, parameters) OperationalError: (psycopg2.OperationalError) server closed the connection unexpectedly This probably means the server terminated abnormally before or while processing the request. [SQL: 'SELECT EXISTS (SELECT history_dataset_association.id, history_dataset_association.history_id, history_dataset_association.dataset_id, history_dataset_association.create_time, history_dataset_association.update_time, history_dataset_association.state, history_dataset_association.copied_from_history_dataset_association_id, history_dataset_association.copied_from_library_dataset_dataset_association_id, history_dataset_association.name, history_dataset_association.info, history_dataset_association.blurb, history_dataset_association.peek, history_dataset_association.tool_version, history_dataset_association.extension, history_dataset_association.metadata, history_dataset_association.parent_id, history_dataset_association.designation, history_dataset_association.deleted, history_dataset_association.visible, history_dataset_association.extended_metadata_id, history_dataset_association.version, history_dataset_association.hid, history_dataset_association.purged, history_dataset_association.hidden_beneath_collection_instance_id \nFROM history_dataset_association, job_to_output_dataset \nWHERE job.id = job_to_output_dataset.job_id AND history_dataset_association.id = job_to_output_dataset.dataset_id AND history_dataset_association.deleted = true) AS anon_1, EXISTS (SELECT history_dataset_collection_association.id \nFROM history_dataset_collection_association, job_to_output_dataset_collection \nWHERE job.id = job_to_output_dataset_collection.job_id AND history_dataset_collection_association.id = job_to_output_dataset_collection.dataset_collection_id AND history_dataset_collection_association.deleted = true) AS anon_2, job.id AS job_id, job.create_time AS job_create_time, job.update_time AS job_update_time, job.history_id AS job_history_id, job.library_folder_id AS job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS job_tool_version, job.state AS job_state, job.info AS job_info, job.copied_from_job_id AS job_copied_from_job_id, job.command_line AS job_command_line, job.dependencies AS job_dependencies, job.param_filename AS job_param_filename, job.runner_name AS job_runner_name_1, job.stdout AS job_stdout, job.stderr AS job_stderr, job.exit_code AS job_exit_code, job.traceback AS job_traceback, job.session_id AS job_session_id, job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name, job.job_runner_external_id AS job_job_runner_external_id, job.destination_id AS job_destination_id, job.destination_params AS job_destination_params, job.object_store_id AS job_object_store_id, job.imported AS job_imported, job.params AS job_params, job.handler AS job_handler \nFROM job \nWHERE job.state = %(state_1)s AND job.handler = %(handler_1)s AND job.id NOT IN (SELECT job.id \nFROM job JOIN job_to_input_dataset ON job.id = job_to_input_dataset.job_id JOIN history_dataset_association ON history_dataset_association.id = job_to_input_dataset.dataset_id JOIN dataset ON dataset.id = history_dataset_association.dataset_id \nWHERE job.state = %(state_2)s AND (history_dataset_association.state = %(_state_1)s OR history_dataset_association.deleted = true OR dataset.state != %(state_3)s OR dataset.deleted = true)) AND job.id NOT IN (SELECT job.id \nFROM job JOIN job_to_input_library_dataset ON job.id = job_to_input_library_dataset.job_id JOIN library_dataset_dataset_association ON library_dataset_dataset_association.id = job_to_input_library_dataset.ldda_id JOIN dataset ON dataset.id = library_dataset_dataset_association.dataset_id \nWHERE job.state = %(state_4)s AND (library_dataset_dataset_association.state IS NOT NULL OR library_dataset_dataset_association.deleted = true OR dataset.state != %(state_5)s OR dataset.deleted = true)) ORDER BY job.id'] [parameters: {'state_3': 'ok', 'handler_1': 'main.web.2', 'state_1': 'new', '_state_1': 'failed_metadata', 'state_2': 'new', 'state_5': 'ok', 'state_4': 'new'}] (Background on this error at: http://sqlalche.me/e/e3q8)
participants (1)
-
Rui Wang