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Created June 21, 2023 18:29
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deadlock error log
# Date: 6/15/23
# PR #16209
# api tests
2023-06-15T21:54:46.7968842Z Traceback (most recent call last):
2023-06-15T21:54:46.7969423Z File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/web/framework/decorators.py", line 337, in decorator
2023-06-15T21:54:46.7969911Z rval = func(self, trans, *args, **kwargs)
2023-06-15T21:54:46.7970491Z File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/webapps/galaxy/api/tools.py", line 563, in create
2023-06-15T21:54:46.7971005Z return self.service._create(trans, payload, **kwd)
2023-06-15T21:54:46.7971600Z File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/webapps/galaxy/services/tools.py", line 175, in _create
2023-06-15T21:54:46.7972124Z preferred_object_store_id=preferred_object_store_id,
2023-06-15T21:54:46.7972702Z File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tools/__init__.py", line 2010, in handle_input
2023-06-15T21:54:46.7973153Z completed_jobs=completed_jobs,
2023-06-15T21:54:46.7973707Z File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tools/execute.py", line 182, in execute
2023-06-15T21:54:46.7974133Z trans.sa_session.commit()
2023-06-15T21:54:46.7974504Z File "<string>", line 2, in commit
2023-06-15T21:54:46.7975269Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 1454, in commit
2023-06-15T21:54:46.7975803Z self._transaction.commit(_to_root=self.future)
2023-06-15T21:54:46.7976569Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 832, in commit
2023-06-15T21:54:46.7977041Z self._prepare_impl()
2023-06-15T21:54:46.7977794Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 811, in _prepare_impl
2023-06-15T21:54:46.7978259Z self.session.flush()
2023-06-15T21:54:46.7979154Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 3449, in flush
2023-06-15T21:54:46.7979629Z self._flush(objects)
2023-06-15T21:54:46.7980365Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 3589, in _flush
2023-06-15T21:54:46.7980920Z transaction.rollback(_capture_exception=True)
2023-06-15T21:54:46.7981714Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/util/langhelpers.py", line 72, in __exit__
2023-06-15T21:54:46.7982175Z with_traceback=exc_tb,
2023-06-15T21:54:46.7982902Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 211, in raise_
2023-06-15T21:54:46.7983353Z raise exception
2023-06-15T21:54:46.7984070Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 3549, in _flush
2023-06-15T21:54:46.7984540Z flush_context.execute()
2023-06-15T21:54:46.7985496Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 456, in execute
2023-06-15T21:54:46.7985952Z rec.execute(self)
2023-06-15T21:54:46.7986683Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 633, in execute
2023-06-15T21:54:46.7987118Z uow,
2023-06-15T21:54:46.7987834Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 250, in save_obj
2023-06-15T21:54:46.7988289Z insert,
2023-06-15T21:54:46.7989533Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 1241, in _emit_insert_statements
2023-06-15T21:54:46.7990233Z execution_options=execution_options,
2023-06-15T21:54:46.7991329Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1710, in _execute_20
2023-06-15T21:54:46.7991915Z return meth(self, args_10style, kwargs_10style, execution_options)
2023-06-15T21:54:46.7992767Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/sql/elements.py", line 335, in _execute_on_connection
2023-06-15T21:54:46.7993334Z self, multiparams, params, execution_options
2023-06-15T21:54:46.7994155Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1587, in _execute_clauseelement
2023-06-15T21:54:46.7994785Z cache_hit=cache_hit,
2023-06-15T21:54:46.7995710Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1949, in _execute_context
2023-06-15T21:54:46.7996239Z e, statement, parameters, cursor, context
2023-06-15T21:54:46.7997061Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 2130, in _handle_dbapi_exception
2023-06-15T21:54:46.7997669Z sqlalchemy_exception, with_traceback=exc_info[2], from_=e
2023-06-15T21:54:46.7998587Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 211, in raise_
2023-06-15T21:54:46.7999023Z raise exception
2023-06-15T21:54:46.8000583Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1906, in _execute_context
2023-06-15T21:54:46.8001054Z cursor, statement, parameters, context
2023-06-15T21:54:46.8002191Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 736, in do_execute
2023-06-15T21:54:46.8003047Z cursor.execute(statement, parameters)
2023-06-15T21:54:46.8003652Z sqlalchemy.exc.OperationalError: (psycopg2.errors.DeadlockDetected) deadlock detected
2023-06-15T21:54:46.8004316Z DETAIL: Process 277 waits for ShareLock on transaction 4411; blocked by process 273.
2023-06-15T21:54:46.8005084Z Process 273 waits for ShareLock on transaction 4410; blocked by process 277.
2023-06-15T21:54:46.8005574Z HINT: See server log for query details.
2023-06-15T21:54:46.8006139Z CONTEXT: while locking tuple (0,142) in relation "history_dataset_collection_association"
2023-06-15T21:54:46.8007127Z SQL statement "SELECT 1 FROM ONLY "public"."history_dataset_collection_association" x WHERE "id" OPERATOR(pg_catalog.=) $1 FOR KEY SHARE OF x"
2023-06-15T21:54:46.8007766Z
2023-06-15T21:54:46.8008379Z [SQL: INSERT INTO job_to_input_dataset_collection (job_id, dataset_collection_id, name) VALUES (%(job_id)s, %(dataset_collection_id)s, %(name)s) RETURNING job_to_input_dataset_collection.id]
2023-06-15T21:54:46.8009371Z [parameters: {'job_id': 197, 'dataset_collection_id': 79, 'name': 'input'}]
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