Created
June 21, 2023 18:29
-
-
Save jdavcs/5594b44c28eae2122189a57c3307e6ee to your computer and use it in GitHub Desktop.
deadlock error log
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# 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'}] |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment