[23.1] Let job handler work queue call job wrapper fail #17083
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This avoids committing the transaction and then have it fail on the next iteration. Should fix the app startup failing in galaxyproject#17079
mvdbeek
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jmchilton
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Nov 25, 2023
mvdbeek
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Nov 26, 2023
I think the premise that we want to do a rollback on exceptions in this
method is wrong (it **may** be correct apprach in other places in the
codebase e.g. in
`Tool.handle_single_execution()`). Here it prevents us from comitting
anything inside the with statement (as the job_wrapper.fail method
does).
Here's the simplified issue:
```shell
❯ python -i scripts/db_shell.py -c config/galaxy.yml
>>> with sa_session() as session, session.begin():
... sa_session.execute(update(Job).where(Job.id == 1).values(state="error"))
... sa_session.commit()
... sa_session.execute(update(Job).where(Job.id == 1).values(state="ok"))
... sa_session.commit()
...
<sqlalchemy.engine.cursor.LegacyCursorResult object at 0x11f1be350>
Traceback (most recent call last):
File "<stdin>", line 4, in <module>
File "<string>", line 2, in execute
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 1711, in execute
conn = self._connection_for_bind(bind, close_with_result=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 1552, in _connection_for_bind
TransactionalContext._trans_ctx_check(self)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/engine/util.py", line 199, in _trans_ctx_check
raise exc.InvalidRequestError(
sqlalchemy.exc.InvalidRequestError: Can't operate on closed transaction inside context manager. Please complete the context manager before emitting further commands.
```
It is probably still worthwhile to have the job recovery be minimal and
do things such as calling the job wrapper fail method that does actual
work to the job handler as in
galaxyproject#17083, but that's
refactoring that can be done on the dev branch and it still seems risky
in the sense that we then need to be very careful in ensuring we don't
commit anywhere else inside the scope of the begin() statement.
Finally I don't think it makes sense that the startup check should
ever cause the boot process to fail. This isn't a misconfiguration
or even anything catastrophic for the remaining jobs and places
unnecessary stress on admins and can basically break at any time
and shouldn't cause a complete service failure.
Fixes galaxyproject#17079
4 tasks
mvdbeek
added a commit
to mvdbeek/galaxy
that referenced
this pull request
Nov 27, 2023
I think the premise that we want to do a rollback on exceptions in this
method is wrong (it **may** be correct apprach in other places in the
codebase e.g. in
`Tool.handle_single_execution()`). Here it prevents us from comitting
anything inside the with statement (as the job_wrapper.fail method
does).
Here's the simplified issue:
```shell
❯ python -i scripts/db_shell.py -c config/galaxy.yml
>>> with sa_session() as session, session.begin():
... sa_session.execute(update(Job).where(Job.id == 1).values(state="error"))
... sa_session.commit()
... sa_session.execute(update(Job).where(Job.id == 1).values(state="ok"))
... sa_session.commit()
...
<sqlalchemy.engine.cursor.LegacyCursorResult object at 0x11f1be350>
Traceback (most recent call last):
File "<stdin>", line 4, in <module>
File "<string>", line 2, in execute
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 1711, in execute
conn = self._connection_for_bind(bind, close_with_result=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 1552, in _connection_for_bind
TransactionalContext._trans_ctx_check(self)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/engine/util.py", line 199, in _trans_ctx_check
raise exc.InvalidRequestError(
sqlalchemy.exc.InvalidRequestError: Can't operate on closed transaction inside context manager. Please complete the context manager before emitting further commands.
```
It is probably still worthwhile to have the job recovery be minimal and
do things such as calling the job wrapper fail method that does actual
work to the job handler as in
galaxyproject#17083, but that's
refactoring that can be done on the dev branch and it still seems risky
in the sense that we then need to be very careful in ensuring we don't
commit anywhere else inside the scope of the begin() statement.
Finally I don't think it makes sense that the startup check should
ever cause the boot process to fail. This isn't a misconfiguration
or even anything catastrophic for the remaining jobs and places
unnecessary stress on admins and can basically break at any time
and shouldn't cause a complete service failure.
Fixes galaxyproject#17079
mvdbeek
added a commit
to mvdbeek/galaxy
that referenced
this pull request
Nov 27, 2023
I think the premise that we want to do a rollback on exceptions in this
method is wrong (it **may** be correct apprach in other places in the
codebase e.g. in
`Tool.handle_single_execution()`). Here it prevents us from comitting
anything inside the with statement (as the job_wrapper.fail method
does).
Here's the simplified issue:
```shell
❯ python -i scripts/db_shell.py -c config/galaxy.yml
>>> with sa_session() as session, session.begin():
... sa_session.execute(update(Job).where(Job.id == 1).values(state="error"))
... sa_session.commit()
... sa_session.execute(update(Job).where(Job.id == 1).values(state="ok"))
... sa_session.commit()
...
<sqlalchemy.engine.cursor.LegacyCursorResult object at 0x11f1be350>
Traceback (most recent call last):
File "<stdin>", line 4, in <module>
File "<string>", line 2, in execute
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 1711, in execute
conn = self._connection_for_bind(bind, close_with_result=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 1552, in _connection_for_bind
TransactionalContext._trans_ctx_check(self)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/engine/util.py", line 199, in _trans_ctx_check
raise exc.InvalidRequestError(
sqlalchemy.exc.InvalidRequestError: Can't operate on closed transaction inside context manager. Please complete the context manager before emitting further commands.
```
It is probably still worthwhile to have the job recovery be minimal and
do things such as calling the job wrapper fail method that does actual
work to the job handler as in
galaxyproject#17083, but that's
refactoring that can be done on the dev branch and it still seems risky
in the sense that we then need to be very careful in ensuring we don't
commit anywhere else inside the scope of the begin() statement.
Finally I don't think it makes sense that the startup check should
ever cause the boot process to fail. This isn't a misconfiguration
or even anything catastrophic for the remaining jobs and places
unnecessary stress on admins and can basically break at any time
and shouldn't cause a complete service failure.
Fixes galaxyproject#17079
|
The mypy error is legitimate though definitely confusing. |
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This avoids committing the transaction and then have it fail on the next iteration. Should fix the app startup failing in #17079
There's more places though where we commit in the startup case. I wonder if all that's even necessary, the job handler should probably handle all of the error conditions ?
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