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[24.0] Don't set file size to zero #18653

Merged
merged 2 commits into from
Aug 6, 2024
Merged

[24.0] Don't set file size to zero #18653

merged 2 commits into from
Aug 6, 2024

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@mvdbeek mvdbeek commented Aug 6, 2024

Fixes #18648

How to test the changes?

(Select all options that apply)

  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.
  • Instructions for manual testing are as follows:
    1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

  • I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

@github-actions github-actions bot added this to the 24.1 milestone Aug 6, 2024
@bgruening bgruening merged commit c3738ad into galaxyproject:release_24.0 Aug 6, 2024
44 of 51 checks passed
@nsoranzo nsoranzo deleted the dont_set_file_size_to_zero branch August 6, 2024 22:17
@davelopez davelopez mentioned this pull request Aug 9, 2024
Merged
4 tasks
mvdbeek added a commit to mvdbeek/galaxy that referenced this pull request Aug 12, 2024
@mvdbeek
Make sure we set file size also for purged outputs
c71f944 
Fixes one of the integration tests:
```
Exception: HistoryDatasetAssociation <galaxy.model.HistoryDatasetAssociation(None) at 0x7f50ddcf56a0> in state ok with null file size, this is not valid
ERROR    galaxy.jobs.runners:__init__.py:177 (1) Unhandled exception calling finish_job
Traceback (most recent call last):
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/runners/pulsar.py", line 702, in finish_job
    job_wrapper.finish(
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/__init__.py", line 2054, in finish
    self.sa_session.commit()
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/scoping.py", line 597, in commit
    return self._proxied.commit()
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 2017, in commit
    trans.commit(_to_root=True)
  File "<string>", line 2, in commit
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/state_changes.py", line 139, in _go
    ret_value = fn(self, *arg, **kw)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1302, in commit
    self._prepare_impl()
  File "<string>", line 2, in _prepare_impl
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/state_changes.py", line 139, in _go
    ret_value = fn(self, *arg, **kw)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1277, in _prepare_impl
    self.session.flush()
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 4341, in flush
    self._flush(objects)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 4369, in _flush
    self.dispatch.before_flush(self, flush_context, objects)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/event/attr.py", line 378, in __call__
    fn(*args, **kw)
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/base.py", line 184, in before_flush
    obj.__strict_check_before_flush__()
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/__init__.py", line 5223, in __strict_check_before_flush__
    raise Exception(
Exception: HistoryDatasetAssociation <galaxy.model.HistoryDatasetAssociation(None) at 0x7f50ddcf56a0> in state ok with null file size, this is not valid

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/runners/__init__.py", line 174, in run_next
    method(arg)
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/runners/pulsar.py", line 713, in finish_job
    job_wrapper.fail("Unable to finish job", exception=True)
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/__init__.py", line 1468, in fail
    self.sa_session.commit()
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/scoping.py", line 597, in commit
    return self._proxied.commit()
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 2017, in commit
    trans.commit(_to_root=True)
  File "<string>", line 2, in commit
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/state_changes.py", line 139, in _go
    ret_value = fn(self, *arg, **kw)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1302, in commit
    self._prepare_impl()
  File "<string>", line 2, in _prepare_impl
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/state_changes.py", line 139, in _go
    ret_value = fn(self, *arg, **kw)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1277, in _prepare_impl
    self.session.flush()
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 4341, in flush
    self._flush(objects)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 4369, in _flush
    self.dispatch.before_flush(self, flush_context, objects)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/event/attr.py", line 378, in __call__
    fn(*args, **kw)
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/base.py", line 184, in before_flush
    obj.__strict_check_before_flush__()
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/__init__.py", line 5223, in __strict_check_before_flush__
    raise Exception(
Exception: HistoryDatasetAssociation <galaxy.model.HistoryDatasetAssociation(None) at 0x7f50ddcf56a0> in state ok with null file size, this is not valid
```

More fallout from galaxyproject#18653
@mvdbeek mvdbeek mentioned this pull request Aug 12, 2024
Merged
4 tasks
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@davelopez davelopez davelopez approved these changes

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@mvdbeek @davelopez @bgruening