mvdbeek c71f944093 Make sure we set file size also for purged outputs ...

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 https://github.com/galaxyproject/galaxy/pull/18653

2024-08-12 12:11:38 +02:00

..

galaxy

Make sure we set file size also for purged outputs

2024-08-12 12:11:38 +02:00

galaxy_ext

Update to black 2024 stable style

2024-01-30 18:09:51 +00:00

galaxy_test

Test that we don't reset the file size

2024-08-06 17:33:02 +02:00

tool_shed

Use get_app_with_request_session as dependency resolver

2024-08-02 12:31:13 +02:00

tool_shed_client

Fix test_install_info test

2024-01-08 15:25:39 +01:00