This test fails because cut fails on the compressed input with
`cut: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpu8gqd71c/tmpmae9egoz/tmpz8sonmgx/database/objects/6/9/8/dataset_69847aef-7b3f-4915-a8ae-394921dbe388.dat: Illegal byte sequence`
with the ``CONVERTER_gz_to_uncompressed`` tool.
Previously, if a user forced an incorrect datatype to a compressed input
dataset (e.g. `fastqsanger` instead of `fastqsanger.gz`), then the output
datatype assigned by this tool would be an invalid one (`fastqsan`).
Fix#17938.
In https://github.com/galaxyproject/galaxy/commit/3fd5b0252f840dbb92aaebf31b9d21034b21c578 we changed the sqlalchemy query construct `one_or_none`
method to use the core statement `.scalar_one_or_none`, which bypasses
the identity map. Since there are a handful of legacy accounts with
duplicate UserRoleAssociation rows on usegalaxy.{org,eu} the
deduplication that occured via the entity map meant that no exception
was raised, while for the core level construct this happened.
Fortunately it's easy enough to simply add a distinct
statement to return to the old behavior.
Here's an ipython session to prove this:
"""
In [4]: ura = sa_session.query(UserRoleAssociation).filter_by(user_id=1, role_id=1).all()
In [5]: ura
Out[5]: [<galaxy.model.UserRoleAssociation(1) at 0x165809190>]
In [6]: new_ura = UserRoleAssociation(sa_session.get(User, 1), sa_session.get(Role, 1))
In [7]: sa_session.add(new_ura)
In [8]: sa_session.flush()
In [9]: role = (
...: sa_session.query(Role)
...: .filter(
...: and_(
...: UserRoleAssociation.table.c.user_id == 1,
...: Role.id == UserRoleAssociation.table.c.role_id,
...: Role.type == Role.types.PRIVATE,
...: )
...: )
...: .one_or_none()
...: )
In [10]: stmt = select(Role).where(
...: and_(
...: UserRoleAssociation.user_id == 1,
...: Role.id == UserRoleAssociation.role_id,
...: Role.type == Role.types.PRIVATE,
...: )
...: )
...: role = sa_session.execute(stmt).scalar_one_or_none()
---------------------------------------------------------------------------
MultipleResultsFound Traceback (most recent call last)
Cell In[10], line 8
1 stmt = select(Role).where(
2 and_(
3 UserRoleAssociation.user_id == 1,
(...)
6 )
7 )
----> 8 role = sa_session.execute(stmt).scalar_one_or_none()
File ~/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/engine/result.py:1225, in Result.scalar_one_or_none(self)
1212 def scalar_one_or_none(self):
1213 """Return exactly one scalar result or ``None``.
1214
1215 This is equivalent to calling :meth:`_engine.Result.scalars` and
(...)
1223
1224 """
-> 1225 return self._only_one_row(
1226 raise_for_second_row=True, raise_for_none=False, scalar=True
1227 )
File ~/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/engine/result.py:614, in ResultInternal._only_one_row(self, raise_for_second_row, raise_for_none, scalar)
612 if next_row is not _NO_ROW:
613 self._soft_close(hard=True)
--> 614 raise exc.MultipleResultsFound(
615 "Multiple rows were found when exactly one was required"
616 if raise_for_none
617 else "Multiple rows were found when one or none "
618 "was required"
619 )
620 else:
621 next_row = _NO_ROW
MultipleResultsFound: Multiple rows were found when one or none was required
In [11]: stmt = select(Role).where(
...: and_(
...: UserRoleAssociation.user_id == 1,
...: Role.id == UserRoleAssociation.role_id,
...: Role.type == Role.types.PRIVATE,
...: )
...: ).distinct()
...: role = sa_session.execute(stmt).scalar_one_or_none()
"""
I think that's what the sqlalchemy docs for [Query.one_or_none](https://docs.sqlalchemy.org/en/14/orm/query.html#sqlalchemy.orm.Query.one_or_none) mean to
communicate with
> Returns None if the query selects no rows. Raises sqlalchemy.orm.exc.MultipleResultsFound if multiple object identities are returned, or if multiple rows are returned for a query that returns only scalar values as opposed to full identity-mapped entities.
Fixes https://github.com/galaxyproject/galaxy/issues/17848
mvdbeek