Running the test without removing the session yields:
```
celery.app.trace ERROR 2024-01-17 11:49:42,502 [pN:main,p:81158,tN:Thread-2 (start)] Task integration.test_celery_tasks.use_session[0f89df2c-4960-4aac-8e1a-ce431dae6749] raised unexpected: PendingRollbackError("Can't reconnect until invalid transaction is rolled back.")
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/celery/app/trace.py", line 477, in trace_task
R = retval = fun(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/celery/__init__.py", line 181, in wrapper
rval = app.magic_partial(func)(*args, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/lagom/wrapping.py", line 28, in _bound_func
return inner_func(*bound_args, **bound_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/lagom/wrapping.py", line 45, in _error_handling_func
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/test/integration/test_celery_tasks.py", line 42, in use_session
sa_session().query(HistoryDatasetAssociation).get(1)
File "<string>", line 2, in get
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/util/deprecations.py", line 468, in warned
return fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/orm/query.py", line 947, in get
return self._get_impl(ident, loading.load_on_pk_identity)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/orm/query.py", line 951, in _get_impl
return self.session._get_impl(
^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 2975, in _get_impl
return db_load_fn(
^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/orm/loading.py", line 530, in load_on_pk_identity
session.execute(
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 1717, in execute
result = conn._execute_20(statement, params or {}, execution_options)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 1710, in _execute_20
return meth(self, args_10style, kwargs_10style, execution_options)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/sql/elements.py", line 334, in _execute_on_connection
return connection._execute_clauseelement(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 1577, in _execute_clauseelement
ret = self._execute_context(
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 1808, in _execute_context
conn = self._revalidate_connection()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 650, in _revalidate_connection
self._invalid_transaction()
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 622, in _invalid_transaction
raise exc.PendingRollbackError(
sqlalchemy.exc.PendingRollbackError: Can't reconnect until invalid transaction is rolled back. (Background on this error at: https://sqlalche.me/e/14/8s2b)
FAILEDINFO: 127.0.0.1:59776 - "GET /api/jobs?state=running HTTP/1.1" 200 OK
```
The fix here is to set a unique scope for the session registry.
This means that the task is guranteed to get a new, unshared session,
and this session gets removed after completing the task.
The docstring of session.remove says:
```
This will first call :meth:`.Session.close` method
on the current :class:`.Session`, which releases any existing
transactional/connection resources still being held; transactions
specifically are rolled back. The :class:`.Session` is then
discarded. Upon next usage within the same scope,
the :class:`.scoped_session` will produce a new
:class:`.Session` object.
```
which I think is what we want after every celery task (for now, at least).
It might make sense to discard the session for any long-running task
that doesn't require database access in the future.
Fix scope
Latest celery fixes exception reporting, but doesn't work on python 3.7.
I'm only adding this to {pinned,dev}-requirements.txt. When merging forward
we can drop the 3.7 dependency.
in tool schema. New lxml is more strict when validating
the xml schema and fails with
```
lxml.etree.XMLSchemaParseError: complex type 'Output': The content model is not determinist., line 5329
```
this is because `filter` and `discover_datasets` are present in
OutputDataElement and OutputCollectionElement, making
```
<xs:sequence>
<xs:group ref="OutputDataElement" minOccurs="0" maxOccurs="unbounded" />
<xs:group ref="OutputCollectionElement" minOccurs="0" maxOccurs="unbounded" />
</xs:sequence>
```
not deterministic.
In any case this isn't an accurate model of what is allowed and parsed,
as you can't use collection-specific discover_datasets options outside
of a dataset collection.
I **think** that the reason for adding
OutputCollectionElement to the sequence is that you can have a `data`
element nested in a `collection` element.
To continue allowing this and making it more precise I've added an
additional `OutputCollectionDataElement` type that is allowed within
`collection`. This then should allow us to remove
`OutputCollectionElement` from the `OutputData` type.
A quick test against IUC and devteam revealed no problem with this
approach per se, however it showed that https://github.com/galaxyproject/tools-iuc/blob/aa8360cb3ec9faf1488938a430855977632706ff/tools/krakentools/extract_kraken_reads.xml#L145
uses `change_format` which is not implemented for collections.
