Fix upload jobs not being picked up by the job handlers:
```
FAILED test/integration/objectstore/test_onedata_objectstore.py::test_tools[multi_output_assign_primary] - galaxy.tool_util.verify.wait.TimeoutAssertionError: Timed out after 60.25 seconds waiting on tool test run.
FAILED test/integration/objectstore/test_onedata_objectstore.py::test_tools[composite_output_tests] - galaxy.tool_util.verify.wait.TimeoutAssertionError: Timed out after 60.25 seconds waiting on tool test run.
FAILED test/integration/objectstore/test_onedata_objectstore.py::test_tools[metadata_bam] - galaxy.tool_util.verify.wait.TimeoutAssertionError: Timed out after 60.25 seconds waiting on tool test run.
```
Found by running:
```
make pyupgrade
ruff check --fix .
ruff check --preview --unsafe-fixes --select=F401 --fix .
make format
make update-client-api-schema
```
The bulk of the changes are replacements of typing deprecated aliases
such as `Dict` and `List` with the standard library classes. These
aliases became redundant in Python 3.9 when the corresponding
pre-existing classes were enhanced to support `[]`, see
https://docs.python.org/3/library/typing.html#deprecated-aliases
Also:
- Update the `pyupgrade` Makefile target to use `--py38-plus` for the
packages needed by Pulsar, including the new galaxy-tool-util-models
package.
- UI for detailed display of errors.
- UI option to test configuration from management menu.
- API + UI for checking configuration before upgrading to new version of template.
- API + UI for checking configuration before updating current template's settings.
- Add an option during update/upgrade to allow forcing the update even if configuration doesn't validate - I don't allow creation of invalid things, but if there are problems with an existing thing - admins and power users should have recourse. It is their data.
stores
The problem is that `object_store.is_private` would check in which
object store the dataset is stored, and that fails if we haven't written
to the object store yet (which is why extended metadata is a
workaround).
Fixes https://github.com/galaxyproject/galaxy/issues/17208
In the extended_metadata + remote tool_evaluation_strategy the
commandline is templated as part of the job, so we need to give the test
more time to start running before we delete outputs (as then we can't
template the command line anymore).
Add a sleep so we can delay output purging until command line is
templated. If we don't sleep we generate a command line where the
output path is just `''`. That needs another fix!
I think I clung to the idea of having two ways to do this too long. I did a bunch of testing with the old way (exposing integer references based on numeric database primary keys). Having a config option that if changed would break everything exisiting is also a symptom of maybe me clinging too hard for too long.
The result of dropping this option is a much cleaner API schema, simpler API objects, and better typing throughout. We can also be more certain of how things entering the Vault are stored - I think being more strucutured about this is good.
Ultimately, the future facing stuff (e.g. OAuth 2.0) is going to require UUIDs so that I can store things like refresh tokens in the store before the object has been fully created.
Nicola Soranzo