Traverse all registered API routes, attempt to load schema information
if available in docstring, register with an `APISpec` instance, and
convert to YAML.
if we're building a web app, but aren't using gunicorn. I don't think
this has a big impact currently, since you can only set base pools via
lib/galaxy/main.py. I think you could set up alternative logging based
on the web stack class though, and this seems cleaner.
Fixes:
```
AttributeError: 'UniverseApplication' object has no attribute 'user_manager'
File "galaxy/web/framework/decorators.py", line 312, in decorator
rval = func(self, trans, *args, **kwargs)
File "galaxy/webapps/galaxy/api/authenticate.py", line 63, in get_api_key
user = self.app.user_manager.get_user_by_identity(identity)
```
This broke when we started re-exporting jobs to update their command
line in https://github.com/galaxyproject/galaxy/pull/12459/commits/65e0ee213ae574bc0a45dfcc60e997863ff96a7c#diff-bfb854f344e56a25a86761f80a639de09add404a7a53ebde45afb908762fc1eaR161:
```
ERROR galaxy.jobs:__init__.py:1836 problem importing job outputs. stdout [] stderr [
Traceback (most recent call last):
File "metadata/set.py", line 1, in <module>
from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/metadata/set_metadata.py", line 121, in set_metadata
set_metadata_portable()
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/metadata/set_metadata.py", line 307, in set_metadata_portable
export_store.export_job(job, include_job_data=False)
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/__init__.py", line 1320, in export_job
self.export_jobs([job], include_job_data=include_job_data)
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/__init__.py", line 1336, in export_jobs
job_attrs = job.serialize(self.security, self.serialization_options)
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/__init__.py", line 339, in serialize
return self._serialize(id_encoder, serialization_options)
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/__init__.py", line 1447, in _serialize
params_objects = remap(params_objects, remap_objects)
File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/boltons/iterutils.py", line 1128, in remap
visited_item = visit(path, key, value)
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/__init__.py", line 1441, in remap_objects
new_id = serialization_options.get_identifier_for_id(id_encoder, obj["id"])
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/__init__.py", line 323, in get_identifier_for_id
raise NotImplementedError()
NotImplementedError
]
```
To test run `GALAXY_CONFIG_METADATA_STRATEGY=extended ./run_tests.sh
-api
lib/galaxy_test/api/test_jobs.py::JobsApiTestCase::test_dce_submission_security`
Nicola Soranzo