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`
I don't think this tool is really used much, but it is loaded in
`tool_conf.xml`.
https://github.com/galaxyproject/galaxy/pull/11877 added type
annotations, and that's a syntax error on 2.7
The alternative would be to fix the rest of the tool for 3.x,
but I think we're just wasting our time there and we shouldn't
touch this again.
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`
xref: https://github.com/galaxyproject/galaxy/issues/13551, fixes
```
galaxy.jobs ERROR 2022-03-15 00:21:29,515 [pN:main,p:2180,tN:LocalRunner.work_thread-3] 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 291, in set_metadata_portable
collect_dynamic_outputs(job_context, output_collections)
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/job_execution/output_collect.py", line 147, in collect_dynamic_outputs
persist_elements_to_hdca(job_context, elements, hdca, collector=DEFAULT_DATASET_COLLECTOR)
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/discover.py", line 719, in persist_elements_to_hdca
filenames,
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/discover.py", line 292, in populate_collection_elements
final_job_state=final_job_state,
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/discover.py", line 354, in _populate_elements
self.add_tags_to_datasets(datasets=element_datasets["datasets"], tag_lists=element_datasets["tag_lists"])
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/discover.py", line 576, in add_tags_to_datasets
self.tag_handler.add_tags_from_list(user, dataset, tags, flush=False)
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 61, in add_tags_from_list
return self.set_tags_from_list(user, item, new_tags_set, flush=flush)
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 75, in set_tags_from_list
self.apply_item_tags(user, item, unicodify(new_tags_str, "utf-8"), flush=flush)
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 207, in apply_item_tags
self.apply_item_tag(user, item, name, value, flush=flush)
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 179, in apply_item_tag
tag = self._get_or_create_tag(lc_name)
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 281, in _get_or_create_tag
tag = self._create_tag(scrubbed_tag_str)
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 246, in _create_tag
tag = self._create_tag_instance(tag_name)
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 428, in _create_tag_instance
tag = super()._create_tag_instance(tag_name)
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 259, in _create_tag_instance
Session = sessionmaker(self.sa_session.bind)
AttributeError: 'NoneType' object has no attribute 'bind'
]
Traceback (most recent call last):
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/__init__.py", line 1828, in finish
import_model_store.perform_import(history=job.history, job=job)
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/__init__.py", line 209, in perform_import
datasets_attrs = self.datasets_properties()
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/__init__.py", line 930, in datasets_properties
datasets_attrs = load(open(datasets_attrs_file_name))
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmp19s6x278/tmpt0rr8vmw/tmp2mjq6ysx/database/job_working_directory1/000/7/metadata/outputs_populated/datasets_attrs.txt'
galaxy.jobs.runners ERROR 2022-03-15 00:21:29,516 [pN:main,p:2180,tN:LocalRunner.work_thread-3] (7/) Job wrapper finish method failed
Traceback (most recent call last):
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/runners/__init__.py", line 594, in _finish_or_resubmit_job
job_stderr=job_stderr,
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/__init__.py", line 1828, in finish
import_model_store.perform_import(history=job.history, job=job)
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/__init__.py", line 209, in perform_import
datasets_attrs = self.datasets_properties()
File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/__init__.py", line 930, in datasets_properties
datasets_attrs = load(open(datasets_attrs_file_name))
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmp19s6x278/tmpt0rr8vmw/tmp2mjq6ysx/database/job_working_directory1/000/7/metadata/outputs_populated/datasets_attrs.txt'
```
mvdbeek