Merge 23.1 into dev #17000
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Merge 23.1 into dev #17000
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…aram_name_fallback [23.1] Backport Fix select parameter doesn't show parameter name in UI
adds `biii` as supported xref reference type
Added a `fixed_delegated_path` variable to the `ConfigSerializer` that lets us reroute users to home if we have a Galaxy set up with: ``` config.enable_oidc and len(config.oidc) == 1 and len(auth_manager.authenticators) == 0 ``` as in; we only have 1 external auth and no local authenticator, hence, we don't want users to be disconnecting the external provider.
…f_fixed_delegated_auth [23.1] Prevent Singular external auth users from disconnecting identity
Fix the following traceback: ``` Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: uvicorn.access INFO 2023-06-30 10:28:03,573 [pN:main.1,p:3528860,tN:MainThread] 193.156.42.8:0 - "HEAD /root/login HTTP/1.0" 500 Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: Exception in supplement: Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: Traceback (most recent call last): Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: File "/cluster/galaxy-test/srv/galaxy/server/lib/galaxy/web/framework/middleware/error.py", line 165, in __call__ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: app_iter = self.application(environ, sr_checker) Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: File "/cluster/galaxy-test/srv/galaxy/venv/lib64/python3.11/site-packages/paste/recursive.py", line 85, in __call__ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: return self.application(environ, start_response) Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: File "/cluster/galaxy-test/srv/galaxy/venv/lib64/python3.11/site-packages/paste/httpexceptions.py", line 640, in __call__ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: return self.application(environ, start_response) Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: File "/cluster/galaxy-test/srv/galaxy/server/lib/galaxy/web/framework/base.py", line 167, in __call__ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: return self.handle_request(environ, start_response) Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: File "/cluster/galaxy-test/srv/galaxy/server/lib/galaxy/web/framework/base.py", line 221, in handle_request Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: rc.environ = environ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: ^^^^^^^^^^ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: File "/cluster/galaxy-test/srv/galaxy/venv/lib64/python3.11/site-packages/routes/__init__.py", line 23, in __setattr__ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: self.load_wsgi_environ(value) Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: File "/cluster/galaxy-test/srv/galaxy/venv/lib64/python3.11/site-packages/routes/__init__.py", line 73, in load_wsgi_environ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: self.__shared_state.host += ':' + environ['SERVER_PORT'] Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ Jun 30 10:28:03 galaxy01-test.educloud.no galaxyctl[3528286]: TypeError: can only concatenate str (not "int") to str ``` Reported by @vazovn : https://matrix.to/#/!rfLDbcWEWZapZrujix:gitter.im/$McOyd5Kmp-w-Z-bYbRUV42K30YhVvwRJtrCaxru-yf4?via=gitter.im&via=matrix.org
…tes_bug [23.1] Workaround issue in Routes
[23.1] Backport Fix maf_thread_for_species.py
…fix-backport [23.1] Empty page render fix - backport
and invalidate `_output_hdas_and_paths` when current session is not the same session that was used to populate `_output_hdas_and_paths`. The Job instance may originate from a session that is associated to another thread, and when that thread closes the session the instance (along with other instances retrieved through loading relationships) becomes detached. I am not sure at all if this will fix ``` DetachedInstanceError: Instance <HistoryDatasetAssociation at 0x7fe68bbf14f0> is not bound to a Session; attribute refresh operation cannot proceed (Background on this error at: https://sqlalche.me/e/14/bhk3) File "galaxy/jobs/runners/__init__.py", line 291, in prepare_job job_wrapper.prepare() File "galaxy/jobs/__init__.py", line 1248, in prepare tool_evaluator.set_compute_environment(compute_environment, get_special=get_special) File "galaxy/tools/evaluation.py", line 162, in set_compute_environment self.param_dict = self.build_param_dict( File "galaxy/tools/evaluation.py", line 204, in build_param_dict self.__populate_output_dataset_wrappers(param_dict, output_datasets, job_working_directory) File "galaxy/tools/evaluation.py", line 447, in __populate_output_dataset_wrappers param_dict[name] = DatasetFilenameWrapper( File "galaxy/tools/wrappers.py", line 403, in __init__ path_rewrite = compute_environment and compute_environment.output_path_rewrite(dataset_instance) File "galaxy/job_execution/compute_environment.py", line 132, in output_path_rewrite return str(self.job_io.get_output_path(dataset)) File "galaxy/job_execution/setup.py", line 226, in get_output_path if hda.id == dataset.id: File "sqlalchemy/orm/attributes.py", line 487, in __get__ return self.impl.get(state, dict_) File "sqlalchemy/orm/attributes.py", line 959, in get value = self._fire_loader_callables(state, key, passive) File "sqlalchemy/orm/attributes.py", line 990, in _fire_loader_callables return state._load_expired(state, passive) File "sqlalchemy/orm/state.py", line 712, in _load_expired self.manager.expired_attribute_loader(self, toload, passive) File "sqlalchemy/orm/loading.py", line 1369, in load_scalar_attributes raise orm_exc.DetachedInstanceError( ``` but it seems to make some sense. JobIO crosses thread boundaries as part of the job wrapper getting put into threading queues. Ideally we'd make sure that no ORM instance crosses the thread boundary (or we systematically re-associated with a session). I also tried flagging these patterns automatically using something like: ``` @event.listens_for(session, "persistent_to_detached") def on_detach(sess, instance): if not getattr(instance, "allow_detatch", False): raise Exception(f"{instance} detached. This ain't good for how we do things ?") ``` but it seems tricky to figure out when this is fine and when it is not.
[23.1] Client publication
…ob_object [23.1] Don't store job in JobIO instance attributes
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(Please replace this header with a description of your pull request. Please include BOTH what you did and why you made the changes. The "why" may simply be citing a relevant Galaxy issue.)
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