Integrate the new async biothings-client support #64
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newgene
reviewed
Nov 13, 2024
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@ctrl-schaff looks good to me. The only thing I want to add is to update pyproject.toml to include specific version of biothings_client package. Note that merging this to main will trigger a CI deployment, it would break without the proper version of biothings_client.
added 11 commits
December 17, 2024 06:51
We change the scope of the application instance to module and the asyncio loop as well to avoid event loop issues from having to scope it per function and the teardown process causing issues between tests https://pytest-asyncio.readthedocs.io/en/latest/how-to-guides/run_class_tests_in_same_loop.html
Due to conflicting issues between more than one event loop with these tests I've done two things. 1) Removed tests that have external querying from the test group. While it will make the unit tests less robust, having external queries was always going to be slighly flakier. This way the core tests leverage the built-in testing clients for exercising the annotator as a web service through the endpoints. The annotator as a standalone library is important but comes second to that 2) Set the loop scope to module to allow for the event loop to exist for groups of tests that are semantically similar.
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Should provide performance improvements for bigger async jobs