fix(ingest): decrease ingest memory usage for large datasets #3505
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fhennig
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looks sensible!
still @corneliusroemer because I think it'd be good if he had a look.
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As discussed with @corneliusroemer offline I will merge |
This was referenced Feb 3, 2025
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resolves #
preview URL: https://ingest-memory-fixes.loculus.org/
Summary
When dealing with organisms with a large number of sequences (e.g. influenza A has 1.3M sequences) even just reading it the entire metadata is highly memory intensive - this PR switches to streaming metadata where ever possible and is similar to the change @corneliusroemer made in #2277 to stream sequences.
Note that in the case where segments are grouped the entire file still must be read into a dictionary.
Testing
How best to test this? Use https://github.com/pathoplexus/pathoplexus/tree/main/data-integrity-tests/regression-testing and switch the URLs to this branch and main :-)
PR Checklist