Ingest VIDRL human sera references

[joverlee521]

Description of proposed changes

First pass for ingesting VIDRL human sera references, focused on 2024 data. I'm hoping that ingesting older data should be as simple as updating the VACCINE_MAPPING, but we'll see...

Related issue(s)

Related to #158

Checklist

• [ ] Checks pass

[joverlee521]

Used this Snakefile to upload 2024 human sera data to test_tdb with changes up to https://github.com/nextstrain/fauna/pull/160/commits/f34c82686f0c5111738cf1813fd4cf9315fea81a

pyenv activate fauna
nextstrain build --cpus 2 --ambient --envdir ../env.d/seasonal-flu/ . --snakefile data/Snakefile --config year='2024' preview=False

This ran through 73 Excel workbooks without raising any errors 🎉
I will dig more into the uploaded data tomorrow to make sure nothing looks too out of place...

[joverlee521]

Of the 73 processed workbooks, 1 did not have any human sera references. From the other 72 workbooks, the upload workflow added 5722 measurements to test_tdb/flu.

I tested download of the titer measurements using the seasonal-flu workflow with a small patch to use the `test_tdb` database.

```diff diff --git a/workflow/snakemake_rules/download_from_fauna.smk b/workflow/snakemake_rules/download_from_fauna.smk index 64e8350..04544df 100644 --- a/workflow/snakemake_rules/download_from_fauna.smk +++ b/workflow/snakemake_rules/download_from_fauna.smk @@ -68,7 +68,7 @@ rule download_titers: output: titers = "data/{lineage}/{center}_{passage}_{assay}_titers.tsv" params: - dbs = _get_tdb_databases, + dbs = 'test_tdb', assays = _get_tdb_assays, virus_passage_category=_get_virus_passage_category, conda: "../envs/nextstrain.yaml" ``` ``` nextstrain build --envdir ../env.d/seasonal-flu/ . data/h3n2/who_human_cell_hi_titers.tsv data/h3n2/who_human_egg_hi_titers.tsv data/h3n2/who_human_cell_fra_titers.tsv data/h3n2/who_human_egg_fra_titers.tsv data/h1n1pdm/who_human_cell_hi_titers.tsv data/h1n1pdm/who_human_egg_hi_titers.tsv data/vic/who_human_cell_hi_titers.tsv data/vic/who_human_egg_hi_titers.tsv --configfile profiles/upload.yaml ```

This downloaded 5694 measurements that were all appropriately selected for the human host files. There were 28 measurements excluded because the virus_passage_category was egg while the serum_passage_category was cell. The seasonal-flu workflow explicitly excludes egg passaged test viruses in cell passaged titer data.

I manually spot checked 3 workbooks per subtype to verify all of the human sera reference measurements were included. At this point, I'm pretty confident that this at least works for the 2024 files.

[joverlee521]

I'll plan to merge and upload the 2024 data as part of tomorrow's ingest.