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read_flat_vidrl: Remove TODOs for verifying vaccine strain
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joverlee521 committed Nov 4, 2024
1 parent ea78b6f commit e7dc41d
Showing 1 changed file with 4 additions and 3 deletions.
7 changes: 4 additions & 3 deletions tdb/vidrl_upload.py
Original file line number Diff line number Diff line change
Expand Up @@ -432,11 +432,12 @@ def standardize_human_serum(record: dict, passage_field: str) -> dict:
return record

new_record = record.copy()
# TODO: Translate passage to egg/cell to support vaccine strain verification
# We are purposely _not_ verifying serum_strain/serum_passage against the VACCINE_MAPPING.
# VIDRL uses reference antigens that are proxies for the human serum
# vaccine strains so these do not always align with the exact egg/cell vaccine strains.
# -Jover, 04 November 2024
new_record["serum_passage"] = new_record[passage_field]
human_serum_id = new_record["serum_abbr"]

# TODO: Verify the serum strain matches the year's vaccine strain
new_record["serum_strain"] = re.sub(r"pool$", "", new_record["serum_strain"])
_, new_record["serum_id"] = parse_human_serum_id(human_serum_id, HUMAN_SERA_YEAR_REGEX)
return new_record
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