From 10a5ad3d3fc57ea4f71123368138687d3dbf0cd5 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Tue, 19 Nov 2024 11:01:42 -0800 Subject: [PATCH] Update flat records column map Using the latest flat file column `original designation` to use the original strain name that has not gone through VIDRL's strain name standardizations. --- tdb/vidrl_upload.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/tdb/vidrl_upload.py b/tdb/vidrl_upload.py index e1ff175..29d7d55 100644 --- a/tdb/vidrl_upload.py +++ b/tdb/vidrl_upload.py @@ -351,7 +351,9 @@ def curate_flat_records(records: Iterator[dict], fstem: str, assay_type: str) -> # The new column names need to be one of the ELIFE_COLUMNS in order to be # included in the temporary output file that's then passed to elife_upload.py column_map = { - "test virus": "virus_strain", + # Using original strain name _without_ VIDRL standardization so that + # the strain name can be standardized to match our sequence strain names + "original designation": "virus_strain", "test virus passage": "virus_passage", "reference antigen": "serum_strain", "reference passage": "human_serum_passage",