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Update flat records column map
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Using the latest flat file column `original designation` to use the
original strain name that has not gone through VIDRL's strain name
standardizations.
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joverlee521 committed Nov 19, 2024
1 parent ad39ce2 commit 10a5ad3
Showing 1 changed file with 3 additions and 1 deletion.
4 changes: 3 additions & 1 deletion tdb/vidrl_upload.py
Original file line number Diff line number Diff line change
Expand Up @@ -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",
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