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Update ingest for VIDRL flat files #164

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Update ingest for VIDRL flat files #164

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d4eb286
read_flat_vidrl: add column map to script
joverlee521 Oct 8, 2024
3ac788f
read_flat_vidrl: Update column map
joverlee521 Oct 8, 2024
facbe78
read_flat_vidrl: replace pandas with csv module
joverlee521 Oct 8, 2024
5c80788
vidrl_upload: refactor human serum id to separate function
joverlee521 Oct 8, 2024
a9d4e14
read_flat_vidrl: standardize human sera strain/id/type
joverlee521 Oct 8, 2024
fd56875
read_flat_vidrl: Include "assay_date"
joverlee521 Oct 8, 2024
e5edcf3
read_flat_vidrl: Validate records
joverlee521 Oct 14, 2024
349c72f
vidrl_upload: refactor curate_flat_records
joverlee521 Oct 15, 2024
d16f37c
read_flat_vidrl: ingest reference_panel.csv file
joverlee521 Oct 15, 2024
ceff42b
read_flat_vidrl: Parse human serum passage from `reference passage`
joverlee521 Oct 16, 2024
fe2685c
read_flat_vidrl: Clean up `virus_strain` that includes "pool" suffix
joverlee521 Nov 4, 2024
ad39ce2
read_flat_vidrl: Check for potential duplicate _reference_panel files
joverlee521 Nov 5, 2024
10a5ad3
Update flat records column map
joverlee521 Nov 19, 2024
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read_flat_vidrl: Update column map 
Update column map based on `0906.xlsx_H1_flat_file.csv` in comparison
to the matching Excel file `20240906\ H1N1.xlsx` available on
VIDRL's OneDrive.
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@joverlee521
joverlee521 committed Nov 19, 2024
commit 3ac788f451c99c5ae4c41d2379e471475dd2ec99
10 changes: 5 additions & 5 deletions tdb/vidrl_upload.py
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Expand Up @@ -314,12 +314,12 @@ def read_flat_vidrl(path, fstem, assay_type):
# 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 = {
"virus": "virus_strain",
"virus.passage": "virus_passage",
"antisera.passage": "serum_passage",
"test virus": "virus_strain",
"test virus passage": "virus_passage",
"reference antigen": "serum_strain",
"antisera passage": "serum_passage",
"ferret": "serum_id",
"value": "titer",
"antisera.name": "serum_strain"
"titre": "titer",
}
filepath = path + fstem + ".csv"

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