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Update ingest for VIDRL flat files#164

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joverlee521 wants to merge 13 commits intomasternextstrain/fauna:masterfrom vidrl-flat-filenextstrain/fauna:vidrl-flat-fileCopy head branch name to clipboard

+312-47

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Commits on Nov 19, 2024

• read_flat_vidrl: add column map to script

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• read_flat_vidrl: Update column map

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• read_flat_vidrl: replace pandas with csv module

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• vidrl_upload: refactor human serum id to separate function

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• read_flat_vidrl: standardize human sera strain/id/type

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• read_flat_vidrl: Include "assay_date"

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• read_flat_vidrl: Validate records

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• vidrl_upload: refactor curate_flat_records

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• read_flat_vidrl: ingest reference_panel.csv file

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• read_flat_vidrl: Parse human serum passage from reference passage

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• read_flat_vidrl: Clean up virus_strain that includes "pool" suffix

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• read_flat_vidrl: Check for potential duplicate _reference_panel files

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• Update flat records column map

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