Code

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

Commits

Commits on Nov 19, 2024

• read_flat_vidrl: add column map to script

  Show description for d4eb286
  joverlee521

  committed
  d4eb286

• read_flat_vidrl: Update column map

  Show description for 3ac788f
  joverlee521

  committed
  3ac788f

• read_flat_vidrl: replace pandas with csv module

  Show description for facbe78
  joverlee521

  committed
  facbe78

• vidrl_upload: refactor human serum id to separate function

  Show description for 5c80788
  joverlee521

  committed
  5c80788

• read_flat_vidrl: standardize human sera strain/id/type

  Show description for a9d4e14
  joverlee521

  committed
  a9d4e14

• read_flat_vidrl: Include "assay_date"

  Show description for fd56875
  joverlee521

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  fd56875

• read_flat_vidrl: Validate records

  Show description for e5edcf3
  joverlee521

  committed
  e5edcf3

• vidrl_upload: refactor curate_flat_records

  Show description for 349c72f
  joverlee521

  committed
  349c72f

• read_flat_vidrl: ingest reference_panel.csv file

  Show description for d16f37c
  joverlee521

  committed
  d16f37c

• read_flat_vidrl: Parse human serum passage from reference passage

  Show description for ceff42b
  joverlee521

  committed
  ceff42b

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

  Show description for fe2685c
  joverlee521

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  fe2685c

• read_flat_vidrl: Check for potential duplicate _reference_panel files

  Show description for ad39ce2
  joverlee521

  committed
  ad39ce2

• Update flat records column map

  Show description for 10a5ad3
  joverlee521

  committed
  10a5ad3