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SQL-based data linkage

mwham requested to merge sql_schemas into master

Overhaul of data linkage back-end:

  • Pandas instead of R Tidyverse for initial loading
  • Defining schemas for all dataasets
    • Except for ynamically inferring clinical data - changes all the time
  • Simple dataframe/SQL load and CSV export, instead of symlinking CSVs
  • Set up system for re-linking columns
  • Sample barcode in LIMS data
  • New assays_done report - takes into account what samples have been dispatched
  • New test data

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