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SN Submission spreadsheet update #379

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@sarahgonicholson sarahgonicholson commented Mar 14, 2025

  • Update commands/write_submission_spreadsheets.py to include capability to add "pseudo-properties" such as expected_file_counts in FileSet that are used for validation in submitr
  • Update the --eqm flag to use data from submitr/config/custom_column_mappings.json so that values are consistent with submitr
  • Reorder properties in PathologyReport schema for ease of submission

item = list(eqm['template'].keys())[0]
properties = get_eqm_properties(item, eqm)
mapping = custom_column_mappings['column_mappings']['external_quality_metric']
### TMP
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TMP ?

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