Added support for configurable enum sources, template-only fields, and AMR metadata JSON generation.

[albatalavera]

Summary

This PR updates schema generation to support configurable enum sources from the input Excel, template-only lab form fields, alphabetically sorted enum values, and automatic generation of amr_genes.json for downstream AMR metadata processing.

Changes

• Added support for ONLY in submitting_lab_form to include fields in the metadata template while excluding them from the generated JSON schema.
• Added support for loading long enum lists from .txt files in conf or from Excel sheets using @sheet:sheet_name:column_name.
• Added support for filtered Excel enum sources using @sheet:sheet_name:column_name:filter_column=filter_value.
• Updated amr_acquired_genes to derive its enum values from amr_gene_list using the configurable Excel enum source syntax.
• Added automatic generation of amr_genes.json in the schema output directory using amr_gene_list.
• Sorted enum values alphabetically, keeping special values such as Not applicable, Not collected, Not provided, Missing, Restricted access, and Other at the end.

PR Checklist

• This comment contains a description of changes (with reason).
• Make sure your code lints (black and flake8).
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[Daniel-VM]

Looks good!

However, since this is specific to AMR genes only, unless I’m wrong, I’ll move this implementation to the schema utils: https://github.com/BU-ISCIII/relecov-tools/tree/develop/relecov_tools/assets/schema_utils

[Daniel-VM]

Nice!!