Add support for custom metadata validation & custom BioSample packages

[jessicarowell]

Description

This PR remedies the existing custom metadata functionality to correctly populate the submission.xml file with BioSample attributes that are added to input metadata Excel file. It performs a minimal validation on them at this time: it replaces the field name with an (optional) alternative ("new_field_name") and fill empty values with user-specified text ("replace_empty_with").

Changes:

1. Remove two keys from example_custom_metadata.json
2. Rewrite portion of validate_metadata.py to simplify custom metadata validation
3. Move submission config file to conf/ folder (and remove department ID and org_ID defaults)
4. Remove the bin/config_files folder as no longer needed
5. Add example JSON and Metadata Excel templates for One Health Enterics BioSample package

Checklist

General Checks

• [] Have you run appropriate tests (unit/integration/end-to-end) to check logic across run environments (Conda/Docker/Singularity on Scicomp/AWS/NF Tower/Local)?

  For each relevant configuration:

  • Can the program run completely through without erroring out?
  • Does it produce the expected outputs, given the inputs provided?

• [] Have you conducted proper linting procedures?

  • Numpy formatted docstrings for functions
  • Comments explaining lines of code
  • Consistent and intuitive naming conventions for variables, functions, classes, methods, attributes, and scripts
  • Single empty line between class functions, two lines between non-class functions, and two lines between imports and code body
  • Camel case formatting for class names

• Have you updated existing documentation (README.md, etc.) or created new ones within docs?

CDC Checks

• Did you check for sensitive data, and remove any?
• If you added or modified HTML, did you check that it was 508 compliant?

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Are there potential vulnerabilities or licensing issues with any new dependencies introduced? If so, please mention them below:

[jessicarowell]

Emergency merging because people are out for the holidays. I may or may not regret this.