feat(prepro): standardized displayNames

[maverbiest]

adding functionality to build displayNames from specimenCollectorSampleId (or subissionId) and metadata in a more structured way, with the option of extracting an ID if specimenCollectorSampleId is in a recognized format

Manual testing

• build_display_name is now used to generate displayNames for WNV on this preview. displayNames look as expected and an the same number of WNV sequences come up on the preview as on main's preview
• I also tested build_display_name on a pathoplexus preview by manually bumping the loculus version to a commit from this branch, where it also worked as expected

PR Checklist

• All necessary documentation has been adapted.
• The implemented feature is covered by appropriate, automated tests.
• Any manual testing that has been done is documented (i.e. what exactly was tested?)

🚀 Preview: https://update-displayname-creati.loculus.org

[claude]

This PR may be related to: #3652 (Include submissionId in displayName), #4089 (Add displayNames for all fields and remove sentenceCase logic)

[claude]

Claude finished @maverbiest's task in 3m 38s —— View job

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Code Review

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The implementation looks solid overall. The use of extract_regex for identifier extraction is a good choice (reusing existing validated logic), and the INSDC vs direct-submission branching is clear. A few issues worth addressing:

Bug — warnings accumulated inside build_display_name (e.g. "identifier could not be parsed") are silently discarded when concatenate() also produces warnings or errors (lines 1327–1328). The early return drops the warnings list. See inline comment.

Dead code — extract_id_field() at line 1598 is never called; it was superseded by extract_regex but left behind. The docstring on line 1193 still references it.

Minor — using identifier directly in the extract_regex call (line 1288) instead of re-evaluating collector_id or submission_id would be clearer. Also a typo: "concatentate" in the docstring.

Testing — no test for the INSDC happy path (clean identifier with no slashes should pass through unchanged).