tier_engine: None tier is unreachable for live PXD accessions; PRIDE enforces mandatory fields

[eneskemalergin]

Summary

The None tier fires when a PXD accession is missing title, organisms, or instruments. PRIDE's submission pipeline enforces all three as mandatory fields — every published PXD dataset has them. After scanning hundreds of live accessions (PXD000001–PXD001200 and targeted keyword searches), no published PXD accession was found with any of these fields absent.

Impact

• The None tier branch in tier_engine.py is dead code for Phase 1 (PXD-only auditing against PRIDE). It is not a bug — the logic is correct
  and the branch is covered by unit tests using synthetic payloads.
• C08 integration tests cannot test None tier against a live PXD accession. The integration test suite should acknowledge this and skip the live None test.

Tiers reachable on live PRIDE (as-of 2026)

Tier	Reachable?	Example accession
Gold	✅	PXD075811 (14 files)
Silver	✅	PXD000001 (8 files)
Bronze	✅	PXD057701 (1070 raw-only files)
None	❌	No live PXD example exists
Unverifiable	✅	Any non-PXD accession (e.g. MSV000001)

Why None still belongs in the model

1. Phase 2+ will ingest non-PRIDE repositories (MassIVE, jPOST, iProX) whose submission pipelines may not enforce these fields.
2. PRIDE's validation could theoretically produce edge cases in the future (reprocessed metadata, withdrawn-then-restored datasets).
3. Unit tests exercise this branch with synthetic payloads — correctness is fully verified without a live example.

Resolution plan

• Phase 1: document as known non-testable live tier; skip it in C08.
• Phase 2: add a live None-tier example from a non-PRIDE repository, or construct a controlled synthetic endpoint for integration test harness.