feat: fetch PRIDE spectra by USI via PROXI (MzSpectrum)

[trishorts]

The nut

Given a USI (Universal Spectrum Identifier), fetch a spectrum from PRIDE and get it back as an mzLib MzSpectrum — the next capability on the PRIDE client after the merged manifest MVP (#1088) and file download (#1093).

What's here

New API on PrideArchiveClient:

• GetSpectrumAsync(usi) → MzSpectrum — the common case: the spectrum's peaks as an mzLib spectrum.
• GetProxiSpectrumAsync(usi) → PrideProxiSpectrum — the raw PROXI object, keeping the controlled-vocabulary attributes (charge state, selected ion m/z, ms level, scan number, instrument) that an MzSpectrum cannot carry.

Supporting pieces:

• PrideProxiSpectrum DTO (status/usi/mzs/intensities/attributes); attributes reuse MzLibUtil.CvParam, exactly as PrideArchiveFile does.
• PrideArchiveExtensions.ToMzSpectrum() — a pure, offline peaks→MzSpectrum transform (mirrors how GetHttpsDownloadUrl is a pure extension beside the networked DownloadFileAsync).

Design notes

• PROXI is a different path root than the v3 archive API (/pride/proxi/archive/v0.1/ vs /pride/ws/archive/v3/), so the request is issued as an absolute URI rather than resolving against the client's archive BaseAddress.
• MzSpectrum assumes ascending m/z and validates nothing, so ToMzSpectrum defensively (a) rejects a mzs/intensities length mismatch and (b) sorts a copy of the peaks (leaving the DTO's arrays untouched), constructing with shouldCopy: false to avoid a redundant copy.
• Adds a MassSpectrometry project reference to UsefulProteomicsDatabases (no dependency cycle — MassSpectrometry depends only on Chemistry + MzLibUtil).

Verified against the live API

Probed the real endpoint before writing the DTO: resultType=full returns a 1-element JSON array of {status, usi, mzs[], intensities[], attributes[cvParam]}; an unknown/unreadable USI returns 404 and a malformed USI 400, both surfacing as HttpRequestException through the existing non-success path.

Tests

• 16 offline fixture-based tests (deserialization, URL construction, error contract, the pure ToMzSpectrum transform incl. sort/length-mismatch/null/empty edges).
• 2 live canaries carrying [Category("ExternalService")] + [Category("Pride")], routed through ExternalServiceTestHelper so a PRIDE/EBI outage skips while a genuine contract break fails — same convention as test(ci): unify Koina under ExternalService; non-blocking live tests that skip on outage #1090/feat(usefulproteomicsdatabases): add PRIDE Archive REST client #1088/feat: download PRIDE Archive files over HTTPS + manifest helpers (stacked on #1088) #1093.

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.51%. Comparing base (525cb7c) to head (048fe6d).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1099   +/-   ##
=======================================
  Coverage   91.50%   91.51%           
=======================================
  Files         439      440    +1     
  Lines       53542    53579   +37     
  Branches     6511     6519    +8     
=======================================
+ Hits        48995    49031   +36     
  Misses       3275     3275           
- Partials     1272     1273    +1     

Files with missing lines	Coverage Δ
...ib/UsefulProteomicsDatabases/PrideArchiveClient.cs	100.00% <100.00%> (ø)
...sefulProteomicsDatabases/PrideArchiveExtensions.cs	95.83% <100.00%> (+0.91%)	⬆️
...ib/UsefulProteomicsDatabases/PrideProxiSpectrum.cs	100.00% <100.00%> (ø)

... and 1 file with indirect coverage changes

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