feat: download PRIDE Archive files over HTTPS + manifest helpers (stacked on #1088)

[trishorts]

Summary

Adds the "get the data" capability to the PRIDE Archive client: download a project's files to disk. Builds directly on the file-manifest MVP in #1088.

⚠️ Stacked on #1088. This branch is based on pride-client (#1088), which is not yet on master, so the diff below temporarily contains both commits. Review only the top commit — feat(usefulproteomicsdatabases): download PRIDE files over HTTPS + manifest helpers. Once #1088 merges, this diff self-reduces to the download changes alone.

The design decision: no FTP subsystem

PRIDE advertises each file's locations only as FTP (PRIDE:0000469) and Aspera (PRIDE:0000468) — there is no HTTPS location field (verified live against PXD012345 and PXD000001). The naive path would be a System.Net.FtpWebRequest downloader, but that API is deprecated and mzLib has no FTP code today.

Instead: PRIDE's FTP host ftp.pride.ebi.ac.uk also serves the identical path over HTTPS (verified: HEAD → 200, Content-Length, Accept-Ranges: bytes). So the client scheme-upgrades ftp:// → https:// and downloads through the existing reused HttpClient. The result:

• ✅ works on real PRIDE data (which is FTP/Aspera-only),
• ✅ no new dependency, no deprecated FTP code,
• ✅ reuses the client's Koina-style HttpClient (success-checked, streamed).

API

• PrideArchiveClient.DownloadFileAsync(file, destinationDirectory, overwrite = true, ct) — downloads one file, returns the written path. Streams to a .partial sibling and moves it into place only on success (no truncated files on interruption). overwrite = false skips an existing file (cheap resume).
• PrideArchiveClient.DownloadProjectFilesAsync(accession, destinationDirectory, filter = null, ...) — manifest → optional filter → download each.
• PrideArchiveExtensions (new): TryGetHttpsDownloadUrl / GetHttpsDownloadUrl (explicit HTTPS → FTP-upgraded-to-HTTPS → NotSupportedException for Aspera-only), plus WhereCategory / WhereExtension / TotalSizeBytes manifest helpers.

Tests

• 17 offline tests via a stub HttpMessageHandler: FTP→HTTPS resolution, explicit-HTTPS preference, Aspera-only rejection, category/extension filters, size aggregation, overwrite policy, non-success (+ no leftover .partial), and filtered project download.
• Live canary PrideArchiveDownloadLiveTests under [Category("ExternalService")] / [Category("Pride")], routed through ExternalServiceTestHelper so an EBI outage skips while a contract break fails. Downloads the smallest file of a real project end-to-end.

🤖 Generated with Claude Code

[codecov]

Codecov Report

❌ Patch coverage is 97.24771% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 91.47%. Comparing base (77fb7db) to head (3cc184c).
⚠️ Report is 2 commits behind head on master.

Files with missing lines	Patch %	Lines
...sefulProteomicsDatabases/PrideArchiveExtensions.cs	94.91%	0 Missing and 3 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1093      +/-   ##
==========================================
+ Coverage   91.46%   91.47%   +0.01%     
==========================================
  Files         427      428       +1     
  Lines       52777    52886     +109     
  Branches     6325     6356      +31     
==========================================
+ Hits        48273    48379     +106     
  Misses       3268     3268              
- Partials     1236     1239       +3     

Files with missing lines	Coverage Δ
...ib/UsefulProteomicsDatabases/PrideArchiveClient.cs	100.00% <100.00%> (ø)
...sefulProteomicsDatabases/PrideArchiveExtensions.cs	94.91% <94.91%> (ø)

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.