fix(usefulproteomicsdatabases): close leaf-guard gap and reorder resume skip

Address the four remaining findings from the PR #1093 re-review:

- DownloadFileAsync now also rejects a bare "." or ".." FileName.
  Path.GetFileName returns these unchanged, so they slipped past the
  leaf-name guard despite the documented "no '..'" contract.
- Move the overwrite==false && File.Exists short-circuit ahead of
  GetHttpsDownloadUrl and Directory.CreateDirectory, so a resume
  (overwrite: false) skips an already-present file that has no HTTPS
  location (e.g. Aspera-only) instead of throwing, and does no needless
  URL resolution or filesystem work.
- Fix the path-traversal test to assert against the real escape target
  derived from the fileName parameter (parent dir for "../evil.raw", a
  nested subdir for "sub/dir/file.raw") rather than a fixed
  _tempDir/evil.raw that neither case ever occupies; add "." and ".." cases.
- Exercise TryGetHttpsDownloadUrl(out ...) in the explicit-HTTPS-preference
  test, and add a resume-skip test for an already-present Aspera-only file.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Author: trishorts

mzLib/Test/DatabaseTests/PrideArchiveDownloadTests.cs

@@ -121,6 +121,8 @@ public void TryGetHttpsDownloadUrl_PrefersExplicitHttpsOverFtp()
             Ftp("pride/data/x/run1.raw"),
             ("PRIDE:0000000", "https://example.org/direct/run1.raw"));
 
+        Assert.That(file.TryGetHttpsDownloadUrl(out string url), Is.True);
+        Assert.That(url, Is.EqualTo("https://example.org/direct/run1.raw"));
         Assert.That(file.GetHttpsDownloadUrl(), Is.EqualTo("https://example.org/direct/run1.raw"));
     }
 
@@ -227,6 +229,24 @@ public async Task DownloadFileAsync_NotOverwrite_ExistingFile_SkipsRequest()
         Assert.That(File.ReadAllText(path), Is.EqualTo("old"));    // untouched
     }
 
+    [Test]
+    public async Task DownloadFileAsync_NotOverwrite_ExistingFile_NoHttpsLocation_SkipsWithoutThrowing()
+    {
+        // resume must skip an already-present file before resolving its URL, so an Aspera-only entry
+        // (no HTTPS location) that is already on disk returns untouched instead of throwing NotSupportedException.
+        Directory.CreateDirectory(_tempDir);
+        string existing = Path.Combine(_tempDir, "run1.raw");
+        File.WriteAllText(existing, "old");
+        var handler = new StubHandler(_ => Bytes(Encoding.UTF8.GetBytes("new")));
+        using var client = new PrideArchiveClient(new HttpClient(handler));
+        var file = MakeFile("run1.raw", "RAW", Aspera("pride/data/x/run1.raw")); // no HTTPS-reachable location
+
+        string path = await client.DownloadFileAsync(file, _tempDir, overwrite: false);
+
+        Assert.That(handler.RequestedUris, Is.Empty);            // skipped before any URL resolution or network call
+        Assert.That(File.ReadAllText(path), Is.EqualTo("old"));  // left untouched
+    }
+
     [Test]
     public async Task DownloadFileAsync_Overwrite_ReplacesExistingFile()
     {
@@ -391,6 +411,8 @@ public void WhereCategory_NullCategory_Skipped()
 
     [TestCase("../evil.raw")]
     [TestCase("sub/dir/file.raw")]
+    [TestCase(".")]   // bare "." survives Path.GetFileName unchanged but is a non-leaf the contract rejects
+    [TestCase("..")]  // bare ".." likewise resolves to the parent directory; must be rejected
     public void DownloadFileAsync_FileNameNotBareLeaf_Throws_WritesNothingOutside(string fileName)
     {
         // REGRESSION: failed before the fix — a path-bearing FileName escaped destinationDirectory via Path.Combine.
@@ -400,7 +422,10 @@ public void DownloadFileAsync_FileNameNotBareLeaf_Throws_WritesNothingOutside(st
 
         Assert.That(async () => await client.DownloadFileAsync(file, _tempDir), Throws.ArgumentException);
         Assert.That(handler.RequestedUris, Is.Empty);                        // rejected before any network call
-        Assert.That(File.Exists(Path.Combine(_tempDir, "evil.raw")), Is.False);
+        // the location an un-prevented Path.Combine would have written to (parent for "../evil.raw",
+        // a nested subdir for "sub/dir/file.raw") — derived from the input so each case checks its own escape target
+        string wouldBeTarget = Path.GetFullPath(Path.Combine(_tempDir, fileName));
+        Assert.That(File.Exists(wouldBeTarget), Is.False);
     }
 
     [Test]

mzLib/UsefulProteomicsDatabases/PrideArchiveClient.cs

@@ -158,18 +158,22 @@ public async Task<string> DownloadFileAsync(PrideArchiveFile file, string destin
             // leaf name is allowed, so a value carrying a directory separator, a ".." segment, or a rooted
             // path cannot escape destinationDirectory when combined below (Path.Combine does not sanitize).
             string safeFileName = Path.GetFileName(file.FileName);
-            if (safeFileName != file.FileName)
+            if (safeFileName != file.FileName || safeFileName == "." || safeFileName == "..")
                 throw new ArgumentException(
                     $"The PRIDE file name '{file.FileName}' is not a bare file name; refusing to write outside the destination directory.",
                     nameof(file));
 
-            string url = file.GetHttpsDownloadUrl(); // throws NotSupportedException if unreachable over HTTPS
-
-            Directory.CreateDirectory(destinationDirectory);
             string destinationPath = Path.Combine(destinationDirectory, safeFileName);
 
+            // Cheap resume: an already-present destination is left untouched. This runs before URL
+            // resolution and directory creation so skipping a downloaded file never fails on a file
+            // that has no HTTPS location (e.g. Aspera-only) or does needless filesystem work.
             if (!overwrite && File.Exists(destinationPath))
-                return destinationPath; // already downloaded; leave it untouched
+                return destinationPath;
+
+            string url = file.GetHttpsDownloadUrl(); // throws NotSupportedException if unreachable over HTTPS
+
+            Directory.CreateDirectory(destinationDirectory);
 
             using HttpResponseMessage response =
                 await _httpClient.GetAsync(url, HttpCompletionOption.ResponseHeadersRead, cancellationToken).ConfigureAwait(false);