fix: read ignore patterns from workspace member Cargo.toml files (#375)

## Description

Previously, ignore patterns (exhortignore / trustify-da-ignore) were
only read from the root Cargo.toml. In a virtual workspace, member
crates have their own Cargo.toml with [dependencies], so ignore comments
there were never detected. This caused the Java client to include
dependencies that should have been ignored at the member level.

Now, when processing each workspace member for stack analysis, its own
Cargo.toml is parsed for ignore patterns and merged with workspace-level
ignores before walking the dependency tree.

**Related issue (if any):** fixes #374 

## Checklist

- [x] I have followed this repository's contributing guidelines.
- [x] I will adhere to the project's code of conduct.

## Additional information

> Anything else?

---------

Co-authored-by: Chao Wang <chaowan@redhat.com>

Author: a-oren

src/main/java/io/github/guacsec/trustifyda/providers/CargoProvider.java

@@ -202,13 +202,60 @@ private void handleVirtualWorkspace(
                   + metadata.workspaceMembers());
         }
         for (String memberId : metadata.workspaceMembers()) {
+          Set<String> memberIgnoredDeps = getMemberIgnoredDeps(memberId, packageMap, ignoredDeps);
           processWorkspaceMember(
-              sbom, root, memberId, nodeMap, packageMap, ignoredDeps, analysisType);
+              sbom, root, memberId, nodeMap, packageMap, memberIgnoredDeps, analysisType);
         }
       }
     }
   }
 
+  /**
+   * Builds the full set of ignored dependencies for a workspace member by reading the member's own
+   * Cargo.toml for ignore patterns and merging them with the workspace-level ignored deps.
+   */
+  private Set<String> getMemberIgnoredDeps(
+      String memberId, Map<String, CargoPackage> packageMap, Set<String> workspaceIgnoredDeps) {
+    CargoPackage memberPkg = packageMap.get(memberId);
+    if (memberPkg == null || memberPkg.manifestPath() == null) {
+      return workspaceIgnoredDeps;
+    }
+    Path memberManifest = Path.of(memberPkg.manifestPath());
+    if (!Files.isRegularFile(memberManifest)) {
+      return workspaceIgnoredDeps;
+    }
+    try {
+      TomlParseResult memberToml = Toml.parse(memberManifest);
+      if (memberToml.hasErrors()) {
+        return workspaceIgnoredDeps;
+      }
+      String memberContent = Files.readString(memberManifest, StandardCharsets.UTF_8);
+      Set<String> memberIgnored = getIgnoredDependencies(memberToml, memberContent);
+      if (memberIgnored.isEmpty()) {
+        return workspaceIgnoredDeps;
+      }
+      if (debugLoggingIsNeeded()) {
+        log.info(
+            "Found "
+                + memberIgnored.size()
+                + " ignored dependencies in member "
+                + memberPkg.name()
+                + ": "
+                + memberIgnored);
+      }
+      Set<String> merged = new HashSet<>(workspaceIgnoredDeps);
+      merged.addAll(memberIgnored);
+      return merged;
+    } catch (IOException e) {
+      log.warning(
+          "Failed to read member Cargo.toml for ignore patterns: "
+              + memberManifest
+              + ": "
+              + e.getMessage());
+      return workspaceIgnoredDeps;
+    }
+  }
+
   void processWorkspaceDependencies(
       Sbom sbom,
       PackageURL root,
@@ -714,7 +761,7 @@ private ProjectInfo parseCargoToml(TomlParseResult result) throws IOException {
     throw new IOException("Invalid Cargo.toml: no [package] or [workspace] section found");
   }
 
-  private Set<String> getIgnoredDependencies(TomlParseResult result, String content) {
+  Set<String> getIgnoredDependencies(TomlParseResult result, String content) {
     Set<String> normalDependencies = collectNormalDependencies(result);
     if (debugLoggingIsNeeded()) {
       log.info("Found " + normalDependencies.size() + " normal dependencies in Cargo.toml");

src/main/java/io/github/guacsec/trustifyda/providers/rust/model/CargoPackage.java

@@ -24,4 +24,5 @@ public record CargoPackage(
     @JsonProperty("name") String name,
     @JsonProperty("version") String version,
     @JsonProperty("id") String id,
+    @JsonProperty("manifest_path") String manifestPath,
     @JsonProperty("dependencies") List<CargoDependency> dependencies) {}

src/test/java/io/github/guacsec/trustifyda/providers/CargoProviderCargoParsingTest.java

@@ -405,23 +405,11 @@ public void testComplexDependencySyntaxWithIgnorePatterns(@TempDir Path tempDir)
         """;
     Files.writeString(cargoToml, content);
 
-    // Create RustProvider and test ignore detection
     CargoProvider provider = new CargoProvider(cargoToml);
-
-    // Read the file content for the updated method signature
     String cargoContent = Files.readString(cargoToml, StandardCharsets.UTF_8);
+    TomlParseResult tomlResult = Toml.parse(cargoToml);
 
-    // Parse TOML using TOMLJ (matching the optimized implementation)
-    org.tomlj.TomlParseResult tomlResult = org.tomlj.Toml.parse(cargoToml);
-
-    // Use reflection to test the private getIgnoredDependencies method with new signature
-    java.lang.reflect.Method method =
-        CargoProvider.class.getDeclaredMethod(
-            "getIgnoredDependencies", org.tomlj.TomlParseResult.class, String.class);
-    method.setAccessible(true);
-
-    @SuppressWarnings("unchecked")
-    Set<String> ignoredDeps = (Set<String>) method.invoke(provider, tomlResult, cargoContent);
+    Set<String> ignoredDeps = provider.getIgnoredDependencies(tomlResult, cargoContent);
 
     System.out.println("Complex syntax test - Ignored dependencies found:");
     for (String dep : ignoredDeps) {
@@ -627,20 +615,10 @@ public void testEdgeCaseCargoTomlFormats(@TempDir Path tempDir) throws Exception
     assertTrue(sbomContent.contains("edge-case-project"), "Should contain project name");
 
     // Test ignore detection with edge case formatting
-    // Read the file content for the updated method signature
     String edgeCargoContent = Files.readString(edgeCaseCargoToml, StandardCharsets.UTF_8);
+    TomlParseResult edgeTomlResult = Toml.parse(edgeCaseCargoToml);
 
-    // Parse TOML using TOMLJ (matching the optimized implementation)
-    org.tomlj.TomlParseResult edgeTomlResult = org.tomlj.Toml.parse(edgeCaseCargoToml);
-
-    java.lang.reflect.Method method =
-        CargoProvider.class.getDeclaredMethod(
-            "getIgnoredDependencies", org.tomlj.TomlParseResult.class, String.class);
-    method.setAccessible(true);
-
-    @SuppressWarnings("unchecked")
-    Set<String> ignoredDeps =
-        (Set<String>) method.invoke(provider, edgeTomlResult, edgeCargoContent);
+    Set<String> ignoredDeps = provider.getIgnoredDependencies(edgeTomlResult, edgeCargoContent);
 
     // Should detect ignore patterns despite varying spacing and formatting
     assertTrue(ignoredDeps.contains("dep1"), "Should ignore dep1 (extra spaces)");
@@ -766,4 +744,69 @@ public void testVirtualWorkspaceWithoutWorkspaceDepsDoesNotThrowNPE(@TempDir Pat
                 sbom, root, new HashMap<>(), new HashSet<>(), tomlResult),
         "processWorkspaceDependencies should handle missing [workspace.dependencies] gracefully");
   }
+
+  @Test
+  public void testMemberCargoTomlIgnorePatternsDetected(@TempDir Path tempDir) throws Exception {
+    // Simulate a member's Cargo.toml with exhortignore on a dependency
+    Path memberDir = tempDir.resolve("crate-a");
+    Files.createDirectories(memberDir);
+    Path memberCargoToml = memberDir.resolve("Cargo.toml");
+    String memberContent =
+        """
+        [package]
+        name = "crate-a"
+        version = "0.1.0"
+        edition = "2021"
+
+        [dependencies]
+        serde = "1.0" # exhortignore
+        tokio = "1.0"
+        reqwest = "0.11" # trustify-da-ignore
+        """;
+    Files.writeString(memberCargoToml, memberContent);
+
+    CargoProvider provider = new CargoProvider(memberCargoToml);
+    TomlParseResult tomlResult = Toml.parse(memberCargoToml);
+    String content = Files.readString(memberCargoToml, StandardCharsets.UTF_8);
+
+    Set<String> ignoredDeps = provider.getIgnoredDependencies(tomlResult, content);
+
+    assertTrue(ignoredDeps.contains("serde"), "serde should be ignored (exhortignore)");
+    assertFalse(ignoredDeps.contains("tokio"), "tokio should NOT be ignored");
+    assertTrue(ignoredDeps.contains("reqwest"), "reqwest should be ignored (trustify-da-ignore)");
+    assertEquals(2, ignoredDeps.size(), "Should find exactly 2 ignored dependencies in member");
+  }
+
+  @Test
+  public void testMemberIgnorePatternsWithTableFormat(@TempDir Path tempDir) throws Exception {
+    Path memberDir = tempDir.resolve("crate-b");
+    Files.createDirectories(memberDir);
+    Path memberCargoToml = memberDir.resolve("Cargo.toml");
+    String memberContent =
+        """
+        [package]
+        name = "crate-b"
+        version = "0.1.0"
+        edition = "2021"
+
+        [dependencies]
+        serde-json-wasm = "1.0"
+
+        [dependencies.aho-corasick] # trustify-da-ignore
+        version = "1.0.0"
+        """;
+    Files.writeString(memberCargoToml, memberContent);
+
+    CargoProvider provider = new CargoProvider(memberCargoToml);
+    TomlParseResult tomlResult = Toml.parse(memberCargoToml);
+    String content = Files.readString(memberCargoToml, StandardCharsets.UTF_8);
+
+    Set<String> ignoredDeps = provider.getIgnoredDependencies(tomlResult, content);
+
+    assertFalse(ignoredDeps.contains("serde-json-wasm"), "serde-json-wasm should NOT be ignored");
+    assertTrue(
+        ignoredDeps.contains("aho-corasick"),
+        "aho-corasick should be ignored (table format with trustify-da-ignore)");
+    assertEquals(1, ignoredDeps.size(), "Should find exactly 1 ignored dependency in member");
+  }
 }