fix: sbomtool merge losing packages and properties

sbomtool/cmd/sbomtool/main.go

@@ -9,6 +9,7 @@ import (
 	"github.com/anchore/syft/syft/pkg"
 	"github.com/anchore/syft/syft/sbom"
 	"github.com/spf13/cobra"
+	_ "modernc.org/sqlite"
 
 	"github.com/bottlerocket-os/bottlerocket-sdk/sbomtool/go/internal/commands/filter"
 	"github.com/bottlerocket-os/bottlerocket-sdk/sbomtool/go/internal/commands/generate"

sbomtool/internal/commands/generate/generate.go

@@ -109,6 +109,9 @@ func Generate(name string, spdx bool, cyclonedx bool, buildDir string, outDir st
 		return false, fmt.Errorf("failed to create SBOM: %w", err)
 	}
 
+	// Set the source name from the --name parameter so it appears in metadata.component
+	sbomData.Source.Name = name
+
 	if spdx {
 		slog.Info("Generating SPDX SBOM", "name", name)
 		if err := createSpdxSbom(*sbomData, name, outDir); err != nil {

sbomtool/internal/commands/merge/merge.go

@@ -12,6 +12,7 @@ import (
 	"github.com/anchore/syft/syft/artifact"
 	"github.com/anchore/syft/syft/pkg"
 	"github.com/anchore/syft/syft/sbom"
+	"github.com/anchore/syft/syft/source"
 
 	"github.com/bottlerocket-os/bottlerocket-sdk/sbomtool/go/internal/deduplication"
 	"github.com/bottlerocket-os/bottlerocket-sdk/sbomtool/go/internal/processor"
@@ -136,25 +137,60 @@ func loadSBOMs(inputFiles []string) ([]*sbom.SBOM, string, error) {
 	return sboms, commonFormat, nil
 }
 
+// sourceToPackage converts an SBOM's Source (metadata.component) to a package.
+// This ensures the subject of each input SBOM is preserved in the merged output.
+func sourceToPackage(src source.Description) *pkg.Package {
+	if src.Name == "" {
+		return nil
+	}
+
+	p := pkg.Package{
+		Name:    src.Name,
+		Version: src.Version,
+		Type:    pkg.UnknownPkg,
+	}
+	p.SetID()
+
+	slog.Debug("Converted source to package", "name", src.Name, "version", src.Version)
+	return &p
+}
+
 // mergeSBOMs combines SBOM metadata and extracts all packages and relationships.
+// Each input SBOM's Source (metadata.component) is converted to a package to preserve
+// the subject of each SBOM in the merged output. Contains relationships are created
+// from the source package to all packages in that SBOM.
 func mergeSBOMs(sboms []*sbom.SBOM) (*sbom.SBOM, []pkg.Package, []artifact.Relationship) {
 	if len(sboms) == 0 {
 		return &sbom.SBOM{}, nil, nil
 	}
 
-	// Use first SBOM as base
+	// Use first SBOM as base for descriptor
 	merged := &sbom.SBOM{
 		Descriptor: sboms[0].Descriptor,
-		Source:     sboms[0].Source,
 	}
 
 	var allPackages []pkg.Package
 	var allRelationships []artifact.Relationship
 
-	// Collect all packages and relationships
+	// Collect all packages and relationships, including Source as a package
 	for _, s := range sboms {
-		allPackages = append(allPackages, s.Artifacts.Packages.Sorted()...)
+		sbomPackages := s.Artifacts.Packages.Sorted()
+		allPackages = append(allPackages, sbomPackages...)
 		allRelationships = append(allRelationships, s.Relationships...)
+
+		// Convert Source (metadata.component) to a package and create contains relationships
+		if srcPkg := sourceToPackage(s.Source); srcPkg != nil {
+			allPackages = append(allPackages, *srcPkg)
+
+			// Create "contains" relationships from source to each package in this SBOM
+			for _, p := range sbomPackages {
+				allRelationships = append(allRelationships, artifact.Relationship{
+					From: *srcPkg,
+					To:   p,
+					Type: artifact.ContainsRelationship,
+				})
+			}
+		}
 	}
 
 	slog.Debug("SBOM merge phase completed",
@@ -174,7 +210,6 @@ func createFinalSBOM(base *sbom.SBOM, canonicalPackages map[string]*pkg.Package,
 
 	return &sbom.SBOM{
 		Descriptor: base.Descriptor,
-		Source:     base.Source,
 		Artifacts: sbom.Artifacts{
 			Packages: collection,
 		},

sbomtool/internal/commands/merge/merge_test.go

@@ -143,8 +143,10 @@ func TestMergeSBOMs(t *testing.T) {
 					createTestPackage("pkg3", "3.0.0", ""),
 				}),
 			},
-			expectedPackageCount:      4,
-			expectedRelationshipCount: 2,
+			// 4 original packages + 2 source packages (test1, test2) = 6
+			// 2 original relationships + 4 contains relationships (2 pkgs × 2 sources) = 6
+			expectedPackageCount:      6,
+			expectedRelationshipCount: 6,
 		},
 		{
 			name:                      "empty SBOM slice",
@@ -259,3 +261,122 @@ func createTestPackagePtr(name, version, cpeStr string) *pkg.Package {
 	p := createTestPackage(name, version, cpeStr)
 	return &p
 }
+
+func TestSourceToPackage(t *testing.T) {
+	// GIVEN: Various source descriptions
+	// WHEN: sourceToPackage is called
+	// THEN: Appropriate packages should be created
+
+	tests := []struct {
+		name       string
+		src        source.Description
+		expectNil  bool
+		expectName string
+		expectVer  string
+	}{
+		{
+			name:       "valid source with name and version",
+			src:        source.Description{Name: "libelf", Version: "0.194"},
+			expectNil:  false,
+			expectName: "libelf",
+			expectVer:  "0.194",
+		},
+		{
+			name:       "valid source with name only",
+			src:        source.Description{Name: "mypackage"},
+			expectNil:  false,
+			expectName: "mypackage",
+			expectVer:  "",
+		},
+		{
+			name:      "empty source",
+			src:       source.Description{},
+			expectNil: true,
+		},
+		{
+			name:      "source with empty name",
+			src:       source.Description{Name: "", Version: "1.0"},
+			expectNil: true,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			result := sourceToPackage(tt.src)
+
+			if tt.expectNil {
+				if result != nil {
+					t.Errorf("expected nil, got package with name %s", result.Name)
+				}
+				return
+			}
+
+			if result == nil {
+				t.Fatal("expected package, got nil")
+			}
+
+			if result.Name != tt.expectName {
+				t.Errorf("expected name %s, got %s", tt.expectName, result.Name)
+			}
+
+			if result.Version != tt.expectVer {
+				t.Errorf("expected version %s, got %s", tt.expectVer, result.Version)
+			}
+		})
+	}
+}
+
+func TestMergeSBOMsPreservesSource(t *testing.T) {
+	// GIVEN: Multiple SBOMs with Source (metadata.component) set
+	// WHEN: mergeSBOMs is called
+	// THEN: Source from each SBOM should be converted to a package with contains relationships
+
+	sbom1 := createTestSBOM("sbom1", []pkg.Package{
+		createTestPackage("pkg1", "1.0.0", ""),
+	})
+	sbom1.Source = source.Description{Name: "libelf", Version: "0.194"}
+
+	sbom2 := createTestSBOM("sbom2", []pkg.Package{
+		createTestPackage("pkg2", "2.0.0", ""),
+	})
+	sbom2.Source = source.Description{Name: "glibc", Version: "2.38"}
+
+	_, packages, relationships := mergeSBOMs([]*sbom.SBOM{sbom1, sbom2})
+
+	// Should have: pkg1, pkg2, libelf (from source), glibc (from source) = 4 packages
+	if len(packages) != 4 {
+		t.Errorf("expected 4 packages (2 original + 2 from source), got %d", len(packages))
+	}
+
+	// Verify libelf and glibc are in the packages
+	foundLibelf := false
+	foundGlibc := false
+	for _, p := range packages {
+		if p.Name == "libelf" && p.Version == "0.194" {
+			foundLibelf = true
+		}
+		if p.Name == "glibc" && p.Version == "2.38" {
+			foundGlibc = true
+		}
+	}
+
+	if !foundLibelf {
+		t.Error("expected libelf package from source, not found")
+	}
+	if !foundGlibc {
+		t.Error("expected glibc package from source, not found")
+	}
+
+	// Verify contains relationships were created
+	// Each SBOM has 1 package + 1 existing relationship from createTestSBOM
+	// Plus 1 contains relationship from source to package = 2 contains relationships total
+	containsCount := 0
+	for _, rel := range relationships {
+		if rel.Type == artifact.ContainsRelationship {
+			containsCount++
+		}
+	}
+	if containsCount != 2 {
+		t.Errorf("expected 2 contains relationships (one per source), got %d", containsCount)
+	}
+}

sbomtool/internal/deduplication/deduplicator.go

@@ -13,6 +13,7 @@ import (
 
 	"github.com/anchore/syft/syft/artifact"
 	"github.com/anchore/syft/syft/cpe"
+	"github.com/anchore/syft/syft/file"
 	"github.com/anchore/syft/syft/pkg"
 )
 
@@ -39,10 +40,10 @@ type DeduplicationStats struct {
 func DeduplicatePackages(packages []pkg.Package) *DeduplicationResult {
 	startTime := time.Now()
 
-	// Filter out document root packages and other metadata packages
+	// Filter out packages with empty names
 	var realPackages []pkg.Package
 	for _, p := range packages {
-		if p.Name != "" && !strings.Contains(string(p.ID()), "DocumentRoot") {
+		if p.Name != "" {
 			realPackages = append(realPackages, p)
 		}
 	}
@@ -236,6 +237,23 @@ func mergePackages(packages []*pkg.Package) *pkg.Package {
 		}
 	}
 
+	// Merge Locations (union of all file locations)
+	allLocations := make([]file.Location, 0)
+	for _, p := range packages {
+		allLocations = append(allLocations, p.Locations.ToSlice()...)
+	}
+	canonical.Locations = file.NewLocationSet(allLocations...)
+
+	// Preserve Metadata from first package with non-nil metadata
+	if canonical.Metadata == nil {
+		for _, p := range packages {
+			if p.Metadata != nil {
+				canonical.Metadata = p.Metadata
+				break
+			}
+		}
+	}
+
 	return &canonical
 }
 

sbomtool/internal/processor/processor.go

@@ -1,5 +1,6 @@
 // Package processor provides Syft-based SBOM processing capabilities optimized for Bottlerocket builds.
 // It configures Syft's catalogers for comprehensive package detection including Go and Rust binary analysis.
+
 package processor
 
 import (
@@ -8,6 +9,7 @@ import (
 	"os"
 
 	"github.com/anchore/syft/syft/format"
+	"github.com/anchore/syft/syft/format/cyclonedxjson"
 	"github.com/anchore/syft/syft/pkg"
 	"github.com/anchore/syft/syft/sbom"
 )
@@ -41,12 +43,23 @@ func LoadSBOM(path string) (*sbom.SBOM, string, error) {
 // SaveSBOM saves an SBOM using Syft's format encoders.
 // It supports all formats that Syft can encode.
 func SaveSBOM(s *sbom.SBOM, path, formatName string) error {
-	// Find the encoder for the specified format
 	var encoder sbom.FormatEncoder
-	for _, enc := range format.Encoders() {
-		if string(enc.ID()) == formatName {
-			encoder = enc
-			break
+	var err error
+
+	if formatName == "cyclonedx-json" {
+		encoder, err = cyclonedxjson.NewFormatEncoderWithConfig(cyclonedxjson.EncoderConfig{
+			Version: "1.6",
+			Pretty:  true,
+		})
+		if err != nil {
+			return fmt.Errorf("failed to create CycloneDX encoder: %w", err)
+		}
+	} else {
+		for _, enc := range format.Encoders() {
+			if string(enc.ID()) == formatName {
+				encoder = enc
+				break
+			}
 		}
 	}