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Merged
ruromero merged 3 commits into from
Apr 30, 2026
Merged

fix(go): distinguish direct from indirect dependencies #449

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11e71d3
fix(go): distinguish direct from indirect dependencies
ruromero Apr 29, 2026
4bceb7a
fix: match JS client empty SBOM structure in CycloneDX output
ruromero Apr 29, 2026
b908270
chore: update expectations and minor fixes
ruromero Apr 30, 2026
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81 changes: 77 additions & 4 deletions src/main/java/io/github/guacsec/trustifyda/providers/GoModulesProvider.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,9 @@

import static io.github.guacsec.trustifyda.impl.ExhortApi.debugLoggingIsNeeded;

import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.github.packageurl.MalformedPackageURLException;
import com.github.packageurl.PackageURL;
import io.github.guacsec.trustifyda.Api;
Expand All @@ -40,9 +43,11 @@
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Set;
import java.util.logging.Logger;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
Expand Down Expand Up @@ -136,16 +141,17 @@ Sbom getDependenciesSbom(Path manifestPath, boolean buildTree) throws IOExceptio
determineMainModuleVersion(manifestPath.getParent());
Sbom sbom;
List<PackageURL> ignoredDeps = getIgnoredDeps(manifestPath);
Set<String> directDepPaths = getDirectDependencyPaths(manifestPath);
boolean matchManifestVersions =
Environment.getBoolean(Provider.PROP_MATCH_MANIFEST_VERSIONS, false);
if (matchManifestVersions) {
String[] goModGraphLines = goModulesResult.split(Operations.GENERIC_LINE_SEPARATOR);
performManifestVersionsCheck(goModGraphLines, manifestPath);
}
if (!buildTree) {
sbom = buildSbomFromList(goModulesResult, ignoredDeps);
sbom = buildSbomFromList(goModulesResult, ignoredDeps, directDepPaths);
} else {
sbom = buildSbomFromGraph(goModulesResult, ignoredDeps, manifestPath);
sbom = buildSbomFromGraph(goModulesResult, ignoredDeps, manifestPath, directDepPaths);
}
return sbom;
}
Expand Down Expand Up @@ -264,7 +270,10 @@ public void determineMainModuleVersion(Path directory) {
}

private Sbom buildSbomFromGraph(
String goModulesResult, List<PackageURL> ignoredDeps, Path manifestPath) {
String goModulesResult,
List<PackageURL> ignoredDeps,
Path manifestPath,
Set<String> directDepPaths) {
// Each entry contains a key of the module, and the list represents the module direct
// dependencies , so
// pairing of the key with each of the dependencies in a list is basically an edge in the graph.
Expand Down Expand Up @@ -300,6 +309,17 @@ private Sbom buildSbomFromGraph(
PackageURL source = toPurl(key, "@");
value.stream()
.filter(dep -> !isGoToolchainEntry(dep))
.filter(
dep -> {
// When processing root-level edges, skip indirect dependencies.
// In Go 1.17+, go mod graph emits edges for all modules in go.mod,
// including those marked // indirect. Only keep edges whose child
// module path is in the direct dependency set.
if (getModulePath(key).equals(getModulePath(rootPackage))) {
return directDepPaths.contains(getModulePath(dep));
}
return true;
})
.forEach(
dep -> {
PackageURL targetPurl = toPurl(dep, "@");
Expand Down Expand Up @@ -422,7 +442,59 @@ private String buildGoModulesDependencies(Path manifestPath) {
return goModulesOutput;
}

private Sbom buildSbomFromList(String golangDeps, List<PackageURL> ignoredDeps) {
/**
* Runs {@code go mod edit -json} and returns the set of module paths that are direct dependencies
* (i.e., entries in the Require array where {@code Indirect} is false or absent). This
* distinguishes direct from indirect dependencies in Go 1.17+ modules, where {@code go mod tidy}
* records all transitively-imported modules in go.mod with an {@code // indirect} marker.
*/
private Set<String> getDirectDependencyPaths(Path manifestPath) {
String[] goModEditCmd = new String[] {goExecutable, "mod", "edit", "-json"};
String goModEditOutput = Operations.runProcessGetOutput(manifestPath.getParent(), goModEditCmd);
if (debugLoggingIsNeeded()) {
log.info(
String.format(
"Package Manager Go Mod Edit -json output : %s%s",
System.lineSeparator(), goModEditOutput));
}
Set<String> directDepPaths = new HashSet<>();
try {
ObjectMapper mapper = new ObjectMapper();
JsonNode root = mapper.readTree(goModEditOutput);
JsonNode requireArray = root.get("Require");
if (requireArray != null && requireArray.isArray()) {
for (JsonNode req : requireArray) {
JsonNode indirectNode = req.get("Indirect");
if (indirectNode == null || !indirectNode.asBoolean()) {
if (req.get("Path") != null) {
directDepPaths.add(req.get("Path").asText());
}
}
}
}
} catch (JsonProcessingException e) {
throw new IllegalStateException("Failed to parse go mod edit -json output", e);
}
if (debugLoggingIsNeeded()) {
log.info(String.format("Direct dependency paths from go mod edit -json: %s", directDepPaths));
}
return directDepPaths;
}

/**
* Extracts the module path from a go mod graph entry by stripping the version suffix. For
* example, {@code "github.com/foo/bar@v1.2.3"} returns {@code "github.com/foo/bar"}.
*/
private static String getModulePath(String graphEntry) {
int atIndex = graphEntry.indexOf("@");
if (atIndex == -1) {
return graphEntry;
}
return graphEntry.substring(0, atIndex);
}

private Sbom buildSbomFromList(
String golangDeps, List<PackageURL> ignoredDeps, Set<String> directDepPaths) {
String[] allModulesFlat = golangDeps.split(Operations.GENERIC_LINE_SEPARATOR);
String parentVertex = getParentVertex(allModulesFlat[0]);
PackageURL root = toPurl(parentVertex, "@");
Expand All @@ -433,6 +505,7 @@ private Sbom buildSbomFromList(String golangDeps, List<PackageURL> ignoredDeps)
sbom.addRoot(root, readLicenseFromManifest());
deps.stream()
.filter(dep -> !isGoToolchainEntry(dep))
.filter(dep -> directDepPaths.contains(getModulePath(dep)))
.forEach(
dep -> {
PackageURL targetPurl = toPurl(dep, "@");
Expand Down
34 changes: 32 additions & 2 deletions src/main/java/io/github/guacsec/trustifyda/sbom/CycloneDXSbom.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,9 @@

import static io.github.guacsec.trustifyda.impl.ExhortApi.debugLoggingIsNeeded;

import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.node.ObjectNode;
import com.github.packageurl.MalformedPackageURLException;
import com.github.packageurl.PackageURL;
import io.github.guacsec.trustifyda.logging.LoggersFactory;
Expand Down Expand Up @@ -67,8 +70,8 @@ public CycloneDXSbom() {
Metadata metadata = new Metadata();
metadata.setTimestamp(new Date());
bom.setMetadata(metadata);
bom.setComponents(new ArrayList<>());
bom.setDependencies(new ArrayList<>());
bom.setComponents(new ArrayList<>());
belongingCriteriaBinaryAlgorithm = getBelongingConditionByName();
this.exhortIgnoreMethod = "insensitive";
}
Expand Down Expand Up @@ -230,6 +233,9 @@ private Sbom removeIgnoredDepsFromSbom(List<String> refsToIgnore) {
d.setDependencies(filteredDeps);
}
});
if (bom.getComponents().isEmpty()) {
bom.setDependencies(new ArrayList<>());
}
return this;
}

Expand Down Expand Up @@ -302,12 +308,36 @@ public Sbom addDependency(PackageURL sourceRef, PackageURL targetRef, String s)
public String getAsJsonString() {
try {
var jsonString = BomGeneratorFactory.createJson(VERSION, bom).toJsonString();
jsonString = ensureComponentsField(jsonString);
if (debugLoggingIsNeeded()) {
log.info("Generated Sbom Json:" + System.lineSeparator() + jsonString);
}
return jsonString;
} catch (GeneratorException e) {
throw new RuntimeException("Unable to genenerate JSON from SBOM", e);
throw new RuntimeException("Unable to generate JSON from SBOM", e);
}
}

private String ensureComponentsField(String json) throws GeneratorException {
try {
var mapper = new ObjectMapper();
var rootNode = (ObjectNode) mapper.readTree(json);
if (!rootNode.has("components")) {
var ordered = mapper.createObjectNode();
rootNode
.properties()
.forEach(
field -> {
ordered.set(field.getKey(), field.getValue());
if (field.getKey().equals("metadata")) {
ordered.set("components", mapper.createArrayNode());
}
});
return mapper.writerWithDefaultPrettyPrinter().writeValueAsString(ordered);
}
return json;
} catch (JsonProcessingException e) {
throw new GeneratorException("Unable to ensure components field in JSON", e);
}
}
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Expand Down
40 changes: 1 addition & 39 deletions src/test/resources/msc/golang/mvs_logic/expected_sbom_stack_analysis.json
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Original file line number Diff line number Diff line change
Expand Up @@ -3989,51 +3989,13 @@
{
"ref": "pkg:golang/github.com/rhecosystemappeng/saasi/deployer@v0.0.0",
"dependsOn": [
"pkg:golang/github.com/davecgh/go-spew@v1.1.1",
"pkg:golang/github.com/emicklei/go-restful/v3@v3.9.0",
"pkg:golang/github.com/gin-gonic/gin@v1.9.1",
"pkg:golang/github.com/go-logr/logr@v1.2.3",
"pkg:golang/github.com/go-openapi/jsonpointer@v0.19.5",
"pkg:golang/github.com/go-openapi/jsonreference@v0.20.0",
"pkg:golang/github.com/go-openapi/swag@v0.19.14",
"pkg:golang/github.com/gogo/protobuf@v1.3.2",
"pkg:golang/github.com/golang/protobuf@v1.5.2",
"pkg:golang/github.com/google/gnostic@v0.5.7-v3refs",
"pkg:golang/github.com/google/go-cmp@v0.5.9",
"pkg:golang/github.com/google/gofuzz@v1.1.0",
"pkg:golang/github.com/google/uuid@v1.1.2",
"pkg:golang/github.com/imdario/mergo@v0.3.6",
"pkg:golang/github.com/jessevdk/go-flags@v1.5.0",
"pkg:golang/github.com/josharian/intern@v1.0.0",
"pkg:golang/github.com/json-iterator/go@v1.1.12",
"pkg:golang/github.com/kr/pretty@v0.3.1",
"pkg:golang/github.com/kr/text@v0.2.0",
"pkg:golang/github.com/mailru/easyjson@v0.7.6",
"pkg:golang/github.com/modern-go/concurrent@v0.0.0-20180306012644-bacd9c7ef1dd",
"pkg:golang/github.com/modern-go/reflect2@v1.0.2",
"pkg:golang/github.com/munnerz/goautoneg@v0.0.0-20191010083416-a7dc8b61c822",
"pkg:golang/github.com/rogpeppe/go-internal@v1.9.0",
"pkg:golang/github.com/spf13/pflag@v1.0.5",
"pkg:golang/golang.org/x/net@v0.10.0",
"pkg:golang/golang.org/x/oauth2@v0.0.0-20220223155221-ee480838109b",
"pkg:golang/golang.org/x/sys@v0.8.0",
"pkg:golang/golang.org/x/term@v0.8.0",
"pkg:golang/golang.org/x/text@v0.9.0",
"pkg:golang/golang.org/x/time@v0.0.0-20220210224613-90d013bbcef8",
"pkg:golang/google.golang.org/appengine@v1.6.7",
"pkg:golang/google.golang.org/protobuf@v1.30.0",
"pkg:golang/gopkg.in/inf.v0@v0.9.1",
"pkg:golang/gopkg.in/yaml.v2@v2.4.0",
"pkg:golang/gopkg.in/yaml.v3@v3.0.1",
"pkg:golang/k8s.io/api@v0.26.1",
"pkg:golang/k8s.io/apimachinery@v0.26.1",
"pkg:golang/k8s.io/client-go@v0.26.1",
"pkg:golang/k8s.io/klog/v2@v2.80.1",
"pkg:golang/k8s.io/kube-openapi@v0.0.0-20221012153701-172d655c2280",
"pkg:golang/k8s.io/utils@v0.0.0-20221107191617-1a15be271d1d",
"pkg:golang/sigs.k8s.io/json@v0.0.0-20220713155537-f223a00ba0e2",
"pkg:golang/sigs.k8s.io/structured-merge-diff/v4@v4.2.3",
"pkg:golang/sigs.k8s.io/yaml@v1.3.0"
"pkg:golang/k8s.io/client-go@v0.26.1"
]
},
{
Expand Down
17 changes: 2 additions & 15 deletions ...sources/tst_manifests/golang/go_mod_light_no_ignore/expected_sbom_component_analysis.json
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Original file line number Diff line number Diff line change
Expand Up @@ -29,23 +29,14 @@
"name" : "tools",
"version" : "v0.0.0-20210112183307-1e6ecd4bf1b0",
"purl" : "pkg:golang/golang.org/x/tools@v0.0.0-20210112183307-1e6ecd4bf1b0"
},
{
"type" : "library",
"bom-ref" : "pkg:golang/gopkg.in/yaml.v3@v3.0.1",
"group" : "gopkg.in",
"name" : "yaml.v3",
"version" : "v3.0.1",
"purl" : "pkg:golang/gopkg.in/yaml.v3@v3.0.1"
}
],
"dependencies" : [
{
"ref" : "pkg:golang/golang.org/x/example@v0.0.0",
"dependsOn" : [
"pkg:golang/github.com/spf13/cobra@v0.0.5",
"pkg:golang/golang.org/x/tools@v0.0.0-20210112183307-1e6ecd4bf1b0",
"pkg:golang/gopkg.in/yaml.v3@v3.0.1"
"pkg:golang/golang.org/x/tools@v0.0.0-20210112183307-1e6ecd4bf1b0"
]
},
{
Expand All @@ -55,10 +46,6 @@
{
"ref" : "pkg:golang/golang.org/x/tools@v0.0.0-20210112183307-1e6ecd4bf1b0",
"dependsOn" : [ ]
},
{
"ref" : "pkg:golang/gopkg.in/yaml.v3@v3.0.1",
"dependsOn" : [ ]
}
]
}
}
3 changes: 1 addition & 2 deletions ...t/resources/tst_manifests/golang/go_mod_light_no_ignore/expected_sbom_stack_analysis.json
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Original file line number Diff line number Diff line change
Expand Up @@ -315,8 +315,7 @@
"ref": "pkg:golang/golang.org/x/example@v0.0.0",
"dependsOn": [
"pkg:golang/github.com/spf13/cobra@v0.0.5",
"pkg:golang/golang.org/x/tools@v0.0.0-20210112183307-1e6ecd4bf1b0",
"pkg:golang/gopkg.in/yaml.v3@v3.0.1"
"pkg:golang/golang.org/x/tools@v0.0.0-20210112183307-1e6ecd4bf1b0"
]
},
{
Expand Down
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