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Merged
ruromero merged 3 commits into from
Apr 20, 2026
Merged

fix(npm): stop skipping dependency subtree when root entry has no version #423

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435e32d
fix(npm): stop skipping dependency subtree when root entry has no ver…
ruromero Apr 16, 2026
b9ff6e2
fix: add missing test fixture for versionless root dep test
ruromero Apr 16, 2026
03c7132
fix: align addRootDependenciesFromKey functionality
ruromero Apr 20, 2026
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6 changes: 3 additions & 3 deletions src/main/java/io/github/guacsec/trustifyda/Provider.java
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Original file line number Diff line number Diff line change
Expand Up @@ -47,13 +47,13 @@ public Content(byte[] buffer, String type) {
/** The ecosystem of this provider, i.e. maven. */
public final Ecosystem.Type ecosystem;

public final Path manifest;
public final Path manifestPath;

protected final ObjectMapper objectMapper = new ObjectMapper();

protected Provider(Ecosystem.Type ecosystem, Path manifest) {
protected Provider(Ecosystem.Type ecosystem, Path manifestPath) {
this.ecosystem = ecosystem;
this.manifest = manifest;
this.manifestPath = manifestPath;
}

/**
Expand Down
23 changes: 12 additions & 11 deletions src/main/java/io/github/guacsec/trustifyda/providers/CargoProvider.java
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Expand Up @@ -146,7 +146,7 @@ private void addDependencies(
handleSingleCrate(sbom, root, metadata, nodeMap, packageMap, ignoredDeps, analysisType);
}

} catch (Exception e) {
} catch (IOException | InterruptedException e) {
log.severe("Unexpected error during " + analysisType + " analysis: " + e.getMessage());
}
}
Expand Down Expand Up @@ -385,7 +385,7 @@ private Path findOutermostCargoTomlDirectory(Path startDir) {
}

private CargoMetadata executeCargoMetadata() throws IOException, InterruptedException {
Path workingDir = manifest.getParent();
Path workingDir = manifestPath.getParent();

if (debugLoggingIsNeeded()) {
log.info("Executing cargo metadata for full dependency resolution with resolved versions");
Expand Down Expand Up @@ -657,20 +657,21 @@ public CargoProvider(Path manifest) {
@Override
public String readLicenseFromManifest() {
String manifestLicense = readLicenseFromToml(null);
return LicenseUtils.getLicense(manifestLicense, manifest);
return LicenseUtils.getLicense(manifestLicense, manifestPath);
}

private String readLicenseFromToml(TomlParseResult existingResult) {
try {
TomlParseResult tomlResult = existingResult != null ? existingResult : Toml.parse(manifest);
TomlParseResult tomlResult =
existingResult != null ? existingResult : Toml.parse(manifestPath);
if (tomlResult.hasErrors()) {
return null;
}
String license = tomlResult.getString("package.license");
return LicenseUtils.getLicense(license, manifest);
return LicenseUtils.getLicense(license, manifestPath);
} catch (IOException e) {
log.warning("Failed to read license from Cargo.toml: " + e.getMessage());
return LicenseUtils.getLicense(null, manifest);
return LicenseUtils.getLicense(null, manifestPath);
}
}

Expand All @@ -687,11 +688,11 @@ public Content provideStack() throws IOException {
}

private Sbom createSbom(AnalysisType analysisType) throws IOException {
if (!Files.exists(manifest) || !Files.isRegularFile(manifest)) {
throw new IOException("Cargo.toml not found: " + manifest);
if (!Files.exists(manifestPath) || !Files.isRegularFile(manifestPath)) {
throw new IOException("Cargo.toml not found: " + manifestPath);
}

TomlParseResult tomlResult = Toml.parse(manifest);
TomlParseResult tomlResult = Toml.parse(manifestPath);
if (tomlResult.hasErrors()) {
throw new IOException(
"Invalid Cargo.toml format: " + tomlResult.errors().get(0).getMessage());
Expand All @@ -706,7 +707,7 @@ private Sbom createSbom(AnalysisType analysisType) throws IOException {
Type.CARGO.getType(), null, projectInfo.name(), projectInfo.version(), null, null);
sbom.addRoot(root, readLicenseFromToml(tomlResult));

String cargoContent = Files.readString(manifest, StandardCharsets.UTF_8);
String cargoContent = Files.readString(manifestPath, StandardCharsets.UTF_8);
Set<String> ignoredDeps = getIgnoredDependencies(tomlResult, cargoContent);
addDependencies(sbom, root, ignoredDeps, tomlResult, analysisType);
return sbom;
Expand Down Expand Up @@ -744,7 +745,7 @@ private ProjectInfo parseCargoToml(TomlParseResult result) throws IOException {
boolean hasWorkspace = result.contains("workspace");
if (hasWorkspace) {
String workspaceVersion = result.getString(WORKSPACE_PACKAGE_VERSION);
String dirName = manifest.toAbsolutePath().getParent().getFileName().toString();
String dirName = manifestPath.toAbsolutePath().getParent().getFileName().toString();
if (debugLoggingIsNeeded()) {
log.info(
"Using workspace fallback: name="
Expand Down
14 changes: 7 additions & 7 deletions src/main/java/io/github/guacsec/trustifyda/providers/GoModulesProvider.java
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Expand Up @@ -73,27 +73,27 @@ public GoModulesProvider(Path manifest) {

@Override
public String readLicenseFromManifest() {
return LicenseUtils.readLicenseFile(manifest);
return LicenseUtils.readLicenseFile(manifestPath);
}

@Override
public Content provideStack() throws IOException {
// check for custom executable
Sbom sbom = getDependenciesSbom(manifest, true);
Sbom sbom = getDependenciesSbom(manifestPath, true);
return new Content(
sbom.getAsJsonString().getBytes(StandardCharsets.UTF_8), Api.CYCLONEDX_MEDIA_TYPE);
}

@Override
public Content provideComponent() throws IOException {
if (!Files.exists(manifest)) {
throw new IllegalArgumentException("Missing required go.mod file: " + manifest);
if (!Files.exists(manifestPath)) {
throw new IllegalArgumentException("Missing required go.mod file: " + manifestPath);
}
if (!Files.isRegularFile(manifest)) {
if (!Files.isRegularFile(manifestPath)) {
throw new IllegalArgumentException(
"The provided manifest is not a regular file: " + manifest);
"The provided manifest is not a regular file: " + manifestPath);
}
var sbom = getDependenciesSbom(manifest, false);
var sbom = getDependenciesSbom(manifestPath, false);
return new Content(
sbom.getAsJsonString().getBytes(StandardCharsets.UTF_8), Api.CYCLONEDX_MEDIA_TYPE);
}
Expand Down
14 changes: 7 additions & 7 deletions src/main/java/io/github/guacsec/trustifyda/providers/GradleProvider.java
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Expand Up @@ -70,12 +70,12 @@ public GradleProvider(Path manifest) {

@Override
public String readLicenseFromManifest() {
return LicenseUtils.readLicenseFile(manifest);
return LicenseUtils.readLicenseFile(manifestPath);
}

@Override
public Content provideStack() throws IOException {
Path tempFile = getDependencies(manifest);
Path tempFile = getDependencies(manifestPath);
try {
if (debugLoggingIsNeeded()) {
String stackAnalysisDependencyTree = Files.readString(tempFile);
Expand All @@ -84,10 +84,10 @@ public Content provideStack() throws IOException {
"Package Manager Gradle Stack Analysis Dependency Tree Output: %s %s",
System.lineSeparator(), stackAnalysisDependencyTree));
}
Map<String, String> propertiesMap = extractProperties(manifest);
Map<String, String> propertiesMap = extractProperties(manifestPath);

var sbom = buildSbomFromTextFormat(tempFile, propertiesMap, AnalysisType.STACK);
var ignored = getIgnoredDeps(manifest);
var ignored = getIgnoredDeps(manifestPath);

return new Content(
sbom.filterIgnoredDeps(ignored).getAsJsonString().getBytes(), Api.CYCLONEDX_MEDIA_TYPE);
Expand Down Expand Up @@ -605,12 +605,12 @@ private List<String> extractLines(Path inputFilePath, String startMarker) throws

@Override
public Content provideComponent() throws IOException {
Path tempFile = getDependencies(manifest);
Path tempFile = getDependencies(manifestPath);
try {
Map<String, String> propertiesMap = extractProperties(manifest);
Map<String, String> propertiesMap = extractProperties(manifestPath);

Sbom sbom = buildSbomFromTextFormat(tempFile, propertiesMap, AnalysisType.COMPONENT);
var ignored = getIgnoredDeps(manifest);
var ignored = getIgnoredDeps(manifestPath);

return new Content(
sbom.filterIgnoredDeps(ignored).getAsJsonString().getBytes(), Api.CYCLONEDX_MEDIA_TYPE);
Expand Down
23 changes: 12 additions & 11 deletions src/main/java/io/github/guacsec/trustifyda/providers/JavaMavenProvider.java
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Expand Up @@ -68,8 +68,8 @@ public JavaMavenProvider(Path manifest) {

@Override
public String readLicenseFromManifest() {
String manifestLicense = readLicenseFromPom(manifest);
return LicenseUtils.getLicense(manifestLicense, manifest);
String manifestLicense = readLicenseFromPom(manifestPath);
return LicenseUtils.getLicense(manifestLicense, manifestPath);
}

/**
Expand Down Expand Up @@ -124,10 +124,11 @@ private String readLicenseFromPom(Path pomPath) {

@Override
public Content provideStack() throws IOException {
var mvnCleanCmd = buildMvnCommandArgs("clean", "-f", manifest.toString(), "--batch-mode", "-q");
var mvnCleanCmd =
buildMvnCommandArgs("clean", "-f", manifestPath.toString(), "--batch-mode", "-q");
var mvnEnvs = getMvnExecEnvs();
// execute the clean command
Operations.runProcess(manifest.getParent(), mvnCleanCmd.toArray(String[]::new), mvnEnvs);
Operations.runProcess(manifestPath.getParent(), mvnCleanCmd.toArray(String[]::new), mvnEnvs);
// create a temp file for storing the dependency tree in
var tmpFile = Files.createTempFile("TRUSTIFY_DA_dot_graph_", null);
// the tree command will build the project and create the dependency tree in the temp file
Expand All @@ -140,12 +141,12 @@ public Content provideStack() throws IOException {
"-DoutputType=text",
String.format("-DoutputFile=%s", tmpFile.toString()),
"-f",
manifest.toString(),
manifestPath.toString(),
"--batch-mode",
"-q"));
// if we have dependencies marked as ignored, exclude them from the tree command
var ignored =
getDependencies(manifest).stream()
getDependencies(manifestPath).stream()
.filter(d -> d.ignored)
.map(DependencyAggregator::toPurlWithoutVersion)
.map(PackageURL::getCoordinates)
Expand All @@ -157,7 +158,7 @@ public Content provideStack() throws IOException {

// execute the tree command
var mvnTreeCmd = buildMvnCommandArgs(mvnTreeCmdArgs.toArray(String[]::new));
Operations.runProcess(manifest.getParent(), mvnTreeCmd.toArray(String[]::new), mvnEnvs);
Operations.runProcess(manifestPath.getParent(), mvnTreeCmd.toArray(String[]::new), mvnEnvs);
if (debugLoggingIsNeeded()) {
String stackAnalysisDependencyTree = Files.readString(tmpFile);
log.info(
Expand Down Expand Up @@ -201,12 +202,12 @@ private Content generateSbomFromEffectivePom() throws IOException {
"help:effective-pom",
String.format("-Doutput=%s", tmpEffPom.toString()),
"-f",
manifest.toString(),
manifestPath.toString(),
"--batch-mode",
"-q");
// execute the effective pom command
Operations.runProcess(
manifest.getParent(), mvnEffPomCmd.toArray(String[]::new), getMvnExecEnvs());
manifestPath.getParent(), mvnEffPomCmd.toArray(String[]::new), getMvnExecEnvs());
if (debugLoggingIsNeeded()) {
String CaEffectivePoM = Files.readString(tmpEffPom);
log.info(
Expand All @@ -216,7 +217,7 @@ private Content generateSbomFromEffectivePom() throws IOException {
}
// if we have dependencies marked as ignored grab ignored dependencies from the original pom
// the effective-pom goal doesn't carry comments
List<DependencyAggregator> dependencies = getDependencies(manifest);
List<DependencyAggregator> dependencies = getDependencies(manifestPath);
var ignored =
dependencies.stream()
.filter(d -> d.ignored)
Expand Down Expand Up @@ -437,7 +438,7 @@ private String selectMvnRuntime(final Path manifestPath) {
if (mvnw != null) {
try {
// verify maven wrapper is accessible
Operations.runProcess(manifest.getParent(), mvnw, ARG_VERSION);
Operations.runProcess(manifestPath.getParent(), mvnw, ARG_VERSION);
if (debugLoggingIsNeeded()) {
log.info(String.format("using maven wrapper from : %s", mvnw));
}
Expand Down
29 changes: 12 additions & 17 deletions src/main/java/io/github/guacsec/trustifyda/providers/JavaScriptProvider.java
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,6 @@
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Collections;
import java.util.Iterator;
import java.util.Map;
import java.util.Map.Entry;
import java.util.TreeMap;
Expand Down Expand Up @@ -128,9 +127,7 @@ private void addDependenciesOf(Sbom sbom, PackageURL from, JsonNode node) {
if (dependencies == null) {
return;
}
Iterator<Entry<String, JsonNode>> fields = dependencies.fields();
while (fields.hasNext()) {
Entry<String, JsonNode> e = fields.next();
for (var e : dependencies.properties()) {
String name = e.getKey();
JsonNode versionNode = e.getValue().get("version");
if (versionNode == null) {
Expand Down Expand Up @@ -174,14 +171,13 @@ private void addDependenciesFromKey(Sbom sbom, JsonNode depTree, String key) {
if (deps == null) {
return;
}
deps.fields()
.forEachRemaining(
deps.properties()
.forEach(
e -> {
JsonNode versionNode = e.getValue().get("version");
if (versionNode == null || versionNode.isNull()) {
return; // skip entries without a resolved version
}
var target = toPurl(e.getKey(), versionNode.asText());
String version =
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(versionNode != null && !versionNode.isNull()) ? versionNode.asText() : null;
var target = toPurl(e.getKey(), version);
sbom.addDependency(manifest.root, target, null);
addDependenciesOf(sbom, target, e.getValue());
});
Expand Down Expand Up @@ -216,16 +212,15 @@ private void addRootDependenciesFromKey(
if (node == null) {
return;
}
node.fields()
.forEachRemaining(
node.properties()
.forEach(
e -> {
String name = e.getKey();
JsonNode versionNode = e.getValue().get("version");
if (versionNode != null) {
String version = versionNode.asText();
PackageURL purl = toPurl(name, version);
direct.put(name, purl);
}
String version =
(versionNode != null && !versionNode.isNull()) ? versionNode.asText() : null;
PackageURL purl = toPurl(name, version);
direct.put(name, purl);
});
}

Expand Down
10 changes: 6 additions & 4 deletions src/main/java/io/github/guacsec/trustifyda/providers/PythonPipProvider.java
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Expand Up @@ -57,15 +57,16 @@ public void setPythonController(PythonControllerBase pythonController) {
@Override
public Content provideStack() throws IOException {
PythonControllerBase controller = getPythonController();
List<Map<String, Object>> dependencies = controller.getDependencies(manifest.toString(), true);
List<Map<String, Object>> dependencies =
controller.getDependencies(manifestPath.toString(), true);
printDependenciesTree(dependencies);
Sbom sbom = SbomFactory.newInstance(Sbom.BelongingCondition.PURL, "sensitive");
sbom.addRoot(
toPurl(getRootComponentName(), getRootComponentVersion()), readLicenseFromManifest());
for (Map<String, Object> component : dependencies) {
addAllDependencies(sbom.getRoot(), component, sbom);
}
String manifestContent = Files.readString(manifest);
String manifestContent = Files.readString(manifestPath);
handleIgnoredDependencies(manifestContent, sbom);
return new Content(
sbom.getAsJsonString().getBytes(StandardCharsets.UTF_8), Api.CYCLONEDX_MEDIA_TYPE);
Expand All @@ -74,7 +75,8 @@ public Content provideStack() throws IOException {
@Override
public Content provideComponent() throws IOException {
PythonControllerBase controller = getPythonController();
List<Map<String, Object>> dependencies = controller.getDependencies(manifest.toString(), false);
List<Map<String, Object>> dependencies =
controller.getDependencies(manifestPath.toString(), false);
printDependenciesTree(dependencies);
Sbom sbom = SbomFactory.newInstance();
sbom.addRoot(
Expand All @@ -85,7 +87,7 @@ public Content provideComponent() throws IOException {
sbom.getRoot(),
toPurl((String) component.get("name"), (String) component.get("version")),
null));
String manifestContent = Files.readString(manifest);
String manifestContent = Files.readString(manifestPath);
handleIgnoredDependencies(manifestContent, sbom);
return new Content(
sbom.getAsJsonString().getBytes(StandardCharsets.UTF_8), Api.CYCLONEDX_MEDIA_TYPE);
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/io/github/guacsec/trustifyda/providers/PythonProvider.java
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Expand Up @@ -43,7 +43,7 @@ protected PythonProvider(Path manifest) {

@Override
public String readLicenseFromManifest() {
return LicenseUtils.readLicenseFile(manifest);
return LicenseUtils.readLicenseFile(manifestPath);
}

protected String getRootComponentName() {
Expand Down
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