Fix Spdx2to3Converter dropping packages with no relationships

src/main/java/org/spdx/library/conversion/Spdx2to3Converter.java

@@ -21,6 +21,7 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 import javax.annotation.Nullable;
 
@@ -29,6 +30,7 @@
 import org.spdx.core.IModelCopyManager;
 import org.spdx.core.InvalidSPDXAnalysisException;
 import org.spdx.library.ListedLicenses;
+import org.spdx.library.SpdxModelFactory;
 import org.spdx.library.model.v2.SpdxConstantsCompatV2;
 import org.spdx.library.model.v2.SpdxCreatorInformation;
 import org.spdx.library.model.v2.pointer.ByteOffsetPointer;
@@ -698,11 +700,58 @@ public SpdxDocument convertAndStore(org.spdx.library.model.v2.SpdxDocument fromD
 		}
 						).collect(Collectors.toList()));
 		for (org.spdx.library.model.v2.license.ExtractedLicenseInfo extractedLicense:fromDoc.getExtractedLicenseInfos()) {
-			convertAndStore(extractedLicense);
+			toDoc.getRootElements().add(convertAndStore(extractedLicense));
 		}
+		convertOrphanElements(fromDoc, toDoc);
 		return toDoc;
 	}
 
+	/**
+	 * Converts any SPDX spec version 2 packages, files, snippets, listed licenses, and listed license
+	 * exceptions belonging to fromDoc which are not reachable through documentDescribes, a relationship,
+	 * or a license expression (i.e. have no edges connecting them to anything else in the document).
+	 * Without this, such elements would be silently dropped from the conversion since they would never
+	 * be visited by the relationship graph traversal performed elsewhere in this class.
+	 * Any such elements found are converted, stored, and added to the toDoc's root elements.
+	 * @param fromDoc SPDX spec version 2 document being converted from
+	 * @param toDoc SPDX spec version 3 document being converted to
+	 * @throws InvalidSPDXAnalysisException on any errors converting the orphan elements
+	 */
+	@SuppressWarnings("unchecked")
+	private void convertOrphanElements(org.spdx.library.model.v2.SpdxDocument fromDoc, SpdxDocument toDoc) throws InvalidSPDXAnalysisException {
+		String documentUri = fromDoc.getDocumentUri();
+		IModelStore fromModelStore = fromDoc.getModelStore();
+		for (String typeFilter : new String[] {SpdxConstantsCompatV2.CLASS_SPDX_PACKAGE,
+				SpdxConstantsCompatV2.CLASS_SPDX_FILE, SpdxConstantsCompatV2.CLASS_SPDX_SNIPPET}) {
+			List<org.spdx.library.model.v2.SpdxElement> fromElements = ((Stream<org.spdx.library.model.v2.SpdxElement>)
+					SpdxModelFactory.getSpdxObjects(fromModelStore, copyManager, typeFilter, documentUri, null))
+					.collect(Collectors.toList());
+			for (org.spdx.library.model.v2.SpdxElement fromElement : fromElements) {
+				if (!alreadyCopied(fromElement.getObjectUri())) {
+					toDoc.getRootElements().add(convertAndStore(fromElement));
+				}
+			}
+		}
+		// Listed licenses and listed license exceptions are stored under the SPDX License List namespace
+		// rather than the document's namespace, so no object URI prefix filter is used to find them.
+		List<org.spdx.library.model.v2.license.SpdxListedLicense> fromListedLicenses = ((Stream<org.spdx.library.model.v2.license.SpdxListedLicense>)
+				SpdxModelFactory.getSpdxObjects(fromModelStore, copyManager, SpdxConstantsCompatV2.CLASS_SPDX_LISTED_LICENSE, null, null))
+				.collect(Collectors.toList());
+		for (org.spdx.library.model.v2.license.SpdxListedLicense fromListedLicense : fromListedLicenses) {
+			if (!alreadyCopied(fromListedLicense.getObjectUri())) {
+				toDoc.getRootElements().add(convertAndStore(fromListedLicense));
+			}
+		}
+		List<org.spdx.library.model.v2.license.ListedLicenseException> fromListedExceptions = ((Stream<org.spdx.library.model.v2.license.ListedLicenseException>)
+				SpdxModelFactory.getSpdxObjects(fromModelStore, copyManager, SpdxConstantsCompatV2.CLASS_SPDX_LISTED_LICENSE_EXCEPTION, null, null))
+				.collect(Collectors.toList());
+		for (org.spdx.library.model.v2.license.ListedLicenseException fromListedException : fromListedExceptions) {
+			if (!alreadyCopied(fromListedException.getObjectUri())) {
+				toDoc.getRootElements().add(convertAndStore(fromListedException));
+			}
+		}
+	}
+
 	/**
 	 * Converts the externalDocRef to a NamespaceMap and store the NamespaceMap.
 	 * The document information is also retained in the externalDocRefMap such that any subsequent 

src/test/java/org/spdx/library/conversion/Spdx2to3ConverterTest.java

@@ -23,10 +23,12 @@
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;
 import java.util.Optional;
+import java.util.Set;
 
 import javax.annotation.Nullable;
 
@@ -606,9 +608,21 @@ public void testConvertAndStoreSpdxDocument() throws InvalidSPDXAnalysisExceptio
 		assertEquals(annotationComment, resultAnnotation.getStatement().get());
 
 		Element[] rootElements = result.getRootElements().toArray(new Element[result.getRootElements().size()]);
-		assertEquals(1, rootElements.length);
-		assertTrue(rootElements[0] instanceof SpdxPackage);
-		SpdxPackage resultPkg = (SpdxPackage)rootElements[0];
+		assertEquals(2, rootElements.length);
+		SpdxPackage resultPkg = null;
+		CustomLicense rootCustomLicense = null;
+		for (Element rootElement:rootElements) {
+			if (rootElement instanceof SpdxPackage) {
+				resultPkg = (SpdxPackage)rootElement;
+			} else if (rootElement instanceof CustomLicense) {
+				rootCustomLicense = (CustomLicense)rootElement;
+			} else {
+				fail("Unexpected root element type "+rootElement.getClass().getName());
+			}
+		}
+		assertTrue(Objects.nonNull(resultPkg));
+		assertTrue(Objects.nonNull(rootCustomLicense));
+		assertEquals(extractedLicName, rootCustomLicense.getName().get());
 		assertEquals(pkgName, resultPkg.getName().get());
 		assertEquals(pkgDownloadLocation, resultPkg.getDownloadLocation().get());
 		assertEquals(pkgCopyright, resultPkg.getCopyrightText().get());
@@ -671,6 +685,135 @@ public void testConvertAndStoreSpdxDocument() throws InvalidSPDXAnalysisExceptio
 		assertTrue(verify.isEmpty());
 	}
 
+	/**
+	 * Test method for {@link org.spdx.library.conversion.Spdx2to3Converter#convertAndStore(org.spdx.library.model.v2.SpdxDocument)}.
+	 * Verifies that a package with no relationships and not included in documentDescribes (i.e. no edges
+	 * connecting it to anything else in the document) is still converted rather than silently dropped.
+	 * @throws InvalidSPDXAnalysisException 
+	 */
+	@Test
+	public void testConvertAndStoreSpdxDocumentOrphanPackage() throws InvalidSPDXAnalysisException {
+		String describedPkgName = "described package";
+		String orphanPkgName = "orphan package";
+
+		org.spdx.library.model.v2.SpdxDocument doc = new org.spdx.library.model.v2.SpdxDocument(fromModelStore, DOCUMENT_URI, copyManager, true);
+		doc.setCreationInfo(doc.createCreationInfo(Arrays.asList(new String[] {SpdxConstantsCompatV2.CREATOR_PREFIX_TOOL + "test"}), 
+				"2010-01-29T18:30:22Z"));
+		org.spdx.library.model.v2.license.AnyLicenseInfo dataLicense = 
+				LicenseInfoFactory.parseSPDXLicenseStringCompatV2("CC0-1.0", fromModelStore, DOCUMENT_URI, copyManager);
+		doc.setDataLicense(dataLicense);
+
+		org.spdx.library.model.v2.license.AnyLicenseInfo noAssertion = 
+				new org.spdx.library.model.v2.license.SpdxNoAssertionLicense();
+		org.spdx.library.model.v2.SpdxPackage describedPkg = doc.createPackage(fromModelStore.getNextId(IdType.SpdxId), 
+				describedPkgName, noAssertion, "copyright", noAssertion)
+				.setFilesAnalyzed(false)
+				.setDownloadLocation("NOASSERTION")
+				.build();
+		doc.setDocumentDescribes(Arrays.asList(new org.spdx.library.model.v2.SpdxItem[] {describedPkg}));
+
+		// orphan package - no relationships, not part of documentDescribes
+		org.spdx.library.model.v2.SpdxPackage orphanPkg = doc.createPackage(fromModelStore.getNextId(IdType.SpdxId), 
+				orphanPkgName, noAssertion, "copyright", noAssertion)
+				.setFilesAnalyzed(false)
+				.setDownloadLocation("NOASSERTION")
+				.build();
+
+		Spdx2to3Converter converter = new Spdx2to3Converter(toModelStore, copyManager, defaultCreationInfo, 
+				SpdxModelFactory.getLatestSpecVersion(), DEFAULT_PREFIX, true);
+		converter.convertAndStore(doc);
+
+		List<SpdxPackage> resultPackages = new ArrayList<>();
+		SpdxModelFactory.getSpdxObjects(toModelStore, copyManager, SpdxConstantsV3.SOFTWARE_SPDX_PACKAGE, DEFAULT_PREFIX, DEFAULT_PREFIX)
+				.forEach(pkg -> resultPackages.add((SpdxPackage)pkg));
+		assertEquals(2, resultPackages.size());
+		Set<String> resultPackageNames = new HashSet<>();
+		for (SpdxPackage pkg:resultPackages) {
+			resultPackageNames.add(pkg.getName().get());
+		}
+		assertTrue(resultPackageNames.contains(describedPkgName));
+		assertTrue(resultPackageNames.contains(orphanPkgName));
+	}
+
+	/**
+	 * Test method for {@link org.spdx.library.conversion.Spdx2to3Converter#convertAndStore(org.spdx.library.model.v2.SpdxDocument)}.
+	 * Verifies that extracted licensing info, listed licenses, and listed license exceptions stored in the
+	 * document's model store but not referenced by any package, file, or snippet are still converted and
+	 * added as root elements rather than silently dropped.
+	 * @throws InvalidSPDXAnalysisException 
+	 */
+	@Test
+	public void testConvertAndStoreSpdxDocumentOrphanLicenses() throws InvalidSPDXAnalysisException {
+		String pkgName = "package";
+		String extractedLicName = "Extracted License Name";
+		String extractedLicText = "Extracted license text";
+		String orphanLicenseId = "Apache-2.0";
+		String orphanExceptionId = "Classpath-exception-2.0";
+
+		org.spdx.library.model.v2.SpdxDocument doc = new org.spdx.library.model.v2.SpdxDocument(fromModelStore, DOCUMENT_URI, copyManager, true);
+		doc.setCreationInfo(doc.createCreationInfo(Arrays.asList(new String[] {SpdxConstantsCompatV2.CREATOR_PREFIX_TOOL + "test"}), 
+				"2010-01-29T18:30:22Z"));
+		org.spdx.library.model.v2.license.AnyLicenseInfo dataLicense = 
+				LicenseInfoFactory.parseSPDXLicenseStringCompatV2("CC0-1.0", fromModelStore, DOCUMENT_URI, copyManager);
+		doc.setDataLicense(dataLicense);
+
+		org.spdx.library.model.v2.license.AnyLicenseInfo noAssertion = 
+				new org.spdx.library.model.v2.license.SpdxNoAssertionLicense();
+		org.spdx.library.model.v2.SpdxPackage pkg = doc.createPackage(fromModelStore.getNextId(IdType.SpdxId), 
+				pkgName, noAssertion, "copyright", noAssertion)
+				.setFilesAnalyzed(false)
+				.setDownloadLocation("NOASSERTION")
+				.build();
+		doc.setDocumentDescribes(Arrays.asList(new org.spdx.library.model.v2.SpdxItem[] {pkg}));
+
+		// extracted license info stored at the document level but not referenced by the package
+		org.spdx.library.model.v2.license.ExtractedLicenseInfo extractedLicense = 
+				new org.spdx.library.model.v2.license.ExtractedLicenseInfo(fromModelStore, DOCUMENT_URI, 
+						fromModelStore.getNextId(IdType.LicenseRef), copyManager, true);
+		extractedLicense.setExtractedText(extractedLicText);
+		extractedLicense.setName(extractedLicName);
+		doc.setExtractedLicenseInfos(Arrays.asList(new org.spdx.library.model.v2.license.ExtractedLicenseInfo[] {extractedLicense}));
+
+		// listed license and listed license exception stored in the document's model store but not
+		// referenced by the package, a relationship, or documentDescribes
+		org.spdx.library.model.v2.license.SpdxListedLicense orphanLicense = 
+				new org.spdx.library.model.v2.license.SpdxListedLicense(fromModelStore, 
+						SpdxConstantsCompatV2.LISTED_LICENSE_NAMESPACE_PREFIX, orphanLicenseId, copyManager, true);
+		org.spdx.library.model.v2.license.ListedLicenseException orphanException = 
+				new org.spdx.library.model.v2.license.ListedLicenseException(fromModelStore, 
+						SpdxConstantsCompatV2.LISTED_LICENSE_NAMESPACE_PREFIX, orphanExceptionId, copyManager, true);
+
+		Spdx2to3Converter converter = new Spdx2to3Converter(toModelStore, copyManager, defaultCreationInfo, 
+				SpdxModelFactory.getLatestSpecVersion(), DEFAULT_PREFIX, true);
+		SpdxDocument result = converter.convertAndStore(doc);
+
+		Element[] rootElements = result.getRootElements().toArray(new Element[result.getRootElements().size()]);
+		assertEquals(4, rootElements.length);
+		boolean foundPkg = false;
+		boolean foundCustomLicense = false;
+		boolean foundListedLicense = false;
+		boolean foundListedException = false;
+		for (Element rootElement:rootElements) {
+			if (rootElement instanceof SpdxPackage) {
+				foundPkg = true;
+				assertEquals(pkgName, ((SpdxPackage)rootElement).getName().get());
+			} else if (rootElement instanceof CustomLicense) {
+				foundCustomLicense = true;
+				assertEquals(extractedLicName, ((CustomLicense)rootElement).getName().get());
+			} else if (rootElement instanceof ListedLicense) {
+				foundListedLicense = true;
+			} else if (rootElement instanceof ListedLicenseException) {
+				foundListedException = true;
+			} else {
+				fail("Unexpected root element type "+rootElement.getClass().getName());
+			}
+		}
+		assertTrue(foundPkg);
+		assertTrue(foundCustomLicense);
+		assertTrue(foundListedLicense);
+		assertTrue(foundListedException);
+	}
+
 	@Test
 	public void testConvertAndStoreExternalDocRef() throws InvalidSPDXAnalysisException {
 		String externalDocumentId = SpdxConstantsCompatV2.EXTERNAL_DOC_REF_PRENUM + "external";