Updated to support API changes needed for the RDF store

Signed-off-by: Gary O'Neall <gary@sourceauditor.com>

Author: goneall

pom.xml

@@ -4,7 +4,7 @@
 
     <groupId>org.spdx</groupId>
     <artifactId>java-spdx-library</artifactId>
-    <version>1.1.8-SNAPSHOT</version>
+    <version>2.0.0-SNAPSHOT</version>
     <packaging>jar</packaging>
 
     <name>java-spdx-library</name>

src/main/java/org/spdx/library/ModelCopyManager.java

@@ -244,7 +244,7 @@ private void copyCollectionProperty(IModelStore toStore, String toObjectUri, IMo
 	 * @param sourceUri URI for the Source object
 	 * @param type Type to copy
 	 * @param toSpecVersion Version of the SPDX spec the to value complies with
-	 * @param toNamespace Namespace to use if an ID needs to be generated for the to object
+	 * @param toNamespace Namespace to use if an ID needs to be generated for the to object - must be a unique prefix to the store
 	 * @return Object URI for the copied object
 	 * @throws InvalidSPDXAnalysisException
 	 */
@@ -258,30 +258,95 @@ public TypedValue copy(IModelStore toStore, IModelStore fromStore,
 
 		String toObjectUri = getCopiedObjectUri(fromStore, sourceUri, toStore);
 		if (Objects.isNull(toObjectUri)) {
-			if (toStore.exists(sourceUri) || IdType.Anonymous.equals(fromStore.getIdType(sourceUri))) {
-				// TODO - the toNamspace will never be used - we need to add a from namespace
-				if (Objects.nonNull(toNamespace)) {
-					if (SpdxConstantsCompatV2.CLASS_EXTERNAL_DOC_REF.equals(type)) {
-						toObjectUri = toNamespace + toStore.getNextId(IdType.DocumentRef);
-					} else {
-						switch (fromStore.getIdType(sourceUri)) {
-							case Anonymous: toObjectUri = toStore.getNextId(IdType.Anonymous); break;
-							case LicenseRef: toObjectUri = toNamespace + toStore.getNextId(IdType.LicenseRef); break;
-							case DocumentRef: toObjectUri = toNamespace + toStore.getNextId(IdType.DocumentRef); break;
-							case SpdxId: toObjectUri = toNamespace + toStore.getNextId(IdType.SpdxId); break;
-							case ListedLicense:
-							case Unkown:
-							default: toObjectUri = toStore.getNextId(IdType.Anonymous);
-						}
-					}
-				} else {
-					toObjectUri = toStore.getNextId(IdType.Anonymous);
-				}
-			} else {
-				toObjectUri = sourceUri;
-			}
+			toObjectUri = toSpecVersion.startsWith("SPDX-2") ? sourceUriToObjectUriV2Compat(sourceUri, 
+					fromStore.getIdType(sourceUri), toStore, toNamespace, SpdxConstantsCompatV2.CLASS_EXTERNAL_DOC_REF.equals(type)) :
+				sourceUriToObjectUri(sourceUri, fromStore.getIdType(sourceUri), toStore, toNamespace);
 			copy(toStore, toObjectUri, fromStore, sourceUri, type, toSpecVersion, toNamespace);
 		}
 		return new TypedValue(toObjectUri, type, toSpecVersion);
 	}
+
+	/**
+	 * @param sourceUri source URI copied from
+	 * @param idType idType from the sourceUri
+	 * @param toStore model store to store the copied item
+	 * @param toNamespace namespace for the generated elements for "to"
+	 * @return an object URI suitable for SPDX V3 and later
+	 * @throws InvalidSPDXAnalysisException 
+	 */
+	private String sourceUriToObjectUri(String sourceUri, IdType idType, IModelStore toStore, 
+			String toNamespace) throws InvalidSPDXAnalysisException {
+		if (IdType.Anonymous.equals(idType)) {
+			return toStore.getNextId(IdType.Anonymous);
+		}
+		if (!toStore.exists(sourceUri)) {
+			return sourceUri;
+		}
+		if (Objects.isNull(toNamespace) || toNamespace.isEmpty() || 
+				sourceUri.startsWith(toNamespace)) {
+			logger.warn(sourceUri + " already exists - possibly overwriting properties due to a copy from a different model store.");
+			return sourceUri;
+		}
+		switch (idType) {
+			case LicenseRef: return toNamespace + toStore.getNextId(IdType.LicenseRef);
+			case DocumentRef: return toNamespace + toStore.getNextId(IdType.DocumentRef);
+			case SpdxId: return toNamespace + toStore.getNextId(IdType.SpdxId);
+			case ListedLicense: return sourceUri;
+			case Anonymous:
+			case Unkown:
+			default: return toStore.getNextId(IdType.Anonymous);
+		}
+	}
+
+	/**
+	 * @param sourceUri source URI copied from
+	 * @param idType idType from the sourceUri
+	 * @param toStore model store to store the copied item
+	 * @param toNamespace namespace for the generated elements for "to"
+	 * @param isExternalDocRef true if the type of the value to be copied is an ExternalDocRef
+	 * @return an object URI suitable for SPDX V2
+	 * @throws InvalidSPDXAnalysisException 
+	 */
+	private String sourceUriToObjectUriV2Compat(String sourceUri, IdType idType, 
+			IModelStore toStore, String toNamespace, boolean isExternalDocRef) throws InvalidSPDXAnalysisException {
+		if ((isExternalDocRef || !(IdType.Anonymous.equals(idType) ||
+				IdType.ListedLicense.equals(idType) || IdType.Unkown.equals(idType)))
+				&& (Objects.isNull(toNamespace) || toNamespace.isEmpty())) {
+			throw new InvalidSPDXAnalysisException("A to namespace or document URI must be provided to copy SPDX element for SPDX spec version 2");
+		}
+		if (sourceUri.startsWith(toNamespace) && !toStore.exists(sourceUri)) {
+			return sourceUri;
+		}
+		if (IdType.ListedLicense.equals(idType)) {
+			return sourceUri;
+		}
+		String toUri = null;
+		if (Objects.nonNull(toNamespace)) {
+			int poundIndex = sourceUri.lastIndexOf('#');
+			if (poundIndex > 0) {
+				toUri = toNamespace + sourceUri.substring(poundIndex + 1);
+			}
+		}
+		
+		boolean notNullAndNotExists = Objects.nonNull(toUri) && !toStore.exists(toUri); // notExists and nonNull
+		if (isExternalDocRef) {
+			if (!toStore.exists(toUri) && IdType.DocumentRef.equals(toStore.getIdType(toUri))) {
+				return toUri;
+			} else {
+				return toNamespace + toStore.getNextId(IdType.DocumentRef);
+			}
+		}
+		switch (idType) {
+			case LicenseRef: return notNullAndNotExists && IdType.LicenseRef.equals(toStore.getIdType(toUri)) ? toUri : 
+				toNamespace + toStore.getNextId(IdType.LicenseRef);
+			case DocumentRef: return notNullAndNotExists && IdType.DocumentRef.equals(toStore.getIdType(toUri)) ? toUri : 
+				toNamespace + toStore.getNextId(IdType.DocumentRef);
+			case SpdxId: return notNullAndNotExists && IdType.SpdxId.equals(toStore.getIdType(toUri)) ? toUri : 
+				toNamespace + toStore.getNextId(IdType.SpdxId);
+			case ListedLicense: return sourceUri;
+			case Anonymous:
+			case Unkown:
+			default: return toStore.getNextId(IdType.Anonymous);
+		}
+	}
 }

src/main/java/org/spdx/storage/listedlicense/SpdxListedLicenseModelStore.java

@@ -41,11 +41,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.spdx.core.DuplicateSpdxIdException;
-import org.spdx.core.IExternalElementInfo;
 import org.spdx.core.InvalidSPDXAnalysisException;
 import org.spdx.core.SpdxIdNotFoundException;
 import org.spdx.core.TypedValue;
-import org.spdx.library.LicenseInfoFactory;
 import org.spdx.library.model.v2.ModelObjectV2;
 import org.spdx.library.model.v2.SpdxConstantsCompatV2;
 import org.spdx.library.model.v2.license.SpdxListedLicenseException;
@@ -156,12 +154,6 @@ public SpdxListedLicenseModelStore() throws InvalidSPDXAnalysisException {
 	 * @throws IOException
 	 */
 	abstract InputStream getExceptionInputStream(String exceptionId) throws IOException;
-	
-	/**
-	 * Map of an objectUri to a map of documentUri's to external element information
-	 */
-	protected Map<String, Map<String, IExternalElementInfo>> objectUriExternalMap = new HashMap<>();
-
 	/**
 	 * Loads all license and exception ID's from the appropriate JSON files
 	 * @throws InvalidSPDXAnalysisException
@@ -249,6 +241,9 @@ private String objectUriToId(String objectUri) throws InvalidSPDXAnalysisExcepti
 		String id;
 		if (objectUri.startsWith(LISTED_LICENSE_NAMESPACE)) {
 			id = objectUri.substring(LISTED_LICENSE_NAMESPACE.length());
+		} else if (objectUri.startsWith(SpdxConstantsCompatV2.LISTED_LICENSE_URL)) {
+			logger.warn("SPDX listed license URL was used instead of the required namespace ('https:' rather than 'http:'");
+			id = objectUri.substring(SpdxConstantsCompatV2.LISTED_LICENSE_URL.length());
 		} else if (getIdType(objectUri) == IdType.Anonymous || 
 				licenseCreator.getObjectUri().equals(objectUri) ||
 				LicenseCreationInfo.CREATION_INFO_URI.equals(objectUri)) {
@@ -1194,19 +1189,24 @@ public boolean isCollectionProperty(String objectUri, PropertyDescriptor propert
 	}
 
 	@Override
-	public IdType getIdType(String id) {
-		Objects.requireNonNull(id, "ID must not be null");
-		if (LicenseInfoFactory.isSpdxListedLicenseId(id) || LicenseInfoFactory.isSpdxListedExceptionId(id)) {
+	public IdType getIdType(String objectUri) {
+		Objects.requireNonNull(objectUri, "Object URI must not be null");
+		if (objectUri.startsWith(LISTED_LICENSE_NAMESPACE)) {
 			return IdType.ListedLicense;
-		} else if (id.startsWith(ANONYMOUS_ID_PREFIX) || LicenseCreationInfo.CREATION_INFO_URI.equals(id)) {
+		} else if (objectUri.startsWith(ANONYMOUS_ID_PREFIX) || LicenseCreationInfo.CREATION_INFO_URI.equals(objectUri)) {
 			return IdType.Anonymous;
-		} else if (id.startsWith(LicenseCreatorAgent.OBJECT_URI_PREFIX)) {
+		} else if (objectUri.startsWith(LicenseCreatorAgent.OBJECT_URI_PREFIX)) {
 			return IdType.SpdxId;
 		} else {
 			return IdType.Unkown;
 		}
 	}
 
+	@Override
+	public boolean isAnon(String objectUri) {
+		return objectUri.startsWith(ANONYMOUS_ID_PREFIX);
+	}
+	
 
 	@Override
 	public IModelStoreLock enterCriticalSection(boolean readLockRequested) {
@@ -1284,44 +1284,4 @@ public void delete(String objectUri) throws InvalidSPDXAnalysisException {
 	public void close() throws Exception {
 		// Nothing to do for the either the in-memory or the web store
 	}
-	
-	/**
-	 * Adds an external reference for a given collection
-	 * @param externalObjectUri URI of the external SPDX Element or License
-	 * @param collectionUri URI of the SPDX document or collection
-	 * @param externalElementInfo info about the external element
-	 * @return the previous external mapping for the collection, null if no previous value is present
-	 */
-	@Override
-	public synchronized @Nullable IExternalElementInfo addExternalReference(String externalObjectUri, String collectionUri, IExternalElementInfo externalElementInfo) {
-		Map<String, IExternalElementInfo> externalObjectToCollectionMap = objectUriExternalMap.get(externalObjectUri);
-		if (Objects.isNull(externalObjectToCollectionMap)) {
-			externalObjectToCollectionMap = new HashMap<>();
-		}
-		return externalObjectToCollectionMap.put(collectionUri, externalElementInfo);
-	}
-	
-	/**
-	 * @param externalObjectUri object URI for an element external to a collection
-	 * @return a map of collection (or document) URI's mapped to their external element info for the given object URI
-	 */
-	@Override
-	public synchronized @Nullable Map<String, IExternalElementInfo> getExternalReferenceMap(String externalObjectUri) {
-		return objectUriExternalMap.get(externalObjectUri);
-	}
-	
-	/**
-	 * @param externalObjectUri URI of the external SPDX Element or License
-	 * @param collectionUri URI of the SPDX document or collection
-	 * @return the externalElementInfo associated with the collection for a given external element
-	 */
-	@Override
-	public synchronized @Nullable IExternalElementInfo getExternalElementInfo(String externalObjectUri, String collectionUri) {
-		Map<String, IExternalElementInfo> externalObjectToCollectionMap = objectUriExternalMap.get(externalObjectUri);
-		if (Objects.isNull(externalObjectToCollectionMap)) {
-			return null;
-		} else {
-			return externalObjectToCollectionMap.get(collectionUri);
-		}
-	}
 }

src/main/java/org/spdx/storage/listedlicense/SpdxV2ListedLicenseModelStore.java

@@ -21,13 +21,11 @@
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
-import java.util.Map;
 import java.util.Objects;
 import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Stream;
 
-import org.spdx.core.IExternalElementInfo;
 import org.spdx.core.InvalidSPDXAnalysisException;
 import org.spdx.core.TypedValue;
 import org.spdx.library.model.v2.ModelObjectV2;
@@ -374,30 +372,11 @@ public void delete(String objectUri) throws InvalidSPDXAnalysisException {
 	}
 
 	/* (non-Javadoc)
-	 * @see org.spdx.storage.IModelStore#addExternalReference(java.lang.String, java.lang.String, org.spdx.core.IExternalElementInfo)
+	 * @see org.spdx.storage.IModelStore#isAnon(java.lang.String)
 	 */
 	@Override
-	public IExternalElementInfo addExternalReference(String externalObjectUri,
-			String collectionUri, IExternalElementInfo externalElementInfo) {
-		return baseStore.addExternalReference(externalObjectUri, collectionUri, externalElementInfo);
-	}
-
-	/* (non-Javadoc)
-	 * @see org.spdx.storage.IModelStore#getExternalReferenceMap(java.lang.String)
-	 */
-	@Override
-	public Map<String, IExternalElementInfo> getExternalReferenceMap(
-			String externalObjectUri) {
-		return baseStore.getExternalReferenceMap(externalObjectUri);
-	}
-
-	/* (non-Javadoc)
-	 * @see org.spdx.storage.IModelStore#getExternalElementInfo(java.lang.String, java.lang.String)
-	 */
-	@Override
-	public IExternalElementInfo getExternalElementInfo(String externalObjectUri,
-			String collectionUri) {
-		return baseStore.getExternalElementInfo(externalObjectUri, collectionUri);
+	public boolean isAnon(String objectUri) {
+		return baseStore.isAnon(objectUri);
 	}
 
 }

src/main/java/org/spdx/storage/listedlicense/SpdxV3ListedLicenseModelStore.java

@@ -21,12 +21,10 @@
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
-import java.util.Map;
 import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Stream;
 
-import org.spdx.core.IExternalElementInfo;
 import org.spdx.core.InvalidSPDXAnalysisException;
 import org.spdx.core.TypedValue;
 import org.spdx.library.model.v2.SpdxConstantsCompatV2;
@@ -380,30 +378,10 @@ public void delete(String objectUri) throws InvalidSPDXAnalysisException {
 	}
 
 	/* (non-Javadoc)
-	 * @see org.spdx.storage.IModelStore#addExternalReference(java.lang.String, java.lang.String, org.spdx.core.IExternalElementInfo)
+	 * @see org.spdx.storage.IModelStore#isAnon(java.lang.String)
 	 */
 	@Override
-	public IExternalElementInfo addExternalReference(String externalObjectUri,
-			String collectionUri, IExternalElementInfo externalElementInfo) {
-		return baseStore.addExternalReference(externalObjectUri, collectionUri, externalElementInfo);
+	public boolean isAnon(String objectUri) {
+		return baseStore.isAnon(objectUri);
 	}
-
-	/* (non-Javadoc)
-	 * @see org.spdx.storage.IModelStore#getExternalReferenceMap(java.lang.String)
-	 */
-	@Override
-	public Map<String, IExternalElementInfo> getExternalReferenceMap(
-			String externalObjectUri) {
-		return baseStore.getExternalReferenceMap(externalObjectUri);
-	}
-
-	/* (non-Javadoc)
-	 * @see org.spdx.storage.IModelStore#getExternalElementInfo(java.lang.String, java.lang.String)
-	 */
-	@Override
-	public IExternalElementInfo getExternalElementInfo(String externalObjectUri,
-			String collectionUri) {
-		return baseStore.getExternalElementInfo(externalObjectUri, collectionUri);
-	}
-
 }

src/main/java/org/spdx/storage/simple/ExtendedSpdxStore.java

@@ -19,14 +19,10 @@
 
 import java.util.Iterator;
 import java.util.List;
-import java.util.Map;
 import java.util.Optional;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-import javax.annotation.Nullable;
-
-import org.spdx.core.IExternalElementInfo;
 import org.spdx.core.InvalidSPDXAnalysisException;
 import org.spdx.core.TypedValue;
 import org.spdx.storage.IModelStore;
@@ -223,6 +219,14 @@ public boolean isCollectionProperty(String objectUri, PropertyDescriptor propert
 	public IdType getIdType(String id) {
 		return baseStore.getIdType(id);
 	}
+	
+	/* (non-Javadoc)
+	 * @see org.spdx.storage.IModelStore#isAnon(java.lang.String)
+	 */
+	@Override
+	public boolean isAnon(String objectUri) {
+		return baseStore.isAnon(objectUri);
+	}
 
 	/* (non-Javadoc)
 	 * @see org.spdx.storage.IModelStore#getCaseSensisitiveId(java.lang.String, java.lang.String)
@@ -268,20 +272,4 @@ public void delete(String objectUri) throws InvalidSPDXAnalysisException {
 	public void close() throws Exception {
 		baseStore.close();
 	}
-	
-	@Override
-	public synchronized @Nullable IExternalElementInfo getExternalElementInfo(String externalObjectUri, String collectionUri) {
-		return baseStore.getExternalElementInfo(externalObjectUri, collectionUri);
-	}
-	
-	@Override
-	public synchronized @Nullable Map<String, IExternalElementInfo> getExternalReferenceMap(String externalObjectUri) {
-		return baseStore.getExternalReferenceMap(externalObjectUri);
-	}
-	
-	@Override
-	public synchronized @Nullable IExternalElementInfo addExternalReference(String externalObjectUri, String collectionUri, IExternalElementInfo externalElementInfo) {
-		return baseStore.addExternalReference(externalObjectUri, collectionUri, externalElementInfo);
-	}
-
 }