Merge pull request #77 from spdx/rc1

Update to SPDX Spec 3.0.1

pom.xml

@@ -141,7 +141,7 @@ This store supports serializing and deserializing files in JSON, YAML and XML fo
     <dependency>
     	<groupId>org.spdx</groupId>
     	<artifactId>java-spdx-library</artifactId>
-    	<version>2.0.0-Alpha</version>
+    	<version>2.0.0-RC1</version>
     </dependency>
     <dependency>
     	<groupId>com.google.code.gson</groupId>

src/main/java/org/spdx/jacksonstore/MultiFormatStore.java

@@ -1,14 +1,14 @@
 /**
  * Copyright (c) 2020 Source Auditor Inc.
- *
+ * <p>
  * SPDX-License-Identifier: Apache-2.0
- * 
+ * <p>
  *   Licensed under the Apache License, Version 2.0 (the "License");
  *   you may not use this file except in compliance with the License.
  *   You may obtain a copy of the License at
- *
+ * <p>
  *       http://www.apache.org/licenses/LICENSE-2.0
- *
+ * <p>
  *   Unless required by applicable law or agreed to in writing, software
  *   distributed under the License is distributed on an "AS IS" BASIS,
  *   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -21,6 +21,7 @@
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.OutputStream;
+import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
@@ -57,8 +58,8 @@
 
 /**
  * Model store that supports multiple serialization formats (JSON, XML, YAML)
- * 
- * Note that the serialization/deserlization methods are synchronized to prevent the format or verbose changing while serilizing
+ * <p>
+ * Note that the serialization/deserialization methods are synchronized to prevent the format or verbose changing while serializing
  * 
  * @author Gary O'Neall
  *
@@ -71,9 +72,9 @@ public enum Verbose {
 		COMPACT,		// SPDX identifiers are used for any SPDX element references, license expressions as text
 		STANDARD,		// Expand referenced SPDX element, license expressions as text
 		FULL			// Expand all licenses to full objects and expand all SPDX elements
-	};
-	
-	public enum Format {
+	}
+
+    public enum Format {
 		JSON,
 		JSON_PRETTY,	// pretty printed JSON format
 		XML,
@@ -92,7 +93,7 @@ public enum Format {
 	private ObjectMapper inputMapper;
 
 	/**
-	 * @param baseStore modelStore to store the results of the desearialization
+	 * @param baseStore modelStore to store the results of the deserialization
 	 * @param format Format - XML, JSON or YAML
 	 * @param verbose How verbose to make the document
 	 */
@@ -120,7 +121,7 @@ private void setMapper() {
 
 	/**
 	 * Default compact version of MultiFormatStore
-	 * @param baseStore modelStore to store the results of the desearialization
+	 * @param baseStore modelStore to store the results of the deserialization
 	 * @param format Format - XML, JSON or YAML
 	 */
 	public MultiFormatStore(IModelStore baseStore, Format format) {
@@ -198,15 +199,12 @@ public synchronized void serialize(OutputStream stream, @Nullable CoreModelObjec
     				jgen = yamlFactory.createGenerator(stream); 
     				break;
     			}
-    			case XML: {
-    				jgen = outputMapper.getFactory().createGenerator(stream).useDefaultPrettyPrinter(); 
-    				break;
-    			}
     			case JSON: {
     				jgen = outputMapper.getFactory().createGenerator(stream);
     				break;
     			}
     			case JSON_PRETTY:
+				case XML:
     			default:  {
     				jgen = outputMapper.getFactory().createGenerator(stream).useDefaultPrettyPrinter(); 
     				break;
@@ -221,7 +219,7 @@ public synchronized void serialize(OutputStream stream, @Nullable CoreModelObjec
 	}
 
 	/**
-	 * @param propertyName
+	 * @param propertyName name of the singular property
 	 * @return property name used for an array or collection of these values
 	 */
 	public static String propertyNameToCollectionPropertyName(String propertyName) {
@@ -256,7 +254,7 @@ public synchronized SpdxDocument deSerialize(InputStream stream, boolean overwri
 		JsonNode root;
 		if (Format.XML.equals(format)) {
 			// Jackson XML mapper does not support deserializing collections or arrays.  Use Json-In-Java to convert to JSON
-			JSONObject jo = XML.toJSONObject(new InputStreamReader(stream, "UTF-8"));
+			JSONObject jo = XML.toJSONObject(new InputStreamReader(stream, StandardCharsets.UTF_8));
 			root = inputMapper.readTree(jo.toString()).get("Document");
 		} else {
 			root  = inputMapper.readTree(stream);
@@ -266,7 +264,7 @@ public synchronized SpdxDocument deSerialize(InputStream stream, boolean overwri
 		}
 		List<String> documentNamespaces = new ArrayList<>();
 		if (root instanceof ArrayNode) {
-			for (JsonNode docNode:(ArrayNode)root) {
+			for (JsonNode docNode: root) {
 				documentNamespaces.add(getNamespaceFromDoc(docNode));
 			}
 		} else {
@@ -299,10 +297,10 @@ public synchronized SpdxDocument deSerialize(InputStream stream, boolean overwri
 		JacksonDeSerializer deSerializer = new JacksonDeSerializer(this, new ModelCopyManager(), format);
 		String docNamespace;
 		if (root instanceof ArrayNode) {
-			for (JsonNode doc:(ArrayNode)root) {
+			for (JsonNode doc: root) {
 				deSerializer.storeDocument(getNamespaceFromDoc(doc), doc);
 			}
-			docNamespace = getNamespaceFromDoc((ArrayNode)root.get(0));
+			docNamespace = getNamespaceFromDoc(root.get(0));
 		} else {
 			deSerializer.storeDocument(getNamespaceFromDoc(root), root);
 			docNamespace = getNamespaceFromDoc(root);
@@ -330,8 +328,8 @@ private String getNamespaceFromDoc(JsonNode docNode) throws InvalidSPDXAnalysisE
 	}
 
 	/**
-	 * @param documentNamespace
-	 * @throws InvalidSPDXAnalysisException 
+	 * @param documentNamespace Document namespace or Uri
+	 * @throws InvalidSPDXAnalysisException on SPDX parsing errors
 	 */
 	public void clear(String documentNamespace) throws InvalidSPDXAnalysisException {
 		List<TypedValue> valuesToDelete = this.getAllItems(documentNamespace, null).collect(Collectors.toList());
@@ -341,8 +339,8 @@ public void clear(String documentNamespace) throws InvalidSPDXAnalysisException
 	}
 
 	/**
-	 * @return list of SPDX V2 document URI's in this model store 
-	 * @throws InvalidSPDXAnalysisException 
+	 * @return set of SPDX V2 document URI's in this model store
+	 * @throws InvalidSPDXAnalysisException on SPDX parsing errors
 	 */
 	public Set<String> getDocumentUris() throws InvalidSPDXAnalysisException {
 		Set<String> retval = new HashSet<>();

src/main/java/org/spdx/jacksonstore/PropertyComparator.java

@@ -1,14 +1,14 @@
 /**
  * Copyright (c) 2020 Source Auditor Inc.
- *
+ * <p>
  * SPDX-License-Identifier: Apache-2.0
- * 
+ * <p>
  *   Licensed under the Apache License, Version 2.0 (the "License");
  *   you may not use this file except in compliance with the License.
  *   You may obtain a copy of the License at
- *
+ * <p>
  *       http://www.apache.org/licenses/LICENSE-2.0
- *
+ * <p>
  *   Unless required by applicable law or agreed to in writing, software
  *   distributed under the License is distributed on an "AS IS" BASIS,
  *   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -30,7 +30,7 @@
 
 /**
  * Comparator for property names for different SPDX class types
- * 
+ * <p>
  * To change the order of properties, change the order in the arrays for the specific type
  * If a property or type isn't in the propertyOrderMap, the alphaNumeric comparison of property names will be used
  * 
@@ -39,22 +39,20 @@
  */
 public class PropertyComparator implements Comparator<String> {
 
-	static final List<String> DOCUMENT_PROPERTY_ORDER = Arrays.asList(new String[] {
-			SpdxConstantsCompatV2.PROP_DOCUMENT_NAMESPACE.getName(),
-			SpdxConstantsCompatV2.PROP_SPDX_SPEC_VERSION.getName(),
-			SpdxConstantsCompatV2.PROP_SPDX_CREATION_INFO.getName(),
-			SpdxConstantsCompatV2.PROP_NAME.getName(),
-			SpdxConstantsCompatV2.PROP_SPDX_DATA_LICENSE.getName(),
-			SpdxConstantsCompatV2.RDFS_PROP_COMMENT.getName(),
-			SpdxConstantsCompatV2.PROP_SPDX_EXTERNAL_DOC_REF.getName(),
-			SpdxConstantsCompatV2.PROP_DOCUMENT_DESCRIBES.getName(),
-			SpdxConstantsCompatV2.PROP_DOCUMENT_PACKAGES.getName(),
-			SpdxConstantsCompatV2.PROP_DOCUMENT_FILES.getName(),
-			SpdxConstantsCompatV2.PROP_DOCUMENT_SNIPPETS.getName(),
-			SpdxConstantsCompatV2.PROP_SPDX_EXTRACTED_LICENSES.getName(),
-			SpdxConstantsCompatV2.PROP_ANNOTATION.getName(),
-			SpdxConstantsCompatV2.PROP_DOCUMENT_RELATIONSHIPS.getName()
-	});
+	static final List<String> DOCUMENT_PROPERTY_ORDER = Arrays.asList(SpdxConstantsCompatV2.PROP_DOCUMENT_NAMESPACE.getName(),
+            SpdxConstantsCompatV2.PROP_SPDX_SPEC_VERSION.getName(),
+            SpdxConstantsCompatV2.PROP_SPDX_CREATION_INFO.getName(),
+            SpdxConstantsCompatV2.PROP_NAME.getName(),
+            SpdxConstantsCompatV2.PROP_SPDX_DATA_LICENSE.getName(),
+            SpdxConstantsCompatV2.RDFS_PROP_COMMENT.getName(),
+            SpdxConstantsCompatV2.PROP_SPDX_EXTERNAL_DOC_REF.getName(),
+            SpdxConstantsCompatV2.PROP_DOCUMENT_DESCRIBES.getName(),
+            SpdxConstantsCompatV2.PROP_DOCUMENT_PACKAGES.getName(),
+            SpdxConstantsCompatV2.PROP_DOCUMENT_FILES.getName(),
+            SpdxConstantsCompatV2.PROP_DOCUMENT_SNIPPETS.getName(),
+            SpdxConstantsCompatV2.PROP_SPDX_EXTRACTED_LICENSES.getName(),
+            SpdxConstantsCompatV2.PROP_ANNOTATION.getName(),
+            SpdxConstantsCompatV2.PROP_DOCUMENT_RELATIONSHIPS.getName());
 	static final Map<String, List<String>> propertyOrderMap;
 	static {
 		HashMap<String, List<String>> hm = new HashMap<>();

src/main/java/org/spdx/jacksonstore/SpdxJsonLDContext.java

@@ -1,14 +1,14 @@
 /**
  * Copyright (c) 2020 Source Auditor Inc.
- *
+ * <p>
  * SPDX-License-Identifier: Apache-2.0
- * 
+ * <p>
  *   Licensed under the Apache License, Version 2.0 (the "License");
  *   you may not use this file except in compliance with the License.
  *   You may obtain a copy of the License at
- *
+ * <p>
  *       http://www.apache.org/licenses/LICENSE-2.0
- *
+ * <p>
  *   Unless required by applicable law or agreed to in writing, software
  *   distributed under the License is distributed on an "AS IS" BASIS,
  *   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -52,12 +52,12 @@ public class SpdxJsonLDContext {
 	}
 
 	/**
-	 * Maps XML Schema primitive types to Java classes supported by the SPDX stores. 
-	 * See https://www.w3.org/TR/xmlschema-2 for a description of XML schema types.
-	 */
-	public static Map<String, Class<? extends Object>> XMLSCHEMA_TYPE_TO_JAVA_CLASS;
+     * Maps XML Schema primitive types to Java classes supported by the SPDX stores.
+     * See <a href="https://www.w3.org/TR/xmlschema-2">xml-schema</a> for a description of XML schema types.
+     */
+	public static Map<String, Class<?>> XMLSCHEMA_TYPE_TO_JAVA_CLASS;
 	static {
-		Map<String, Class<? extends Object>> schemaToClass = new HashMap<>();
+		Map<String, Class<?>> schemaToClass = new HashMap<>();
 		schemaToClass.put("string", String.class);
 		schemaToClass.put("boolean", Boolean.class);
 		schemaToClass.put("decimal", String.class);
@@ -110,7 +110,7 @@ public class SpdxJsonLDContext {
 	static private SpdxJsonLDContext instance;
 	static final String JSON_LD_PATH = "/resources/spdx-2-3-revision-2-onotology.context.json";
 	static final ObjectMapper JSON_MAPPER = new ObjectMapper();
-	private JsonNode contexts;
+	private final JsonNode contexts;
 
 	private SpdxJsonLDContext() throws InvalidSPDXAnalysisException {
 		try (InputStream is = SpdxJsonLDContext.class.getResourceAsStream(JSON_LD_PATH)) {
@@ -144,8 +144,8 @@ public static synchronized SpdxJsonLDContext getInstance() throws InvalidSPDXAna
 	}
 
 	/**
-	 * @param propertyName
-	 * @return type type for the property name if the type is specified in the JSON-LD context
+	 * @param propertyName Name of the property
+	 * @return type for the property name if the type is specified in the JSON-LD context
 	 */
 	public Optional<String> getType(String propertyName) {
 		JsonNode propContext = this.contexts.get(propertyName);
@@ -182,7 +182,7 @@ public Optional<String> getType(String propertyName) {
 	}
 
 	/**
-	 * @param property
+	 * @param property JSON name of the property
 	 * @return true if the property is a list
 	 */
 	public boolean isList(String property) {
@@ -195,12 +195,11 @@ public boolean isList(String property) {
 			return false;
 		}
 		if (jnContainer.isArray()) {
-			Iterator<JsonNode> iter = jnContainer.iterator();
-			while (iter.hasNext()) {
-				if (LIST_CONTAINER_TYPES.contains(iter.next().asText())) {
-					return true;
-				}
-			}
+            for (JsonNode jsonNode : jnContainer) {
+                if (LIST_CONTAINER_TYPES.contains(jsonNode.asText())) {
+                    return true;
+                }
+            }
 			return false;
 		} else {
 			return LIST_CONTAINER_TYPES.contains(jnContainer.asText());