Merge pull request #91 from spdx/issue90

Set the XMLInputFactory property for RDF files

src/main/java/org/spdx/tools/SpdxConverter.java

@@ -28,6 +28,7 @@
 import org.spdx.library.InvalidSPDXAnalysisException;
 import org.spdx.library.ModelCopyManager;
 import org.spdx.library.SpdxConstants;
+import org.spdx.spdxRdfStore.RdfStore;
 import org.spdx.storage.ISerializableModelStore;
 import org.spdx.tools.SpdxToolsHelper.SerFileType;
 
@@ -143,9 +144,22 @@ public static void convert(String fromFilePath, String toFilePath, SerFileType f
 		}
 		FileInputStream input = null;
 		FileOutputStream output = null;
+		String oldXmlInputFactory = null;
+		boolean propertySet = false;
 		try {
 			ISerializableModelStore fromStore = SpdxToolsHelper.fileTypeToStore(fromFileType);
 			ISerializableModelStore toStore = SpdxToolsHelper.fileTypeToStore(toFileType);
+			if (fromStore instanceof RdfStore || toStore instanceof RdfStore) {
+				// Setting the property value will avoid the error message
+				// See issue #90 for more information
+				try {
+					oldXmlInputFactory = System.setProperty(SpdxToolsHelper.XML_INPUT_FACTORY_PROPERTY_KEY, 
+					        "com.sun.xml.internal.stream.XMLInputFactoryImpl");
+					propertySet = true;
+				} catch (SecurityException e) {
+					propertySet = false; // we'll just deal with the extra error message
+				}
+			}
 			input = new FileInputStream(fromFile);
 			output = new FileOutputStream(toFile);
 			String documentUri = fromStore.deSerialize(input, false);
@@ -177,6 +191,13 @@ public static void convert(String fromFilePath, String toFilePath, SerFileType f
 			}
 			throw new SpdxConverterException(msg, ex);
 		} finally {
+			if (propertySet) {
+				if (Objects.isNull(oldXmlInputFactory)) {
+					System.clearProperty(SpdxToolsHelper.XML_INPUT_FACTORY_PROPERTY_KEY);
+				} else {
+					System.setProperty(SpdxToolsHelper.XML_INPUT_FACTORY_PROPERTY_KEY, oldXmlInputFactory);
+				}
+			}
 			if (Objects.nonNull(input)) {
 				try {
 					input.close();

src/main/java/org/spdx/tools/SpdxToolsHelper.java

@@ -21,6 +21,7 @@
 
 import java.io.File;
 import java.io.FileInputStream;
+import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.Collections;
@@ -53,6 +54,8 @@ public enum SerFileType {
 		JSON, RDFXML, XML, XLS, XLSX, YAML, TAG, RDFTTL
 	}
 
+	static final String XML_INPUT_FACTORY_PROPERTY_KEY = "javax.xml.stream.XMLInputFactory";
+
 	static Map<String, SerFileType> EXT_TO_FILETYPE;
 	static {
 		HashMap<String, SerFileType> temp = new HashMap<>();
@@ -167,10 +170,7 @@ public static SpdxDocument deserializeDocument(File file)
 			throws InvalidSPDXAnalysisException, IOException,
 			InvalidFileNameException {
 		ISerializableModelStore store = fileTypeToStore(fileToFileType(file));
-		try (InputStream is = new FileInputStream(file)) {
-			String documentUri = store.deSerialize(is, false);
-			return new SpdxDocument(store, documentUri, null, false);
-		}
+		return readDocumentFromFile(store, file);
 	}
 	/**
 	 * @param file
@@ -186,9 +186,43 @@ public static SpdxDocument deserializeDocument(File file,
 			SerFileType fileType)
 			throws InvalidSPDXAnalysisException, IOException {
 		ISerializableModelStore store = fileTypeToStore(fileType);
+		return readDocumentFromFile(store, file);
+	}
+
+	/**
+	 * Reads an SPDX Document from a file
+	 * @param store Store where the document is to be stored
+	 * @param file File to read the store from
+	 * @return SPDX Document from the store
+	 * @throws FileNotFoundException If the file is not found
+	 * @throws IOException If there is an error reading the file
+	 * @throws InvalidSPDXAnalysisException If there is a problem in the SPDX document structure
+	 */
+	public static SpdxDocument readDocumentFromFile(ISerializableModelStore store, File file) throws FileNotFoundException, IOException, InvalidSPDXAnalysisException {
+		String oldXmlInputFactory = null;
+		boolean propertySet = false;
 		try (InputStream is = new FileInputStream(file)) {
+			if (store instanceof RdfStore) {
+				// Setting the property value will avoid the error message
+				// See issue #90 for more information
+				try {
+					oldXmlInputFactory = System.setProperty(XML_INPUT_FACTORY_PROPERTY_KEY, 
+					        "com.sun.xml.internal.stream.XMLInputFactoryImpl");
+					propertySet = true;
+				} catch (SecurityException e) {
+					propertySet = false; // we'll just deal with the extra error message
+				}
+			}
 			String documentUri = store.deSerialize(is, false);
 			return new SpdxDocument(store, documentUri, null, false);
+		} finally {
+			if (propertySet) {
+				if (Objects.isNull(oldXmlInputFactory)) {
+					System.clearProperty(XML_INPUT_FACTORY_PROPERTY_KEY);
+				} else {
+					System.setProperty(XML_INPUT_FACTORY_PROPERTY_KEY, oldXmlInputFactory);
+				}
+			}
 		}
 	}
 }

src/main/java/org/spdx/tools/Verify.java

@@ -28,6 +28,7 @@
 import org.spdx.library.InvalidSPDXAnalysisException;
 import org.spdx.library.Version;
 import org.spdx.library.model.SpdxDocument;
+import org.spdx.spdxRdfStore.RdfStore;
 import org.spdx.storage.ISerializableModelStore;
 import org.spdx.tagvaluestore.TagValueStore;
 import org.spdx.tools.SpdxToolsHelper.SerFileType;
@@ -124,9 +125,8 @@ public static List<String> verify(String filePath, SerFileType fileType) throws
 			throw new SpdxVerificationException("Error converting fileType to store",e);
 		}
 		SpdxDocument doc = null;
-		try (InputStream is = new FileInputStream(file)) {
-			String documentUri = store.deSerialize(is, false);
-			doc = new SpdxDocument(store, documentUri, null, false);
+		try {
+			doc = SpdxToolsHelper.readDocumentFromFile(store, file);
 		} catch (FileNotFoundException e) {
 			throw new SpdxVerificationException("File "+filePath+ " not found.",e);
 		} catch (IOException e) {