src/main/java/org/purl/wf4ever/robundle/manifest/odf/ODFManifest.java - incubator-taverna-language - Git at Google

 package org.purl.wf4ever.robundle.manifest.odf;

 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
 import java.math.BigInteger;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.logging.Level;
 import java.util.logging.Logger;

 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBException;
 import javax.xml.bind.Marshaller;
 import javax.xml.bind.Unmarshaller;

 import oasis.names.tc.opendocument.xmlns.manifest._1.FileEntry;
 import oasis.names.tc.opendocument.xmlns.manifest._1.Manifest;
 import oasis.names.tc.opendocument.xmlns.manifest._1.ObjectFactory;

 import org.purl.wf4ever.robundle.Bundle;
 import org.purl.wf4ever.robundle.manifest.PathMetadata;

 import com.sun.xml.bind.marshaller.NamespacePrefixMapper;

 public class ODFManifest {

 	public static class ManifestNamespacePrefixMapperJAXB_RI extends
 			NamespacePrefixMapper {
 		@Override
 		public String[] getPreDeclaredNamespaceUris() {
 			// TODO Auto-generated method stub
 			return super.getPreDeclaredNamespaceUris();
 		}

 		@Override
 		public String getPreferredPrefix(String namespaceUri,
 				String suggestion, boolean requirePrefix) {
 			if (namespaceUri
 					.equals("urn:oasis:names:tc:opendocument:xmlns:manifest:1.0")) {
 				return "manifest";
 			}
 			return suggestion;
 		}

 	}

 	public static final String CONTAINER_XML = "META-INF/container.xml";
 	private static JAXBContext jaxbContext;
 	private static Logger logger = Logger.getLogger(ODFManifest.class
 			.getCanonicalName());

 	public static final String MANIFEST_XML = "META-INF/manifest.xml";

 	private static final String ODF_MANIFEST_VERSION = "1.2";
 	private static boolean warnedPrefixMapper;
 	public static boolean containsManifest(Bundle bundle) {
 		return Files.isRegularFile(manifestXmlPath(bundle));
 	}
 	protected static synchronized Marshaller createMarshaller()
 			throws JAXBException {
 		Marshaller marshaller = getJaxbContext().createMarshaller();
 		setPrefixMapper(marshaller);
 		return marshaller;
 	}
 	protected static synchronized Unmarshaller createUnMarshaller()
 			throws JAXBException {
 		Unmarshaller unmarshaller = getJaxbContext().createUnmarshaller();
 		return unmarshaller;
 	}

 	protected static synchronized JAXBContext getJaxbContext()
 			throws JAXBException {
 		if (jaxbContext == null) {
 			jaxbContext = JAXBContext
 					.newInstance(oasis.names.tc.opendocument.xmlns.manifest._1.ObjectFactory.class
 					// ,
 					// org.oasis_open.names.tc.opendocument.xmlns.container.ObjectFactory.class,
 					// org.w3._2000._09.xmldsig_.ObjectFactory.class,
 					// org.w3._2001._04.xmlenc_.ObjectFactory.class
 					);
 		}
 		return jaxbContext;
 	}

 	private static Path manifestXmlPath(Bundle bundle) {
 		return bundle.getRoot().resolve(MANIFEST_XML);
 	}

 	protected static void setPrefixMapper(Marshaller marshaller) {
 		boolean setPrefixMapper = false;

 		try {
 			// This only works with JAXB RI, in which case we can set the
 			// namespace prefix mapper
 			Class.forName("com.sun.xml.bind.marshaller.NamespacePrefixMapper");
 			marshaller.setProperty("com.sun.xml.bind.namespacePrefixMapper",
 					new ManifestNamespacePrefixMapperJAXB_RI());
 			// Note: A similar mapper for the built-in java
 			// (com.sun.xml.bind.internal.namespacePrefixMapper)
 			// is no longer included here, as it will not (easily) compile with
 			// Maven.
 			setPrefixMapper = true;
 		} catch (Exception e) {
 			logger.log(Level.FINE, "Can't find NamespacePrefixMapper", e);
 		}

 		if (!setPrefixMapper && !warnedPrefixMapper) {
 			logger.info("Could not set prefix mapper (missing or incompatible JAXB) "
 					+ "- will use prefixes ns0, ns1, ..");
 			warnedPrefixMapper = true;
 		}
 	}

 	private Bundle bundle;

 	// protected void prepareContainerXML() throws IOException {
 	//
 	//
 	// /* Check if we should prune <rootFiles> */
 	// Iterator<Object> iterator = containerXml.getValue().getRootFilesOrAny()
 	// .iterator();
 	// boolean foundAlready = false;
 	// while (iterator.hasNext()) {
 	// Object anyOrRoot = iterator.next();
 	// if (!(anyOrRoot instanceof JAXBElement)) {
 	// continue;
 	// }
 	// @SuppressWarnings("rawtypes")
 	// JAXBElement elem = (JAXBElement) anyOrRoot;
 	// if (!elem.getDeclaredType().equals(RootFiles.class)) {
 	// continue;
 	// }
 	// RootFiles rootFiles = (RootFiles) elem.getValue();
 	// if (foundAlready
 	// || (rootFiles.getOtherAttributes().isEmpty() && rootFiles
 	// .getAnyOrRootFile().isEmpty())) {
 	// // Delete it!
 	// System.err.println("Deleting unneccessary <rootFiles>");
 	// iterator.remove();
 	// }
 	// foundAlready = true;
 	// }
 	//
 	// Marshaller marshaller;
 	// OutputStream outStream = null;
 	// try {
 	// marshaller = createMarshaller();
 	// // XMLStreamWriter xmlStreamWriter = XMLOutputFactory
 	// // .newInstance().createXMLStreamWriter(outStream);
 	// // xmlStreamWriter.setDefaultNamespace(containerElem.getName()
 	// // .getNamespaceURI());
 	// //
 	// // xmlStreamWriter.setPrefix("dsig",
 	// // "http://www.w3.org/2000/09/xmldsig#");
 	// // xmlStreamWriter.setPrefix("xmlenc",
 	// // "http://www.w3.org/2001/04/xmlenc#");
 	// outStream = odfPackage.insertOutputStream(CONTAINER_XML);
 	//
 	// // FIXME: Set namespace prefixes and default namespace
 	//
 	// marshaller.setProperty("jaxb.formatted.output", true);
 	//
 	// // TODO: Ensure using default namespace
 	// marshaller.marshal(containerXml, outStream);
 	//
 	// } catch (IOException e) {
 	// throw e;
 	// } catch (Exception e) {
 	// throw new IOException("Could not parse " + CONTAINER_XML, e);
 	// } finally {
 	// if (outStream != null) {
 	// outStream.close();
 	// }
 	// }
 	// }
 	//
 	// @SuppressWarnings("unchecked")
 	// protected void parseContainerXML() throws IOException {
 	// createdContainerXml = false;
 	// InputStream containerStream = getResourceAsInputStream(CONTAINER_XML);
 	// if (containerStream == null) {
 	// // Make an empty containerXml
 	// Container container = containerFactory.createContainer();
 	// containerXml = containerFactory.createContainer(container);
 	// createdContainerXml = true;
 	// return;
 	// }
 	// try {
 	// Unmarshaller unMarshaller = createUnMarshaller();
 	// containerXml = (JAXBElement<Container>) unMarshaller
 	// .unmarshal(containerStream);
 	// } catch (JAXBException e) {
 	// throw new IOException("Could not parse " + CONTAINER_XML, e);
 	// }
 	//
 	// }

 	private org.purl.wf4ever.robundle.manifest.Manifest manifest;

 	private ObjectFactory manifestFactory = new oasis.names.tc.opendocument.xmlns.manifest._1.ObjectFactory();

 	public ODFManifest(org.purl.wf4ever.robundle.manifest.Manifest manifest) {
 		this.manifest = manifest;
 		this.bundle = manifest.getBundle();
 	}

 	public Path createManifestXML() throws IOException {
 		Manifest odfManifest = manifestFactory.createManifest();
 		odfManifest.setVersion(ODF_MANIFEST_VERSION);
 		for (PathMetadata pathMetadata : manifest.getAggregates()) {
 			Path path = pathMetadata.getFile();
 			if (path == null) {
 				logger.finest("Skipping non-path entry "
 						+ pathMetadata.getUri());
 			}
 			// if (! Files.isRegularFile(path)) {
 			// logger.fine("Not adding " + path +
 			// " to  manifest, not a regular file");
 			// }
 			FileEntry entry = manifestFactory.createFileEntry();
 			entry.setFullPath(bundle.getRoot().relativize(path).toString());
 			if (pathMetadata.getMediatype() != null) {
 				entry.setMediaType(pathMetadata.getMediatype());
 			} else {
 				entry.setMediaType("application/octet-stream");
 			}

 			try {
 				entry.setSize(BigInteger.valueOf(Files.size(path)));
 			} catch (IOException e) {
 				logger.log(Level.WARNING, "Can't find size of " + path, e);
 			}
 			if (pathMetadata.getConformsTo() != null) {
 				entry.setVersion(pathMetadata.getConformsTo().toString());
 			}
 			odfManifest.getFileEntry().add(entry);
 		}
 		Path manifestXml = manifestXmlPath(bundle);
 		Files.createDirectories(manifestXml.getParent());
 		try (OutputStream outStream = Files.newOutputStream(manifestXml)) {
 			try {
 				createMarshaller().marshal(odfManifest, outStream);
 			} catch (JAXBException e) {
 				throw new RuntimeException("Could not serialize ODF Manifest",
 						e);
 			}
 		}
 		return manifestXml;

 	}

 	public void readManifestXML() throws IOException {
 		Path manifestXml = manifestXmlPath(bundle);
 		Manifest odfManifest;
 		try (InputStream inStream = Files.newInputStream(manifestXml)) {
 			odfManifest = (Manifest) createUnMarshaller().unmarshal(inStream);
 		} catch (JAXBException e) {
 			// logger.warning("Could not parse " + manifestXml);
 			throw new IOException("Could not parse " + manifestXml, e);
 		}
 		if (!manifest.getManifest().contains(manifestXml)) {
 			manifest.getManifest().add(manifestXml);
 		}
 		for (FileEntry f : odfManifest.getFileEntry()) {
 			Path path = bundle.getRoot().resolve(f.getFullPath());
 			if (!Files.exists(path)) {
 				logger.warning(MANIFEST_XML + " listed " + path
 						+ ", but it does not exist in bundle");
 				continue;
 			}
 			PathMetadata metadata = manifest.getAggregation(path);
 			if (f.getMediaType() != null && f.getMediaType().contains("/")) {
 				metadata.setMediatype(f.getMediaType());
 			}
 			if (f.getEncryptionData() != null) {
 				logger.warning("Unsupported encryption for " + path);
 				continue;
 			}
 			if (f.getVersion() != null) {
 				try {
 					metadata.setConformsTo(new URI(f.getVersion()));
 				} catch (URISyntaxException e) {
 					logger.warning("Ignoring unsupported version "
 							+ f.getVersion());
 				}
 			}
 			if (Files.isRegularFile(path) && f.getSize() != null) {
 				long actualSize = Files.size(path);
 				long expectedSize = f.getSize().longValue();
 				if (expectedSize != actualSize) {
 					logger.warning("Wrong file size for " + path
 							+ ", expected: " + expectedSize + ", actually: "
 							+ actualSize);

 				}
 			}
 		}
 	}

 }
	package org.purl.wf4ever.robundle.manifest.odf;

	import java.io.IOException;
	import java.io.InputStream;
	import java.io.OutputStream;
	import java.math.BigInteger;
	import java.net.URI;
	import java.net.URISyntaxException;
	import java.nio.file.Files;
	import java.nio.file.Path;
	import java.util.logging.Level;
	import java.util.logging.Logger;

	import javax.xml.bind.JAXBContext;
	import javax.xml.bind.JAXBException;
	import javax.xml.bind.Marshaller;
	import javax.xml.bind.Unmarshaller;

	import oasis.names.tc.opendocument.xmlns.manifest._1.FileEntry;
	import oasis.names.tc.opendocument.xmlns.manifest._1.Manifest;
	import oasis.names.tc.opendocument.xmlns.manifest._1.ObjectFactory;

	import org.purl.wf4ever.robundle.Bundle;
	import org.purl.wf4ever.robundle.manifest.PathMetadata;

	import com.sun.xml.bind.marshaller.NamespacePrefixMapper;

	public class ODFManifest {

	public static class ManifestNamespacePrefixMapperJAXB_RI extends
	NamespacePrefixMapper {
	@Override
	public String[] getPreDeclaredNamespaceUris() {
	// TODO Auto-generated method stub
	return super.getPreDeclaredNamespaceUris();
	}

	@Override
	public String getPreferredPrefix(String namespaceUri,
	String suggestion, boolean requirePrefix) {
	if (namespaceUri
	.equals("urn:oasis:names:tc:opendocument:xmlns:manifest:1.0")) {
	return "manifest";
	}
	return suggestion;
	}

	}

	public static final String CONTAINER_XML = "META-INF/container.xml";
	private static JAXBContext jaxbContext;
	private static Logger logger = Logger.getLogger(ODFManifest.class
	.getCanonicalName());

	public static final String MANIFEST_XML = "META-INF/manifest.xml";

	private static final String ODF_MANIFEST_VERSION = "1.2";
	private static boolean warnedPrefixMapper;
	public static boolean containsManifest(Bundle bundle) {
	return Files.isRegularFile(manifestXmlPath(bundle));
	}
	protected static synchronized Marshaller createMarshaller()
	throws JAXBException {
	Marshaller marshaller = getJaxbContext().createMarshaller();
	setPrefixMapper(marshaller);
	return marshaller;
	}
	protected static synchronized Unmarshaller createUnMarshaller()
	throws JAXBException {
	Unmarshaller unmarshaller = getJaxbContext().createUnmarshaller();
	return unmarshaller;
	}

	protected static synchronized JAXBContext getJaxbContext()
	throws JAXBException {
	if (jaxbContext == null) {
	jaxbContext = JAXBContext
	.newInstance(oasis.names.tc.opendocument.xmlns.manifest._1.ObjectFactory.class
	// ,
	// org.oasis_open.names.tc.opendocument.xmlns.container.ObjectFactory.class,
	// org.w3._2000._09.xmldsig_.ObjectFactory.class,
	// org.w3._2001._04.xmlenc_.ObjectFactory.class
	);
	}
	return jaxbContext;
	}

	private static Path manifestXmlPath(Bundle bundle) {
	return bundle.getRoot().resolve(MANIFEST_XML);
	}

	protected static void setPrefixMapper(Marshaller marshaller) {
	boolean setPrefixMapper = false;

	try {
	// This only works with JAXB RI, in which case we can set the
	// namespace prefix mapper
	Class.forName("com.sun.xml.bind.marshaller.NamespacePrefixMapper");
	marshaller.setProperty("com.sun.xml.bind.namespacePrefixMapper",
	new ManifestNamespacePrefixMapperJAXB_RI());
	// Note: A similar mapper for the built-in java
	// (com.sun.xml.bind.internal.namespacePrefixMapper)
	// is no longer included here, as it will not (easily) compile with
	// Maven.
	setPrefixMapper = true;
	} catch (Exception e) {
	logger.log(Level.FINE, "Can't find NamespacePrefixMapper", e);
	}

	if (!setPrefixMapper && !warnedPrefixMapper) {
	logger.info("Could not set prefix mapper (missing or incompatible JAXB) "
	+ "- will use prefixes ns0, ns1, ..");
	warnedPrefixMapper = true;
	}
	}

	private Bundle bundle;

	// protected void prepareContainerXML() throws IOException {
	//
	//
	// /* Check if we should prune <rootFiles> */
	// Iterator<Object> iterator = containerXml.getValue().getRootFilesOrAny()
	// .iterator();
	// boolean foundAlready = false;
	// while (iterator.hasNext()) {
	// Object anyOrRoot = iterator.next();
	// if (!(anyOrRoot instanceof JAXBElement)) {
	// continue;
	// }
	// @SuppressWarnings("rawtypes")
	// JAXBElement elem = (JAXBElement) anyOrRoot;
	// if (!elem.getDeclaredType().equals(RootFiles.class)) {
	// continue;
	// }
	// RootFiles rootFiles = (RootFiles) elem.getValue();
	// if (foundAlready
	// \|\| (rootFiles.getOtherAttributes().isEmpty() && rootFiles
	// .getAnyOrRootFile().isEmpty())) {
	// // Delete it!
	// System.err.println("Deleting unneccessary <rootFiles>");
	// iterator.remove();
	// }
	// foundAlready = true;
	// }
	//
	// Marshaller marshaller;
	// OutputStream outStream = null;
	// try {
	// marshaller = createMarshaller();
	// // XMLStreamWriter xmlStreamWriter = XMLOutputFactory
	// // .newInstance().createXMLStreamWriter(outStream);
	// // xmlStreamWriter.setDefaultNamespace(containerElem.getName()
	// // .getNamespaceURI());
	// //
	// // xmlStreamWriter.setPrefix("dsig",
	// // "http://www.w3.org/2000/09/xmldsig#");
	// // xmlStreamWriter.setPrefix("xmlenc",
	// // "http://www.w3.org/2001/04/xmlenc#");
	// outStream = odfPackage.insertOutputStream(CONTAINER_XML);
	//
	// // FIXME: Set namespace prefixes and default namespace
	//
	// marshaller.setProperty("jaxb.formatted.output", true);
	//
	// // TODO: Ensure using default namespace
	// marshaller.marshal(containerXml, outStream);
	//
	// } catch (IOException e) {
	// throw e;
	// } catch (Exception e) {
	// throw new IOException("Could not parse " + CONTAINER_XML, e);
	// } finally {
	// if (outStream != null) {
	// outStream.close();
	// }
	// }
	// }
	//
	// @SuppressWarnings("unchecked")
	// protected void parseContainerXML() throws IOException {
	// createdContainerXml = false;
	// InputStream containerStream = getResourceAsInputStream(CONTAINER_XML);
	// if (containerStream == null) {
	// // Make an empty containerXml
	// Container container = containerFactory.createContainer();
	// containerXml = containerFactory.createContainer(container);
	// createdContainerXml = true;
	// return;
	// }
	// try {
	// Unmarshaller unMarshaller = createUnMarshaller();
	// containerXml = (JAXBElement<Container>) unMarshaller
	// .unmarshal(containerStream);
	// } catch (JAXBException e) {
	// throw new IOException("Could not parse " + CONTAINER_XML, e);
	// }
	//
	// }

	private org.purl.wf4ever.robundle.manifest.Manifest manifest;

	private ObjectFactory manifestFactory = new oasis.names.tc.opendocument.xmlns.manifest._1.ObjectFactory();

	public ODFManifest(org.purl.wf4ever.robundle.manifest.Manifest manifest) {
	this.manifest = manifest;
	this.bundle = manifest.getBundle();
	}

	public Path createManifestXML() throws IOException {
	Manifest odfManifest = manifestFactory.createManifest();
	odfManifest.setVersion(ODF_MANIFEST_VERSION);
	for (PathMetadata pathMetadata : manifest.getAggregates()) {
	Path path = pathMetadata.getFile();
	if (path == null) {
	logger.finest("Skipping non-path entry "
	+ pathMetadata.getUri());
	}
	// if (! Files.isRegularFile(path)) {
	// logger.fine("Not adding " + path +
	// " to manifest, not a regular file");
	// }
	FileEntry entry = manifestFactory.createFileEntry();
	entry.setFullPath(bundle.getRoot().relativize(path).toString());
	if (pathMetadata.getMediatype() != null) {
	entry.setMediaType(pathMetadata.getMediatype());
	} else {
	entry.setMediaType("application/octet-stream");
	}

	try {
	entry.setSize(BigInteger.valueOf(Files.size(path)));
	} catch (IOException e) {
	logger.log(Level.WARNING, "Can't find size of " + path, e);
	}
	if (pathMetadata.getConformsTo() != null) {
	entry.setVersion(pathMetadata.getConformsTo().toString());
	}
	odfManifest.getFileEntry().add(entry);
	}
	Path manifestXml = manifestXmlPath(bundle);
	Files.createDirectories(manifestXml.getParent());
	try (OutputStream outStream = Files.newOutputStream(manifestXml)) {
	try {
	createMarshaller().marshal(odfManifest, outStream);
	} catch (JAXBException e) {
	throw new RuntimeException("Could not serialize ODF Manifest",
	e);
	}
	}
	return manifestXml;

	}

	public void readManifestXML() throws IOException {
	Path manifestXml = manifestXmlPath(bundle);
	Manifest odfManifest;
	try (InputStream inStream = Files.newInputStream(manifestXml)) {
	odfManifest = (Manifest) createUnMarshaller().unmarshal(inStream);
	} catch (JAXBException e) {
	// logger.warning("Could not parse " + manifestXml);
	throw new IOException("Could not parse " + manifestXml, e);
	}
	if (!manifest.getManifest().contains(manifestXml)) {
	manifest.getManifest().add(manifestXml);
	}
	for (FileEntry f : odfManifest.getFileEntry()) {
	Path path = bundle.getRoot().resolve(f.getFullPath());
	if (!Files.exists(path)) {
	logger.warning(MANIFEST_XML + " listed " + path
	+ ", but it does not exist in bundle");
	continue;
	}
	PathMetadata metadata = manifest.getAggregation(path);
	if (f.getMediaType() != null && f.getMediaType().contains("/")) {
	metadata.setMediatype(f.getMediaType());
	}
	if (f.getEncryptionData() != null) {
	logger.warning("Unsupported encryption for " + path);
	continue;
	}
	if (f.getVersion() != null) {
	try {
	metadata.setConformsTo(new URI(f.getVersion()));
	} catch (URISyntaxException e) {
	logger.warning("Ignoring unsupported version "
	+ f.getVersion());
	}
	}
	if (Files.isRegularFile(path) && f.getSize() != null) {
	long actualSize = Files.size(path);
	long expectedSize = f.getSize().longValue();
	if (expectedSize != actualSize) {
	logger.warning("Wrong file size for " + path
	+ ", expected: " + expectedSize + ", actually: "
	+ actualSize);

	}
	}
	}
	}

	}