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

 package org.purl.wf4ever.robundle.manifest;

 import java.io.IOException;
 import java.io.Writer;
 import java.net.URI;
 import java.nio.charset.Charset;
 import java.nio.file.FileVisitResult;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.SimpleFileVisitor;
 import java.nio.file.StandardOpenOption;
 import java.nio.file.attribute.BasicFileAttributes;
 import java.nio.file.attribute.FileTime;
 import java.util.ArrayList;
 import java.util.GregorianCalendar;
 import java.util.HashSet;
 import java.util.LinkedHashMap;
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
 import java.util.Set;
 import java.util.logging.Logger;

 import org.purl.wf4ever.robundle.Bundle;
 import org.purl.wf4ever.robundle.Bundles;
 import org.purl.wf4ever.robundle.manifest.combine.CombineManifest;
 import org.purl.wf4ever.robundle.manifest.odf.ODFManifest;

 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonInclude.Include;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.annotation.JsonPropertyOrder;
 import com.fasterxml.jackson.annotation.JsonValue;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.SerializationFeature;

 @JsonPropertyOrder(value = { "@context", "id", "manifest", "createdOn",
 		"createdBy", "createdOn", "authoredOn", "authoredBy", "history",
 		"aggregates", "annotations", "@graph" })
 public class Manifest {

 	public abstract class FileTimeMixin {
 		@JsonValue
 		public abstract String toString();
 	}

 	public abstract class PathMixin {
 		@JsonValue
 		public abstract String toString();
 	}

 	private static Logger logger = Logger.getLogger(Manifest.class
 			.getCanonicalName());

 	private static final String MANIFEST_JSON = "manifest.json";

 	private static final String META_INF = "/META-INF";

 	private static final String MIMETYPE = "/mimetype";
 	private static final String RO = "/.ro";
 	private static URI ROOT = URI.create("/");

 	public static FileTime now() {
 		return FileTime.fromMillis(new GregorianCalendar().getTimeInMillis());
 	}

 	protected static Path withSlash(Path dir) {
 		if (dir == null) {
 			return null;
 		}
 		if (Files.isDirectory(dir)) {
 			Path fname = dir.getFileName();
 			if (fname == null) {
 				return dir;
 			}
 			String fnameStr = fname.toString();
 			if (fnameStr.endsWith("/")) {
 				return dir;
 			}
 			return dir.resolveSibling(fnameStr + "/");
 		}
 		return dir;
 	}

 	private Map<URI, PathMetadata> aggregates = new LinkedHashMap<>();
 	private List<PathAnnotation> annotations = new ArrayList<>();
 	private List<Agent> authoredBy = new ArrayList<>();
 	private FileTime authoredOn;
 	private Bundle bundle;
 	private Agent createdBy = null;
 	private FileTime createdOn = now();
 	private List<String> graph;
 	private List<Path> history = new ArrayList<>();
 	private URI id = URI.create("/");
 	private List<Path> manifest = new ArrayList<>();

 	public Manifest(Bundle bundle) {
 		this.bundle = bundle;
 	}

 	public List<PathMetadata> getAggregates() {
 		return new ArrayList<>(aggregates.values());
 	}

 	public PathMetadata getAggregation(Path file) {
 		URI fileUri = file.toUri();
 		return getAggregation(fileUri);
 	}

 	public PathMetadata getAggregation(URI uri) {
 		uri = relativeToBundleRoot(uri);
 		PathMetadata metadata = aggregates.get(uri);
 		if (metadata == null) {
 			metadata = new PathMetadata();
 			if (!uri.isAbsolute() && uri.getFragment() == null) {
 				Path path = Bundles.uriToBundlePath(bundle, uri);
 				metadata.setFile(path);
 				metadata.setMediatype(guessMediaType(path));
 			} else {
 				metadata.setUri(uri);
 			}
 			aggregates.put(uri, metadata);
 		}
 		return metadata;
 	}

 	public List<PathAnnotation> getAnnotations() {
 		return annotations;
 	}

 	public List<Agent> getAuthoredBy() {
 		return authoredBy;
 	}

 	public FileTime getAuthoredOn() {
 		return authoredOn;
 	}

 	@JsonIgnore
 	public URI getBaseURI() {
 		return getBundle().getRoot().toUri();
 	}

 	@JsonIgnore
 	public Bundle getBundle() {
 		return bundle;
 	}

 	@JsonProperty(value = "@context")
 	public List<Object> getContext() {
 		ArrayList<Object> context = new ArrayList<>();
 		// HashMap<Object, Object> map = new HashMap<>();
 		// map.put("@base", getBaseURI());
 		// context.add(map);
 		context.add(URI.create("https://w3id.org/bundle/context"));
 		return context;
 	}

 	public Agent getCreatedBy() {
 		return createdBy;
 	}

 	public FileTime getCreatedOn() {
 		return createdOn;
 	}

 	public List<String> getGraph() {
 		return graph;
 	}

 	public List<Path> getHistory() {
 		return history;
 	}

 	public URI getId() {
 		return id;
 	}

 	public List<Path> getManifest() {
 		return manifest;
 	}

 	/**
 	 * Guess media type based on extension
 	 *
 	 * @see http://wf4ever.github.io/ro/bundle/#media-types
 	 *
 	 * @param file
 	 *            A Path to a file
 	 * @return media-type, e.g. <code>application/xml</code> or
 	 *         <code>text/plain; charset="utf-8"</code>
 	 */
 	public String guessMediaType(Path file) {
 		if (file.getFileName() == null) {
 			return null;
 		}
 		String filename = file.getFileName().toString()
 				.toLowerCase(Locale.ENGLISH);
 		if (filename.endsWith(".txt")) {
 			return "text/plain; charset=\"utf-8\"";
 		}
 		if (filename.endsWith(".ttl")) {
 			return "text/turtle; charset=\"utf-8\"";
 		}
 		if (filename.endsWith(".rdf") || filename.endsWith(".owl")) {
 			return "application/rdf+xml";
 		}
 		if (filename.endsWith(".json")) {
 			return "application/json";
 		}
 		if (filename.endsWith(".jsonld")) {
 			return "application/ld+json";
 		}
 		if (filename.endsWith(".xml")) {
 			return "application/xml";
 		}

 		// A few extra, common ones

 		if (filename.endsWith(".png")) {
 			return "image/png";
 		}
 		if (filename.endsWith(".svg")) {
 			return "image/svg+xml";
 		}
 		if (filename.endsWith(".jpg") || filename.endsWith(".jpeg")) {
 			return "image/jpeg";
 		}
 		if (filename.endsWith(".pdf")) {
 			return "application/pdf";
 		}
 		return "application/octet-stream";
 	}

 	public void populateFromBundle() throws IOException {
 		final Set<Path> potentiallyEmptyFolders = new LinkedHashSet<>();

 		final Set<URI> existingAggregationsToPrune = new HashSet<>(
 				aggregates.keySet());

 		Files.walkFileTree(bundle.getRoot(), new SimpleFileVisitor<Path>() {
 			@Override
 			public FileVisitResult postVisitDirectory(Path dir, IOException exc)
 					throws IOException {
 				super.postVisitDirectory(dir, exc);
 				if (potentiallyEmptyFolders.remove(dir)) {
 					URI uri = relativeToBundleRoot(dir.toUri());
 					existingAggregationsToPrune.remove(uri);
 					PathMetadata metadata = aggregates.get(uri);
 					if (metadata == null) {
 						metadata = new PathMetadata();
 						aggregates.put(uri, metadata);
 					}
 					metadata.setFile(withSlash(dir));
 					metadata.setFolder(withSlash(dir.getParent()));
 					metadata.setProxy();
 					metadata.setCreatedOn(Files.getLastModifiedTime(dir));
 					potentiallyEmptyFolders.remove(withSlash(dir.getParent()));
 					return FileVisitResult.CONTINUE;
 				}
 				return FileVisitResult.CONTINUE;
 			}

 			@Override
 			public FileVisitResult preVisitDirectory(Path dir,
 					BasicFileAttributes attrs) throws IOException {
 				if (dir.startsWith(RO) || dir.startsWith(META_INF)) {
 					return FileVisitResult.SKIP_SUBTREE;
 				}
 				potentiallyEmptyFolders.add(withSlash(dir));
 				potentiallyEmptyFolders.remove(withSlash(dir.getParent()));
 				return FileVisitResult.CONTINUE;
 			}

 			@Override
 			public FileVisitResult visitFile(Path file,
 					BasicFileAttributes attrs) throws IOException {
 				potentiallyEmptyFolders.remove(withSlash(file.getParent()));
 				if (file.startsWith(MIMETYPE)) {
 					return FileVisitResult.CONTINUE;
 				}
 				if (manifest.contains(file)) {
 					// Don't aggregate the manifests
 					return FileVisitResult.CONTINUE;
 				}
 				// super.visitFile(file, attrs);
 				URI uri = relativeToBundleRoot(file.toUri());
 				existingAggregationsToPrune.remove(uri);
 				PathMetadata metadata = aggregates.get(uri);
 				if (metadata == null) {
 					metadata = new PathMetadata();
 					aggregates.put(uri, metadata);
 				}
 				metadata.setFile(file);
 				if (metadata.getMediatype() == null) {
 					// Don't override if already set
 					metadata.setMediatype(guessMediaType(file));
 				}
 				metadata.setFolder(withSlash(file.getParent()));
 				metadata.setProxy();
 				metadata.setCreatedOn(Files.getLastModifiedTime(file));
 				potentiallyEmptyFolders.remove(file.getParent());
 				return FileVisitResult.CONTINUE;
 			}
 		});
 		for (URI preExisting : existingAggregationsToPrune) {
 			PathMetadata meta = aggregates.get(preExisting);
 			if (meta.getFile() != null) {
 				// Don't remove 'virtual' resources, only aggregations
 				// that went to files
 				aggregates.remove(preExisting);
 			}
 		}
 	}

 	public URI relativeToBundleRoot(URI uri) {
 		uri = ROOT.resolve(bundle.getRoot().toUri().relativize(uri));
 		return uri;
 	}

 	public void setAggregates(List<PathMetadata> aggregates) {
 		this.aggregates.clear();

 		for (PathMetadata meta : aggregates) {
 			URI uri = null;
 			if (meta.getFile() != null) {
 				uri = relativeToBundleRoot(meta.getFile().toUri());
 			} else if (meta.getUri() != null) {
 				uri = relativeToBundleRoot(meta.getUri());
 			} else {
 				uri = relativeToBundleRoot(meta.getProxy());
 			}
 			if (uri == null) {
 				logger.warning("Unknown URI for aggregation " + meta);
 				continue;
 			}
 			this.aggregates.put(uri, meta);
 		}

 	}

 	public void setAnnotations(List<PathAnnotation> annotations) {
 		this.annotations = annotations;
 	}

 	public void setAuthoredBy(List<Agent> authoredBy) {
 		if (authoredBy == null) {
 			throw new NullPointerException("authoredBy can't be null");
 		}
 		this.authoredBy = authoredBy;
 	}

 	public void setAuthoredOn(FileTime authoredOn) {
 		this.authoredOn = authoredOn;
 	}

 	public void setBundle(Bundle bundle) {
 		this.bundle = bundle;
 	}

 	public void setCreatedBy(Agent createdBy) {
 		this.createdBy = createdBy;
 	}

 	public void setCreatedOn(FileTime createdOn) {
 		this.createdOn = createdOn;
 	}

 	public void setGraph(List<String> graph) {
 		this.graph = graph;
 	}

 	public void setHistory(List<Path> history) {
 		if (history == null) {
 			throw new NullPointerException("history can't be null");
 		}
 		this.history = history;
 	}

 	public void setId(URI id) {
 		this.id = id;
 	}

 	public void setManifest(List<Path> manifest) {
 		this.manifest = manifest;
 	}

 	public void writeAsCombineManifest() throws IOException {
 		new CombineManifest(this).createManifestXML();
 	}

 	/**
 	 * Write as an RO Bundle JSON-LD manifest
 	 *
 	 * @return The path of the written manifest (e.g. ".ro/manifest.json")
 	 * @throws IOException
 	 */
 	public Path writeAsJsonLD() throws IOException {
 		Path jsonld = bundle.getFileSystem().getPath(RO, MANIFEST_JSON);
 		Files.createDirectories(jsonld.getParent());
 		// Files.createFile(jsonld);
 		if (!getManifest().contains(jsonld)) {
 			getManifest().add(0, jsonld);
 		}
 		ObjectMapper om = new ObjectMapper();
 		om.addMixInAnnotations(Path.class, PathMixin.class);
 		om.addMixInAnnotations(FileTime.class, FileTimeMixin.class);
 		om.enable(SerializationFeature.INDENT_OUTPUT);
 		om.disable(SerializationFeature.WRITE_EMPTY_JSON_ARRAYS);
 		om.disable(SerializationFeature.FAIL_ON_EMPTY_BEANS);
 		om.disable(SerializationFeature.WRITE_NULL_MAP_VALUES);

 		om.setSerializationInclusion(Include.NON_NULL);
 		try (Writer w = Files
 				.newBufferedWriter(jsonld, Charset.forName("UTF-8"),
 						StandardOpenOption.WRITE,
 						StandardOpenOption.TRUNCATE_EXISTING,
 						StandardOpenOption.CREATE)) {
 			om.writeValue(w, this);
 		}
 		return jsonld;
 	}

 	/**
 	 * Write as a ODF manifest.xml
 	 *
 	 * @see http
 	 *      ://docs.oasis-open.org/office/v1.2/os/OpenDocument-v1.2-os-part3.
 	 *      html#__RefHeading__752807_826425813
 	 * @return The path of the written manifest (e.g. "META-INF/manifest.xml")
 	 * @throws IOException
 	 */
 	public Path writeAsODFManifest() throws IOException {
 		return new ODFManifest(this).createManifestXML();
 	}
 }
	package org.purl.wf4ever.robundle.manifest;

	import java.io.IOException;
	import java.io.Writer;
	import java.net.URI;
	import java.nio.charset.Charset;
	import java.nio.file.FileVisitResult;
	import java.nio.file.Files;
	import java.nio.file.Path;
	import java.nio.file.SimpleFileVisitor;
	import java.nio.file.StandardOpenOption;
	import java.nio.file.attribute.BasicFileAttributes;
	import java.nio.file.attribute.FileTime;
	import java.util.ArrayList;
	import java.util.GregorianCalendar;
	import java.util.HashSet;
	import java.util.LinkedHashMap;
	import java.util.LinkedHashSet;
	import java.util.List;
	import java.util.Locale;
	import java.util.Map;
	import java.util.Set;
	import java.util.logging.Logger;

	import org.purl.wf4ever.robundle.Bundle;
	import org.purl.wf4ever.robundle.Bundles;
	import org.purl.wf4ever.robundle.manifest.combine.CombineManifest;
	import org.purl.wf4ever.robundle.manifest.odf.ODFManifest;

	import com.fasterxml.jackson.annotation.JsonIgnore;
	import com.fasterxml.jackson.annotation.JsonInclude.Include;
	import com.fasterxml.jackson.annotation.JsonProperty;
	import com.fasterxml.jackson.annotation.JsonPropertyOrder;
	import com.fasterxml.jackson.annotation.JsonValue;
	import com.fasterxml.jackson.databind.ObjectMapper;
	import com.fasterxml.jackson.databind.SerializationFeature;

	@JsonPropertyOrder(value = { "@context", "id", "manifest", "createdOn",
	"createdBy", "createdOn", "authoredOn", "authoredBy", "history",
	"aggregates", "annotations", "@graph" })
	public class Manifest {

	public abstract class FileTimeMixin {
	@JsonValue
	public abstract String toString();
	}

	public abstract class PathMixin {
	@JsonValue
	public abstract String toString();
	}

	private static Logger logger = Logger.getLogger(Manifest.class
	.getCanonicalName());

	private static final String MANIFEST_JSON = "manifest.json";

	private static final String META_INF = "/META-INF";

	private static final String MIMETYPE = "/mimetype";
	private static final String RO = "/.ro";
	private static URI ROOT = URI.create("/");

	public static FileTime now() {
	return FileTime.fromMillis(new GregorianCalendar().getTimeInMillis());
	}

	protected static Path withSlash(Path dir) {
	if (dir == null) {
	return null;
	}
	if (Files.isDirectory(dir)) {
	Path fname = dir.getFileName();
	if (fname == null) {
	return dir;
	}
	String fnameStr = fname.toString();
	if (fnameStr.endsWith("/")) {
	return dir;
	}
	return dir.resolveSibling(fnameStr + "/");
	}
	return dir;
	}

	private Map<URI, PathMetadata> aggregates = new LinkedHashMap<>();
	private List<PathAnnotation> annotations = new ArrayList<>();
	private List<Agent> authoredBy = new ArrayList<>();
	private FileTime authoredOn;
	private Bundle bundle;
	private Agent createdBy = null;
	private FileTime createdOn = now();
	private List<String> graph;
	private List<Path> history = new ArrayList<>();
	private URI id = URI.create("/");
	private List<Path> manifest = new ArrayList<>();

	public Manifest(Bundle bundle) {
	this.bundle = bundle;
	}

	public List<PathMetadata> getAggregates() {
	return new ArrayList<>(aggregates.values());
	}

	public PathMetadata getAggregation(Path file) {
	URI fileUri = file.toUri();
	return getAggregation(fileUri);
	}

	public PathMetadata getAggregation(URI uri) {
	uri = relativeToBundleRoot(uri);
	PathMetadata metadata = aggregates.get(uri);
	if (metadata == null) {
	metadata = new PathMetadata();
	if (!uri.isAbsolute() && uri.getFragment() == null) {
	Path path = Bundles.uriToBundlePath(bundle, uri);
	metadata.setFile(path);
	metadata.setMediatype(guessMediaType(path));
	} else {
	metadata.setUri(uri);
	}
	aggregates.put(uri, metadata);
	}
	return metadata;
	}

	public List<PathAnnotation> getAnnotations() {
	return annotations;
	}

	public List<Agent> getAuthoredBy() {
	return authoredBy;
	}

	public FileTime getAuthoredOn() {
	return authoredOn;
	}

	@JsonIgnore
	public URI getBaseURI() {
	return getBundle().getRoot().toUri();
	}

	@JsonIgnore
	public Bundle getBundle() {
	return bundle;
	}

	@JsonProperty(value = "@context")
	public List<Object> getContext() {
	ArrayList<Object> context = new ArrayList<>();
	// HashMap<Object, Object> map = new HashMap<>();
	// map.put("@base", getBaseURI());
	// context.add(map);
	context.add(URI.create("https://w3id.org/bundle/context"));
	return context;
	}

	public Agent getCreatedBy() {
	return createdBy;
	}

	public FileTime getCreatedOn() {
	return createdOn;
	}

	public List<String> getGraph() {
	return graph;
	}

	public List<Path> getHistory() {
	return history;
	}

	public URI getId() {
	return id;
	}

	public List<Path> getManifest() {
	return manifest;
	}

	/**
	* Guess media type based on extension
	*
	* @see http://wf4ever.github.io/ro/bundle/#media-types
	*
	* @param file
	* A Path to a file
	* @return media-type, e.g. <code>application/xml</code> or
	* <code>text/plain; charset="utf-8"</code>
	*/
	public String guessMediaType(Path file) {
	if (file.getFileName() == null) {
	return null;
	}
	String filename = file.getFileName().toString()
	.toLowerCase(Locale.ENGLISH);
	if (filename.endsWith(".txt")) {
	return "text/plain; charset=\"utf-8\"";
	}
	if (filename.endsWith(".ttl")) {
	return "text/turtle; charset=\"utf-8\"";
	}
	if (filename.endsWith(".rdf") \|\| filename.endsWith(".owl")) {
	return "application/rdf+xml";
	}
	if (filename.endsWith(".json")) {
	return "application/json";
	}
	if (filename.endsWith(".jsonld")) {
	return "application/ld+json";
	}
	if (filename.endsWith(".xml")) {
	return "application/xml";
	}

	// A few extra, common ones

	if (filename.endsWith(".png")) {
	return "image/png";
	}
	if (filename.endsWith(".svg")) {
	return "image/svg+xml";
	}
	if (filename.endsWith(".jpg") \|\| filename.endsWith(".jpeg")) {
	return "image/jpeg";
	}
	if (filename.endsWith(".pdf")) {
	return "application/pdf";
	}
	return "application/octet-stream";
	}

	public void populateFromBundle() throws IOException {
	final Set<Path> potentiallyEmptyFolders = new LinkedHashSet<>();

	final Set<URI> existingAggregationsToPrune = new HashSet<>(
	aggregates.keySet());

	Files.walkFileTree(bundle.getRoot(), new SimpleFileVisitor<Path>() {
	@Override
	public FileVisitResult postVisitDirectory(Path dir, IOException exc)
	throws IOException {
	super.postVisitDirectory(dir, exc);
	if (potentiallyEmptyFolders.remove(dir)) {
	URI uri = relativeToBundleRoot(dir.toUri());
	existingAggregationsToPrune.remove(uri);
	PathMetadata metadata = aggregates.get(uri);
	if (metadata == null) {
	metadata = new PathMetadata();
	aggregates.put(uri, metadata);
	}
	metadata.setFile(withSlash(dir));
	metadata.setFolder(withSlash(dir.getParent()));
	metadata.setProxy();
	metadata.setCreatedOn(Files.getLastModifiedTime(dir));
	potentiallyEmptyFolders.remove(withSlash(dir.getParent()));
	return FileVisitResult.CONTINUE;
	}
	return FileVisitResult.CONTINUE;
	}

	@Override
	public FileVisitResult preVisitDirectory(Path dir,
	BasicFileAttributes attrs) throws IOException {
	if (dir.startsWith(RO) \|\| dir.startsWith(META_INF)) {
	return FileVisitResult.SKIP_SUBTREE;
	}
	potentiallyEmptyFolders.add(withSlash(dir));
	potentiallyEmptyFolders.remove(withSlash(dir.getParent()));
	return FileVisitResult.CONTINUE;
	}

	@Override
	public FileVisitResult visitFile(Path file,
	BasicFileAttributes attrs) throws IOException {
	potentiallyEmptyFolders.remove(withSlash(file.getParent()));
	if (file.startsWith(MIMETYPE)) {
	return FileVisitResult.CONTINUE;
	}
	if (manifest.contains(file)) {
	// Don't aggregate the manifests
	return FileVisitResult.CONTINUE;
	}
	// super.visitFile(file, attrs);
	URI uri = relativeToBundleRoot(file.toUri());
	existingAggregationsToPrune.remove(uri);
	PathMetadata metadata = aggregates.get(uri);
	if (metadata == null) {
	metadata = new PathMetadata();
	aggregates.put(uri, metadata);
	}
	metadata.setFile(file);
	if (metadata.getMediatype() == null) {
	// Don't override if already set
	metadata.setMediatype(guessMediaType(file));
	}
	metadata.setFolder(withSlash(file.getParent()));
	metadata.setProxy();
	metadata.setCreatedOn(Files.getLastModifiedTime(file));
	potentiallyEmptyFolders.remove(file.getParent());
	return FileVisitResult.CONTINUE;
	}
	});
	for (URI preExisting : existingAggregationsToPrune) {
	PathMetadata meta = aggregates.get(preExisting);
	if (meta.getFile() != null) {
	// Don't remove 'virtual' resources, only aggregations
	// that went to files
	aggregates.remove(preExisting);
	}
	}
	}

	public URI relativeToBundleRoot(URI uri) {
	uri = ROOT.resolve(bundle.getRoot().toUri().relativize(uri));
	return uri;
	}

	public void setAggregates(List<PathMetadata> aggregates) {
	this.aggregates.clear();

	for (PathMetadata meta : aggregates) {
	URI uri = null;
	if (meta.getFile() != null) {
	uri = relativeToBundleRoot(meta.getFile().toUri());
	} else if (meta.getUri() != null) {
	uri = relativeToBundleRoot(meta.getUri());
	} else {
	uri = relativeToBundleRoot(meta.getProxy());
	}
	if (uri == null) {
	logger.warning("Unknown URI for aggregation " + meta);
	continue;
	}
	this.aggregates.put(uri, meta);
	}

	}

	public void setAnnotations(List<PathAnnotation> annotations) {
	this.annotations = annotations;
	}

	public void setAuthoredBy(List<Agent> authoredBy) {
	if (authoredBy == null) {
	throw new NullPointerException("authoredBy can't be null");
	}
	this.authoredBy = authoredBy;
	}

	public void setAuthoredOn(FileTime authoredOn) {
	this.authoredOn = authoredOn;
	}

	public void setBundle(Bundle bundle) {
	this.bundle = bundle;
	}

	public void setCreatedBy(Agent createdBy) {
	this.createdBy = createdBy;
	}

	public void setCreatedOn(FileTime createdOn) {
	this.createdOn = createdOn;
	}

	public void setGraph(List<String> graph) {
	this.graph = graph;
	}

	public void setHistory(List<Path> history) {
	if (history == null) {
	throw new NullPointerException("history can't be null");
	}
	this.history = history;
	}

	public void setId(URI id) {
	this.id = id;
	}

	public void setManifest(List<Path> manifest) {
	this.manifest = manifest;
	}

	public void writeAsCombineManifest() throws IOException {
	new CombineManifest(this).createManifestXML();
	}

	/**
	* Write as an RO Bundle JSON-LD manifest
	*
	* @return The path of the written manifest (e.g. ".ro/manifest.json")
	* @throws IOException
	*/
	public Path writeAsJsonLD() throws IOException {
	Path jsonld = bundle.getFileSystem().getPath(RO, MANIFEST_JSON);
	Files.createDirectories(jsonld.getParent());
	// Files.createFile(jsonld);
	if (!getManifest().contains(jsonld)) {
	getManifest().add(0, jsonld);
	}
	ObjectMapper om = new ObjectMapper();
	om.addMixInAnnotations(Path.class, PathMixin.class);
	om.addMixInAnnotations(FileTime.class, FileTimeMixin.class);
	om.enable(SerializationFeature.INDENT_OUTPUT);
	om.disable(SerializationFeature.WRITE_EMPTY_JSON_ARRAYS);
	om.disable(SerializationFeature.FAIL_ON_EMPTY_BEANS);
	om.disable(SerializationFeature.WRITE_NULL_MAP_VALUES);

	om.setSerializationInclusion(Include.NON_NULL);
	try (Writer w = Files
	.newBufferedWriter(jsonld, Charset.forName("UTF-8"),
	StandardOpenOption.WRITE,
	StandardOpenOption.TRUNCATE_EXISTING,
	StandardOpenOption.CREATE)) {
	om.writeValue(w, this);
	}
	return jsonld;
	}

	/**
	* Write as a ODF manifest.xml
	*
	* @see http
	* ://docs.oasis-open.org/office/v1.2/os/OpenDocument-v1.2-os-part3.
	* html#__RefHeading__752807_826425813
	* @return The path of the written manifest (e.g. "META-INF/manifest.xml")
	* @throws IOException
	*/
	public Path writeAsODFManifest() throws IOException {
	return new ODFManifest(this).createManifestXML();
	}
	}