public void convert(Path file) throws IOException {
try (Bundle bundle = Bundles.openBundle(file)) {
// System.out.println(bundle.getManifest().toString());
bundle.getManifest().writeAsJsonLD();
bundle.getManifest().writeAsCombineManifest();
}
}
public void readTo(
InputStream manifestResourceAsStream, Manifest manifest, URI manifestResourceBaseURI)
throws IOException, RiotException {
OntModel model = new RDFToManifest().getOntModel();
model.add(jsonLdAsJenaModel(manifestResourceAsStream, manifestResourceBaseURI));
// model.write(System.out, "TURTLE");
// System.out.println();
URI root = manifestResourceBaseURI.resolve("/");
Individual ro = findRO(model, root);
if (ro == null)
throw new IOException("root ResearchObject not found - " + "Not a valid RO Bundle manifest");
for (Individual manifestResource : listObjectProperties(ro, isDescribedBy)) {
String uriStr = manifestResource.getURI();
if (uriStr == null) {
logger.warning("Skipping manifest without URI: " + manifestResource);
continue;
}
// URI relative = relativizeFromBase(uriStr, root);
Path path = manifest.getBundle().getFileSystem().provider().getPath(URI.create(uriStr));
manifest.getManifest().add(path);
}
List<Agent> creators = getAgents(root, ro, createdBy);
if (!creators.isEmpty()) {
manifest.setCreatedBy(creators.get(0));
if (creators.size() > 1) logger.warning("Ignoring additional createdBy agents");
}
RDFNode created = ro.getPropertyValue(createdOn);
manifest.setCreatedOn(literalAsFileTime(created));
List<Path> history = new ArrayList<Path>();
for (Individual histItem : listObjectProperties(ro, hasProvenance))
history.add(
Bundles.uriToBundlePath(
manifest.getBundle(), relativizeFromBase(histItem.getURI(), root)));
manifest.setHistory(history);
List<Agent> authors = getAgents(root, ro, authoredBy);
if (!authors.isEmpty()) manifest.setAuthoredBy(authors);
RDFNode authored = ro.getPropertyValue(authoredOn);
manifest.setAuthoredOn(literalAsFileTime(authored));
for (Individual aggrResource : listObjectProperties(ro, aggregates)) {
String uriStr = aggrResource.getURI();
// PathMetadata meta = new PathMetadata();
if (uriStr == null) {
logger.warning("Skipping aggregation without URI: " + aggrResource);
continue;
}
PathMetadata meta = manifest.getAggregation(relativizeFromBase(uriStr, root));
Set<Individual> proxies = listObjectProperties(aggrResource, hasProxy);
if (!proxies.isEmpty()) {
// We can only deal with the first one
Individual proxy = proxies.iterator().next();
String proxyUri = null;
if (proxy.getURI() != null) proxyUri = proxy.getURI();
else if (proxy.getSameAs() != null) proxyUri = proxy.getSameAs().getURI();
if (proxyUri != null) setPathProxy(meta, relativizeFromBase(proxyUri, root));
}
creators = getAgents(root, aggrResource, createdBy);
if (!creators.isEmpty()) {
meta.setCreatedBy(creators.get(0));
if (creators.size() > 1) logger.warning("Ignoring additional createdBy agents for " + meta);
}
meta.setCreatedOn(literalAsFileTime(aggrResource.getPropertyValue(createdOn)));
for (Individual standard : listObjectProperties(aggrResource, conformsTo))
if (standard.getURI() != null)
meta.setConformsTo(relativizeFromBase(standard.getURI(), root));
RDFNode mediaType = aggrResource.getPropertyValue(format);
if (mediaType != null && mediaType.isLiteral())
meta.setMediatype(mediaType.asLiteral().getLexicalForm());
}
for (Individual ann : listObjectProperties(ro, hasAnnotation)) {
/*
* Normally just one body per annotation, but just in case we'll
* iterate and split them out (as our PathAnnotation can only keep a
* single setContent() at a time)
*/
for (Individual body : listObjectProperties(model.getOntResource(ann), hasBody)) {
if (body.getURI() == null) {
logger.warning("Can't find annotation body for anonymous " + body);
continue;
}
PathAnnotation pathAnn = new PathAnnotation();
pathAnn.setContent(relativizeFromBase(body.getURI(), root));
if (ann.getURI() != null) pathAnn.setUri(relativizeFromBase(ann.getURI(), root));
else if (ann.getSameAs() != null && ann.getSameAs().getURI() != null)
pathAnn.setUri(relativizeFromBase(ann.getSameAs().getURI(), root));
// Handle multiple about/hasTarget
for (Individual target : listObjectProperties(ann, hasTarget))
if (target.getURI() != null)
pathAnn.getAboutList().add(relativizeFromBase(target.getURI(), root));
manifest.getAnnotations().add(pathAnn);
}
}
}