public static void writeNanopub(Nanopub nanopub, OutputStream out, RDFFormat format)
throws RDFHandlerException {
RDFWriter writer = Rio.createWriter(format, out);
writer.startRDF();
String s = nanopub.getUri().toString();
writer.handleNamespace("this", s);
writer.handleNamespace("sub", s + ".");
writer.handleNamespace("blank", s + "..");
writer.handleNamespace("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
writer.handleNamespace("rdfs", "http://www.w3.org/2000/01/rdf-schema#");
writer.handleNamespace("rdfg", "http://www.w3.org/2004/03/trix/rdfg-1/");
writer.handleNamespace("xsd", "http://www.w3.org/2001/XMLSchema#");
writer.handleNamespace("owl", "http://www.w3.org/2002/07/owl#");
writer.handleNamespace("dc", "http://purl.org/dc/terms/");
writer.handleNamespace("pav", "http://swan.mindinformatics.org/ontologies/1.2/pav/");
writer.handleNamespace("np", "http://www.nanopub.org/nschema#");
for (Statement st : NanopubUtils.getStatements(nanopub)) {
writer.handleStatement(st);
}
writer.endRDF();
}
public void publishNanopub(Nanopub nanopub) throws IOException {
if (serverInfo == null) {
if (serverUrls == null || serverUrls.isEmpty()) {
serverIterator = new ServerIterator();
} else {
serverIterator = new ServerIterator(serverUrls);
}
serverInfo = serverIterator.next();
}
artifactCode = TrustyUriUtils.getArtifactCode(nanopub.getUri().toString());
if (verbose) {
System.out.println("---");
System.out.println("Trying to publish nanopub: " + artifactCode);
}
while (serverInfo != null) {
String serverUrl = serverInfo.getPublicUrl();
try {
if (!ServerInfo.load(serverUrl).isPostNanopubsEnabled()) {
serverInfo = serverIterator.next();
continue;
}
} catch (ServerInfoException ex) {
serverInfo = serverIterator.next();
continue;
}
if (verbose) {
System.out.println("Trying server: " + serverUrl);
}
try {
HttpPost post = new HttpPost(serverUrl);
String nanopubString = NanopubUtils.writeToString(nanopub, RDFFormat.TRIG);
post.setEntity(new StringEntity(nanopubString, "UTF-8"));
post.setHeader("Content-Type", RDFFormat.TRIG.getDefaultMIMEType());
HttpResponse response = HttpClientBuilder.create().build().execute(post);
int code = response.getStatusLine().getStatusCode();
if (code >= 200 && code < 300) {
if (usedServers.containsKey(serverUrl)) {
usedServers.put(serverUrl, usedServers.get(serverUrl) + 1);
} else {
usedServers.put(serverUrl, 1);
}
if (verbose) {
System.out.println("Published: " + artifactCode);
}
return;
} else {
if (verbose) {
System.out.println(
"Response: " + code + " " + response.getStatusLine().getReasonPhrase());
}
}
} catch (IOException ex) {
if (verbose) {
System.out.println(ex.getClass().getName() + ": " + ex.getMessage());
}
} catch (OpenRDFException ex) {
if (verbose) {
System.out.println(ex.getClass().getName() + ": " + ex.getMessage());
}
}
serverInfo = serverIterator.next();
}
serverInfo = null;
throw new IOException("Failed to publish the nanopub");
}