/* (non-Javadoc)
* @see com.semagia.mio.rdf.IMappingReader#read()
*/
@Override
public void read(final Source source) throws IOException, MIOException {
// TODO: check for characterstream / bytestream
_parser.setRDFHandler(new RDFStatementHandler());
final InputStream stream = new BufferedInputStream(new URL(source.getIRI()).openStream());
_handler.start();
try {
_parser.parse(stream, source.getBaseIRI());
} catch (OpenRDFException ex) {
if (ex.getCause() instanceof MIOException) {
throw (MIOException) ex.getCause();
}
if (ex instanceof RDFParseException) {
throw new MIOParseException(
ex,
((RDFParseException) ex).getLineNumber(),
((RDFParseException) ex).getColumnNumber());
}
throw new MIOException(ex);
} finally {
if (stream != null) {
stream.close();
}
}
_buildMapping();
_handler.end();
_mappings.clear();
}
private void run() throws IOException {
failed = false;
for (String s : nanopubs) {
count = 0;
try {
if (sparqlEndpointUrl != null) {
if (sparqlRepo == null) {
sparqlRepo = new SPARQLRepository(sparqlEndpointUrl);
sparqlRepo.initialize();
}
processNanopub(new NanopubImpl(sparqlRepo, new URIImpl(s)));
} else {
if (verbose) {
System.out.println("Reading file: " + s);
}
MultiNanopubRdfHandler.process(
new File(s),
new NanopubHandler() {
@Override
public void handleNanopub(Nanopub np) {
if (failed) return;
processNanopub(np);
}
});
if (count == 0) {
System.out.println("NO NANOPUB FOUND: " + s);
break;
}
}
} catch (OpenRDFException ex) {
System.out.println("RDF ERROR: " + s);
ex.printStackTrace(System.err);
break;
} catch (MalformedNanopubException ex) {
System.out.println("INVALID NANOPUB: " + s);
ex.printStackTrace(System.err);
break;
}
if (failed) {
System.out.println("FAILED TO PUBLISH NANOPUBS");
break;
}
}
for (String s : usedServers.keySet()) {
int c = usedServers.get(s);
System.out.println(c + " nanopub" + (c == 1 ? "" : "s") + " published at " + s);
}
if (sparqlRepo != null) {
try {
sparqlRepo.shutDown();
} catch (RepositoryException ex) {
ex.printStackTrace();
}
}
}
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");
}