Examples with RDFFormat org.openrdf.rio.RDFFormat used on opensource projects

Example 1 with RDFFormat

use of org.openrdf.rio.RDFFormat in project nanopub-server by tkuhn.

the class LoadFiles method checkFilesToLoad.

private void checkFilesToLoad() {
    logger.info("Check whether there are files to load...");
    for (File f : loadDir.listFiles()) {
        stillAlive();
        if (f.isDirectory())
            continue;
        logger.info("Try to load file: " + f);
        try {
            final File processingFile = new File(processingDir, f.getName());
            f.renameTo(processingFile);
            RDFFormat format = Rio.getParserFormatForFileName(processingFile.getName());
            MultiNanopubRdfHandler.process(format, processingFile, new NanopubHandler() {

                @Override
                public void handleNanopub(Nanopub np) {
                    if (!ourPattern.matchesUri(np.getUri().toString()))
                        return;
                    try {
                        db.loadNanopub(np);
                    } catch (Exception ex) {
                        throw new RuntimeException(ex);
                    }
                    stillAlive();
                }
            });
            processingFile.renameTo(new File(doneDir, f.getName()));
            logger.info("File loaded: " + processingFile);
        } catch (Exception ex) {
            logger.error("Failed to load file: " + f, ex);
        }
    }
}

Example 2 with RDFFormat

use of org.openrdf.rio.RDFFormat in project incubator-rya by apache.

the class KafkaLoadStatements method fromFile.

@Override
public void fromFile(final Path statementsPath, final String visibilities) throws RyaStreamsException {
    requireNonNull(statementsPath);
    requireNonNull(visibilities);
    if (!statementsPath.toFile().exists()) {
        throw new RyaStreamsException("Could not load statements at path '" + statementsPath + "' because that " + "does not exist. Make sure you've entered the correct path.");
    }
    // Create an RDF Parser whose format is derived from the statementPath's file extension.
    final RDFFormat format = RDFFormat.forFileName(statementsPath.getFileName().toString());
    final RDFParser parser = Rio.createParser(format);
    // Set a handler that writes the statements to the specified kafka topic.
    parser.setRDFHandler(new RDFHandlerBase() {

        @Override
        public void startRDF() throws RDFHandlerException {
            log.trace("Starting loading statements.");
        }

        @Override
        public void handleStatement(final Statement stmnt) throws RDFHandlerException {
            final VisibilityStatement visiStatement = new VisibilityStatement(stmnt, visibilities);
            producer.send(new ProducerRecord<>(topic, visiStatement));
        }

        @Override
        public void endRDF() throws RDFHandlerException {
            producer.flush();
            log.trace("Done.");
        }
    });
    // Do the parse and load.
    try {
        parser.parse(Files.newInputStream(statementsPath), "");
    } catch (RDFParseException | RDFHandlerException | IOException e) {
        throw new RyaStreamsException("Could not load the RDF file's Statements into Rya Streams.", e);
    }
}

Example 3 with RDFFormat

use of org.openrdf.rio.RDFFormat in project incubator-rya by apache.

the class ConformanceTest method run.

@Override
public int run(final String[] args) throws Exception {
    // Validate command
    if (args.length < 1 || args.length > 2) {
        System.out.println("Usage:\n");
        System.out.println("\tConformanceTest [configuration options] " + "<test-file> <temp-dir>\n");
        System.out.println("to load test data from an RDF file " + "(configuration property " + MRUtils.FORMAT_PROP + " specifies the format, default RDF/XML); or\n");
        System.out.println("\tConformanceTest [configuration options] <temp-dir>\n");
        System.out.println("to load test data from a Rya instance (specified " + "using standard configuration properties).\n");
        System.out.println("For each test given, run the reasoner over the " + "premise ontology using a temporary Mini Accumulo instance " + "at <temp-dir>, then report conformance results.");
        System.exit(1);
    }
    final Set<Value> conformanceTestURIs = new HashSet<>();
    Collection<OwlTest> conformanceTests = new LinkedList<>();
    final List<OwlTest> successes = new LinkedList<>();
    final List<OwlTest> failures = new LinkedList<>();
    final Configuration conf = getConf();
    Repository repo;
    File workingDir;
    // If tests are in a file, stick them in a repository for querying
    if (args.length == 2) {
        workingDir = new File(PathUtils.clean(args[1]));
        RDFFormat inputFormat = RDFFormat.RDFXML;
        final String formatString = conf.get(MRUtils.FORMAT_PROP);
        if (formatString != null) {
            inputFormat = RDFFormat.valueOf(formatString);
        }
        repo = new SailRepository(new MemoryStore());
        repo.initialize();
        final RepositoryConnection conn = repo.getConnection();
        FileInputStream fileInput = new FileInputStream(PathUtils.clean(args[0]));
        conn.add(fileInput, "", inputFormat);
        fileInput.close();
        conn.close();
    } else // Otherwise, get a Rya repository
    {
        workingDir = new File(PathUtils.clean(args[0]));
        repo = MRReasoningUtils.getRepository(conf);
        repo.initialize();
    }
    // Query for the tests we're interested in
    final RepositoryConnection conn = repo.getConnection();
    conformanceTestURIs.addAll(getTestURIs(conn, TEST_INCONSISTENCY));
    conformanceTestURIs.addAll(getTestURIs(conn, TEST_CONSISTENCY));
    conformanceTestURIs.addAll(getTestURIs(conn, TEST_ENTAILMENT));
    conformanceTestURIs.addAll(getTestURIs(conn, TEST_NONENTAILMENT));
    conformanceTests = getTests(conn, conformanceTestURIs);
    conn.close();
    repo.shutDown();
    // Set up a MiniAccumulo cluster and set up conf to connect to it
    final String username = "root";
    final String password = "root";
    final MiniAccumuloCluster mini = new MiniAccumuloCluster(workingDir, password);
    mini.start();
    conf.set(MRUtils.AC_INSTANCE_PROP, mini.getInstanceName());
    conf.set(MRUtils.AC_ZK_PROP, mini.getZooKeepers());
    conf.set(MRUtils.AC_USERNAME_PROP, username);
    conf.set(MRUtils.AC_PWD_PROP, password);
    conf.setBoolean(MRUtils.AC_MOCK_PROP, false);
    conf.set(MRUtils.TABLE_PREFIX_PROPERTY, "temp_");
    // Run the conformance tests
    int result;
    for (final OwlTest test : conformanceTests) {
        System.out.println(test.uri);
        result = runTest(conf, args, test);
        if (result != 0) {
            return result;
        }
        if (test.success) {
            successes.add(test);
            System.out.println("(SUCCESS)");
        } else {
            failures.add(test);
            System.out.println("(FAIL)");
        }
    }
    mini.stop();
    System.out.println("\n" + successes.size() + " successful tests:");
    for (final OwlTest test : successes) {
        System.out.println("\t[SUCCESS] " + test.type() + " " + test.name);
    }
    System.out.println("\n" + failures.size() + " failed tests:");
    for (final OwlTest test : failures) {
        System.out.println("\t[FAIL] " + test.type() + " " + test.name);
        System.out.println("\t\t(" + test.description + ")");
        for (final Statement triple : test.error) {
            if (test.types.contains(TEST_ENTAILMENT)) {
                System.out.println("\t\tExpected: " + triple);
            } else if (test.types.contains(TEST_NONENTAILMENT)) {
                System.out.println("\t\tUnexpected: " + triple);
            }
        }
    }
    return 0;
}

Example 4 with RDFFormat

use of org.openrdf.rio.RDFFormat in project stanbol by apache.

the class RdfResourceImporter method importResource.

@Override
public ResourceState importResource(InputStream is, String resourceName) throws IOException {
    log.info("> importing {}:", resourceName);
    RDFFormat rdfFormat = Rio.getParserFormatForFileName(resourceName);
    if (rdfFormat == null) {
        log.info("  ... unable to detect RDF format for {}", resourceName);
        log.info("  ... resource '{}' will not be imported", resourceName);
        return ResourceState.IGNORED;
    } else {
        RepositoryConnection con = null;
        try {
            con = repository.getConnection();
            con.begin();
            con.add(new InputStreamReader(is, UTF8), baseUri, rdfFormat, contexts);
            con.commit();
            return ResourceState.LOADED;
        } catch (RDFParseException e) {
            log.error("  ... unable to parser RDF file " + resourceName + " (format: " + rdfFormat + ")", e);
            return ResourceState.ERROR;
        } catch (RepositoryException e) {
            throw new IllegalArgumentException("Repository Exception while " + resourceName + "!", e);
        } finally {
            if (con != null) {
                try {
                    con.close();
                } catch (RepositoryException e1) {
                /* ignore */
                }
            }
        }
    }
}

Example 5 with RDFFormat

use of org.openrdf.rio.RDFFormat in project stanbol by apache.

the class RdfIndexingSource method loadRepositoryConfig.

/**
 * @param repoConfigFile
 * @return
 */
private RepositoryConfig loadRepositoryConfig(File repoConfigFile) {
    Repository configRepo = new SailRepository(new MemoryStore());
    RepositoryConnection con = null;
    try {
        configRepo.initialize();
        con = configRepo.getConnection();
        // We need to load the configuration into a context
        org.openrdf.model.URI configContext = con.getValueFactory().createURI("urn:stanbol.entityhub:indexing.source.sesame:config.context");
        RDFFormat format = Rio.getParserFormatForFileName(repoConfigFile.getName());
        try {
            con.add(new InputStreamReader(new FileInputStream(repoConfigFile), Charset.forName("UTF-8")), baseUri, format, configContext);
        } catch (RDFParseException e) {
            throw new IllegalArgumentException("Unable to parsed '" + repoConfigFile + "' using RDF format '" + format + "'!", e);
        } catch (IOException e) {
            throw new IllegalArgumentException("Unable to access '" + repoConfigFile + "'!", e);
        }
        con.commit();
    } catch (RepositoryException e) {
        throw new IllegalStateException("Unable to load '" + repoConfigFile + "' to inmemory Sail!", e);
    } finally {
        if (con != null) {
            try {
                con.close();
            } catch (RepositoryException e) {
            /* ignore */
            }
        }
    }
    Set<String> repoNames;
    RepositoryConfig repoConfig;
    try {
        repoNames = RepositoryConfigUtil.getRepositoryIDs(configRepo);
        if (repoNames.size() == 1) {
            repoConfig = RepositoryConfigUtil.getRepositoryConfig(configRepo, repoNames.iterator().next());
            repoConfig.validate();
        } else if (repoNames.size() > 1) {
            throw new IllegalArgumentException("Repository configuration file '" + repoConfigFile + "' MUST only contain a single repository configuration!");
        } else {
            throw new IllegalArgumentException("Repository configuration file '" + repoConfigFile + "' DOES NOT contain a repository configuration!");
        }
    } catch (RepositoryException e) {
        throw new IllegalStateException("Unable to read RepositoryConfiguration form the " + "in-memory Sail!", e);
    } catch (RepositoryConfigException e) {
        throw new IllegalArgumentException("Repository Configuration in '" + repoConfigFile + "is not valid!", e);
    } finally {
        try {
            configRepo.shutDown();
        } catch (RepositoryException e) {
        /* ignore */
        }
    }
    if (repoConfig.getRepositoryImplConfig() == null) {
        throw new IllegalArgumentException("Missing RepositoryImpl config for " + "config " + repoConfig.getID() + " of file " + repoConfigFile + "!");
    }
    return repoConfig;
}