io.opencaesar.owl.save.OwlSaveApp Maven / Gradle / Ivy
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/**
* Copyright 2024 California Institute of Technology ("Caltech").
* U.S. Government sponsorship acknowledged.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package io.opencaesar.owl.save;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.OutputStream;
import java.net.Authenticator;
import java.net.ConnectException;
import java.net.URI;
import java.net.http.HttpClient;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
import org.apache.jena.atlas.web.HttpException;
import org.apache.jena.http.HttpEnv;
import org.apache.jena.query.Dataset;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdfconnection.LibSec;
import org.apache.jena.rdfconnection.RDFConnection;
import org.apache.jena.rdfconnection.RDFConnectionRemote;
import org.apache.jena.rdfconnection.RDFConnectionRemoteBuilder;
import org.apache.jena.riot.Lang;
import org.apache.jena.riot.RDFLanguages;
import org.apache.log4j.Appender;
import org.apache.log4j.AppenderSkeleton;
import org.apache.log4j.Level;
import org.apache.log4j.LogManager;
import org.apache.log4j.Logger;
import org.apache.log4j.xml.DOMConfigurator;
import com.beust.jcommander.IParameterValidator;
import com.beust.jcommander.JCommander;
import com.beust.jcommander.Parameter;
import com.beust.jcommander.ParameterException;
/**
* Utility for saving an OWL dataset from a Fuseki server
*/
public class OwlSaveApp {
/**
* Allowed input file extensions for ontologies.
*/
private final static String DEFAULT_EXTENSION = "ttl";
@Parameter(
names = {"--endpoint-url", "-e"},
description = "URL (endpointURL) of the dataset in a triple store (Required)",
required = true,
order = 1)
private String endpointURL;
@Parameter(
names = {"--username", "-u"},
description = "Env var whose value is a username for authenticating the SPARQL endpoint (Optional)",
required = false,
order = 2)
private String authenticationUsername;
@Parameter(
names = {"--password", "-p"},
description = "Env var whose value is a password for authenticating the SPARQL endpoint (Optional)",
required = false,
order = 3)
private String authenticationPassword;
@Parameter(
names = {"--catalog-path", "-c"},
description = "Path to the OWL XML catalog file (Required)",
validateWith = CatalogPath.class,
required = true,
order = 4)
private String catalogPath;
@Parameter(
names = {"--file-extension", "-f"},
description = "File extension of the saved files. Default is ttl, options: owl, rdf, xml, rj, ttl, n3, nt, trig, nq, trix, jsonld (Optional)",
validateWith = FileExtensionValidator.class,
required = false,
order = 7)
private String fileExtension = DEFAULT_EXTENSION;
@Parameter(
names = {"-d", "--debug"},
description = "Shows debug logging statements",
order = 9)
private boolean debug;
@Parameter(
names = {"--help", "-h"},
description = "Displays summary of options",
help = true,
order = 10)
private boolean help;
private final static Logger LOGGER = Logger.getLogger(OwlSaveApp.class);
static {
DOMConfigurator.configure(ClassLoader.getSystemClassLoader().getResource("log4j.xml"));
}
private final static Map languages = new HashMap<>();
static {
languages.put("owl", RDFLanguages.RDFXML.getName());
languages.put("rdf", RDFLanguages.RDFXML.getName());
languages.put("xml", RDFLanguages.RDFXML.getName());
languages.put("rj", RDFLanguages.RDFJSON.getName());
languages.put("ttl", RDFLanguages.TTL.getName());
languages.put("n3", RDFLanguages.N3.getName());
languages.put("nt", RDFLanguages.NT.getName());
languages.put("trig", RDFLanguages.TRIG.getName());
languages.put("nq", RDFLanguages.NQ.getName());
languages.put("trix", RDFLanguages.TRIX.getName());
languages.put("jsonld", RDFLanguages.JSONLD.getName());
}
/**
* Application for loading ontologies to a Fuseki server.
*
* @param args Application arguments.
* @throws Exception Error
*/
public static void main(final String... args) throws Exception {
final OwlSaveApp app = new OwlSaveApp();
final JCommander builder = JCommander.newBuilder().addObject(app).build();
builder.parse(args);
if (app.help) {
builder.usage();
return;
}
if (app.debug) {
final Appender appender = LogManager.getRootLogger().getAppender("stdout");
((AppenderSkeleton) appender).setThreshold(Level.DEBUG);
}
app.run();
}
/**
* Creates a new OwlSaveApp object
*/
public OwlSaveApp() {
}
private void run() throws Exception {
LOGGER.info("=================================================================");
LOGGER.info(" S T A R T");
LOGGER.info(" OWL Save " + getAppVersion());
LOGGER.info("=================================================================");
LOGGER.info(("Catalog path = " + catalogPath));
LOGGER.info(("Endpoint URL = " + endpointURL));
LOGGER.info(("File Extension = " + fileExtension));
// Get an RDF Connection
RDFConnection conn = getRDFConnection();
// Load Owl Catalog
final File catalogFile = new File(catalogPath);
if (!catalogFile.exists() ) {
createOutputCatalog(catalogFile);
}
OwlCatalog catalog = OwlCatalog.create(new File(catalogPath));
try {
// Fetches the dataset
LOGGER.info("Fetching dataset at "+endpointURL);
Dataset dataset = conn.fetchDataset();
// save the ontologies
int count = 0;
Iterator resources = dataset.listNames();
while (resources.hasNext()) {
count++;
String uri = resources.next();
String resolved = catalog.resolveURI(uri);
File dst = new File(new URI(resolved+"."+fileExtension));
dst.getParentFile().mkdirs();
dst.createNewFile();
OutputStream out = new FileOutputStream(dst, false);
LOGGER.info("Saving "+dst.getCanonicalPath());
Model model = dataset.getNamedModel(uri);
model.write(out, languages.get(fileExtension));
}
System.out.println("Saved "+count+" owl file(s)");
} catch (HttpException e) {
if (e.getCause() instanceof ConnectException) {
System.out.println("Connection Exception: check that the endpoint ("+endpointURL+") is reachable");
}
throw e;
} finally {
// Close connection
conn.close();
conn.end();
}
LOGGER.info("=================================================================");
LOGGER.info(" E N D");
LOGGER.info("=================================================================");
}
private RDFConnection getRDFConnection() {
RDFConnectionRemoteBuilder builder = RDFConnectionRemote.create()
.destination(endpointURL);
final String username = authenticationUsername != null ? System.getenv(authenticationUsername) : null;
final String password = authenticationPassword != null ? System.getenv(authenticationPassword) : null;
if (null != username && null != password) {
Authenticator authenticator = LibSec.authenticator(username, password);
HttpClient client = HttpEnv.httpClientBuilder()
.authenticator(authenticator)
.build();
builder = builder.httpClient(client);
}
return builder.build();
}
private void createOutputCatalog(final File outputCatalogFile) throws Exception {
LOGGER.info(("Saving: " + outputCatalogFile));
BufferedWriter bw = new BufferedWriter(new FileWriter(outputCatalogFile));
bw.write("\n");
bw.write("\n");
bw.write("\t ");
bw.close();
}
private String getAppVersion() {
var version = this.getClass().getPackage().getImplementationVersion();
return (version != null) ? version : "";
}
/**
* A parameter validator for an OASIS XML catalog path.
*/
public static class CatalogPath implements IParameterValidator {
/**
* Creates a new FileExtensionValidator object
*/
public CatalogPath() {
}
@Override
public void validate(final String name, final String value) throws ParameterException {
File file = new File(value);
if (!file.getName().endsWith("catalog.xml")) {
throw new ParameterException("Parameter " + name + " should be a valid OWL catalog path");
}
final File folder = file.getParentFile();
folder.mkdirs();
}
}
/**
* A parameter validator for a file extension for an RDF language syntax.
*/
public static class FileExtensionValidator implements IParameterValidator {
/**
* Creates a new FileExtensionValidator object
*/
public FileExtensionValidator() {
}
@Override
public void validate(final String name, final String value) throws ParameterException {
Lang lang = RDFLanguages.fileExtToLang(value);
if (lang == null) {
throw new ParameterException("File extension " + name + " is not a valid one");
}
}
}
}