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org.bridgedb.uri.loader.RdfParser Maven / Gradle / Ivy
// BridgeDb,
// An abstraction layer for identifier mapping services, both local and online.
//
// Copyright 2006-2009 BridgeDb developers
// Copyright 2012-2013 Christian Y. A. Brenninkmeijer
// Copyright 2012-2013 OpenPhacts
//
// 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 org.bridgedb.uri.loader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import java.util.Optional;
import org.apache.log4j.Logger;
import org.bridgedb.uri.loader.transative.TransativeConfig;
import org.bridgedb.utils.BridgeDBException;
import org.eclipse.rdf4j.common.exception.RDF4JException;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.eclipse.rdf4j.rio.RDFFormat;
import org.eclipse.rdf4j.rio.RDFHandler;
import org.eclipse.rdf4j.rio.RDFParser;
import org.eclipse.rdf4j.rio.RDFParserFactory;
import org.eclipse.rdf4j.rio.RDFParserRegistry;
import org.eclipse.rdf4j.rio.turtle.TurtleParser;
public class RdfParser {
private final RDFHandler handler;
public static RDFParser DEFAULT_PARSER = new TurtleParser();
private static final String GET_FORMAT_FROM_ADDRESS = null;
public RdfParser(RDFHandler handler){
this.handler = handler;
}
static final Logger logger = Logger.getLogger(RdfParser.class);
public void parse(String baseURI, File file) throws BridgeDBException{
parse(baseURI, file, GET_FORMAT_FROM_ADDRESS);
}
public void parse(String baseURI, File file, String rdfFormatName) throws BridgeDBException{
logger.info("Parsing: " + file.getAbsolutePath());
FileReader reader = null;
try {
reader = new FileReader(file);
RDFParser parser = getParser(file.getName(), rdfFormatName);
parser.setRDFHandler(handler);
parser.setParseErrorListener(new LinksetParserErrorListener());
parser.parse (reader, baseURI);
} catch (IOException ex) {
throw new BridgeDBException("Error reading " + file.getAbsolutePath() + " " + ex.getMessage(), ex);
} catch (RDF4JException ex) {
throw new BridgeDBException("Error parsing " + file.getAbsolutePath() + " " + ex.getMessage(), ex);
} finally {
try {
if (reader != null){
reader.close();
}
} catch (IOException ex) {
throw new BridgeDBException("Error closing inputStream ", ex);
}
}
}
public void parse(String uri) throws BridgeDBException {
parse(uri, GET_FORMAT_FROM_ADDRESS);
}
public void parse(String uri, String rdfFormatName) throws BridgeDBException {
InputStream stream = getInputStream(uri);
parse(stream, uri, rdfFormatName);
}
public void parse(InputStream stream, String mappingSource, String rdfFormatName) throws BridgeDBException {
logger.info("Parsing: " + mappingSource);
try {
RDFParser parser = getParser(mappingSource, rdfFormatName);
parser.setRDFHandler(handler);
parser.setParseErrorListener(new LinksetParserErrorListener());
parser.parse (stream, mappingSource);
} catch (IOException ex) {
throw new BridgeDBException("Error reading " + mappingSource + " " + ex.getMessage(), ex);
} catch (RDF4JException ex) {
throw new BridgeDBException("Error parsing " + mappingSource + " " + ex.getMessage(), ex);
} finally {
try {
stream.close();
} catch (IOException ex) {
throw new BridgeDBException("Error closing inputStream ", ex);
}
}
}
public InputStream getInputStream(String uri) throws BridgeDBException {
URL url;
try {
url = new URL(uri);
} catch (MalformedURLException ex) {
throw new BridgeDBException ("Unable to convert String to Uri:" + uri, ex);
}
InputStream inputStream;
try {
return url.openStream();
} catch (IOException ex) {
throw new BridgeDBException ("Unable to convert String to Uri:" + uri, ex);
}
}
public static IRI fileToURL(File file) throws BridgeDBException{
String baseURI = TransativeConfig.getTransitiveBaseUri();
if (baseURI == null || baseURI.isEmpty()){
return fileToURI(file);
}
if (file.getParent().equals(TransativeConfig.getTransativeDirectory())){
return SimpleValueFactory.getInstance().createIRI(baseURI + file.getName());
} else {
return RdfParser.fileToURI(file);
}
}
private static IRI fileToURI(File file) throws BridgeDBException{
try {
String uri = file.toURI().toURL().toExternalForm();
return SimpleValueFactory.getInstance().createIRI(uri);
} catch (MalformedURLException ex) {
throw new BridgeDBException("Unable to convert file to URI", ex);
}
}
public static RDFParser getParser(String address, String rdfFormatName) throws BridgeDBException{
RDFParserRegistry reg = RDFParserRegistry.getInstance();
RDFFormat format = null;
if (rdfFormatName == null || rdfFormatName.isEmpty()){
if (address.endsWith(".gz")){
address = address.substring(0, address.length()-3);
}
if (address.endsWith(".n3")){
address = "try.ttl";
}
Optional fileFormat = reg.getFileFormatForFileName(address);
if (fileFormat.isEmpty()){
//added bridgeDB/OPS specific extension here if required.
logger.warn("OpenRDF does not know the RDF Format for " + address);
logger.warn("Using the default format " + DEFAULT_PARSER);
return DEFAULT_PARSER;
}
format = fileFormat.get();
} else {
List rdfFormats = new ArrayList<>();
rdfFormats.add(RDFFormat.N3);
rdfFormats.add(RDFFormat.NQUADS);
rdfFormats.add(RDFFormat.NTRIPLES);
rdfFormats.add(RDFFormat.JSONLD);
rdfFormats.add(RDFFormat.RDFA);
rdfFormats.add(RDFFormat.RDFJSON);
rdfFormats.add(RDFFormat.RDFXML);
rdfFormats.add(RDFFormat.TRIG);
rdfFormats.add(RDFFormat.TRIX);
rdfFormats.add(RDFFormat.TURTLE);
for (RDFFormat rdfFormat: rdfFormats){
if (rdfFormat.getName().equalsIgnoreCase(rdfFormatName)){
format = rdfFormat;
}
if (format == null){
throw new BridgeDBException("No RdfFormat with name " + rdfFormatName + " known");
}
}
}
Optional factory = reg.get(format);
return factory.get().getParser();
}
}
