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/*
* This file is part of the OWL API.
*
* The contents of this file are subject to the LGPL License, Version 3.0.
*
* Copyright (C) 2011, The University of Manchester
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see http://www.gnu.org/licenses/.
*
*
* Alternatively, the contents of this file may be used under the terms of the Apache License, Version 2.0
* in which case, the provisions of the Apache License Version 2.0 are applicable instead of those above.
*
* Copyright 2011, University of Manchester
*
* 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.semanticweb.owlapi.util;
import java.io.BufferedInputStream;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Serializable;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.StringTokenizer;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;
import org.semanticweb.owlapi.io.BOMSafeInputStream;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLOntologyIRIMapper;
import org.semanticweb.owlapi.model.OWLRuntimeException;
import org.semanticweb.owlapi.vocab.Namespaces;
import org.semanticweb.owlapi.vocab.OWLXMLVocabulary;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.DefaultHandler;
/**
* A mapper which given a root folder attempts to automatically discover and map
* files to ontologies. The mapper is only capable of mapping ontologies in
* RDF/XML and OWL/XML (other serialisations are not supported).
*
* @author Matthew Horridge, The University Of Manchester, Bio-Health
* Informatics Group, Date: 26-Apr-2007
*/
public class AutoIRIMapper extends DefaultHandler implements
OWLOntologyIRIMapper, Serializable {
private static final long serialVersionUID = 30406L;
private final Set fileExtensions;
private boolean mapped;
private final boolean recursive;
private final Map handlerMap;
private final Map ontologyIRI2PhysicalURIMap;
private Map oboFileMap;
private final String directoryPath;
private String currentFilePath;
private transient SAXParserFactory parserFactory;
private transient File directory;
private transient File currentFile;
/**
* Creates an auto-mapper which examines ontologies that reside in the
* specified root folder (and possibly sub-folders).
*
* @param rootDirectory
* The root directory which should be searched for ontologies.
* @param recursive
* Sub directories will be searched recursively if {@code true}.
*/
public AutoIRIMapper(File rootDirectory, boolean recursive) {
directory = rootDirectory;
directoryPath = directory.getAbsolutePath();
this.recursive = recursive;
ontologyIRI2PhysicalURIMap = new HashMap();
oboFileMap = new HashMap();
fileExtensions = new HashSet();
fileExtensions.add("owl");
fileExtensions.add("xml");
fileExtensions.add("rdf");
fileExtensions.add("omn");
mapped = false;
handlerMap = new HashMap();
handlerMap.put(Namespaces.RDF + "RDF",
new RDFXMLOntologyRootElementHandler());
handlerMap.put(OWLXMLVocabulary.ONTOLOGY.toString(),
new OWLXMLOntologyRootElementHandler());
}
protected SAXParserFactory getParserFactory() {
if (parserFactory == null) {
parserFactory = SAXParserFactory.newInstance();
parserFactory.setNamespaceAware(true);
}
return parserFactory;
}
protected File getDirectory() {
if (directory == null) {
directory = new File(directoryPath);
}
return directory;
}
protected File getCurrentFile() {
if (currentFile == null && currentFilePath != null) {
currentFile = new File(currentFilePath);
}
return currentFile;
}
/**
* The mapper only examines files that have specified file extensions. This
* method returns the file extensions that cause a file to be examined.
*
* @return A {@code Set} of file extensions.
*/
public Set getFileExtensions() {
return fileExtensions;
}
/**
* Sets the extensions of files that are to be examined for ontological
* content. (By default the extensions are, owl, xml and rdf). Only files
* that have the specified extensions will be examined to see if they
* contain ontologies.
*
* @param extensions
* the set of extensions
*/
public void setFileExtensions(Set extensions) {
fileExtensions.clear();
fileExtensions.addAll(extensions);
}
/**
* Gets the set of ontology IRIs that this mapper has found.
*
* @return A {@code Set} of ontology (logical) URIs
*/
public Set getOntologyIRIs() {
if (!mapped) {
mapFiles();
}
return new HashSet(ontologyIRI2PhysicalURIMap.keySet());
}
/** update the map. */
public void update() {
mapFiles();
}
@Override
public IRI getDocumentIRI(IRI ontologyIRI) {
if (!mapped) {
mapFiles();
}
if (ontologyIRI.toString().endsWith(".obo")) {
String path = ontologyIRI.toURI().getPath();
if (path != null) {
int lastSepIndex = path.lastIndexOf('/');
String name = path.substring(lastSepIndex + 1, path.length());
IRI documentIRI = oboFileMap.get(name);
if (documentIRI != null) {
return documentIRI;
}
}
}
return ontologyIRI2PhysicalURIMap.get(ontologyIRI);
}
private void mapFiles() {
mapped = true;
ontologyIRI2PhysicalURIMap.clear();
processFile(getDirectory());
}
private void processFile(File f) {
if (f.isHidden()) {
return;
}
File[] files = f.listFiles();
if (files != null) {
for (File file : files) {
if (file.isDirectory() && recursive) {
processFile(file);
} else {
if (file.getName().endsWith(".obo")) {
oboFileMap.put(file.getName(), IRI.create(file));
} else if (file.getName().endsWith(".omn")) {
parseManchesterSyntaxFile(file);
} else {
for (String ext : fileExtensions) {
if (file.getName().endsWith(ext)) {
parseFile(file);
break;
}
}
}
}
}
}
}
private void parseFile(File file) {
InputStream is = null;
try {
is = new FileInputStream(file);
try {
currentFile = file;
currentFilePath = file.getAbsolutePath();
SAXParser parser = getParserFactory().newSAXParser();
parser.parse(
new BufferedInputStream(new BOMSafeInputStream(is)),
this);
} catch (ParserConfigurationException e) {
throw new OWLRuntimeException(e);
} catch (SAXException e) {
// if we can't parse a file, then we can't map it
} catch (IOException e) {
// if we can't parse a file, then we can't map it
}
} catch (FileNotFoundException e) {
// if we can't parse a file, then we can't map it
} finally {
if (is != null) {
try {
is.close();
} catch (IOException e) {
e.printStackTrace();
}
}
}
}
private void parseManchesterSyntaxFile(File file) {
BufferedReader br = null;
try {
// Ontology:
br = new BufferedReader(new InputStreamReader(new FileInputStream(
file), "UTF-8"));
String line = br.readLine();
IRI ontologyIRI = null;
while (line != null) {
StringTokenizer tokenizer = new StringTokenizer(line, " \r\n",
false);
line = br.readLine();
while (tokenizer.hasMoreTokens()) {
String tok = tokenizer.nextToken();
if (tok.startsWith("<") && tok.endsWith(">")) {
ontologyIRI = IRI.create(tok.substring(1,
tok.length() - 1));
ontologyIRI2PhysicalURIMap.put(ontologyIRI,
IRI.create(file));
break;
}
}
if (ontologyIRI != null) {
break;
}
}
} catch (IOException e) {
// if we can't parse a file, then we can't map it } finally {
try {
if (br != null) {
br.close();
}
} catch (IOException e2) {
e2.printStackTrace();
}
}
}
@Override
public void startElement(String uri, String localName, String qName,
Attributes attributes) throws SAXException {
OntologyRootElementHandler handler = handlerMap.get(uri + localName);
if (handler != null) {
IRI ontologyIRI = handler.handle(attributes);
if (ontologyIRI != null) {
ontologyIRI2PhysicalURIMap.put(ontologyIRI,
IRI.create(getCurrentFile()));
}
throw new SAXException();
}
}
@Override
public String toString() {
StringBuilder sb = new StringBuilder();
sb.append("AutoURIMapper: (");
sb.append(ontologyIRI2PhysicalURIMap.size());
sb.append(" ontologies)\n");
for (IRI iri : ontologyIRI2PhysicalURIMap.keySet()) {
sb.append(" ");
sb.append(iri.toQuotedString());
sb.append(" -> ");
sb.append(ontologyIRI2PhysicalURIMap.get(iri));
sb.append("\n");
}
return sb.toString();
}
/**
* A simple interface which extracts an ontology URI from a set of element
* attributes.
*/
private interface OntologyRootElementHandler {
/**
* Gets the ontology URI.
*
* @param attributes
* The attributes which will be examined for the ontology URI.
* @return The ontology URI or {@code null} if no ontology URI could be
* found.
*/
IRI handle(Attributes attributes);
}
/**
* A handler to handle RDF/XML files. The xml:base (if present) is taken to
* be the ontology URI of the ontology document being parsed.
*/
private static class RDFXMLOntologyRootElementHandler implements
OntologyRootElementHandler, Serializable {
private static final long serialVersionUID = 30406L;
public RDFXMLOntologyRootElementHandler() {}
@Override
public IRI handle(Attributes attributes) {
String baseValue = attributes.getValue(Namespaces.XML.toString(),
"base");
if (baseValue == null) {
return null;
}
return IRI.create(baseValue);
}
}
/** A handler that can handle OWL/XML files. */
private static class OWLXMLOntologyRootElementHandler implements
OntologyRootElementHandler, Serializable {
private static final long serialVersionUID = 30406L;
public OWLXMLOntologyRootElementHandler() {}
@Override
public IRI handle(Attributes attributes) {
String ontURI = attributes.getValue(Namespaces.OWL.toString(),
"ontologyIRI");
if (ontURI == null) {
ontURI = attributes.getValue("ontologyIRI");
}
if (ontURI == null) {
return null;
}
return IRI.create(ontURI);
}
}
}
