Java tutorial
/* * 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 esiptestbed.mudrod.ontology.process; import java.io.File; import java.io.PrintStream; import java.util.ArrayList; import java.util.HashMap; import java.util.Hashtable; import java.util.Iterator; import java.util.LinkedList; import java.util.List; import java.util.Locale; import java.util.Map; import java.util.Properties; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.CommandLineParser; import org.apache.commons.cli.DefaultParser; import org.apache.commons.cli.HelpFormatter; import org.apache.commons.cli.Option; import org.apache.commons.cli.Options; import org.apache.jena.ontology.Individual; import org.apache.jena.ontology.OntClass; import org.apache.jena.ontology.OntModel; import org.apache.jena.ontology.OntModelSpec; import org.apache.jena.ontology.OntResource; import org.apache.jena.ontology.Restriction; import org.apache.jena.rdf.model.Literal; import org.apache.jena.rdf.model.ModelFactory; import org.apache.jena.rdf.model.Resource; import org.apache.jena.shared.PrefixMapping; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import esiptestbed.mudrod.main.MudrodEngine; import esiptestbed.mudrod.ontology.Ontology; import esiptestbed.mudrod.ontology.OntologyFactory; /** * The LocalOntology implementation enables us to work with Ontology files * whcih are cached locally and available on the runtime classpath e.g. * in <code>src/main/resource/ontology/...</code>. * From here we can test and iterate on how use of ontology can enhance search. * * @author lewismc */ public class LocalOntology implements Ontology { public static final Logger LOG = LoggerFactory.getLogger(LocalOntology.class); public static final String DELIMITER_SEARCHTERM = " "; private static final String ONT_DIR = "ontDir"; private static Hashtable searchTerms = new Hashtable<>(); private static OntologyParser parser; private static OntModel ontologyModel; private static Ontology ontology = null; private static Map mAnonIDs = new HashMap<>(); private static int mAnonCount = 0; public LocalOntology() { //only initialize all the static variables //if first time called to this ontology constructor if (ontology == null) { if (LOG.isDebugEnabled()) { LOG.debug("Creating new ontology"); } parser = new OwlParser(); ontology = this; } if (ontologyModel == null) ontologyModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, null); } public static Ontology getInstance() { if (ontology == null) { ontology = new LocalOntology(); } return ontology; } /** * */ @Override public void load(String[] urls) { for (int i = 0; i < urls.length; i++) { String url = urls[i].trim(); if (!"".equals(url)) load(ontologyModel, url); } parser.parse(ontologyModel); } private void load(Object m, String url) { try { if (LOG.isDebugEnabled()) { LOG.debug("Reading {}", url); } ((OntModel) m).read(url); } catch (Exception e) { LOG.error("Failed whilst attempting to read ontology {}", url, e); } } public static OntologyParser getParser() { if (parser == null) { parser = new OwlParser(); } return parser; } public static OntModel getModel() { return ontologyModel; } /** * Not yet implemented. */ @Override public void merge(esiptestbed.mudrod.ontology.Ontology o) { // not yet implemented } /** * Retrieve all subclasses of entity(ies) hashed to searchTerm */ @Override public Iterator<String> subclasses(String entitySearchTerm) { Map classMap = retrieve(entitySearchTerm); Map subclasses = new HashMap<>(); Iterator<OntResource> iter = classMap.keySet().iterator(); while (iter.hasNext()) { OntResource resource = iter.next(); if (resource instanceof OntClass) { //get subclasses for (Iterator i = ((OntClass) resource).listSubClasses(); i.hasNext();) { OntResource subclass = (OntResource) i.next(); for (Iterator j = subclass.listLabels(null); j.hasNext();) { Literal l = (Literal) j.next(); subclasses.put(l.toString(), "1"); } } //get individuals for (Iterator i = ((OntClass) resource).listInstances(); i.hasNext();) { OntResource subclass = (OntResource) i.next(); for (Iterator j = subclass.listLabels(null); j.hasNext();) { Literal l = (Literal) j.next(); subclasses.put(l.toString(), "1"); } } } else if (resource instanceof Individual) { for (Iterator i = resource.listSameAs(); i.hasNext();) { OntResource subclass = (OntResource) i.next(); for (Iterator j = subclass.listLabels(null); j.hasNext();) { Literal l = (Literal) j.next(); subclasses.put(l.toString(), "1"); } } } } return subclasses.keySet().iterator(); } /** * retrieves synonyms from wordnet via sweet's web interface */ @Override public Iterator synonyms(String queryKeyPhrase) { //need to have a html quote method instead String qKeyPhrase = queryKeyPhrase.replaceAll("\\s+", "\\+"); Map classMap = retrieve(qKeyPhrase); Map synonyms = new HashMap<>(); Iterator iter = classMap.keySet().iterator(); while (iter.hasNext()) { OntResource resource = (OntResource) iter.next(); //listLabels for (Iterator i = resource.listLabels(null); i.hasNext();) { Literal l = (Literal) i.next(); synonyms.put(l.toString(), "1"); } if (resource instanceof Individual) { //get all individuals same as this one for (Iterator i = resource.listSameAs(); i.hasNext();) { Individual individual = (Individual) i.next(); //add labels for (Iterator j = individual.listLabels(null); j.hasNext();) { Literal l = (Literal) i.next(); synonyms.put(l.toString(), "1"); } } } else if (resource instanceof OntClass) { //list equivalent classes for (Iterator i = ((OntClass) resource).listEquivalentClasses(); i.hasNext();) { OntClass equivClass = (OntClass) i.next(); //add labels for (Iterator j = equivClass.listLabels(null); j.hasNext();) { Literal l = (Literal) j.next(); synonyms.put(l.toString(), "1"); } } } } return synonyms.keySet().iterator(); } public static void addSearchTerm(String label, OntResource resource) { Map<OntResource, String> m = retrieve(label); if (m == null) { m = new HashMap<>(); } m.put(resource, "1"); searchTerms.put(label.toLowerCase(), m); } public static Map<OntResource, String> retrieve(String label) { @SuppressWarnings("unchecked") Map<OntResource, String> m = (Map<OntResource, String>) searchTerms.get(label.toLowerCase()); if (m == null) { m = new HashMap<>(); } return m; } protected static void renderHierarchy(PrintStream out, OntClass cls, List occurs, int depth) { renderClassDescription(out, cls, depth); out.println(); // recurse to the next level down if (cls.canAs(OntClass.class) && !occurs.contains(cls)) { for (Iterator i = cls.listSubClasses(true); i.hasNext();) { OntClass sub = (OntClass) i.next(); // we push this expression on the occurs list before we recurse occurs.add(cls); renderHierarchy(out, sub, occurs, depth + 1); occurs.remove(cls); } for (Iterator i = cls.listInstances(); i.hasNext();) { Individual individual = (Individual) i.next(); renderURI(out, individual.getModel(), individual.getURI()); out.print(" ["); for (Iterator j = individual.listLabels(null); j.hasNext();) { out.print(((Literal) j.next()).getString() + ", "); } out.print("] "); out.println(); } } } public static void renderClassDescription(PrintStream out, OntClass c, int depth) { indent(out, depth); if (c.isRestriction()) { renderRestriction(out, (Restriction) c.as(Restriction.class)); } else { if (!c.isAnon()) { out.print("Class "); renderURI(out, c.getModel(), c.getURI()); out.print(c.getLocalName()); out.print(" ["); for (Iterator i = c.listLabels(null); i.hasNext();) { out.print(((Literal) i.next()).getString() + ", "); } out.print("] "); } else { renderAnonymous(out, c, "class"); } } } protected static void renderRestriction(PrintStream out, Restriction r) { if (!r.isAnon()) { out.print("Restriction "); renderURI(out, r.getModel(), r.getURI()); } else { renderAnonymous(out, r, "restriction"); } out.print(" on property "); renderURI(out, r.getModel(), r.getOnProperty().getURI()); } protected static void renderURI(PrintStream out, PrefixMapping prefixes, String uri) { out.print(prefixes.expandPrefix(uri)); } protected static void renderAnonymous(PrintStream out, Resource anon, String name) { String anonID = (String) mAnonIDs.get(anon.getId()); if (anonID == null) { anonID = "a-" + mAnonCount++; mAnonIDs.put(anon.getId(), anonID); } out.print("Anonymous "); out.print(name); out.print(" with ID "); out.print(anonID); } protected static void indent(PrintStream out, int depth) { for (int i = 0; i < depth; i++) { out.print(" "); } } public static void main(String[] args) throws Exception { // boolean options Option helpOpt = new Option("h", "help", false, "show this help message"); // argument options Option ontDirOpt = Option.builder(ONT_DIR).required(true).numberOfArgs(1).hasArg(true) .desc("A directory containing .owl files.").argName(ONT_DIR).build(); // create the options Options options = new Options(); options.addOption(helpOpt); options.addOption(ontDirOpt); String ontDir; CommandLineParser parser = new DefaultParser(); try { CommandLine line = parser.parse(options, args); if (line.hasOption(ONT_DIR)) { ontDir = line.getOptionValue(ONT_DIR).replace("\\", "/"); } else { ontDir = LocalOntology.class.getClassLoader().getResource("ontology").getFile(); } if (!ontDir.endsWith("/")) { ontDir += "/"; } } catch (Exception e) { LOG.error("Error whilst processing main method of LocalOntology.", e); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("LocalOntology: 'ontDir' argument is mandatory. ", options, true); return; } File fileDir = new File(ontDir); //Fail if the input is not a directory. if (fileDir.isDirectory()) { List<String> owlFiles = new ArrayList<>(); for (File owlFile : fileDir.listFiles()) { owlFiles.add(owlFile.toString()); } MudrodEngine mEngine = new MudrodEngine(); Properties props = mEngine.loadConfig(); Ontology ontology = new OntologyFactory(props).getOntology(); //convert to correct iput for ontology loading. String[] owlArray = new String[owlFiles.size()]; owlArray = owlFiles.toArray(owlArray); ontology.load(owlArray); String[] terms = new String[] { "Glacier ice" }; //Demonstrate that we can do basic ontology heirarchy navigation and log output. for (Iterator<OntClass> i = getParser().rootClasses(getModel()); i.hasNext();) { //print Ontology Class Hierarchy OntClass c = i.next(); renderHierarchy(System.out, c, new LinkedList<>(), 0); for (Iterator<OntClass> subClass = c.listSubClasses(true); subClass.hasNext();) { OntClass sub = subClass.next(); //This means that the search term is present as an OntClass if (terms[0].equalsIgnoreCase(sub.getLabel(null))) { //Add the search term(s) above to the term cache. for (int j = 0; j < terms.length; j++) { addSearchTerm(terms[j], sub); } //Query the ontology and return subclasses of the search term(s) for (int k = 0; k < terms.length; k++) { Iterator<String> iter = ontology.subclasses(terms[k]); while (iter.hasNext()) { LOG.info("Subclasses >> " + iter.next()); } } //print any synonymic relationships to demonstrate that we can //undertake synonym-based query expansion for (int l = 0; l < terms.length; l++) { Iterator<String> iter = ontology.synonyms(terms[l]); while (iter.hasNext()) { LOG.info("Synonym >> " + iter.next()); } } } } } mEngine.end(); } } }