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[DL-Learner SVN] SF.net SVN: dl-learner:[3962] trunk/scripts/src/main/java/org/dllearner/ scripts/pattern/OWLAxiomPatternUsageEvaluation.java
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From: <lor...@us...> - 2013-05-08 19:07:57
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Revision: 3962
http://sourceforge.net/p/dl-learner/code/3962
Author: lorenz_b
Date: 2013-05-08 19:07:53 +0000 (Wed, 08 May 2013)
Log Message:
-----------
Refactored pattern eval.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-08 17:47:19 UTC (rev 3961)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-08 19:07:53 UTC (rev 3962)
@@ -3,6 +3,7 @@
import static java.util.Arrays.asList;
import java.io.File;
+import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
@@ -27,6 +28,7 @@
import java.util.Map.Entry;
import java.util.Random;
import java.util.Set;
+import java.util.TreeSet;
import java.util.concurrent.TimeUnit;
import java.util.prefs.Preferences;
@@ -34,7 +36,6 @@
import joptsimple.OptionParser;
import joptsimple.OptionSet;
-import org.aksw.commons.collections.diff.ModelDiff;
import org.apache.log4j.Logger;
import org.coode.owlapi.turtle.TurtleOntologyFormat;
import org.dllearner.core.EvaluatedAxiom;
@@ -79,6 +80,9 @@
import com.google.common.collect.HashMultiset;
import com.google.common.collect.Multiset;
+import com.google.common.hash.HashCode;
+import com.google.common.hash.HashFunction;
+import com.google.common.hash.Hashing;
import com.hp.hpl.jena.query.ParameterizedSparqlString;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
@@ -96,24 +100,18 @@
public class OWLAxiomPatternUsageEvaluation {
- private static final Logger logger = Logger.getLogger(OWLAxiomPatternUsageEvaluation.AxiomTypeCategory.class
- .getName());
+ private static final Logger logger = Logger.getLogger(OWLAxiomPatternUsageEvaluation.class.getName());
- enum AxiomTypeCategory{
- TBox, RBox, ABox
- }
private OWLObjectRenderer axiomRenderer = new ManchesterOWLSyntaxOWLObjectRendererImpl();
private OWLDataFactory df = new OWLDataFactoryImpl();
- private Connection conn;
- private ExtractionDBCache cache = new ExtractionDBCache("pattern-cache");
+ private ExtractionDBCache cache = new ExtractionDBCache("pattern-cache/db");
private SparqlEndpoint endpoint = SparqlEndpoint.getEndpointDBpedia();
private SparqlEndpointKS ks = new SparqlEndpointKS(endpoint, cache);//new LocalModelBasedSparqlEndpointKS(model);
private String ns = "http://dbpedia.org/ontology/";
- private boolean fancyLatex = false;
private DecimalFormat format = new DecimalFormat("00.0%");
private long waitingTime = TimeUnit.SECONDS.toMillis(3);
private double threshold = 0.6;
@@ -125,33 +123,8 @@
private int queryLimit = 10000;
public OWLAxiomPatternUsageEvaluation() {
- initDBConnection();
}
- private void initDBConnection() {
- try {
- InputStream is = this.getClass().getClassLoader().getResourceAsStream("db_settings.ini");
- Preferences prefs = new IniPreferences(is);
- String dbServer = prefs.node("database").get("server", null);
- String dbName = prefs.node("database").get("name", null);
- String dbUser = prefs.node("database").get("user", null);
- String dbPass = prefs.node("database").get("pass", null);
-
- Class.forName("com.mysql.jdbc.Driver");
- String url = "jdbc:mysql://" + dbServer + "/" + dbName;
- conn = DriverManager.getConnection(url, dbUser, dbPass);
- } catch (ClassNotFoundException e) {
- e.printStackTrace();
- } catch (SQLException e) {
- e.printStackTrace();
- } catch (InvalidFileFormatException e) {
- e.printStackTrace();
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- } catch (IOException e) {
- e.printStackTrace();
- }
- }
public void run(SparqlEndpoint endpoint, OWLOntology ontology, File outputFile, int maxNrOfTestedClasses){
ks = new SparqlEndpointKS(endpoint, cache);
@@ -315,6 +288,21 @@
for (NamedClass cls : classes) {
logger.info("Extracting fragment for " + cls + "...");
Model fragment = ModelFactory.createDefaultModel();
+ //try to load from cache
+ HashFunction hf = Hashing.md5();
+ HashCode hc = hf.newHasher().putString(cls.getName()).hash();
+ File file = new File("pattern-cache/" + hc.toString() + ".ttl");
+ if(file.exists()){
+ try {
+ fragment.read(new FileInputStream(file), null, "TURTLE");
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+ class2Fragment.put(cls, fragment);
+ logger.info("...got " + fragment.size() + " triples.");
+ continue;
+ }
+
//build the CONSTRUCT query
Query query = buildConstructQuery(cls, depth);
query.setLimit(queryLimit);
@@ -323,7 +311,8 @@
int offset = 0;
boolean hasMoreResults = true;
while(hasMoreResults && (System.currentTimeMillis() - startTime)<= maxFragmentExtractionTime){
- query.setOffset(offset);System.out.println(query);
+ query.setOffset(offset);
+ logger.info(query);
Model m = executeConstructQuery(query);
fragment.add(m);
if(m.size() == 0){
@@ -338,6 +327,11 @@
}
logger.info("...got " + fragment.size() + " triples.");
class2Fragment.put(cls, fragment);
+ try {
+ fragment.write(new FileOutputStream(file), "TURTLE");
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
}
return class2Fragment;
}
@@ -554,6 +548,72 @@
Set<OWLEntity> signature = patternSuperClass.getSignature();
signature.remove(patternSubClass);
+ query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(patternSubClass, patternSuperClass), signature);
+ logger.info("Running query\n" + query);
+ Map<OWLEntity, String> variablesMapping = converter.getVariablesMapping();
+ com.hp.hpl.jena.query.ResultSet rs = QueryExecutionFactory.create(query, fragment).execSelect();
+ QuerySolution qs;
+ Set<String> resources = new HashSet<String>();
+ Multiset<OWLAxiom> instantiations = HashMultiset.create();
+ while (rs.hasNext()) {
+ qs = rs.next();
+ resources.add(qs.getResource("x").getURI());
+ // get the IRIs for each variable
+ Map<OWLEntity, IRI> entity2IRIMap = new HashMap<OWLEntity, IRI>();
+ entity2IRIMap.put(pattern.getSubClass().asOWLClass(), cls.getIRI());
+ boolean skip = false;
+ for (OWLEntity entity : signature) {
+ String var = variablesMapping.get(entity);
+ if(qs.get(var) == null){
+ logger.warn("Variable " + var + " is not bound.");
+ skip = true;
+ break;
+ }
+ if(qs.get(var).isLiteral()){
+ skip = true;
+ break;
+ }
+ Resource resource = qs.getResource(var);
+ if(entity.isOWLObjectProperty() && resource.hasURI(RDF.type.getURI())){
+ skip = true;
+ break;
+ }
+ entity2IRIMap.put(entity, IRI.create(resource.getURI()));
+ }
+ if(!skip){
+ // instantiate the pattern
+ OWLObjectDuplicator duplicator = new OWLObjectDuplicator(entity2IRIMap, df);
+ OWLAxiom patternInstantiation = duplicator.duplicateObject(pattern);
+ instantiations.add(patternInstantiation);
+ }
+ }
+ // compute the score
+ int total = resources.size();
+ for (OWLAxiom axiom : instantiations.elementSet()) {
+ int frequency = instantiations.count(axiom);
+ Score score = computeScore(total, Math.min(total, frequency));
+ axioms2Score.put(axiom, score);
+ }
+
+ return axioms2Score;
+ }
+
+ private Map<OWLAxiom, Score> applyPattern2(OWLSubClassOfAxiom pattern, OWLClass cls, Model fragment) {
+ Map<OWLAxiom, Score> axioms2Score = new HashMap<OWLAxiom, Score>();
+
+ OWLClassExpression patternSubClass = pattern.getSubClass();
+ OWLClassExpression patternSuperClass = pattern.getSuperClass();
+
+ patternSubClass = cls;
+
+ // 2. execute SPARQL query on local model
+ Query query = QueryFactory.create(
+ "SELECT (COUNT(DISTINCT ?x) AS ?cnt) WHERE {" + converter.convert("?x", patternSubClass) + "}",
+ Syntax.syntaxARQ);
+ int subClassCnt = QueryExecutionFactory.create(query, fragment).execSelect().next().getLiteral("cnt").getInt();
+
+ Set<OWLEntity> signature = patternSuperClass.getSignature();
+ signature.remove(patternSubClass);
query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(patternSubClass, patternSuperClass), signature, true);
logger.info("Running query\n" + query);
Map<OWLEntity, String> variablesMapping = converter.getVariablesMapping();
@@ -679,7 +739,7 @@
public List<OWLAxiom> getPatternsToEvaluate(OWLOntology ontology){
List<OWLAxiom> axiomPatterns = new ArrayList<OWLAxiom>();
- axiomPatterns.addAll(ontology.getLogicalAxioms());
+ axiomPatterns.addAll(new TreeSet<OWLAxiom>(ontology.getLogicalAxioms()));
return axiomPatterns;
}
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