Menu
▾
▴
[DL-Learner SVN] SF.net SVN: dl-learner:[3931] trunk/components-core/src/main/java/org/ dllearner
|
From: <lor...@us...> - 2013-05-02 07:36:03
|
Revision: 3931
http://sourceforge.net/p/dl-learner/code/3931
Author: lorenz_b
Date: 2013-05-02 07:35:58 +0000 (Thu, 02 May 2013)
Log Message:
-----------
Some improvements in pattern detection workflow.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-04-30 11:06:03 UTC (rev 3930)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-05-02 07:35:58 UTC (rev 3931)
@@ -14,9 +14,11 @@
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
+import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Queue;
+import java.util.Set;
import java.util.prefs.Preferences;
import org.dllearner.kb.dataset.OWLOntologyDataset;
@@ -26,6 +28,7 @@
import org.ini4j.InvalidFileFormatException;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.OWLObjectRenderer;
+import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLDataFactory;
@@ -70,6 +73,7 @@
private Connection conn;
private PreparedStatement selectOntologyIdPs;
private PreparedStatement insertOntologyPs;
+ private PreparedStatement insertOntologyErrorPs;
private PreparedStatement selectPatternIdPs;
private PreparedStatement insertPatternIdPs;
private PreparedStatement insertOntologyPatternPs;
@@ -91,7 +95,9 @@
createTables();
try {
selectOntologyIdPs = conn.prepareStatement("SELECT id FROM Ontology WHERE url=?");
- insertOntologyPs = conn.prepareStatement("INSERT INTO Ontology (url, iri, repository) VALUES(?,?,?)");
+ insertOntologyPs = conn.prepareStatement("INSERT INTO Ontology (url, iri, repository, logical_axioms, tbox_axioms, rbox_axioms" +
+ ", abox_axioms, classes, object_properties, data_properties, individuals) VALUES(?,?,?,?,?,?,?,?,?,?,?)");
+ insertOntologyErrorPs = conn.prepareStatement("INSERT INTO Ontology (url, iri, repository) VALUES(?,?,?)");
selectPatternIdPs = conn.prepareStatement("SELECT id FROM Pattern WHERE pattern=?");
insertPatternIdPs = conn.prepareStatement("INSERT INTO Pattern (pattern,pattern_pretty) VALUES(?,?)");
insertOntologyPatternPs = conn.prepareStatement("INSERT INTO Ontology_Pattern (ontology_id, pattern_id, occurrences) VALUES(?,?,?)");
@@ -156,6 +162,14 @@
+ "url VARCHAR(2000) NOT NULL,"
+ "iri VARCHAR(2000) NOT NULL,"
+ "repository VARCHAR(200) NOT NULL,"
+ + "logical_axioms MEDIUMINT DEFAULT 0,"
+ + "tbox_axioms MEDIUMINT DEFAULT 0,"
+ + "rbox_axioms MEDIUMINT DEFAULT 0,"
+ + "abox_axioms MEDIUMINT DEFAULT 0,"
+ + "classes MEDIUMINT DEFAULT 0,"
+ + "object_properties MEDIUMINT DEFAULT 0,"
+ + "data_properties MEDIUMINT DEFAULT 0,"
+ + "individuals MEDIUMINT DEFAULT 0,"
+ "PRIMARY KEY(id),"
+ "INDEX(url)) DEFAULT CHARSET=utf8");
@@ -222,10 +236,10 @@
String url = physicalURI.toString();
//add ontology loading/parsing/... error entry
try {
- insertOntologyPs.setString(1, url);
- insertOntologyPs.setString(2, "ERROR:" + ex.getClass().getSimpleName() + "->" + ex.getMessage());
- insertOntologyPs.setString(3, repository.getName());
- insertOntologyPs.execute();
+ insertOntologyErrorPs.setString(1, url);
+ insertOntologyErrorPs.setString(2, "ERROR:" + ex.getClass().getSimpleName() + (ex.getMessage() != null ? ("->" + ex.getMessage()) : ""));
+ insertOntologyErrorPs.setString(3, repository.getName());
+ insertOntologyErrorPs.execute();
} catch (SQLException e) {
e.printStackTrace();
}
@@ -233,7 +247,10 @@
private int addOntology(URI physicalURI, OWLOntology ontology){
String url = physicalURI.toString();
- String ontologyIRI = ontology.getOntologyID().getOntologyIRI().toString();
+ String ontologyIRI = "Anonymous";
+ if(!ontology.getOntologyID().isAnonymous()){
+ ontologyIRI = ontology.getOntologyID().getOntologyIRI().toString();
+ }
//check for existing entry
try {
selectOntologyIdPs.setString(1, url);
@@ -249,6 +266,20 @@
insertOntologyPs.setString(1, url);
insertOntologyPs.setString(2, ontologyIRI);
insertOntologyPs.setString(3, repository.getName());
+ Set<OWLAxiom> logicalAxioms = new HashSet<OWLAxiom>();
+ logicalAxioms.addAll(ontology.getLogicalAxioms());
+ Set<OWLAxiom> tbox = AxiomType.getAxiomsOfTypes(logicalAxioms, new ArrayList<AxiomType>(AxiomType.TBoxAxiomTypes).toArray(new AxiomType[AxiomType.TBoxAxiomTypes.size()]));
+ Set<OWLAxiom> rbox = AxiomType.getAxiomsOfTypes(logicalAxioms, new ArrayList<AxiomType>(AxiomType.RBoxAxiomTypes).toArray(new AxiomType[AxiomType.RBoxAxiomTypes.size()]));
+ Set<OWLAxiom> abox = AxiomType.getAxiomsOfTypes(logicalAxioms, new ArrayList<AxiomType>(AxiomType.ABoxAxiomTypes).toArray(new AxiomType[AxiomType.ABoxAxiomTypes.size()]));
+
+ insertOntologyPs.setInt(4, ontology.getLogicalAxiomCount());
+ insertOntologyPs.setInt(5, tbox.size());
+ insertOntologyPs.setInt(6, rbox.size());
+ insertOntologyPs.setInt(7, abox.size());
+ insertOntologyPs.setInt(8, ontology.getClassesInSignature(true).size());
+ insertOntologyPs.setInt(9, ontology.getObjectPropertiesInSignature(true).size());
+ insertOntologyPs.setInt(10, ontology.getDataPropertiesInSignature(true).size());
+ insertOntologyPs.setInt(11, ontology.getIndividualsInSignature(true).size());
insertOntologyPs.execute();
} catch (SQLException e) {
e.printStackTrace();
@@ -293,9 +324,11 @@
Multiset<OWLAxiom> allAxiomPatterns = HashMultiset.create();
for (OntologyRepositoryEntry entry : entries) {
URI uri = entry.getPhysicalURI();
+// if(uri.toString().startsWith("http://rest.bioontology.org/bioportal/ontologies/download/42764")){
if (!ontologyProcessed(uri)) {
System.out.println("Loading \"" + entry.getOntologyShortName() + "\" from "+ uri);
try {
+ manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = manager.loadOntology(IRI.create(uri));
Multiset<OWLAxiom> axiomPatterns = HashMultiset.create();
for (OWLLogicalAxiom axiom : ontology.getLogicalAxioms()) {
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java 2013-04-30 11:06:03 UTC (rev 3930)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java 2013-05-02 07:35:58 UTC (rev 3931)
@@ -1,8 +1,10 @@
package org.dllearner.utilities.owl;
+import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import java.util.Stack;
import org.aksw.commons.collections.diff.ModelDiff;
@@ -31,6 +33,7 @@
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLIndividual;
import org.semanticweb.owlapi.model.OWLLiteral;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
import org.semanticweb.owlapi.model.OWLObjectAllValuesFrom;
import org.semanticweb.owlapi.model.OWLObjectComplementOf;
import org.semanticweb.owlapi.model.OWLObjectExactCardinality;
@@ -62,7 +65,7 @@
private String sparql = "";
private Stack<String> variables = new Stack<String>();
- private Map<OWLEntity, String> variablesMapping;
+ private Map<OWLEntity, String> variablesMapping = new HashMap<OWLEntity, String>();
private int classCnt = 0;
private int propCnt = 0;
@@ -71,6 +74,7 @@
private OWLDataFactory df = new OWLDataFactoryImpl();
private Map<Integer, Boolean> intersection;
+ private Set<? extends OWLEntity> variableEntities;
public OWLClassExpressionToSPARQLConverter() {
}
@@ -90,13 +94,37 @@
}
public Query asQuery(String rootVariable, OWLClassExpression expr){
- String queryString = "SELECT DISTINCT " + rootVariable + " WHERE {";
- queryString += convert(rootVariable, expr);
+ return asQuery(rootVariable, expr, Collections.<OWLEntity>emptySet());
+ }
+
+ public Query asQuery(String rootVariable, OWLClassExpression expr, Set<? extends OWLEntity> variableEntities){
+ this.variableEntities = variableEntities;
+ String queryString = "SELECT DISTINCT ";
+ String triplePattern = convert(rootVariable, expr);
+ if(variableEntities.isEmpty()){
+ queryString += rootVariable + " WHERE {";
+ } else {
+ for (OWLEntity owlEntity : variableEntities) {
+ String var = variablesMapping.get(owlEntity);
+ queryString += var + " ";
+ }
+ queryString += "COUNT(" + rootVariable + ") WHERE {";
+ }
+
+ queryString += triplePattern;
queryString += "}";
+ if(!variableEntities.isEmpty()){
+ queryString += "GROUP BY ";
+ for (OWLEntity owlEntity : variableEntities) {
+ String var = variablesMapping.get(owlEntity);
+ queryString += var;
+ }
+ }System.out.println(queryString);
return QueryFactory.create(queryString, Syntax.syntaxARQ);
}
private void reset(){
+ variablesMapping.clear();
variables.clear();
classCnt = 0;
propCnt = 0;
@@ -143,7 +171,7 @@
private String triple(String subject, String predicate, String object){
return (subject.startsWith("?") ? subject : "<" + subject + ">") + " " +
(predicate.startsWith("?") || predicate.equals("a") ? predicate : "<" + predicate + ">") + " " +
- (object.startsWith("?") ? object : "<" + object + ">") + ".\n";
+ (object.startsWith("?") ? object : object) + ".\n";
}
private String triple(String subject, String predicate, OWLLiteral object){
@@ -152,12 +180,46 @@
render(object) + ".\n";
}
+ private String triple(String subject, String predicate, OWLEntity object){
+ return (subject.startsWith("?") ? subject : "<" + subject + ">") + " " +
+ (predicate.startsWith("?") || predicate.equals("a") ? predicate : "<" + predicate + ">") + " " +
+ render(object) + ".\n";
+ }
+
+ private String triple(String subject, OWLEntity predicate, OWLEntity object){
+ return (subject.startsWith("?") ? subject : "<" + subject + ">") + " " +
+ render(predicate) + " " +
+ render(object) + ".\n";
+ }
+
+ private String triple(String subject, OWLEntity predicate, String object){
+ return (subject.startsWith("?") ? subject : "<" + subject + ">") + " " +
+ render(predicate) + " " +
+ object + ".\n";
+ }
+
+ private String triple(String subject, OWLEntity predicate, OWLLiteral object){
+ return (subject.startsWith("?") ? subject : "<" + subject + ">") + " " +
+ render(predicate) + " " +
+ render(object) + ".\n";
+ }
+
private String triple(String subject, String predicate, OWLIndividual object){
return (subject.startsWith("?") ? subject : "<" + subject + ">") + " " +
(predicate.startsWith("?") || predicate.equals("a") ? predicate : "<" + predicate + ">") + " " +
"<" + object.toStringID() + ">.\n";
}
+ private String render(OWLEntity entity){
+ String s;
+ if(variableEntities.contains(entity)){
+ s = getVariable(entity);
+ } else {
+ s = "<" + entity.toStringID() + ">";
+ }
+ return s;
+ }
+
private String render(OWLLiteral literal){
return "\"" + literal + "\"^^<" + literal.getDatatype().toStringID() + ">";
}
@@ -176,7 +238,7 @@
@Override
public void visit(OWLClass ce) {
- sparql += triple(variables.peek(), "a", ce.toStringID());
+ sparql += triple(variables.peek(), "a", render(ce));
}
@Override
@@ -220,9 +282,9 @@
OWLObjectPropertyExpression propertyExpression = ce.getProperty();
if(propertyExpression.isAnonymous()){
//property expression is inverse of a property
- sparql += triple(objectVariable, propertyExpression.getNamedProperty().toStringID(), variables.peek());
+ sparql += triple(objectVariable, propertyExpression.getNamedProperty(), variables.peek());
} else {
- sparql += triple(variables.peek(), propertyExpression.getNamedProperty().toStringID(), objectVariable);
+ sparql += triple(variables.peek(), propertyExpression.getNamedProperty(), objectVariable);
}
OWLClassExpression filler = ce.getFiller();
if(filler.isAnonymous()){
@@ -230,7 +292,7 @@
filler.accept(this);
variables.pop();
} else {
- sparql += triple(objectVariable, "a", filler.asOWLClass().toStringID());
+ sparql += triple(objectVariable, "a", filler.asOWLClass());
}
}
@@ -240,7 +302,7 @@
String subject = variables.peek();
String objectVariable = buildIndividualVariable();
OWLObjectPropertyExpression propertyExpression = ce.getProperty();
- String predicate = propertyExpression.getNamedProperty().toStringID();
+ OWLObjectProperty predicate = propertyExpression.getNamedProperty();
OWLClassExpression filler = ce.getFiller();
if(propertyExpression.isAnonymous()){
//property expression is inverse of a property
@@ -269,12 +331,12 @@
@Override
public void visit(OWLObjectHasValue ce) {
OWLObjectPropertyExpression propertyExpression = ce.getProperty();
- OWLIndividual value = ce.getValue();
+ OWLNamedIndividual value = ce.getValue().asOWLNamedIndividual();
if(propertyExpression.isAnonymous()){
//property expression is inverse of a property
- sparql += triple(value.toStringID(), propertyExpression.getNamedProperty().toStringID(), variables.peek());
+ sparql += triple(value.toStringID(), propertyExpression.getNamedProperty(), variables.peek());
} else {
- sparql += triple(variables.peek(), propertyExpression.getNamedProperty().toStringID(), value.toStringID());
+ sparql += triple(variables.peek(), propertyExpression.getNamedProperty(), value);
}
}
@@ -287,9 +349,9 @@
sparql += "{SELECT " + subjectVariable + " WHERE {";
if(propertyExpression.isAnonymous()){
//property expression is inverse of a property
- sparql += triple(objectVariable, propertyExpression.getNamedProperty().toStringID(), subjectVariable);
+ sparql += triple(objectVariable, propertyExpression.getNamedProperty(), subjectVariable);
} else {
- sparql += triple(subjectVariable, propertyExpression.getNamedProperty().toStringID(), objectVariable);
+ sparql += triple(subjectVariable, propertyExpression.getNamedProperty(), objectVariable);
}
OWLClassExpression filler = ce.getFiller();
if(filler.isAnonymous()){
@@ -299,7 +361,7 @@
filler.accept(this);
variables.pop();
} else {
- sparql += triple(objectVariable, "a", filler.asOWLClass().toStringID());
+ sparql += triple(objectVariable, "a", filler.asOWLClass());
}
sparql += "} GROUP BY " + subjectVariable + " HAVING(COUNT(" + objectVariable + ")>=" + cardinality + ")}";
@@ -315,9 +377,9 @@
sparql += "{SELECT " + subjectVariable + " WHERE {";
if(propertyExpression.isAnonymous()){
//property expression is inverse of a property
- sparql += triple(objectVariable, propertyExpression.getNamedProperty().toStringID(), subjectVariable);
+ sparql += triple(objectVariable, propertyExpression.getNamedProperty(), subjectVariable);
} else {
- sparql += triple(subjectVariable, propertyExpression.getNamedProperty().toStringID(), objectVariable);
+ sparql += triple(subjectVariable, propertyExpression.getNamedProperty(), objectVariable);
}
OWLClassExpression filler = ce.getFiller();
if(filler.isAnonymous()){
@@ -327,7 +389,7 @@
filler.accept(this);
variables.pop();
} else {
- sparql += triple(objectVariable, "a", filler.asOWLClass().toStringID());
+ sparql += triple(objectVariable, "a", filler.asOWLClass());
}
sparql += "} GROUP BY " + subjectVariable + " HAVING(COUNT(" + objectVariable + ")=" + cardinality + ")}";
@@ -342,9 +404,9 @@
sparql += "{SELECT " + subjectVariable + " WHERE {";
if(propertyExpression.isAnonymous()){
//property expression is inverse of a property
- sparql += triple(objectVariable, propertyExpression.getNamedProperty().toStringID(), subjectVariable);
+ sparql += triple(objectVariable, propertyExpression.getNamedProperty(), subjectVariable);
} else {
- sparql += triple(subjectVariable, propertyExpression.getNamedProperty().toStringID(), objectVariable);
+ sparql += triple(subjectVariable, propertyExpression.getNamedProperty(), objectVariable);
}
OWLClassExpression filler = ce.getFiller();
if(filler.isAnonymous()){
@@ -354,7 +416,7 @@
filler.accept(this);
variables.pop();
} else {
- sparql += triple(objectVariable, "a", filler.asOWLClass().toStringID());
+ sparql += triple(objectVariable, "a", filler.asOWLClass());
}
sparql += "} GROUP BY " + subjectVariable + " HAVING(COUNT(" + objectVariable + ")<=" + cardinality + ")}";
@@ -364,7 +426,7 @@
public void visit(OWLObjectHasSelf ce) {
String subject = variables.peek();
OWLObjectPropertyExpression property = ce.getProperty();
- sparql += triple(subject, property.getNamedProperty().toStringID(), subject);
+ sparql += triple(subject, property.getNamedProperty(), subject);
}
@Override
@@ -390,7 +452,7 @@
public void visit(OWLDataSomeValuesFrom ce) {
String objectVariable = buildIndividualVariable();
OWLDataPropertyExpression propertyExpression = ce.getProperty();
- sparql += triple(variables.peek(), propertyExpression.asOWLDataProperty().toStringID(), objectVariable);
+ sparql += triple(variables.peek(), propertyExpression.asOWLDataProperty(), objectVariable);
OWLDataRange filler = ce.getFiller();
variables.push(objectVariable);
filler.accept(this);
@@ -426,7 +488,7 @@
public void visit(OWLDataHasValue ce) {
OWLDataPropertyExpression propertyExpression = ce.getProperty();
OWLLiteral value = ce.getValue();
- sparql += triple(variables.peek(), propertyExpression.asOWLDataProperty().toStringID(), value);
+ sparql += triple(variables.peek(), propertyExpression.asOWLDataProperty(), value);
}
@Override
@@ -436,7 +498,7 @@
OWLDataPropertyExpression propertyExpression = ce.getProperty();
int cardinality = ce.getCardinality();
sparql += "{SELECT " + subjectVariable + " WHERE {";
- sparql += triple(subjectVariable, propertyExpression.asOWLDataProperty().toStringID(), objectVariable);
+ sparql += triple(subjectVariable, propertyExpression.asOWLDataProperty(), objectVariable);
OWLDataRange filler = ce.getFiller();
variables.push(objectVariable);
filler.accept(this);
@@ -452,7 +514,7 @@
OWLDataPropertyExpression propertyExpression = ce.getProperty();
int cardinality = ce.getCardinality();
sparql += "{SELECT " + subjectVariable + " WHERE {";
- sparql += triple(subjectVariable, propertyExpression.asOWLDataProperty().toStringID(), objectVariable);
+ sparql += triple(subjectVariable, propertyExpression.asOWLDataProperty(), objectVariable);
OWLDataRange filler = ce.getFiller();
variables.push(objectVariable);
filler.accept(this);
@@ -468,7 +530,7 @@
OWLDataPropertyExpression propertyExpression = ce.getProperty();
int cardinality = ce.getCardinality();
sparql += "{SELECT " + subjectVariable + " WHERE {";
- sparql += triple(subjectVariable, propertyExpression.asOWLDataProperty().toStringID(), objectVariable);
+ sparql += triple(subjectVariable, propertyExpression.asOWLDataProperty(), objectVariable);
OWLDataRange filler = ce.getFiller();
variables.push(objectVariable);
filler.accept(this);
@@ -642,6 +704,13 @@
query = converter.asQuery(rootVar, expr).toString();
System.out.println(expr + "\n" + query);
+ //variable entity
+ expr = df.getOWLObjectIntersectionOf(
+ df.getOWLObjectSomeValuesFrom(propR, clsB),
+ clsB);
+ query = converter.asQuery(rootVar, expr, Collections.singleton(propR)).toString();
+ System.out.println(expr + "\n" + query);
+
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
