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[DL-Learner SVN] SF.net SVN: dl-learner: [637] trunk/src/dl-learner/org/dllearner
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From: <jen...@us...> - 2008-02-24 19:29:09
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Revision: 637
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=637&view=rev
Author: jenslehmann
Date: 2008-02-24 11:29:04 -0800 (Sun, 24 Feb 2008)
Log Message:
-----------
- prepared reasoner datatype support
- implemented getRoleMembers in OWL API reasoner - now fully DIG 1.1 compliant
- discovered another bug in OWL API export (adds an empty prefix)
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/refinement/RhoDown.java
trunk/src/dl-learner/org/dllearner/core/Reasoner.java
trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java
trunk/src/dl-learner/org/dllearner/core/ReasoningService.java
trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
trunk/src/dl-learner/org/dllearner/test/OWLAPIBugDemo.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/refinement/RhoDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/refinement/RhoDown.java 2008-02-24 17:49:30 UTC (rev 636)
+++ trunk/src/dl-learner/org/dllearner/algorithms/refinement/RhoDown.java 2008-02-24 19:29:04 UTC (rev 637)
@@ -550,6 +550,15 @@
}
m.put(3,m3);
}
+
+ // boolean datatypes, e.g. testPositive = true
+ if(useBooleanDatatypes) {
+// Set<Description> m3 = new TreeSet<Description>(conceptComparator);
+ // TODO: code for getting boolean datatypes
+// m.put(3,m3);
+ // TODO: do not use put here because we overwrite the
+ // EXISTS quantor stuff
+ }
}
if(maxLength>2) {
Modified: trunk/src/dl-learner/org/dllearner/core/Reasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/Reasoner.java 2008-02-24 17:49:30 UTC (rev 636)
+++ trunk/src/dl-learner/org/dllearner/core/Reasoner.java 2008-02-24 19:29:04 UTC (rev 637)
@@ -24,6 +24,7 @@
import java.util.Set;
import java.util.SortedSet;
+import org.dllearner.core.owl.DatatypeProperty;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Individual;
@@ -88,5 +89,11 @@
public Set<ObjectProperty> getAtomicRoles();
+ // currently, we do not require that datatype properties can be returned;
+ // the main reason is that DIG does not distinguish between datatype and
+ // object properties (of course one could implement it but it is not easy)
+ public Set<DatatypeProperty> getDatatypeProperties() throws ReasoningMethodUnsupportedException;
+
public SortedSet<Individual> getIndividuals();
+
}
Modified: trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java 2008-02-24 17:49:30 UTC (rev 636)
+++ trunk/src/dl-learner/org/dllearner/core/ReasonerComponent.java 2008-02-24 19:29:04 UTC (rev 637)
@@ -25,6 +25,7 @@
import java.util.SortedSet;
import java.util.TreeSet;
+import org.dllearner.core.owl.DatatypeProperty;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Individual;
@@ -120,4 +121,8 @@
throw new ReasoningMethodUnsupportedException();
}
+ public Set<DatatypeProperty> getDatatypeProperties() throws ReasoningMethodUnsupportedException {
+ throw new ReasoningMethodUnsupportedException();
+ }
+
}
Modified: trunk/src/dl-learner/org/dllearner/core/ReasoningService.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/ReasoningService.java 2008-02-24 17:49:30 UTC (rev 636)
+++ trunk/src/dl-learner/org/dllearner/core/ReasoningService.java 2008-02-24 19:29:04 UTC (rev 637)
@@ -486,6 +486,7 @@
// Reasoning-Resultate
// zur�ckgegeben werden k�nnten
private void handleExceptions(ReasoningMethodUnsupportedException e) {
+ e.printStackTrace();
throw new Error("Reasoning method not supported.");
}
Modified: trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2008-02-24 17:49:30 UTC (rev 636)
+++ trunk/src/dl-learner/org/dllearner/examples/Carcinogenesis.java 2008-02-24 19:29:04 UTC (rev 637)
@@ -196,8 +196,10 @@
}
// disjoint classes axioms
- DisjointClassesAxiom disjointAtomTypes = getDisjointClassesAxiom(atomTypes);
- kb.addAxiom(disjointAtomTypes);
+ // OWL API is also buggy here, it adds a strange unused prefix
+ // and cannot parser its own generated file
+// DisjointClassesAxiom disjointAtomTypes = getDisjointClassesAxiom(atomTypes);
+// kb.addAxiom(disjointAtomTypes);
// all different axiom (UNA)
// exporting differentIndividuals axioms is broken in OWL API
@@ -443,6 +445,7 @@
return new DoubleDatatypePropertyAssertion(dp, ind, value);
}
+ @SuppressWarnings({"unused"})
private static DisjointClassesAxiom getDisjointClassesAxiom(Set<String> classes) {
Set<Description> descriptions = new HashSet<Description>();
for(String namedClass : classes)
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-02-24 17:49:30 UTC (rev 636)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2008-02-24 19:29:04 UTC (rev 637)
@@ -35,6 +35,7 @@
import org.dllearner.core.ReasoningService;
import org.dllearner.core.config.ConfigEntry;
import org.dllearner.core.config.InvalidConfigOptionValueException;
+import org.dllearner.core.owl.DatatypeProperty;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.Intersection;
@@ -59,8 +60,8 @@
* model of the knowledge base (TODO: more explanation), which is neither correct nor
* complete, but sufficient in many cases. A big advantage of the algorithm is that it
* does not need even need to perform any set modifications (union, intersection, difference),
- * so it avoids any object creation, which makes it very fast compared to standard
- * reasoners (TODO: maybe add some benchmarks once it is implemented).
+ * so it avoids any Java object creation, which makes it extremely fast compared to standard
+ * reasoners.
*
* Note: This algorithm works only on concepts in negation normal form!
*
@@ -74,10 +75,11 @@
private Set<NamedClass> atomicConcepts;
private Set<ObjectProperty> atomicRoles;
+ private Set<DatatypeProperty> datatypeProperties;
private SortedSet<Individual> individuals;
private ReasoningService rs;
- private ReasonerComponent rc;
+ private OWLAPIReasoner rc;
private Set<KnowledgeSource> sources;
// we use sorted sets (map indices) here, because they have only log(n)
@@ -94,7 +96,6 @@
this.sources = sources;
}
-
/* (non-Javadoc)
* @see org.dllearner.core.Component#applyConfigEntry(org.dllearner.core.config.ConfigEntry)
*/
@@ -109,17 +110,10 @@
@Override
public void init() throws ComponentInitException {
rc = new OWLAPIReasoner(sources);
- // DIG will only be used to get the role pairs;
- // outside the constructor, OWL API will be used because
- // it is fast than DIG
- DIGReasoner rcDIG = new DIGReasoner(sources);
- try {
- rc.init();
- rcDIG.init();
- } catch (ComponentInitException e1) {
- e1.printStackTrace();
- }
+ rc.init();
+
atomicConcepts = rc.getAtomicConcepts();
+ datatypeProperties = rc.getDatatypeProperties();
atomicRoles = rc.getAtomicRoles();
individuals = rc.getIndividuals();
rs = new ReasoningService(rc);
@@ -135,7 +129,7 @@
}
for (ObjectProperty atomicRole : rs.getAtomicRoles()) {
- opPos.put(atomicRole, rcDIG.getRoleMembers(atomicRole));
+ opPos.put(atomicRole, rc.getRoleMembers(atomicRole));
}
long dematDuration = System.currentTimeMillis() - dematStartTime;
@@ -233,6 +227,11 @@
return atomicRoles;
}
+ @Override
+ public Set<DatatypeProperty> getDatatypeProperties() {
+ return datatypeProperties;
+ }
+
/* (non-Javadoc)
* @see org.dllearner.core.Reasoner#getIndividuals()
*/
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-02-24 17:49:30 UTC (rev 636)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-02-24 19:29:04 UTC (rev 637)
@@ -27,6 +27,7 @@
import java.util.Comparator;
import java.util.HashSet;
import java.util.LinkedList;
+import java.util.Map;
import java.util.Set;
import java.util.SortedSet;
import java.util.TreeMap;
@@ -42,6 +43,7 @@
import org.dllearner.core.config.StringConfigOption;
import org.dllearner.core.owl.AssertionalAxiom;
import org.dllearner.core.owl.ClassAssertionAxiom;
+import org.dllearner.core.owl.DatatypeProperty;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.EquivalentClassesAxiom;
import org.dllearner.core.owl.FunctionalObjectPropertyAxiom;
@@ -76,6 +78,7 @@
import org.semanticweb.owl.model.OWLAxiom;
import org.semanticweb.owl.model.OWLClass;
import org.semanticweb.owl.model.OWLDataFactory;
+import org.semanticweb.owl.model.OWLDataProperty;
import org.semanticweb.owl.model.OWLDescription;
import org.semanticweb.owl.model.OWLIndividual;
import org.semanticweb.owl.model.OWLNamedObject;
@@ -120,6 +123,8 @@
// primitives
Set<NamedClass> atomicConcepts = new TreeSet<NamedClass>(conceptComparator);
Set<ObjectProperty> atomicRoles = new TreeSet<ObjectProperty>(roleComparator);
+ Set<DatatypeProperty> datatypeProperties = new TreeSet<DatatypeProperty>();
+// Set<DatatypeProperty> datatypeProperties = new TreeSet<DatatypeProperty>();
SortedSet<Individual> individuals = new TreeSet<Individual>();
public OWLAPIReasoner(Set<KnowledgeSource> sources) {
@@ -164,7 +169,8 @@
}
};
Set<OWLClass> classes = new TreeSet<OWLClass>(namedObjectComparator);
- Set<OWLObjectProperty> properties = new TreeSet<OWLObjectProperty>(namedObjectComparator);
+ Set<OWLObjectProperty> owlObjectProperties = new TreeSet<OWLObjectProperty>(namedObjectComparator);
+ Set<OWLDataProperty> owlDatatypeProperties = new TreeSet<OWLDataProperty>(namedObjectComparator);
Set<OWLIndividual> owlIndividuals = new TreeSet<OWLIndividual>(namedObjectComparator);
Set<OWLOntology> allImports = new HashSet<OWLOntology>();
@@ -178,7 +184,8 @@
OWLOntology ontology = manager.loadOntologyFromPhysicalURI(url.toURI());
allImports.addAll(manager.getImportsClosure(ontology));
classes.addAll(ontology.getReferencedClasses());
- properties.addAll(ontology.getReferencedObjectProperties());
+ owlObjectProperties.addAll(ontology.getReferencedObjectProperties());
+ owlDatatypeProperties.addAll(ontology.getReferencedDataProperties());
owlIndividuals.addAll(ontology.getReferencedIndividuals());
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
@@ -202,7 +209,8 @@
allImports.add(ontology);
atomicConcepts.addAll(kb.findAllAtomicConcepts());
atomicRoles.addAll(kb.findAllAtomicRoles());
- individuals.addAll(kb.findAllIndividuals());
+ individuals.addAll(kb.findAllIndividuals());
+ // TODO: add method to find datatypes
}
}
@@ -264,11 +272,18 @@
// read in primitives
for(OWLClass owlClass : classes)
atomicConcepts.add(new NamedClass(owlClass.getURI().toString()));
- for(OWLObjectProperty owlProperty : properties)
+ for(OWLObjectProperty owlProperty : owlObjectProperties)
atomicRoles.add(new ObjectProperty(owlProperty.getURI().toString()));
+ for(OWLDataProperty owlProperty : owlDatatypeProperties) {
+ // empty ranges are returned for ames test positive
+// Set<OWLDataRange> ranges = owlProperty.getRanges(allImports);
+// System.out.println(owlProperty);
+// System.out.println(ranges);
+ datatypeProperties.add(new DatatypeProperty(owlProperty.getURI().toString()));
+ System.exit(0);
+ }
for(OWLIndividual owlIndividual : owlIndividuals)
individuals.add(new Individual(owlIndividual.getURI().toString()));
-
}
/* (non-Javadoc)
@@ -285,6 +300,11 @@
return atomicRoles;
}
+ @Override
+ public Set<DatatypeProperty> getDatatypeProperties() {
+ return datatypeProperties;
+ }
+
/* (non-Javadoc)
* @see org.dllearner.core.Reasoner#getIndividuals()
*/
@@ -482,6 +502,31 @@
}
}
+ @Override
+ public Map<Individual, SortedSet<Individual>> getRoleMembers(ObjectProperty atomicRole) {
+ OWLObjectProperty prop = getOWLAPIDescription(atomicRole);
+ Map<Individual, SortedSet<Individual>> map = new TreeMap<Individual, SortedSet<Individual>>();
+ for(Individual i : individuals) {
+ OWLIndividual ind = factory.getOWLIndividual(URI.create(i.getName()));
+
+ // get all related individuals via OWL API
+ Set<OWLIndividual> inds = null;
+ try {
+ inds = reasoner.getRelatedIndividuals(ind, prop);
+ } catch (OWLReasonerException e) {
+ e.printStackTrace();
+ }
+
+ // convert data back to DL-Learner structures
+ SortedSet<Individual> is = new TreeSet<Individual>();
+ for(OWLIndividual oi : inds)
+ is.add(new Individual(oi.getURI().toString()));
+ map.put(i, is);
+ }
+ return map;
+ }
+
+
// OWL API often returns a set of sets of classes, where each inner
// set consists of equivalent classes; this method picks one class
// from each inner set to flatten the set of sets
@@ -561,8 +606,7 @@
}
}
- @Deprecated
- public static OWLObjectProperty getOWLAPIDescription(ObjectProperty role) {
+ private static OWLObjectProperty getOWLAPIDescription(ObjectProperty role) {
return staticFactory.getOWLObjectProperty(URI.create(role.getName()));
}
Modified: trunk/src/dl-learner/org/dllearner/test/OWLAPIBugDemo.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/OWLAPIBugDemo.java 2008-02-24 17:49:30 UTC (rev 636)
+++ trunk/src/dl-learner/org/dllearner/test/OWLAPIBugDemo.java 2008-02-24 19:29:04 UTC (rev 637)
@@ -24,15 +24,31 @@
OWLOntology ontology = manager.createOntology(ontologyURI);
OWLDataFactory factory = manager.getOWLDataFactory();
+ // create a set of two individuals
OWLIndividual a = factory.getOWLIndividual(URI.create(ontologyURI + "#a"));
OWLIndividual b = factory.getOWLIndividual(URI.create(ontologyURI + "#b"));
Set<OWLIndividual> inds = new HashSet<OWLIndividual>();
inds.add(a);
inds.add(b);
+ // create a set of two classes
+ OWLClass c = factory.getOWLClass(URI.create(ontologyURI + "#c"));
+ OWLClass d = factory.getOWLClass(URI.create(ontologyURI + "#d"));
+ Set<OWLClass> classes = new HashSet<OWLClass>();
+ classes.add(c);
+ classes.add(d);
+
+ // state that a and b are different
OWLAxiom axiom = factory.getOWLDifferentIndividualsAxiom(inds);
AddAxiom addAxiom = new AddAxiom(ontology, axiom);
manager.applyChange(addAxiom);
+
+ // state that c and d are disjoint
+ OWLAxiom axiom2 = factory.getOWLDisjointClassesAxiom(classes);
+ AddAxiom addAxiom2 = new AddAxiom(ontology, axiom2);
+ manager.applyChange(addAxiom2);
+
+ // save ontology
manager.saveOntology(ontology);
}
catch (OWLException e) {
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