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[DL-Learner SVN] SF.net SVN: dl-learner:[1682] trunk/src/dl-learner/org/dllearner
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From: <jen...@us...> - 2009-04-06 10:58:50
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Revision: 1682
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1682&view=rev
Author: jenslehmann
Date: 2009-04-06 10:58:30 +0000 (Mon, 06 Apr 2009)
Log Message:
-----------
fixed some problems detected by unit tests
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
trunk/src/dl-learner/org/dllearner/reasoning/FastRetrievalReasoner.java
trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
trunk/src/dl-learner/org/dllearner/test/junit/AllTestsRunner.java
trunk/src/dl-learner/org/dllearner/test/junit/ELDescriptionTreeTests.java
trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java
trunk/src/dl-learner/org/dllearner/test/junit/ReasonerTests.java
trunk/src/dl-learner/org/dllearner/test/junit/RefinementOperatorTests.java
trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java
trunk/src/dl-learner/org/dllearner/utilities/Helper.java
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2009-04-03 07:48:52 UTC (rev 1681)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastInstanceChecker.java 2009-04-06 10:58:30 UTC (rev 1682)
@@ -266,7 +266,7 @@
public boolean hasTypeImpl(Description description, Individual individual)
throws ReasoningMethodUnsupportedException {
-// System.out.println(description + " " + individual);
+// System.out.println("FIC: " + description + " " + individual);
if (description instanceof NamedClass) {
return classInstancesPos.get((NamedClass) description).contains(individual);
Modified: trunk/src/dl-learner/org/dllearner/reasoning/FastRetrievalReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/FastRetrievalReasoner.java 2009-04-03 07:48:52 UTC (rev 1681)
+++ trunk/src/dl-learner/org/dllearner/reasoning/FastRetrievalReasoner.java 2009-04-06 10:58:30 UTC (rev 1682)
@@ -1,3 +1,22 @@
+/**
+ * Copyright (C) 2007-2009, Jens Lehmann
+ *
+ * This file is part of DL-Learner.
+ *
+ * DL-Learner 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.
+ *
+ * DL-Learner 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/>.
+ *
+ */
package org.dllearner.reasoning;
import java.util.HashSet;
@@ -22,6 +41,13 @@
import org.dllearner.utilities.Helper;
import org.dllearner.utilities.datastructures.SortedSetTuple;
+/**
+ *
+ * Reasoner for fast retrieval inference (other tasks redirected to OWL API reasoner). Not actively used anymore.
+ *
+ * @author Jens Lehmann
+ *
+ */
public class FastRetrievalReasoner extends ReasonerComponent {
private FastRetrievalReasonerConfigurator configurator;
@@ -36,16 +62,13 @@
Set<ObjectProperty> atomicRoles;
SortedSet<Individual> individuals;
- ReasonerComponent rs;
ReasonerComponent rc;
-
-
public FastRetrievalReasoner(Set<KnowledgeSource> sources) {
super(sources);
this.configurator = new FastRetrievalReasonerConfigurator(this);
- rc = ComponentFactory.getDIGReasoner(sources);
+ rc = ComponentFactory.getOWLAPIReasoner(sources);
try {
rc.init();
} catch (ComponentInitException e1) {
@@ -57,7 +80,7 @@
individuals = rc.getIndividuals();
// rs = new ReasonerComponent(rc);
try {
- abox = Helper.createFlatABox(rs);
+ abox = Helper.createFlatABox(rc);
} catch (ReasoningMethodUnsupportedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
@@ -130,7 +153,7 @@
// Negation neg = new Negation(subConcept);
// Intersection c = new Intersection(neg,superConcept);
// return fastRetrieval.calculateSets(c).getPosSet().isEmpty();
- return rs.isSuperClassOf(superConcept, subConcept);
+ return rc.isSuperClassOf(superConcept, subConcept);
}
// @Override
@@ -154,7 +177,7 @@
@Override
public boolean isSatisfiableImpl() {
- return rs.isSatisfiable();
+ return rc.isSatisfiable();
}
@Override
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2009-04-03 07:48:52 UTC (rev 1681)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/RhoDRDown.java 2009-04-06 10:58:30 UTC (rev 1682)
@@ -185,6 +185,8 @@
public RhoDRDown(ReasonerComponent reasoningService) {
// this(reasoningService, reasoningService.getClassHierarchy(), null, true, true, true, true, true, 3, true, true, true, true, null);
this.rs = reasoningService;
+ this.subHierarchy = rs.getClassHierarchy();
+ init();
}
public RhoDRDown(ReasonerComponent reasoner, ClassHierarchy subHierarchy, Description startClass, RefinementOperatorConfigurator configurator) {
Modified: trunk/src/dl-learner/org/dllearner/test/junit/AllTestsRunner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/AllTestsRunner.java 2009-04-03 07:48:52 UTC (rev 1681)
+++ trunk/src/dl-learner/org/dllearner/test/junit/AllTestsRunner.java 2009-04-06 10:58:30 UTC (rev 1682)
@@ -48,7 +48,12 @@
JUnitCore.main("org.dllearner.test.junit.ComponentTests",
"org.dllearner.test.junit.ReasonerTests",
- "org.dllearner.test.junit.RefinementOperatorTests");
+ "org.dllearner.test.junit.RefinementOperatorTests",
+ "org.dllearner.test.junit.ELDescriptionTreeTests",
+ "org.dllearner.test.junit.ELDownTests",
+ "org.dllearner.test.junit.MinimizeTests",
+ "org.dllearner.test.junit.SimulationTests",
+ "org.dllearner.test.junit.UtilitiesTests");
}
}
Modified: trunk/src/dl-learner/org/dllearner/test/junit/ELDescriptionTreeTests.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/ELDescriptionTreeTests.java 2009-04-03 07:48:52 UTC (rev 1681)
+++ trunk/src/dl-learner/org/dllearner/test/junit/ELDescriptionTreeTests.java 2009-04-06 10:58:30 UTC (rev 1682)
@@ -85,7 +85,7 @@
ConceptTransformation.cleanConcept(d);
ELDescriptionTree tree = new ELDescriptionTree(rs, d);
// clone performance (false for simple unit test, true for clone performance test)
- boolean testPerformance = true;
+ boolean testPerformance = false;
ELDescriptionTree treeCloned = null;
if(testPerformance) {
int runs = 1000000;
Modified: trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java 2009-04-03 07:48:52 UTC (rev 1681)
+++ trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java 2009-04-06 10:58:30 UTC (rev 1682)
@@ -284,6 +284,7 @@
}
}
+ // not part of the regular test suite, since Galen 2 is required
// @Test
public void test4() throws ComponentInitException, ParseException, IOException {
@@ -312,6 +313,7 @@
}
+ // not part of the regular test suite, since Galen 2 is required
// @Test
public void asTest() throws ComponentInitException, MalformedURLException {
Modified: trunk/src/dl-learner/org/dllearner/test/junit/ReasonerTests.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/ReasonerTests.java 2009-04-03 07:48:52 UTC (rev 1681)
+++ trunk/src/dl-learner/org/dllearner/test/junit/ReasonerTests.java 2009-04-06 10:58:30 UTC (rev 1682)
@@ -39,8 +39,8 @@
import org.dllearner.kb.OWLFile;
import org.dllearner.parser.KBParser;
import org.dllearner.parser.ParseException;
+import org.dllearner.reasoning.DIGReasoner;
import org.dllearner.reasoning.FastInstanceChecker;
-import org.dllearner.reasoning.OWLAPIReasoner;
import org.junit.Test;
/**
@@ -78,8 +78,13 @@
* Performs an instance checks on all reasoner components to verify that
* they all return the correct result.
*/
-// @Test
+ @Test
public void instanceCheckTest() {
+
+ // DIG can be excluded from test since it requires a separate DIG reasoner and is no
+ // longer the default reasoning mechanism
+ boolean excludeDIG = true;
+
try {
ComponentManager cm = ComponentManager.getInstance();
KB kb = getSimpleKnowledgeBase();
@@ -91,6 +96,9 @@
Individual i = new Individual(KBParser.getInternalURI("stephen"));
List<Class<? extends ReasonerComponent>> reasonerClasses = cm.getReasonerComponents();
for (Class<? extends ReasonerComponent> reasonerClass : reasonerClasses) {
+ if(excludeDIG && reasonerClass.equals(DIGReasoner.class)) {
+ continue;
+ }
ReasonerComponent reasoner = cm.reasoner(reasonerClass, ks);
reasoner.init();
// long startTime = System.nanoTime();
@@ -116,7 +124,7 @@
* @throws ComponentInitException
* @throws ParseException
*/
-// @Test
+ @Test
public void fastInstanceCheckTest() throws ComponentInitException, ParseException {
String file = "examples/carcinogenesis/carcinogenesis.owl";
ComponentManager cm = ComponentManager.getInstance();
@@ -128,7 +136,7 @@
e.printStackTrace();
}
ks.init();
- ReasonerComponent reasoner = cm.reasoner(OWLAPIReasoner.class, ks);
+ ReasonerComponent reasoner = cm.reasoner(FastInstanceChecker.class, ks);
reasoner.init();
baseURI = reasoner.getBaseURI();
@@ -137,7 +145,7 @@
List<List<Individual>> negIndividuals = new LinkedList<List<Individual>>();
// TODO manually verify that the results are indeed correct
- testDescriptions.add(KBParser.parseConcept("\"http://dl-learner.org/carcinogenesis#Compound\" AND (\"http://dl-learner.org/carcinogenesis#amesTestPositive\" = true OR >= 2 \"http://dl-learner.org/carcinogenesis#hasStructure\" \"http://dl-learner.org/carcinogenesis#Ar_halide\"))"));
+ testDescriptions.add(KBParser.parseConcept("(\"http://dl-learner.org/carcinogenesis#Compound\" AND ((\"http://dl-learner.org/carcinogenesis#amesTestPositive\" IS TRUE) OR >= 2 \"http://dl-learner.org/carcinogenesis#hasStructure\".\"http://dl-learner.org/carcinogenesis#Ar_halide\"))"));
posIndividuals.add(getIndSet("d113","d133","d171","d262","d265","d294","d68","d77","d79"));
negIndividuals.add(getIndSet("d139","d199","d202","d203","d283","d42"));
@@ -150,16 +158,18 @@
List<Individual> neg = negIndividuals.get(i);
for(Individual ind : pos) {
+ System.out.println("description: " + description.toString(baseURI, null) + " individual: " + ind.toString(baseURI, null));
assertTrue(reasoner.hasType(description, ind));
}
for(Individual ind : neg) {
+ System.out.println("description: " + description.toString(baseURI, null) + " individual: " + ind.toString(baseURI, null));
assertTrue(!reasoner.hasType(description, ind));
}
}
}
-// @Test
+ @Test
public void fastInstanceCheck2() throws ComponentInitException, ParseException {
String file = "examples/epc/sap_epc.owl";
ComponentManager cm = ComponentManager.getInstance();
@@ -217,7 +227,8 @@
}
private String uri(String name) {
- return "\""+baseURI+name+"\"";
+// return "\""+baseURI+name+"\"";
+ return baseURI+name;
}
}
Modified: trunk/src/dl-learner/org/dllearner/test/junit/RefinementOperatorTests.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/RefinementOperatorTests.java 2009-04-03 07:48:52 UTC (rev 1681)
+++ trunk/src/dl-learner/org/dllearner/test/junit/RefinementOperatorTests.java 2009-04-06 10:58:30 UTC (rev 1682)
@@ -102,13 +102,13 @@
RhoDRDown op = new RhoDRDown(reasoner);
Description concept = KBParser.parseConcept("(\"http://localhost/aris/sap_model.owl#EPC\" AND EXISTS \"http://localhost/aris/sap_model.owl#hasModelElements\".\"http://localhost/aris/sap_model.owl#Object\")");
- Set<Description> results = op.refine(concept, 6);
+ Set<Description> results = op.refine(concept,10);
for(Description result : results) {
- System.out.println(result);
+ System.out.println(result.toString("http://localhost/aris/sap_model.owl#",null));
}
- int desiredResultSize = 141;
+ int desiredResultSize = 116;
if(results.size() != desiredResultSize) {
System.out.println(results.size() + " results found, but should be " + desiredResultSize + ".");
}
Modified: trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java 2009-04-03 07:48:52 UTC (rev 1681)
+++ trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java 2009-04-06 10:58:30 UTC (rev 1682)
@@ -122,10 +122,10 @@
KnowledgeSource source;
// parse KB string if one has been specified
- if(!kbString.isEmpty()) {
+ if(!kbString.isEmpty() || ont.equals(TestOntology.EMPTY)) {
KB kb = KBParser.parseKBFile(kbString);
source = new KBFile(kb);
- // parse OWL file otherwise
+ // do nothing for empty ontology
} else {
source = cm.knowledgeSource(OWLFile.class);
try {
Modified: trunk/src/dl-learner/org/dllearner/utilities/Helper.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/Helper.java 2009-04-03 07:48:52 UTC (rev 1681)
+++ trunk/src/dl-learner/org/dllearner/utilities/Helper.java 2009-04-06 10:58:30 UTC (rev 1682)
@@ -556,18 +556,22 @@
long dematStartTime = System.currentTimeMillis();
FlatABox aBox = new FlatABox(); // FlatABox.getInstance();
- for (NamedClass atomicConcept : rs.getNamedClasses()) {
- aBox.atomicConceptsPos.put(atomicConcept.getName(), getStringSet(rs
- .getIndividuals(atomicConcept)));
- Negation negatedAtomicConcept = new Negation(atomicConcept);
- aBox.atomicConceptsNeg.put(atomicConcept.getName(), getStringSet(rs
- .getIndividuals(negatedAtomicConcept)));
- aBox.concepts.add(atomicConcept.getName());
+ if(!rs.getNamedClasses().isEmpty()) {
+ for (NamedClass atomicConcept : rs.getNamedClasses()) {
+ aBox.atomicConceptsPos.put(atomicConcept.getName(), getStringSet(rs
+ .getIndividuals(atomicConcept)));
+ Negation negatedAtomicConcept = new Negation(atomicConcept);
+ aBox.atomicConceptsNeg.put(atomicConcept.getName(), getStringSet(rs
+ .getIndividuals(negatedAtomicConcept)));
+ aBox.concepts.add(atomicConcept.getName());
+ }
}
- for (ObjectProperty atomicRole : rs.getObjectProperties()) {
- aBox.rolesPos.put(atomicRole.getName(), getStringMap(rs.getPropertyMembers(atomicRole)));
- aBox.roles.add(atomicRole.getName());
+ if(!rs.getObjectProperties().isEmpty()) {
+ for (ObjectProperty atomicRole : rs.getObjectProperties()) {
+ aBox.rolesPos.put(atomicRole.getName(), getStringMap(rs.getPropertyMembers(atomicRole)));
+ aBox.roles.add(atomicRole.getName());
+ }
}
aBox.domain = getStringSet(rs.getIndividuals());
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