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From: <lor...@us...> - 2013-06-28 11:54:20
|
Revision: 4010
http://sourceforge.net/p/dl-learner/code/4010
Author: lorenz_b
Date: 2013-06-28 11:54:18 +0000 (Fri, 28 Jun 2013)
Log Message:
-----------
Omit timeout in single query mode for now til pagination in Cluas' API is fixed.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalDataPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.java
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/InverseFunctionalObjectPropertyAxiomLearner.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalDataPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalDataPropertyAxiomLearner.java 2013-06-28 11:53:26 UTC (rev 4009)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalDataPropertyAxiomLearner.java 2013-06-28 11:54:18 UTC (rev 4010)
@@ -135,7 +135,7 @@
}
private void runSPARQL1_1_Mode() {
- int numberOfSubjects = reasoner.getSubjectCountForProperty(propertyToDescribe, getRemainingRuntimeInMilliSeconds());
+ int numberOfSubjects = reasoner.getSubjectCountForProperty(propertyToDescribe);//TODO, getRemainingRuntimeInMilliSeconds());
if(numberOfSubjects == -1){
logger.warn("Early termination: Got timeout while counting number of distinct subjects for given property.");
return;
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.java 2013-06-28 11:53:26 UTC (rev 4009)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/FunctionalObjectPropertyAxiomLearner.java 2013-06-28 11:54:18 UTC (rev 4010)
@@ -137,7 +137,7 @@
private void runSPARQL1_1_Mode() {
// get number of instances of s with <s p o>
- int numberOfSubjects = reasoner.getSubjectCountForProperty(propertyToDescribe, getRemainingRuntimeInMilliSeconds());
+ int numberOfSubjects = reasoner.getSubjectCountForProperty(propertyToDescribe);//TODO, getRemainingRuntimeInMilliSeconds());
if(numberOfSubjects == -1){
logger.warn("Early termination: Got timeout while counting number of distinct subjects for given property.");
return;
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/InverseFunctionalObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/InverseFunctionalObjectPropertyAxiomLearner.java 2013-06-28 11:53:26 UTC (rev 4009)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/InverseFunctionalObjectPropertyAxiomLearner.java 2013-06-28 11:54:18 UTC (rev 4010)
@@ -136,7 +136,7 @@
private void runSPARQL1_1_Mode() {
// get number of instances of s with <s p o>
- int numberOfObjects = reasoner.getObjectCountForProperty(propertyToDescribe, getRemainingRuntimeInMilliSeconds());
+ int numberOfObjects = reasoner.getObjectCountForProperty(propertyToDescribe);//TODO, getRemainingRuntimeInMilliSeconds());
if(numberOfObjects == -1){
logger.warn("Early termination: Got timeout while counting number of distinct objects for given property.");
return;
@@ -164,12 +164,12 @@
}
public static void main(String[] args) throws Exception{
- SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpediaLiveAKSW());
+ SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpedia());
InverseFunctionalObjectPropertyAxiomLearner l = new InverseFunctionalObjectPropertyAxiomLearner(ks);
l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/profession"));
l.setMaxExecutionTimeInSeconds(10);
l.init();
- l.setForceSPARQL_1_0_Mode(true);
+// l.setForceSPARQL_1_0_Mode(true);
l.start();
System.out.println(l.getCurrentlyBestEvaluatedAxioms(1));
}
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|
|
From: <lor...@us...> - 2013-06-28 11:53:30
|
Revision: 4009
http://sourceforge.net/p/dl-learner/code/4009
Author: lorenz_b
Date: 2013-06-28 11:53:26 +0000 (Fri, 28 Jun 2013)
Log Message:
-----------
Added methods without timeout.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-06-28 08:47:48 UTC (rev 4008)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-06-28 11:53:26 UTC (rev 4009)
@@ -214,7 +214,20 @@
return cnt;
}
+
+ public int getSubjectCountForProperty(Property p){
+ int cnt = -1;
+ String query = String.format(
+ "SELECT (COUNT(DISTINCT ?s) AS ?cnt) WHERE {?s <%s> ?o.}",
+ p.getName());
+ ResultSet rs = executeSelectQuery(query);
+ if(rs.hasNext()){
+ cnt = rs.next().getLiteral("cnt").getInt();
+ }
+ return cnt;
+ }
+
public int getObjectCountForProperty(ObjectProperty p, long timeout){
int cnt = -1;
String query = String.format(
@@ -227,7 +240,20 @@
return cnt;
}
+
+ public int getObjectCountForProperty(ObjectProperty p){
+ int cnt = -1;
+ String query = String.format(
+ "SELECT (COUNT(DISTINCT ?o) AS ?cnt) WHERE {?s <%s> ?o.}",
+ p.getName());
+ ResultSet rs = executeSelectQuery(query);
+ if(rs.hasNext()){
+ cnt = rs.next().getLiteral("cnt").getInt();
+ }
+ return cnt;
+ }
+
public int getPopularity(NamedClass nc){
if(classPopularityMap != null && classPopularityMap.containsKey(nc)){
return classPopularityMap.get(nc);
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|
|
From: <lor...@us...> - 2013-06-28 08:47:52
|
Revision: 4008
http://sourceforge.net/p/dl-learner/code/4008
Author: lorenz_b
Date: 2013-06-28 08:47:48 +0000 (Fri, 28 Jun 2013)
Log Message:
-----------
Catch timeout exception.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/properties/InverseObjectPropertyAxiomLearner.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/properties/InverseObjectPropertyAxiomLearner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/properties/InverseObjectPropertyAxiomLearner.java 2013-06-27 18:48:26 UTC (rev 4007)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/properties/InverseObjectPropertyAxiomLearner.java 2013-06-28 08:47:48 UTC (rev 4008)
@@ -42,7 +42,7 @@
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
-@ComponentAnn(name="inverse objectproperty domain axiom learner", shortName="oplinv", version=0.1)
+@ComponentAnn(name="inverse objectproperty axiom learner", shortName="oplinv", version=0.1)
public class InverseObjectPropertyAxiomLearner extends AbstractAxiomLearningAlgorithm {
private static final Logger logger = LoggerFactory.getLogger(InverseObjectPropertyAxiomLearner.class);
@@ -78,7 +78,7 @@
}
if(!forceSPARQL_1_0_Mode && ks.supportsSPARQL_1_1()){
- runSingleQueryMode();
+ runSPARQL1_1_Mode();
} else {
runSPARQL1_0_Mode();
}
@@ -157,12 +157,12 @@
}
public static void main(String[] args) throws Exception{
- SparqlEndpointKS ks = new SparqlEndpointKS(new SparqlEndpoint(new URL("http://[2001:638:902:2010:0:168:35:138]/sparql")));
+ SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpediaLiveAKSW());
InverseObjectPropertyAxiomLearner l = new InverseObjectPropertyAxiomLearner(ks);
- l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/animal"));
- l.setMaxExecutionTimeInSeconds(10);
- l.setForceSPARQL_1_0_Mode(true);
+ l.setPropertyToDescribe(new ObjectProperty("http://dbpedia.org/ontology/routeEnd"));
+ l.setMaxExecutionTimeInSeconds(60);
+// l.setForceSPARQL_1_0_Mode(true);
// l.setReturnOnlyNewAxioms(true);
l.init();
l.start();
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|
|
From: <lor...@us...> - 2013-06-27 18:48:28
|
Revision: 4007
http://sourceforge.net/p/dl-learner/code/4007
Author: lorenz_b
Date: 2013-06-27 18:48:26 +0000 (Thu, 27 Jun 2013)
Log Message:
-----------
Added method to get classes filtered by namespace remotely.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-06-27 18:47:37 UTC (rev 4006)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-06-27 18:48:26 UTC (rev 4007)
@@ -504,6 +504,18 @@
}
return types;
}
+
+ public Set<NamedClass> getOWLClasses(String namespace) {
+ Set<NamedClass> types = new HashSet<NamedClass>();
+ String query = String.format("SELECT DISTINCT ?class WHERE {?class a <%s>. FILTER(REGEX(?class,'%s'))}",OWL.Class.getURI(), namespace);
+ ResultSet rs = executeSelectQuery(query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ types.add(new NamedClass(qs.getResource("class").getURI()));
+ }
+ return types;
+ }
/**
* Returns a set of classes which are siblings, i.e. on the same level
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|
|
From: <lor...@us...> - 2013-06-27 18:47:39
|
Revision: 4006
http://sourceforge.net/p/dl-learner/code/4006
Author: lorenz_b
Date: 2013-06-27 18:47:37 +0000 (Thu, 27 Jun 2013)
Log Message:
-----------
Updated enrichment script.
Modified Paths:
--------------
trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2013-06-27 18:31:00 UTC (rev 4005)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2013-06-27 18:47:37 UTC (rev 4006)
@@ -341,7 +341,7 @@
// loop over all entities and call appropriate algorithms
- Set<NamedClass> classes = reasoner.getTypes();//st.getAllClasses();
+ Set<NamedClass> classes = allowedNamespaces.isEmpty() ? reasoner.getOWLClasses() : reasoner.getOWLClasses(allowedNamespaces.iterator().next());//st.getAllClasses();
filterByNamespaces(classes);//classes = Sets.newHashSet(new NamedClass("http://dbpedia.org/ontology/Arachnid"));
int entities = 0;
for(NamedClass nc : classes) {
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|
From: <lor...@us...> - 2013-06-27 18:31:02
|
Revision: 4005
http://sourceforge.net/p/dl-learner/code/4005
Author: lorenz_b
Date: 2013-06-27 18:31:00 +0000 (Thu, 27 Jun 2013)
Log Message:
-----------
Updated enrichment script.
Modified Paths:
--------------
trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2013-06-21 13:36:20 UTC (rev 4004)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2013-06-27 18:31:00 UTC (rev 4005)
@@ -52,13 +52,13 @@
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
+import java.util.Set;
+import java.util.SortedSet;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;
-import java.util.Set;
-import java.util.SortedSet;
import joptsimple.OptionException;
import joptsimple.OptionParser;
@@ -66,8 +66,6 @@
import joptsimple.OptionSpec;
import org.aksw.commons.jena_owlapi.Conversion;
-import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
-import org.apache.jena.riot.Lang;
import org.apache.jena.riot.checker.CheckerLiterals;
import org.apache.jena.riot.system.ErrorHandlerFactory;
import org.apache.log4j.ConsoleAppender;
@@ -75,7 +73,7 @@
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
import org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxOntologyFormat;
-import org.coode.owlapi.turtle.TurtleOntologyFormat;
+import org.dllearner.algorithms.DisjointClassesLearner;
import org.dllearner.algorithms.celoe.CELOE;
import org.dllearner.algorithms.properties.AsymmetricObjectPropertyAxiomLearner;
import org.dllearner.algorithms.properties.DataPropertyDomainAxiomLearner;
@@ -158,9 +156,7 @@
import com.clarkparsia.owlapiv3.XSD;
import com.google.common.collect.Sets;
-import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.query.ResultSetFormatter;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
@@ -306,7 +302,7 @@
dataPropertyAlgorithms.add(SubDataPropertyOfAxiomLearner.class);
classAlgorithms = new LinkedList<Class<? extends LearningAlgorithm>>();
-// classAlgorithms.add(DisjointClassesLearner.class);
+ classAlgorithms.add(DisjointClassesLearner.class);
// classAlgorithms.add(SimpleSubclassLearner.class);
classAlgorithms.add(CELOE.class);
@@ -359,26 +355,26 @@
break;
}
}
-// entities = 0;
-// Set<ObjectProperty> objectProperties = st.getAllObjectProperties();
-// filterByNamespaces(objectProperties);
-// for(ObjectProperty property : objectProperties) {
-// runObjectPropertyAlgorithms(ks, property);
-// entities++;
-// if(maxEntitiesPerType != -1 && entities > maxEntitiesPerType) {
-// break;
-// }
-// }
-// entities = 0;
-// Set<DatatypeProperty> dataProperties = st.getAllDataProperties();
-// filterByNamespaces(dataProperties);
-// for(DatatypeProperty property : dataProperties) {
-// runDataPropertyAlgorithms(ks, property);
-// entities++;
-// if(maxEntitiesPerType != -1 && entities > maxEntitiesPerType) {
-// break;
-// }
-// }
+ entities = 0;
+ Set<ObjectProperty> objectProperties = st.getAllObjectProperties();
+ filterByNamespaces(objectProperties);
+ for(ObjectProperty property : objectProperties) {
+ runObjectPropertyAlgorithms(ks, property);
+ entities++;
+ if(maxEntitiesPerType != -1 && entities > maxEntitiesPerType) {
+ break;
+ }
+ }
+ entities = 0;
+ Set<DatatypeProperty> dataProperties = st.getAllDataProperties();
+ filterByNamespaces(dataProperties);
+ for(DatatypeProperty property : dataProperties) {
+ runDataPropertyAlgorithms(ks, property);
+ entities++;
+ if(maxEntitiesPerType != -1 && entities > maxEntitiesPerType) {
+ break;
+ }
+ }
} else {
if(resource instanceof ObjectProperty) {
System.out.println(resource + " appears to be an object property. Running appropriate algorithms.\n");
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|
From: <lor...@us...> - 2013-06-21 13:36:23
|
Revision: 4004
http://sourceforge.net/p/dl-learner/code/4004
Author: lorenz_b
Date: 2013-06-21 13:36:20 +0000 (Fri, 21 Jun 2013)
Log Message:
-----------
Added namespace filter.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-06-18 15:14:54 UTC (rev 4003)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-06-21 13:36:20 UTC (rev 4004)
@@ -94,7 +94,6 @@
@ConfigOption(name = "useCache", description = "Whether to use a DB cache", defaultValue = "true", required = false, propertyEditorClass = BooleanEditor.class)
private boolean useCache = true;
- private ExtractionDBCache cache;
private QueryExecutionFactory qef;
private SparqlEndpointKS ks;
@@ -111,18 +110,11 @@
public SPARQLReasoner(SparqlEndpointKS ks) {
- this.ks = ks;
-
- if(useCache){
- cache = new ExtractionDBCache("cache");
- }
- classPopularityMap = new HashMap<NamedClass, Integer>();
- objectPropertyPopularityMap = new HashMap<ObjectProperty, Integer>();
+ this(ks, (String)null);
}
-
- public SPARQLReasoner(SparqlEndpointKS ks, ExtractionDBCache cache) {
+
+ public SPARQLReasoner(SparqlEndpointKS ks, String cacheDirectory) {
this.ks = ks;
- this.cache = cache;
classPopularityMap = new HashMap<NamedClass, Integer>();
objectPropertyPopularityMap = new HashMap<ObjectProperty, Integer>();
@@ -130,10 +122,10 @@
if(ks.isRemote()){
SparqlEndpoint endpoint = ks.getEndpoint();
qef = new QueryExecutionFactoryHttp(endpoint.getURL().toString(), endpoint.getDefaultGraphURIs());
- if(cache != null){
+ if(cacheDirectory != null){
try {
long timeToLive = TimeUnit.DAYS.toMillis(30);
- CacheCoreEx cacheBackend = CacheCoreH2.create(cache.getCacheDirectory(), timeToLive, true);
+ CacheCoreEx cacheBackend = CacheCoreH2.create(cacheDirectory, timeToLive, true);
CacheEx cacheFrontend = new CacheExImpl(cacheBackend);
qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
} catch (ClassNotFoundException e) {
@@ -149,6 +141,10 @@
}
}
+ public SPARQLReasoner(SparqlEndpointKS ks, ExtractionDBCache cache) {
+ this(ks, cache.getCacheDirectory());
+ }
+
public SPARQLReasoner(OntModel model) {
this.model = model;
@@ -1410,7 +1406,7 @@
}
public void setCache(ExtractionDBCache cache) {
- this.cache = cache;
+// this.cache = cache;
}
public void setUseCache(boolean useCache) {
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From: <dc...@us...> - 2013-06-18 15:15:01
|
Revision: 4003
http://sourceforge.net/p/dl-learner/code/4003
Author: dcherix
Date: 2013-06-18 15:14:54 +0000 (Tue, 18 Jun 2013)
Log Message:
-----------
Added examples for the sparqr webapp
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/kb/sparql/simple/ABoxQueryGenerator.java
trunk/examples/sparql/AristotlePosNeg.conf
trunk/interfaces/pom.xml
trunk/interfaces/src/main/java/org/dllearner/server/Rest.java
Added Paths:
-----------
trunk/examples/sparqr/
trunk/examples/sparqr/AristotlePosNeg.conf
trunk/examples/sparqr/StGeorge.conf
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/simple/ABoxQueryGenerator.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/simple/ABoxQueryGenerator.java 2013-06-17 10:35:31 UTC (rev 4002)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/simple/ABoxQueryGenerator.java 2013-06-18 15:14:54 UTC (rev 4003)
@@ -26,7 +26,7 @@
if (aboxfilter != null) {
builder.append(aboxfilter);
}
- builder.append("FILTER (! (?p=rdf:type))");
+ builder.append("FILTER ( (?p!=rdf:type))");
builder.append("}");
monABoxQueryGeneration.stop();
return builder.toString();
Modified: trunk/examples/sparql/AristotlePosNeg.conf
===================================================================
--- trunk/examples/sparql/AristotlePosNeg.conf 2013-06-17 10:35:31 UTC (rev 4002)
+++ trunk/examples/sparql/AristotlePosNeg.conf 2013-06-18 15:14:54 UTC (rev 4003)
@@ -11,7 +11,7 @@
// SPARQL options
sparql.type = "SPARQL endpoint fragment"
-sparql.url = "http://dbpedia.openlinksw.com:8890/sparql"
+sparql.url = "http://dbpedia.org/sparql"
sparql.defaultGraphURIs = {"http://dbpedia.org"}
sparql.recursionDepth = 1
//TODOREFACTOR check if predefinedFilter works at all
@@ -29,8 +29,8 @@
reasoner.type = "fast instance checker"
reasoner.sources = {sparql}
+reasoner.forAllSemantics="SomeOnly"
-
// we want to learn from positive and negative examples
lp.type = "posNegStandard"
lp.positiveExamples = {
Added: trunk/examples/sparqr/AristotlePosNeg.conf
===================================================================
--- trunk/examples/sparqr/AristotlePosNeg.conf (rev 0)
+++ trunk/examples/sparqr/AristotlePosNeg.conf 2013-06-18 15:14:54 UTC (rev 4003)
@@ -0,0 +1,107 @@
+/**
+ * Some people from Greece.
+ * Note: DBpedia is always subject to change, solutions will change over time
+
+ * Possible Solution:
+ * Theorist OR (Mathematician AND Physicist)
+ */
+
+
+/******************
+ * SPARQL options *
+ ******************/
+// sparql component to use
+sparql.type = "sparqls"
+// endpoint
+sparql.endpointURL = "http://dbpedia.org/sparql"
+// default graph uri for the SPARQL queries
+sparql.defaultGraphURI = "http://dbpedia.org"
+// recursion depth
+sparql.recursionDepth = 2
+// url(s) of the schema definition of the used ontologies.
+sparql.ontologySchemaUrls = {"http://downloads.dbpedia.org/3.6/dbpedia_3.6.owl" }
+
+//SPARQL Filters for the instances. Those filters excludes all literals, and all Catergory instances. Thereto a instance must begin with http://dbpedia.org/Resource
+sparql.aboxfilter = "FILTER (
+!isLiteral(?o) &&
+!regex(str(?p), 'http://dbpedia.org/property/website') &&
+!regex(str(?p), 'http://dbpedia.org/property/wikipage') &&
+!regex(str(?p), 'http://dbpedia.org/property/wikiPageUsesTemplate') &&
+!regex(str(?p), 'http://dbpedia.org/property/reference') &&
+!regex(str(?p), 'http://www.w3.org/2004/02/skos/core') &&
+!regex(str(?p), 'http://www.w3.org/2002/07/owl#sameAs') &&
+!regex(str(?p), 'http://xmlns.com/foaf/0.1/') &&
+!regex(str(?p), 'http://dbpedia.org/property/wordnet_type') &&
+!regex(str(?p), 'http://dbpedia.org/property/wikilink') &&
+regex(str(?o), '^http://dbpedia.org/resource/') &&
+!regex(str(?o),'^http://dbpedia.org/resource/Category:')
+) "
+// SPARQL Filters for the classes. With this filter only class in the dbpedia ontology are accepted and at example not from YAGO
+sparql.tboxfilter = "FILTER ( !regex(str(?class), '^http://upload.wikimedia.org/wikipedia') &&
+!regex(str(?class), '^http://dbpedia.org/resource/Template') &&
+!regex(str(?class), '^http://dbpedia.org/resource/Category:') &&
+!regex(str(?class), '^http://umbel.org/umbel/')
+ ) . "
+
+//A list of the start instances
+sparql.instances = {
+"http://dbpedia.org/resource/Democritus",
+"http://dbpedia.org/resource/Zeno_of_Elea",
+"http://dbpedia.org/resource/Plato",
+"http://dbpedia.org/resource/Socrates",
+"http://dbpedia.org/resource/Archytas",
+"http://dbpedia.org/resource/Pythagoras",
+"http://dbpedia.org/resource/Archimedes",
+"http://dbpedia.org/resource/EuClid",
+"http://dbpedia.org/resource/Heraclitus"
+}
+
+/********************
+ * Reasoner options *
+ ********************/
+reasoner.type = "fast instance checker"
+reasoner.sources = {sparql}
+reasoner.forAllSemantics="Standard"
+
+/*****************************
+ * Learning problems options *
+ *****************************/
+// we want to learn from positive and negative examples
+lp.type = "posNegStandard"
+
+//the positives examples
+lp.positiveExamples = {
+"http://dbpedia.org/resource/Archytas",
+"http://dbpedia.org/resource/Pythagoras",
+"http://dbpedia.org/resource/Archimedes",
+"http://dbpedia.org/resource/Thales"
+}
+
+//the negatives examples
+lp.negativeExamples = {
+"http://dbpedia.org/resource/Democritus",
+"http://dbpedia.org/resource/Zeno_of_Elea",
+"http://dbpedia.org/resource/Plato",
+"http://dbpedia.org/resource/Socrates",
+"http://dbpedia.org/resource/EuClid",
+"http://dbpedia.org/resource/Heraclitus"
+}
+lp.reasoner = reasoner
+
+/*******************************
+ * refinement operator options *
+ *******************************/
+
+// create a refinement operator and configure it
+op.type = "rho"
+op.useHasValueConstructor = true
+op.reasoner = reasoner
+
+/***************************
+ * learn algorithm options *
+ ***************************/
+// we use the OCEL algorithm
+alg.type = "ocel"
+alg.reasoner = reasoner
+
+
Added: trunk/examples/sparqr/StGeorge.conf
===================================================================
--- trunk/examples/sparqr/StGeorge.conf (rev 0)
+++ trunk/examples/sparqr/StGeorge.conf 2013-06-18 15:14:54 UTC (rev 4003)
@@ -0,0 +1,151 @@
+
+
+/******************
+ * SPARQL options *
+ ******************/
+// sparql component to use
+sparql.type = "sparqls"
+// endpoint
+sparql.endpointURL = "http://dbpedia.org/sparql"
+// default graph uri for the SPARQL queries
+sparql.defaultGraphURI = "http://dbpedia.org"
+// recursion depth
+sparql.recursionDepth = 2
+// url(s) of the schema definition of the used ontologies.
+sparql.ontologySchemaUrls = {"http://downloads.dbpedia.org/3.6/dbpedia_3.6.owl" }
+
+sparql.aboxfilter = "FILTER (
+!isLiteral(?o) &&
+!regex(str(?p), 'http://dbpedia.org/property/website') &&
+!regex(str(?p), 'http://dbpedia.org/property/wikipage') &&
+!regex(str(?p), 'http://dbpedia.org/property/wikiPageUsesTemplate') &&
+!regex(str(?p), 'http://dbpedia.org/property/reference') &&
+!regex(str(?p), 'http://www.w3.org/2004/02/skos/core') &&
+!regex(str(?p), 'http://www.w3.org/2002/07/owl#sameAs') &&
+!regex(str(?p), 'http://xmlns.com/foaf/0.1/') &&
+!regex(str(?p), 'http://dbpedia.org/property/wordnet_type') &&
+!regex(str(?p), 'http://dbpedia.org/property/wikilink') &&
+regex(str(?o), '^http://dbpedia.org/resource/')
+) "
+
+sparql.tboxfilter = "FILTER ( !regex(str(?class), '^http://upload.wikimedia.org/wikipedia') &&
+!regex(str(?class), '^http://dbpedia.org/resource/Template') &&
+!regex(str(?class), '^http://dbpedia.org/resource/Category:') &&
+!regex(str(?class), '^http://umbel.org/umbel/') &&
+!regex(str(?class), '^http://dbpedia.org/class/yago')
+ ) . "
+
+//A list of the start instances
+sparql.instances = {"http://dbpedia.org/resource/Gorden_Tallis",
+"http://dbpedia.org/resource/Matthew_Elliott_(rugby_league)",
+"http://dbpedia.org/resource/Graeme_Bradley",
+"http://dbpedia.org/resource/Elton_Rasmussen",
+"http://dbpedia.org/resource/Noel_Goldthorpe",
+"http://dbpedia.org/resource/Shane_Kenward",
+"http://dbpedia.org/resource/Anthony_Mundine",
+"http://dbpedia.org/resource/Steve_Edge_(rugby_league)",
+"http://dbpedia.org/resource/Robbie_Simpson_(rugby_league)",
+"http://dbpedia.org/resource/Ivan_Henjak",
+"http://dbpedia.org/resource/Dick_Huddart",
+"http://dbpedia.org/resource/Mark_Coyne_(rugby_league)",
+"http://dbpedia.org/resource/Henry_Tatana",
+"http://dbpedia.org/resource/Col_Maxwell",
+"http://dbpedia.org/resource/Wayne_Bartrim",
+"http://dbpedia.org/resource/Mitch_Brennan",
+"http://dbpedia.org/resource/Steve_Morris",
+"http://dbpedia.org/resource/Brian_Johnston_(rugby_league)",
+"http://dbpedia.org/resource/Herb_Narvo",
+"http://dbpedia.org/resource/Chris_Johns_(rugby_league)",
+"http://dbpedia.org/resource/Martin_Offiah",
+"http://dbpedia.org/resource/Gorden_Tallis",
+"http://dbpedia.org/resource/Lance_Thompson",
+"http://dbpedia.org/resource/Rod_Reddy",
+"http://dbpedia.org/resource/Wally_Fullerton_Smith",
+"http://dbpedia.org/resource/Neil_Tierney",
+"http://dbpedia.org/resource/Daniel_Wagon",
+"http://dbpedia.org/resource/Ian_Herron",
+"http://dbpedia.org/resource/Eric_Grothe%2C_Jr.",
+"http://dbpedia.org/resource/Michael_Ennis",
+"http://dbpedia.org/resource/Michael_Buettner",
+"http://dbpedia.org/resource/Chris_Mortimer",
+"http://dbpedia.org/resource/Feleti_Mateo",
+"http://dbpedia.org/resource/John_Barclay_(cricketer)",
+"http://dbpedia.org/resource/Lewis_Collins_(aviator)",
+"http://dbpedia.org/resource/Johann_Mohr",
+"http://dbpedia.org/resource/John_Williams_(VC)",
+"http://dbpedia.org/resource/Paula_Pequeno",
+"http://dbpedia.org/resource/Ben_Ross",
+"http://dbpedia.org/resource/Colin_Forsyth",
+"http://dbpedia.org/resource/Brian_Davies_(rugby_league)",
+"http://dbpedia.org/resource/Harry_Taylor_(rugby_league)",
+"http://dbpedia.org/resource/Wayne_Proctor_(rugby_league)"
+ }
+
+reasoner.type = "fast instance checker"
+reasoner.sources = {sparql}
+
+lp.type = "posNegStandard"
+
+lp.positiveExamples = {
+"http://dbpedia.org/resource/Matthew_Elliott_(rugby_league)",
+"http://dbpedia.org/resource/Graeme_Bradley",
+"http://dbpedia.org/resource/Elton_Rasmussen",
+"http://dbpedia.org/resource/Noel_Goldthorpe",
+"http://dbpedia.org/resource/Shane_Kenward",
+"http://dbpedia.org/resource/Anthony_Mundine",
+"http://dbpedia.org/resource/Steve_Edge_(rugby_league)",
+"http://dbpedia.org/resource/Robbie_Simpson_(rugby_league)",
+"http://dbpedia.org/resource/Ivan_Henjak",
+"http://dbpedia.org/resource/Dick_Huddart",
+"http://dbpedia.org/resource/Mark_Coyne_(rugby_league)",
+"http://dbpedia.org/resource/Henry_Tatana",
+"http://dbpedia.org/resource/Col_Maxwell",
+"http://dbpedia.org/resource/Wayne_Bartrim",
+"http://dbpedia.org/resource/Mitch_Brennan",
+"http://dbpedia.org/resource/Steve_Morris",
+"http://dbpedia.org/resource/Brian_Johnston_(rugby_league)",
+"http://dbpedia.org/resource/Herb_Narvo",
+"http://dbpedia.org/resource/Chris_Johns_(rugby_league)",
+"http://dbpedia.org/resource/Martin_Offiah",
+"http://dbpedia.org/resource/Gorden_Tallis",
+"http://dbpedia.org/resource/Lance_Thompson",
+"http://dbpedia.org/resource/Rod_Reddy",
+"http://dbpedia.org/resource/Wally_Fullerton_Smith",
+"http://dbpedia.org/resource/Neil_Tierney"
+}
+
+lp.negativeExamples = {
+"http://dbpedia.org/resource/Daniel_Wagon",
+"http://dbpedia.org/resource/Ian_Herron",
+"http://dbpedia.org/resource/Eric_Grothe%2C_Jr.",
+"http://dbpedia.org/resource/Michael_Ennis",
+"http://dbpedia.org/resource/Michael_Buettner",
+"http://dbpedia.org/resource/Chris_Mortimer",
+"http://dbpedia.org/resource/Feleti_Mateo",
+"http://dbpedia.org/resource/John_Barclay_(cricketer)",
+"http://dbpedia.org/resource/Lewis_Collins_(aviator)",
+"http://dbpedia.org/resource/Johann_Mohr",
+"http://dbpedia.org/resource/John_Williams_(VC)",
+"http://dbpedia.org/resource/Paula_Pequeno",
+"http://dbpedia.org/resource/Ben_Ross",
+"http://dbpedia.org/resource/Colin_Forsyth",
+"http://dbpedia.org/resource/Brian_Davies_(rugby_league)",
+"http://dbpedia.org/resource/Harry_Taylor_(rugby_league)",
+"http://dbpedia.org/resource/Wayne_Proctor_(rugby_league)"
+ }
+
+lp.reasoner = reasoner
+
+
+op.type = "rho"
+op.useNegation = false
+op.useAllConstructor = false
+op.useCardinalityRestrictions = false
+op.useHasValueConstructor = true
+op.reasoner = reasoner
+
+
+alg.type = "ocel"
+alg.reasoner = reasoner
+alg.maxExecutionTimeInSeconds = 30
+alg.noisePercentage = 10.0
Property changes on: trunk/examples/sparqr/StGeorge.conf
___________________________________________________________________
Added: svn:executable
## -0,0 +1 ##
+*
\ No newline at end of property
Modified: trunk/interfaces/pom.xml
===================================================================
--- trunk/interfaces/pom.xml 2013-06-17 10:35:31 UTC (rev 4002)
+++ trunk/interfaces/pom.xml 2013-06-18 15:14:54 UTC (rev 4003)
@@ -356,7 +356,7 @@
<build>
<finalName>dl-learner</finalName>
<plugins>
- <plugin>
+ <!-- <plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>1.6</version>
@@ -376,7 +376,7 @@
</configuration>
</execution>
</executions>
- </plugin>
+ </plugin>-->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>xmlbeans-maven-plugin</artifactId>
@@ -521,8 +521,8 @@
<!-- Exclude Project-D from Project-B -->
<artifactId>slf4j-log4j12</artifactId>
</exclusion>
- <exclusion>
- <groupId>net.sourceforge</groupId>
+ <exclusion>
+ <groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi</artifactId>
</exclusion>
</exclusions>
Modified: trunk/interfaces/src/main/java/org/dllearner/server/Rest.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/server/Rest.java 2013-06-17 10:35:31 UTC (rev 4002)
+++ trunk/interfaces/src/main/java/org/dllearner/server/Rest.java 2013-06-18 15:14:54 UTC (rev 4003)
@@ -94,7 +94,7 @@
learningResult.put("manchester", ed.getDescription().toManchesterSyntaxString(null, null));
learningResult.put("kbsyntax", ed.getDescription().toKBSyntaxString());
// learningResult.put("sparql", sqd.getSparqlQuery(ed.getDescription()));
- learningResult.put("sparql", sparqlConv.asQuery("?subject", OWLAPIConverter.getOWLAPIDescription(ed.getDescription())));
+ learningResult.put("sparql", " "+ sparqlConv.asQuery("?subject", OWLAPIConverter.getOWLAPIDescription(ed.getDescription()))+" ");
learningResult.put("accuracy", ed.getAccuracy());
learningResult.put("truePositives", EvaluatedDescriptionPosNeg.getJSONArray(ed.getCoveredPositives()));
learningResult.put("falsePositives", EvaluatedDescriptionPosNeg.getJSONArray(ed.getNotCoveredPositives()));
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|
|
From: <lor...@us...> - 2013-06-17 10:35:34
|
Revision: 4002
http://sourceforge.net/p/dl-learner/code/4002
Author: lorenz_b
Date: 2013-06-17 10:35:31 +0000 (Mon, 17 Jun 2013)
Log Message:
-----------
Updated eval script.
Modified Paths:
--------------
trunk/scripts/pom.xml
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/pom.xml
===================================================================
--- trunk/scripts/pom.xml 2013-06-16 10:40:01 UTC (rev 4001)
+++ trunk/scripts/pom.xml 2013-06-17 10:35:31 UTC (rev 4002)
@@ -146,7 +146,7 @@
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
- <version>1.2</version>
+ <version>1.2.1</version>
<executions>
<execution>
@@ -159,7 +159,7 @@
<executable>java</executable>
<arguments>
<argument>-Xms512m</argument>
- <argument>-Xmx3000m</argument>
+ <argument>-Xmx10000m</argument>
</arguments>
</configuration>
</plugin>
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-06-16 10:40:01 UTC (rev 4001)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-06-17 10:35:31 UTC (rev 4002)
@@ -74,6 +74,7 @@
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
import org.semanticweb.owlapi.model.OWLLiteral;
+import org.semanticweb.owlapi.model.OWLLogicalAxiom;
import org.semanticweb.owlapi.model.OWLObjectComplementOf;
import org.semanticweb.owlapi.model.OWLObjectIntersectionOf;
import org.semanticweb.owlapi.model.OWLOntology;
@@ -373,7 +374,7 @@
e.printStackTrace();
}
}
- System.exit(0);
+// System.exit(0);
Monitor patternTimeMon = MonitorFactory.getTimeMonitor("pattern-runtime");
//for each pattern
@@ -438,10 +439,46 @@
}
}
+// private List<OWLAxiom> createSample(OWLOntology ontology, Collection<NamedClass> classes){
+// List<OWLAxiom> sample = new ArrayList<OWLAxiom>();
+//
+// Set<OWLAxiom> axioms = ontology.getAxioms();
+// //filter out trivial axioms, e.g. A SubClassOf Thing or A EquivalentTo A and B
+// filterOutTrivialAxioms(axioms);
+// //filter out axioms below threshold
+// filterOutAxiomsBelowThreshold(axioms, sampleThreshold);
+// //get for each class some random axioms
+// for (NamedClass cls : classes) {
+// List<OWLAxiom> relatedAxioms = new ArrayList<OWLAxiom>(ontology.getReferencingAxioms(df.getOWLClass(IRI
+// .create(cls.getName()))));
+// Multimap<Double, OWLAxiom> accuracyWithAxioms = TreeMultimap.create();
+// for (OWLAxiom axiom : relatedAxioms) {
+// double accuracy = getAccuracy(axiom);
+// if(accuracy >= sampleThreshold){
+// accuracyWithAxioms.put(accuracy, axiom);
+// }
+// }
+// //pick the set of axioms with highest score
+// NavigableSet<Double> keySet = (NavigableSet<Double>)accuracyWithAxioms.keySet();
+// if(!keySet.isEmpty()){
+// Double score = keySet.first();
+// Collection<OWLAxiom> axiomsWithHighestScore = accuracyWithAxioms.get(score);
+// List<OWLAxiom> axiomList = new ArrayList<OWLAxiom>(axiomsWithHighestScore);
+// Collections.shuffle(axiomList, new Random(123));
+// if(!axiomList.isEmpty()){
+// sample.add(axiomList.get(0));
+// }
+// }
+// }
+//
+// Collections.shuffle(sample, new Random(123));
+// return sample.subList(0, Math.min(sampleSize, sample.size()));
+// }
+
private List<OWLAxiom> createSample(OWLOntology ontology, Collection<NamedClass> classes){
List<OWLAxiom> sample = new ArrayList<OWLAxiom>();
- Set<OWLAxiom> axioms = ontology.getAxioms();
+ Set<OWLLogicalAxiom> axioms = ontology.getLogicalAxioms();
//filter out trivial axioms, e.g. A SubClassOf Thing or A EquivalentTo A and B
filterOutTrivialAxioms(axioms);
//filter out axioms below threshold
@@ -526,8 +563,8 @@
return axiomList.subList(0, Math.min(sampleSize, axiomList.size()));
}
- private void filterOutAxiomsBelowThreshold(Set<OWLAxiom> axioms, double threshold) {
- for (Iterator<OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
+ private void filterOutAxiomsBelowThreshold(Set<? extends OWLAxiom> axioms, double threshold) {
+ for (Iterator<? extends OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
OWLAxiom axiom = iter.next();
if(getAccuracy(axiom) < threshold){
iter.remove();
@@ -535,8 +572,8 @@
}
}
- private void filterOutTrivialAxioms(Set<OWLAxiom> axioms) {
- for (Iterator<OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
+ private void filterOutTrivialAxioms(Set<? extends OWLAxiom> axioms) {
+ for (Iterator<? extends OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
OWLAxiom axiom = iter.next();
if (axiom.isOfType(AxiomType.EQUIVALENT_CLASSES)) {
if(((OWLEquivalentClassesAxiom) axiom).getClassExpressions().size() == 1){
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-06-16 10:40:04
|
Revision: 4001
http://sourceforge.net/p/dl-learner/code/4001
Author: lorenz_b
Date: 2013-06-16 10:40:01 +0000 (Sun, 16 Jun 2013)
Log Message:
-----------
Updated eval script.
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 2013-06-14 15:02:24 UTC (rev 4000)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-06-16 10:40:01 UTC (rev 4001)
@@ -33,6 +33,7 @@
import java.util.Random;
import java.util.Set;
import java.util.TreeSet;
+import java.util.concurrent.ExecutionException;
import java.util.concurrent.TimeUnit;
import java.util.prefs.Preferences;
@@ -90,6 +91,10 @@
import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
import com.google.common.base.Charsets;
import com.google.common.base.Joiner;
+import com.google.common.cache.Cache;
+import com.google.common.cache.CacheBuilder;
+import com.google.common.cache.CacheLoader;
+import com.google.common.cache.LoadingCache;
import com.google.common.collect.HashMultiset;
import com.google.common.collect.Multimap;
import com.google.common.collect.Multiset;
@@ -153,7 +158,13 @@
private Connection conn;
private PreparedStatement ps;
-
+
+ private LoadingCache<NamedClass, Model> fragments;
+
+ private File samplesDir;
+ private File instantiationsDir;
+
+
public OWLAxiomPatternUsageEvaluation() {
try {
BZip2CompressorInputStream is = new BZip2CompressorInputStream(new URL(ontologyURL).openStream());
@@ -169,6 +180,11 @@
}
initDBConnection();
+
+ samplesDir = new File("pattern-instantiations-samples");
+ samplesDir.mkdir();
+ instantiationsDir = new File("pattern-instantiations");
+ instantiationsDir.mkdir();
}
private void initDBConnection() {
@@ -218,13 +234,21 @@
List<OWLAxiom> patterns = getPatternsToEvaluate(patternOntology);
//get all classes in KB
- Collection<NamedClass> classes = reasoner.getTypes(ns);
+ Collection<NamedClass> classes = reasoner.getOWLClasses();
- //randomize and extract a chunk
+ //get n random classes which contain at least x instances
+ int minNrOfInstances = 5;
List<NamedClass> classesList = new ArrayList<NamedClass>(classes);
Collections.shuffle(classesList, new Random(123));
- classesList = classesList.subList(0, maxNrOfTestedClasses);
- classes = classesList;
+ classes = new TreeSet<NamedClass>();
+ for (NamedClass cls : classesList) {
+ if(reasoner.getIndividualsCount(cls) >= minNrOfInstances){
+ classes.add(cls);
+ }
+ if(classes.size() == maxNrOfTestedClasses){
+ break;
+ }
+ }
classes = Collections.singleton(new NamedClass("http://dbpedia.org/ontology/BaseballPlayer"));
//get the maximum modal depth in the pattern axioms
@@ -264,8 +288,7 @@
logger.info("...on class " + cls + "...");
OWLClass owlClass = df.getOWLClass(IRI.create(cls.getName()));
Model fragment = class2Fragment.get(cls);
- Map<OWLAxiom, Score> result = applyPattern(pattern, owlClass, fragment);
- Set<OWLAxiom> annotatedAxioms = asAnnotatedAxioms(result);
+ Set<OWLAxiom> annotatedAxioms = applyPattern(pattern, owlClass, fragment);
filterOutTrivialAxioms(annotatedAxioms);
filterOutAxiomsBelowThreshold(annotatedAxioms, threshold);
int nrOfAxiomsLocal = annotatedAxioms.size();
@@ -277,7 +300,7 @@
patternClassTimeMon.stop();
write2DB(pattern, owlClass, patternClassTimeMon.getLastValue(), nrOfAxiomsLocal, nrOfAxiomsGlobal);
}
- ontology = save(pattern, learnedAxioms, file);
+ ontology = save(pattern, learnedAxioms);
} else {
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
try {
@@ -288,7 +311,7 @@
}
patternTimeMon.stop();
if(sampling){
- List<OWLAxiom> sample = createSample(ontology);//, classes);
+ List<OWLAxiom> sample = createSample(ontology, classes);
List<String> lines = new ArrayList<String>();
for (OWLAxiom axiom : sample) {
double accuracy = getAccuracy(axiom);
@@ -303,6 +326,95 @@
}
}
+ public void runUsingFragmentExtraction2(SparqlEndpoint endpoint, OWLOntology patternOntology, File outputFile, int maxNrOfTestedClasses){
+ ks = new SparqlEndpointKS(endpoint, cache);
+ SPARQLReasoner reasoner = new SPARQLReasoner(ks, cache);
+
+ //get the axiom patterns to evaluate
+ List<OWLAxiom> patterns = getPatternsToEvaluate(patternOntology);
+
+ //get all classes in KB
+ Collection<NamedClass> classes = reasoner.getOWLClasses();
+
+ //get n random classes which contain at least x instances
+ int minNrOfInstances = 5;
+ List<NamedClass> classesList = new ArrayList<NamedClass>(classes);
+ Collections.shuffle(classesList, new Random(123));
+ classes = new TreeSet<NamedClass>();
+ for (NamedClass cls : classesList) {
+ if(!cls.getName().startsWith("http://dbpedia.org/ontology/"))continue;
+ if (reasoner.getIndividualsCount(cls) >= minNrOfInstances) {
+ classes.add(cls);
+ }
+ if (classes.size() == maxNrOfTestedClasses) {
+ break;
+ }
+ }
+// classes = Collections.singleton(new NamedClass("http://dbpedia.org/ontology/BaseballPlayer"));
+
+ //get the maximum modal depth in the pattern axioms
+ final int maxModalDepth = maxModalDepth(patterns);
+
+ //create cache and fill the cache
+ fragments = CacheBuilder.newBuilder()
+ .maximumSize(maxNrOfTestedClasses)
+ .expireAfterWrite(100, TimeUnit.HOURS)
+ .build(
+ new CacheLoader<NamedClass, Model>() {
+ public Model load(NamedClass cls) {
+ return extractFragment(cls, maxModalDepth);
+ }
+ });
+ Model fragment;
+ for (NamedClass cls : classes) {
+ try {
+ fragment = fragments.get(cls);
+ } catch (ExecutionException e) {
+ e.printStackTrace();
+ }
+ }
+ System.exit(0);
+
+ Monitor patternTimeMon = MonitorFactory.getTimeMonitor("pattern-runtime");
+ //for each pattern
+ for (OWLAxiom pattern : patterns) {
+ patternTimeMon.start();
+ //run if not already exists a result on disk
+ File file = getPatternInstantiationsFile(pattern);
+ OWLOntology ontology = null;
+ if(!file.exists()){
+ ontology = applyPattern(pattern, classes);
+ } else {
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ try {
+ ontology = man.loadOntologyFromOntologyDocument(file);
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ }
+ }
+ patternTimeMon.stop();
+ if(sampling){
+
+ List<OWLAxiom> sample = createSample(ontology, classes);
+ List<String> lines = new ArrayList<String>();
+ for (OWLAxiom axiom : sample) {
+ double accuracy = getAccuracy(axiom);
+ lines.add(axiomRenderer.render(axiom) + "," + format.format(accuracy));
+ }
+ try {
+ Files.write(Joiner.on("\n").join(lines), new File(samplesDir, axiomRenderer.render(pattern).replace(" ", "_") + "-instantiations-sample.csv"), Charsets.UTF_8);
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+ }
+ }
+
+
+ private File getPatternInstantiationsFile(OWLAxiom pattern){
+ return new File(instantiationsDir, axiomRenderer.render(pattern).replace(" ", "_") + "-instantiations.ttl");
+ }
+
private Set<OWLAxiom> asAnnotatedAxioms(Map<OWLAxiom, Score> axioms2Score){
Set<OWLAxiom> annotatedAxioms = new HashSet<OWLAxiom>();
for (Entry<OWLAxiom, Score> entry : axioms2Score.entrySet()) {
@@ -326,34 +438,39 @@
}
}
- private List<OWLAxiom> createSample(OWLOntology ontology){
+ private List<OWLAxiom> createSample(OWLOntology ontology, Collection<NamedClass> classes){
+ List<OWLAxiom> sample = new ArrayList<OWLAxiom>();
+
Set<OWLAxiom> axioms = ontology.getAxioms();
+ //filter out trivial axioms, e.g. A SubClassOf Thing or A EquivalentTo A and B
filterOutTrivialAxioms(axioms);
- for (Iterator<OWLAxiom> iter = axioms.iterator(); iter.hasNext();) {
- OWLAxiom axiom = iter.next();
- double accuracy = getAccuracy(axiom);
- if(accuracy < sampleThreshold){
- iter.remove();
- } else {
- String axiomString = axiomRenderer.render(axiom);
- boolean remove = false;
- for (String s : entites2Ignore) {
- if(axiomString.contains(s)){
- remove = true;
- break;
+ //filter out axioms below threshold
+ filterOutAxiomsBelowThreshold(axioms, sampleThreshold);
+ //get for each class some random axioms
+ int limit = sampleSize / classes.size();
+ while(!axioms.isEmpty() && sample.size() < sampleSize){
+ for (NamedClass cls : classes) {
+ List<OWLAxiom> relatedAxioms = new ArrayList<OWLAxiom>(ontology.getReferencingAxioms(df.getOWLClass(IRI.create(cls.getName()))));
+ relatedAxioms.retainAll(axioms);
+ Collections.shuffle(relatedAxioms, new Random(123));
+ int cnt = 0;
+ Iterator<OWLAxiom> iter = relatedAxioms.iterator();
+ while(iter.hasNext() && cnt < limit){
+ OWLAxiom axiom = iter.next();
+ if(!sample.contains(axiom)){
+ sample.add(axiom);
+ axioms.remove(axiom);
+ cnt++;
}
}
- if(remove){
- iter.remove();
- }
}
}
- List<OWLAxiom> axiomList = new ArrayList<OWLAxiom>(axioms);
- Collections.shuffle(axiomList, new Random(123));
- return axiomList.subList(0, Math.min(sampleSize, axiomList.size()));
+
+ Collections.shuffle(sample, new Random(123));
+ return sample.subList(0, Math.min(sampleSize, sample.size()));
}
- private List<OWLAxiom> createSample(OWLOntology ontology, Collection<NamedClass> classes){
+ private List<OWLAxiom> createSample2(OWLOntology ontology, Collection<NamedClass> classes){
List<OWLAxiom> axiomList = new ArrayList<OWLAxiom>();
for (NamedClass cls : classes) {
OWLClass owlClass = df.getOWLClass(IRI.create(cls.getName()));
@@ -507,74 +624,92 @@
private Map<NamedClass, Model> extractFragments(Collection<NamedClass> classes, int depth){
Map<NamedClass, Model> class2Fragment = new HashMap<NamedClass, Model>();
- //get the maximum modal depth in the patterns
+ Model fragment;
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();
- }
- filterModel(fragment);
- class2Fragment.put(cls, fragment);
- logger.info("...got " + fragment.size() + " triples.");
- continue;
- }
-
- //build the CONSTRUCT query
- Query query = buildConstructQuery(cls, depth);
- query.setLimit(queryLimit);
- //get triples until time elapsed
- long startTime = System.currentTimeMillis();
- int offset = 0;
- boolean hasMoreResults = true;
- while(hasMoreResults && (System.currentTimeMillis() - startTime)<= maxFragmentExtractionTime){
- query.setOffset(offset);
- logger.info(query);
- Model m = executeConstructQuery(query);
- fragment.add(m);
- if(m.size() == 0){
- hasMoreResults = false;
- }
- offset += queryLimit;
- try {
- Thread.sleep(1000);
- } catch (InterruptedException e) {
- e.printStackTrace();
- }
- }
- logger.info("...got " + fragment.size() + " triples.");
+ fragment = extractFragment(cls, depth);
+ class2Fragment.put(cls, fragment);
+ }
+ return class2Fragment;
+ }
+
+ private Model extractFragment(NamedClass cls, int depth){
+ 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.write(new FileOutputStream(file), "TURTLE");
+ fragment.read(new FileInputStream(file), null, "TURTLE");
} catch (FileNotFoundException e) {
e.printStackTrace();
}
filterModel(fragment);
- class2Fragment.put(cls, fragment);
+ logger.info("...got " + fragment.size() + " triples.");
+ return fragment;
}
- return class2Fragment;
+
+ //build the CONSTRUCT query
+ Query query = buildConstructQuery(cls, depth);
+ query.setLimit(queryLimit);
+ //get triples until time elapsed
+ long startTime = System.currentTimeMillis();
+ int offset = 0;
+ boolean hasMoreResults = true;
+ while(hasMoreResults && (System.currentTimeMillis() - startTime)<= maxFragmentExtractionTime){
+ query.setOffset(offset);
+ logger.info(query);
+ Model m = executeConstructQuery(query);
+ fragment.add(m);
+ if(m.size() == 0){
+ hasMoreResults = false;
+ }
+ offset += queryLimit;
+ try {
+ Thread.sleep(500);
+ } catch (InterruptedException e) {
+ e.printStackTrace();
+ }
+ }
+ logger.info("...got " + fragment.size() + " triples.");
+ try {
+ fragment.write(new FileOutputStream(file), "TURTLE");
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+ filterModel(fragment);
+ return fragment;
}
private void filterModel(Model model){
+ Set<String> blackList = Sets.newHashSet(
+ "http://dbpedia.org/ontology/thumbnail",
+ "http://dbpedia.org/ontology/wikiPageRedirects",
+ "http://dbpedia.org/ontology/wikiPageExternalLink",
+ "http://dbpedia.org/ontology/wikiPageWikiLink",
+ "http://dbpedia.org/ontology/wikiPageRevisionID",
+ "http://dbpedia.org/ontology/wikiPageID",
+ "http://dbpedia.org/ontology/wikiPageDisambiguates",
+ "http://dbpedia.org/ontology/wikiPageInterLanguageLink",
+ "http://dbpedia.org/ontology/abstract"
+ );
List<Statement> statements2Remove = new ArrayList<Statement>();
for (Statement st : model.listStatements().toSet()) {
- if(st.getObject().isLiteral()){
- statements2Remove.add(st);
+ if(st.getPredicate().equals(RDF.type)){
+ if(st.getObject().isURIResource() && !st.getObject().asResource().getURI().startsWith("http://dbpedia.org/ontology/")){
+ statements2Remove.add(st);
+ }
+ } else {
+ if(!st.getPredicate().getURI().startsWith("http://dbpedia.org/ontology/")){
+ statements2Remove.add(st);
+ } else {
+ if(blackList.contains(st.getPredicate().getURI())){
+ statements2Remove.add(st);
+ }
+ }
}
- if(st.getPredicate().equals(RDF.type) && !st.getObject().asResource().getURI().startsWith("http://dbpedia.org/ontology/")){
- statements2Remove.add(st);
- }
- if(st.getPredicate().hasURI("http://xmlns.com/foaf/0.1/depiction") || st.getPredicate().hasURI("http://dbpedia.org/ontology/thumbnail")){
- statements2Remove.add(st);
- } else if(!st.getPredicate().equals(RDF.type) && !st.getPredicate().getURI().startsWith("http://dbpedia.org/ontology/")){
- statements2Remove.add(st);
- }
+
}
model.remove(statements2Remove);
}
@@ -775,7 +910,43 @@
return axioms2Score;
}
- private Map<OWLAxiom, Score> applyPattern(OWLAxiom pattern, OWLClass cls, Model fragment) {
+ private OWLOntology applyPattern(OWLAxiom pattern, Collection<NamedClass> classes) {
+ logger.info("Applying pattern " + pattern + "...");
+ Set<OWLAxiom> learnedAxioms = new HashSet<OWLAxiom>();
+ Monitor patternClassTimeMon = MonitorFactory.getTimeMonitor("class-pattern-runtime");
+ // for each class
+ for (NamedClass cls : classes) {
+ logger.info("...on class " + cls + "...");
+ try {
+ OWLClass owlClass = df.getOWLClass(IRI.create(cls.getName()));
+
+ //get the fragment
+ Model fragment = fragments.get(cls);
+
+ //apply the pattern
+ patternClassTimeMon.start();
+ Set<OWLAxiom> annotatedAxioms = applyPattern(pattern, owlClass, fragment);
+ patternClassTimeMon.stop();
+
+ filterOutTrivialAxioms(annotatedAxioms);
+ filterOutAxiomsBelowThreshold(annotatedAxioms, threshold);
+ int nrOfAxiomsLocal = annotatedAxioms.size();
+ annotatedAxioms = computeScoreGlobal(annotatedAxioms, owlClass);
+ filterOutAxiomsBelowThreshold(annotatedAxioms, threshold);
+ int nrOfAxiomsGlobal = annotatedAxioms.size();
+ learnedAxioms.addAll(annotatedAxioms);
+ printAxioms(annotatedAxioms, threshold);
+
+ write2DB(pattern, owlClass, patternClassTimeMon.getLastValue(), nrOfAxiomsLocal, nrOfAxiomsGlobal);
+ } catch (ExecutionException e) {
+ e.printStackTrace();
+ }
+ }
+ OWLOntology ontology = save(pattern, learnedAxioms);
+ return ontology;
+ }
+
+ private Set<OWLAxiom> applyPattern(OWLAxiom pattern, OWLClass cls, Model fragment) {
Map<OWLAxiom, Score> axioms2Score = new HashMap<OWLAxiom, Score>();
OWLClassExpression patternSubClass = null;
@@ -798,7 +969,7 @@
patternSuperClass = ((OWLSubClassOfAxiom) pattern).getSuperClass();
} else {
logger.warn("Pattern " + pattern + " not supported yet.");
- return axioms2Score;
+ return asAnnotatedAxioms(axioms2Score);
}
Set<OWLEntity> signature = patternSuperClass.getSignature();
@@ -851,7 +1022,7 @@
axioms2Score.put(axiom, score);
}
- return axioms2Score;
+ return asAnnotatedAxioms(axioms2Score);
}
private void write2DB(OWLAxiom pattern, OWLClass cls, double runtime, int nrOfAxiomsLocal, int nrOfAxiomsGlobal){
@@ -964,11 +1135,11 @@
return template.asQuery();
}
- private OWLOntology save(OWLAxiom pattern, Set<OWLAxiom> learnedAxioms, File file){
+ private OWLOntology save(OWLAxiom pattern, Set<OWLAxiom> learnedAxioms){
try {
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
OWLOntology ontology = man.createOntology(learnedAxioms);
- man.saveOntology(ontology, new TurtleOntologyFormat(), new FileOutputStream(file));
+ man.saveOntology(ontology, new TurtleOntologyFormat(), new FileOutputStream(getPatternInstantiationsFile(pattern)));
return ontology;
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
@@ -1133,15 +1304,18 @@
superClass = ((OWLSubClassOfAxiom)axiom).getSuperClass();
}
//count subclass+superClass
- Query query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(cls, superClass), true);System.out.println(query);
+ System.out.println("Counting instances of " + df.getOWLObjectIntersectionOf(cls, superClass) + "...");
+ Query query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(cls, superClass), true);
rs = executeSelectQuery(query);
int overlap = rs.next().getLiteral("cnt").getInt();
+ System.out.println("..." + overlap + " instances.");
//count subclass
- query = converter.asQuery("?x", cls, true);
if(subClassCnt == -1){
- System.out.println(query);
+ System.out.println("Counting instances of " + cls);
+ query = converter.asQuery("?x", cls, true);
rs = executeSelectQuery(query);
subClassCnt = rs.next().getLiteral("cnt").getInt();
+ System.out.println("..." + subClassCnt + " instances.");
}
//compute recall
@@ -1152,9 +1326,11 @@
continue;
}
//count superClass
- query = converter.asQuery("?x", superClass, true);System.out.println(query);
+ System.out.println("Counting instances of " + superClass);
+ query = converter.asQuery("?x", superClass, true);
rs = executeSelectQuery(query);
int superClassCnt = rs.next().getLiteral("cnt").getInt();
+ System.out.println("..." + superClassCnt + " instances.");
//compute precision
double precision = wald(superClassCnt, overlap);
@@ -1320,7 +1496,7 @@
System.exit(0);
}
int maxNrOfTestedClasses = (Integer) options.valueOf("limit");
- new OWLAxiomPatternUsageEvaluation().runUsingFragmentExtraction(endpoint, patternsOntology, outputFile, maxNrOfTestedClasses);
+ new OWLAxiomPatternUsageEvaluation().runUsingFragmentExtraction2(endpoint, patternsOntology, outputFile, maxNrOfTestedClasses);
}
}
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|
|
From: <jen...@us...> - 2013-06-14 15:02:27
|
Revision: 4000
http://sourceforge.net/p/dl-learner/code/4000
Author: jenslehmann
Date: 2013-06-14 15:02:24 +0000 (Fri, 14 Jun 2013)
Log Message:
-----------
added another semantic for all quantors to fast instance checker
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
trunk/components-core/src/test/java/org/dllearner/test/junit/SomeOnlyReasonerTest.java
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java 2013-06-14 12:41:49 UTC (rev 3999)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java 2013-06-14 15:02:24 UTC (rev 4000)
@@ -139,7 +139,11 @@
"use those which have at least one r-filler and do not have an r-filler not in C.",defaultValue = "standard",propertyEditorClass = StringTrimmerEditor.class)
private ForallSemantics forallSemantics = ForallSemantics.Standard;
- public enum ForallSemantics { Standard, SomeOnly }
+ public enum ForallSemantics {
+ Standard, // standard all quantor
+ NonEmpty, // p only C for instance a returns false if there is no fact p(a,x) for any x
+ SomeOnly // p only C for instance a returns false if there is no fact p(a,x) with x \ in C
+ }
/**
* Creates an instance of the fast instance checker.
@@ -401,6 +405,7 @@
return true;
}
SortedSet<Individual> roleFillers = opPos.get(op).get(individual);
+
if (roleFillers == null) {
if(forallSemantics == ForallSemantics.Standard) {
return true;
@@ -408,12 +413,20 @@
return false;
}
}
+ boolean hasCorrectFiller = false;
for (Individual roleFiller : roleFillers) {
- if (!hasTypeImpl(child, roleFiller)) {
+ if (hasTypeImpl(child, roleFiller)) {
+ hasCorrectFiller = true;
+ } else {
return false;
- }
+ }
}
- return true;
+
+ if(forallSemantics == ForallSemantics.SomeOnly) {
+ return hasCorrectFiller;
+ } else {
+ return true;
+ }
} else if (description instanceof ObjectMinCardinalityRestriction) {
ObjectPropertyExpression ope = ((ObjectCardinalityRestriction) description).getRole();
if (!(ope instanceof ObjectProperty)) {
Modified: trunk/components-core/src/test/java/org/dllearner/test/junit/SomeOnlyReasonerTest.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/test/junit/SomeOnlyReasonerTest.java 2013-06-14 12:41:49 UTC (rev 3999)
+++ trunk/components-core/src/test/java/org/dllearner/test/junit/SomeOnlyReasonerTest.java 2013-06-14 15:02:24 UTC (rev 4000)
@@ -31,6 +31,7 @@
*
*/
public class SomeOnlyReasonerTest {
+
@Test
public void someOnlyTest() throws ComponentInitException, LearningProblemUnsupportedException {
// TODO: use aksw-commons-sparql instead of sparql-scala
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|
|
From: <dc...@us...> - 2013-06-14 12:41:53
|
Revision: 3999
http://sourceforge.net/p/dl-learner/code/3999
Author: dcherix
Date: 2013-06-14 12:41:49 +0000 (Fri, 14 Jun 2013)
Log Message:
-----------
Changed in the Rest api class to use the OWLClassExpressionToSparqlConverter
Modified Paths:
--------------
trunk/interfaces/src/main/java/org/dllearner/server/Rest.java
Modified: trunk/interfaces/src/main/java/org/dllearner/server/Rest.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/server/Rest.java 2013-06-14 09:24:13 UTC (rev 3998)
+++ trunk/interfaces/src/main/java/org/dllearner/server/Rest.java 2013-06-14 12:41:49 UTC (rev 3999)
@@ -9,6 +9,8 @@
import org.dllearner.core.LearningAlgorithm;
import org.dllearner.kb.sparql.SparqlQueryDescriptionConvertVisitor;
import org.dllearner.learningproblems.EvaluatedDescriptionPosNeg;
+import org.dllearner.utilities.owl.OWLAPIConverter;
+import org.dllearner.utilities.owl.OWLClassExpressionToSPARQLConverter;
import org.json.simple.JSONObject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -73,7 +75,7 @@
"} ";
learningResult.put("success", "1");
- learningResult.put("manchester", manchester);
+ learningResult.put("manchester", manchester);
learningResult.put("kbsyntax", "other syntax");
learningResult.put("sparql", sparql);
learningResult.put("accuracy", 1.0);
@@ -87,11 +89,12 @@
SparqlQueryDescriptionConvertVisitor sqd = new SparqlQueryDescriptionConvertVisitor();
sqd.setLimit(limit);
-
- learningResult.put("success", "1");
+ OWLClassExpressionToSPARQLConverter sparqlConv = new OWLClassExpressionToSPARQLConverter();
+ learningResult.put("success", "1");
learningResult.put("manchester", ed.getDescription().toManchesterSyntaxString(null, null));
learningResult.put("kbsyntax", ed.getDescription().toKBSyntaxString());
- learningResult.put("sparql", sqd.getSparqlQuery(ed.getDescription()));
+// learningResult.put("sparql", sqd.getSparqlQuery(ed.getDescription()));
+ learningResult.put("sparql", sparqlConv.asQuery("?subject", OWLAPIConverter.getOWLAPIDescription(ed.getDescription())));
learningResult.put("accuracy", ed.getAccuracy());
learningResult.put("truePositives", EvaluatedDescriptionPosNeg.getJSONArray(ed.getCoveredPositives()));
learningResult.put("falsePositives", EvaluatedDescriptionPosNeg.getJSONArray(ed.getNotCoveredPositives()));
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|
|
From: <dc...@us...> - 2013-06-14 09:24:15
|
Revision: 3998
http://sourceforge.net/p/dl-learner/code/3998
Author: dcherix
Date: 2013-06-14 09:24:13 +0000 (Fri, 14 Jun 2013)
Log Message:
-----------
Test for the ForallSemantics property of the FastInstanceChecker
Added Paths:
-----------
trunk/components-core/src/test/java/org/dllearner/test/junit/SomeOnlyReasonerTest.java
Added: trunk/components-core/src/test/java/org/dllearner/test/junit/SomeOnlyReasonerTest.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/test/junit/SomeOnlyReasonerTest.java (rev 0)
+++ trunk/components-core/src/test/java/org/dllearner/test/junit/SomeOnlyReasonerTest.java 2013-06-14 09:24:13 UTC (rev 3998)
@@ -0,0 +1,116 @@
+/**
+ *
+ */
+package org.dllearner.test.junit;
+
+import static org.junit.Assert.assertTrue;
+
+import java.util.ArrayList;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.dllearner.algorithms.celoe.CELOE;
+import org.dllearner.core.AbstractReasonerComponent;
+import org.dllearner.core.ComponentInitException;
+import org.dllearner.core.ComponentManager;
+import org.dllearner.core.LearningProblemUnsupportedException;
+import org.dllearner.core.owl.Description;
+import org.dllearner.core.owl.Individual;
+import org.dllearner.core.owl.ObjectAllRestriction;
+import org.dllearner.kb.sparql.simple.SparqlSimpleExtractor;
+import org.dllearner.learningproblems.PosNegLPStandard;
+import org.dllearner.reasoning.FastInstanceChecker;
+import org.dllearner.reasoning.FastInstanceChecker.ForallSemantics;
+import org.dllearner.refinementoperators.RhoDRDown;
+import org.dllearner.utilities.datastructures.Datastructures;
+import org.dllearner.utilities.datastructures.SortedSetTuple;
+import org.junit.Test;
+
+/**
+ * @author didiers
+ *
+ */
+public class SomeOnlyReasonerTest {
+ @Test
+ public void someOnlyTest() throws ComponentInitException, LearningProblemUnsupportedException {
+ // TODO: use aksw-commons-sparql instead of sparql-scala
+
+ SortedSet<Individual> posExamples = new TreeSet<Individual>();
+ posExamples.add(new Individual("http://dbpedia.org/resource/Archytas"));
+ posExamples.add(new Individual("http://dbpedia.org/resource/Pythagoras"));
+ posExamples.add(new Individual("http://dbpedia.org/resource/Philolaus"));
+
+ SortedSet<Individual> negExamples = new TreeSet<Individual>();
+ negExamples.add(new Individual("http://dbpedia.org/resource/Democritus"));
+ negExamples.add(new Individual("http://dbpedia.org/resource/Zeno_of_Elea"));
+ negExamples.add(new Individual("http://dbpedia.org/resource/Plato"));
+ negExamples.add(new Individual("http://dbpedia.org/resource/Socrates"));
+
+ SortedSetTuple<Individual> examples = new SortedSetTuple<Individual>(posExamples,
+ negExamples);
+
+ ComponentManager cm = ComponentManager.getInstance();
+
+ SparqlSimpleExtractor ks = cm.knowledgeSource(SparqlSimpleExtractor.class);
+ ks.setInstances(new ArrayList<String>(Datastructures.individualSetToStringSet(examples
+ .getCompleteSet())));
+ // ks.getConfigurator().setPredefinedEndpoint("DBPEDIA"); // TODO:
+ // probably the official endpoint is too slow?
+ ks.setEndpointURL("http://dbpedia.org/sparql");
+ // ks.setUseLits(false);
+ // ks.setUseCacheDatabase(true);
+ ks.setRecursionDepth(1);
+ ArrayList<String> ontologyUrls = new ArrayList<String>();
+ ontologyUrls.add("http://downloads.dbpedia.org/3.6/dbpedia_3.6.owl");
+ ks.setOntologySchemaUrls(ontologyUrls);
+ ks.setAboxfilter("FILTER ( !isLiteral(?o) && regex(str(?o), "
+ + "'^http://dbpedia.org/resource/') && "
+ + "! regex(str(?o), '^http://dbpedia.org/resource/Category') ) ");
+ ks.setTboxfilter("FILTER ( regex(str(?class), '^http://dbpedia.org/ontology/') ) . ");
+
+ ks.init();
+
+ AbstractReasonerComponent rc = cm.reasoner(FastInstanceChecker.class, ks);
+ ((FastInstanceChecker)rc).setForAllSemantics(ForallSemantics.SomeOnly);
+ rc.init();
+
+
+ PosNegLPStandard lp = cm.learningProblem(PosNegLPStandard.class, rc);
+ lp.setPositiveExamples(posExamples);
+ lp.setNegativeExamples(negExamples);
+ lp.setAccuracyMethod("fmeasure");
+ lp.setUseApproximations(false);
+ lp.init();
+
+ CELOE la = cm.learningAlgorithm(CELOE.class, lp, rc);
+ // CELOEConfigurator cc = la.getConfigurator();
+ la.setMaxExecutionTimeInSeconds(100);
+ la.init();
+ RhoDRDown op = (RhoDRDown) la.getOperator();
+
+ op.setUseNegation(false);
+ op.setUseAllConstructor(true);
+ op.setUseCardinalityRestrictions(false);
+ op.setUseHasValueConstructor(true);
+ la.setNoisePercentage(20);
+ la.init();
+ la.start();
+
+ cm.freeAllComponents();
+ Description desc = la.getCurrentlyBestDescription();
+ assertTrue( this.containsObjectAllRestriction(desc));
+
+ }
+
+ private boolean containsObjectAllRestriction(Description d){
+ if(d instanceof ObjectAllRestriction){
+ return false;
+ }
+ for(Description child:d.getChildren()){
+ if(!this.containsObjectAllRestriction(child)){
+ return false;
+ }
+ }
+ return true;
+ }
+}
Property changes on: trunk/components-core/src/test/java/org/dllearner/test/junit/SomeOnlyReasonerTest.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <dc...@us...> - 2013-06-14 05:12:17
|
Revision: 3997
http://sourceforge.net/p/dl-learner/code/3997
Author: dcherix
Date: 2013-06-14 05:12:12 +0000 (Fri, 14 Jun 2013)
Log Message:
-----------
sparql for ObjectAllRestriction added
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2013-06-13 13:36:48 UTC (rev 3996)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/SparqlQueryDescriptionConvertVisitor.java 2013-06-14 05:12:12 UTC (rev 3997)
@@ -69,613 +69,628 @@
*
*/
public class SparqlQueryDescriptionConvertVisitor implements DescriptionVisitor {
-
-
- private static Logger logger = Logger.getLogger(ComponentManager.class);
-
- private int limit = 5;
- private int offset = -1;
- private boolean labels = false;
- private boolean distinct = false;
- private boolean count = false;
- private String customFilter = null;
-
-
- private SortedSet<String> transitiveProperties =null;
- private Map<String,Set<String>> subclassMap = null;
-
- private Stack<String> stack = new Stack<String>();
- private String query = "";
- private int currentObject = 0;
- private List<String> foundNamedClasses = new ArrayList<String>();
-
- /**
- * resets internal variables
- */
- private void reset(){
- currentObject = 0;
- stack = new Stack<String>();
- stack.push("subject");
- query = "";
- foundNamedClasses = new ArrayList<String>() ;
- }
-
- public SparqlQueryDescriptionConvertVisitor() {
- stack.push("subject");
- }
-
- /**
- * @param descriptionKBSyntax description which is parsed and passed to getSparqlQuery( Description description)
- * @return
- * @throws ParseException
- */
- public String getSparqlQuery( String descriptionKBSyntax) throws ParseException {
- Description description = KBParser.parseConcept(descriptionKBSyntax);
- return getSparqlQuery( description);
- }
-
- /**
- * takes a description and transforms it into SPARQL
- * @param description
- * @return
- */
- public String getSparqlQuery( Description description) {
- description.accept(this);
- expandSubclasses();
- String ret = "";
- String customFilterTmp = pointalize(customFilter);
- query = pointalize(query);
- if(count){
- ret = "SELECT count(distinct(?subject)) as ?count { "+ query + " \n"+customFilterTmp+" \n } " ;
- }else{
- ret = "SELECT "+distinct()+"?subject "+((labels)?"?label":"")+" { "+labels()+ query + " \n"+customFilterTmp+"\n } " + limit();
- }
- reset();
- return ret;
- }
-
-
- /**
- * finalizes the patterns with a point
- * @param toBePointed
- * @return
- */
- private static String pointalize(String toBePointed){
- if(toBePointed==null){
- return "";
- }
- return (toBePointed.trim().endsWith("."))?toBePointed:toBePointed+" . ";
- }
-
- private void expandSubclasses(){
- if(subclassMap == null){
- return;
- }
- int counter = 0;
- int index = 0;
- String var = "";
- String uriPattern = "";
- StringBuffer tmp ;
- StringBuffer filter = new StringBuffer() ;
- Set<String> subClasses;
- for(String nc: foundNamedClasses){
- index = query.indexOf("<"+nc+">");
- subClasses = subclassMap.get(nc);
- if(index == -1){
- logger.error("named class was found before, but is not in query any more?? "+nc);
- }else if(subClasses != null){
- var = "?expanded"+counter;
- uriPattern = "<"+nc+">";
- tmp = new StringBuffer();
- tmp.append(query.substring(0, index));
- tmp.append(var);
- tmp.append(query.substring(index+(uriPattern.length())));
- query = tmp.toString();
- filter.append(makeFilter(var, subClasses, nc));
- }else{
- logger.debug("no mapping found ("+nc+") "+this.getClass().getSimpleName());
- }
-
- counter++;
- }
- query += filter.toString();
- }
-
- private String makeFilter(String var, Set<String> classes, String superClassUri){
- StringBuffer buf = new StringBuffer("\nFILTER ( "+var+" IN ( ");
- for (String string : classes) {
- buf.append("<"+string+">, ");
- }
- buf.append("<"+superClassUri+"> ) ). ");
- return buf.toString();
- }
-
- private String limit() {
- if (limit > 0 && offset > 0){
- return " LIMIT " + limit + " OFFSET "+offset+" ";
- }else if(limit > 0 ){
- return " LIMIT " + limit + " ";
- }else {
- return "";
- }
- }
- private String labels() {
- return (labels)?"\n?subject rdfs:label ?label . ":"";
- }
- private String distinct() {
- return (distinct)?"DISTINCT ":"";
- }
-
- /**
- * @param limit <= 0 means no limit
- */
- public void setLimit(int limit) {
- this.limit = limit;
- }
-
- public void noLimit() {
- this.limit = -1;
- }
-
- /**
- * also retrieve labels (untested)
- *
- * @param labels
- */
- public void setLabels(boolean labels) {
- this.labels = labels;
- }
-
- /**
- * result is distinct
- * @param distinct
- */
- public void setDistinct(boolean distinct) {
- this.distinct = distinct;
- }
-
- /**
- * virtuoso optimisation for transitive properties
- * @param transitiveProperties
- */
- public void setTransitiveProperties(SortedSet<String> transitiveProperties) {
- this.transitiveProperties = transitiveProperties;
- }
-
-
- /**
- * needed for expanding subclasses, if store does no reasoning
- * @param subclassMap
- */
- public void setSubclassMap(Map<String, Set<String>> subclassMap) {
- this.subclassMap = subclassMap;
- }
-
- public void setCount(boolean count) {
- this.count = count;
- }
-
- public void setOffset(int offset) {
- this.offset = offset;
- }
-
- public void setCustomFilter(String customFilter) {
- this.customFilter = customFilter;
- }
-
- public static String getSparqlQuery(String descriptionKBSyntax, int limit, boolean labels, boolean distinct) throws ParseException {
- Description d = KBParser.parseConcept(descriptionKBSyntax);
- return getSparqlQuery(d, limit, labels, distinct);
- }
-
- public static String getSparqlQuery(Description description, int limit, boolean labels, boolean distinct) {
- SparqlQueryDescriptionConvertVisitor visitor = new SparqlQueryDescriptionConvertVisitor();
- visitor.setDistinct(distinct);
- visitor.setLabels(labels);
- visitor.setLimit(limit);
- return visitor.getSparqlQuery(description);
- }
-
- /**
- * COMMENT: write some more includes subclasses, costly function, because
- * subclasses have to be received first. TODO mentioned method cannot be
- * found by Javadoc tool conceptRewrite(String descriptionKBSyntax,
- * SparqlEndpoint se, Cache c, boolean simple)
- *
- * @param descriptionKBSyntax
- * @see #getSparqlQuery(Description description, int limit)
- * @param resultLimit
- * @see #getSparqlQuery(Description description, int limit)
- * @param maxDepth
- * @throws ParseException
- */
-
- public static String getSparqlQueryIncludingSubclasses(String descriptionKBSyntax, int resultLimit,
- SPARQLTasks st, int maxDepth) throws ParseException {
- String rewritten = SparqlQueryDescriptionConvertRDFS
- .conceptRewrite(descriptionKBSyntax, st, maxDepth);
-
- return getSparqlQuery(rewritten, resultLimit, false, false);
-
- }
-
-
- public static void testHasValue() throws Exception{
-// String ttt = "(\"http://dbpedia.org/ontology/Plant\" AND (\"http://dbpedia.org/ontology/kingdom\" hasValue \"http://dbpedia.org/resource/Plantae\" OR EXISTS \"http://dbpedia.org/ontology/family\".\"http://dbpedia.org/ontology/FloweringPlant\"))";
- String ttt = "(\"http://dbpedia.org/ontology/Plant\" AND ((\"http://dbpedia.org/ontology/kingdom\" HASVALUE \"http://dbpedia.org/resource/Plantae\") OR EXISTS \"http://dbpedia.org/ontology/family\".\"http://dbpedia.org/ontology/FloweringPlant\"))";
- SparqlQueryDescriptionConvertVisitor testVisitor = new SparqlQueryDescriptionConvertVisitor();
- String q = testVisitor.getSparqlQuery(ttt);
- System.out.println(q);
- Description description = KBParser.parseConcept(ttt);
- System.out.println(description.toString());
- System.out.println(description.toKBSyntaxString());
- System.out.println(description.toKBSyntaxString(null,null));
- if (true) {
- System.exit(0);
- }
-
- }
- public static void testTrans() throws Exception{
-// String ttt = "(\"http://dbpedia.org/ontology/Plant\" AND (\"http://dbpedia.org/ontology/kingdom\" hasValue \"http://dbpedia.org/resource/Plantae\" OR EXISTS \"http://dbpedia.org/ontology/family\".\"http://dbpedia.org/ontology/FloweringPlant\"))";
-// String ttt = "(\"http://dbpedia.org/ontology/Plant\" AND ((\"http://dbpedia.org/ontology/kingdom\" HASVALUE \"http://dbpedia.org/resource/Plantae\") OR EXISTS \"http://dbpedia.org/ontology/family\".\"http://dbpedia.org/ontology/FloweringPlant\"))";
- String ttt = "EXISTS \"http://dbpedia.org/ontology/kingdom\".\"http://dbpedia.org/resource/Plantae\"";
- SparqlQueryDescriptionConvertVisitor testVisitor = new SparqlQueryDescriptionConvertVisitor();
- testVisitor.setTransitiveProperties(new TreeSet<String>(Arrays.asList(new String[]{"http://dbpedia.org/ontology/kingdom" })));
- String q = testVisitor.getSparqlQuery(ttt);
- System.out.println(q);
- Description description = KBParser.parseConcept(ttt);
- System.out.println(description.toString());
- System.out.println(description.toKBSyntaxString());
- System.out.println(description.toKBSyntaxString(null,null));
- if (true) {
- System.exit(0);
- }
-
- }
-
- /**
- * Used for testing the Sparql Query converter.
- *
- * @param args
- */
- public static void main(String[] args) throws Exception{
-
- try {
-// testTrans();
- testHasValue();
-
-
- //SparqlQueryConverter.test();
-
- SortedSet<String> s = new TreeSet<String>();
- HashMap<String, String> result = new HashMap<String, String>();
- HashMap<String, String> subclassMap = new HashMap<String, String>();
- subclassMap.put("http://nlp2rdf.org/ontology/Sentence","<http://nlp2rdf.org/ontology/Subsentence>");
- String conj = "(\"http://dbpedia.org/class/yago/Person100007846\" AND \"http://dbpedia.org/class/yago/Head110162991\")";
-
- s.add("EXISTS \"http://dbpedia.org/property/disambiguates\".TOP");
- s.add("EXISTS \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
- s.add("EXISTS \"http://dbpedia.org/property/successor\"." + conj);
- s.add("ALL \"http://dbpedia.org/property/disambiguates\".TOP");
- s.add("ALL \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
- s.add("\"http://dbpedia.org/class/yago/Person100007846\"");
- s.add(conj);
- s.add("(\"http://dbpedia.org/class/yago/Person100007846\" OR \"http://dbpedia.org/class/yago/Head110162991\")");
- s.add("NOT \"http://dbpedia.org/class/yago/Person100007846\"");
- s.add("(\"http://dbpedia.org/class/yago/HeadOfState110164747\" AND (\"http://dbpedia.org/class/yago/Negotiator110351874\" AND \"http://dbpedia.org/class/yago/Representative110522035\"))");
-
- s.clear();
-// s.add("(\"http://nlp2rdf.org/ontology/Sentence\" AND (EXISTS \"http://nlp2rdf.org/ontology/syntaxTreeHasPart\".\"http://nachhalt.sfb632.uni-potsdam.de/owl/stts.owl#Pronoun\" AND EXISTS \"http://nlp2rdf.org/ontology/syntaxTreeHasPart\".\"http://nlp2rdf.org/ontology/sentencefinalpunctuation_tag\"))");
-// s.add("(\"http://nlp2rdf.org/ontology/Sentence\" AND (\"http://nlp2rdf.org/ontology/hasLemma\" VALUE \"test\" )");
-
- String prefix = "http://nlp2rdf.org/ontology/";
- String test = "(\"Sentence\" AND (EXISTS \"syntaxTreeHasPart\".\"VVPP\" AND EXISTS \"syntaxTreeHasPart\".(\"stts:AuxilliaryVerb\" AND \"hasLemma\" = werden)))";
-
- ObjectProperty stp = new ObjectProperty(prefix+"syntaxTreeHasPart");
- DatatypeProperty dtp = new DatatypeProperty(prefix+"hasLemma");
- StringValueRestriction svr = new StringValueRestriction(dtp,"werden" );
- Intersection inner = new Intersection(new NamedClass(prefix+"Auxillary"), svr);
- Intersection middle = new Intersection(
- new ObjectSomeRestriction(stp, new NamedClass(prefix+"VVPP")),
- new ObjectSomeRestriction(stp, inner));
- Intersection outer = new Intersection(
- new NamedClass(prefix+"Sentence"),
- middle
- );
-
- System.out.println(outer.toKBSyntaxString(null,null));
- System.out.println(test);
-
- Map<String, Set<String>> testMap = new HashMap<String, Set<String>>();
- testMap.put(prefix+"Sentence", new HashSet<String>(Arrays.asList(new String[]{"whatever","loser"})));
-// s.add(outer.toKBSyntaxString(null,null));
- SparqlQueryDescriptionConvertVisitor testVisitor = new SparqlQueryDescriptionConvertVisitor();
- testVisitor.setSubclassMap(testMap);
- String q = testVisitor.getSparqlQuery(outer.toKBSyntaxString());
- System.out.println(q);
- if (true) {
- System.exit(0);
- }
-// <http://nlp2rdf.org/ontology/sentencefinalpunctuation_tag>
- String query = "";
- SparqlQueryDescriptionConvertVisitor visit = new SparqlQueryDescriptionConvertVisitor();
- visit.setLabels(false);
- visit.setDistinct(false);
-// visit.setClassToSubclassesVirtuoso(subclassMap);
-
-
-
- for (String kbsyntax : s) {
- query = visit.getSparqlQuery(kbsyntax);
- result.put(kbsyntax, query);
- }
- System.out.println("************************");
- for (String string : result.keySet()) {
- System.out.println("KBSyntayString: " + string);
- System.out.println("Query:\n" + result.get(string));
- System.out.println("************************");
- }
- System.out.println("Finished");
- } catch (ParseException e) {
- e.printStackTrace();
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
- * .Negation)
- */
- public void visit(Negation description) {
- logger.trace("Negation");
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
- * .ObjectAllRestriction)
- */
- public void visit(ObjectAllRestriction description) {
- logger.trace("ObjectAllRestriction");
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
- * .ObjectSomeRestriction)
- */
- public void visit(ObjectSomeRestriction description) {
- logger.trace("ObjectSomeRestriction");
- String option = "";
- if(transitiveProperties!= null && transitiveProperties.contains(description.getRole().toString()) ){
- option =" OPTION (TRANSITIVE , t_in(?" + stack.peek()+"), t_out(?object" + currentObject + "), T_MIN(0), T_MAX(6), T_DIRECTION 1 , T_NO_CYCLES) ";
- }
-
- if(description.getChild(0) instanceof Thing){
- //I removed a point here at the end
- query += "\n?" + stack.peek() + " <" + description.getRole() + "> [] " + option + " ";
- }else{
- query += "\n?" + stack.peek() + " <" + description.getRole() + "> ?object" + currentObject + option + " . ";
- stack.push("object" + currentObject);
- currentObject++;
- description.getChild(0).accept(this);
- stack.pop();
- }
-
- logger.trace(description.getRole().toString());
- logger.trace(description.getChild(0).toString());
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
- * .Nothing)
- */
- public void visit(Nothing description) {
- logger.trace("Nothing");
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
- * .Thing)
- */
- public void visit(Thing description) {
- logger.trace("Thing");
-
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
- * .Intersection)
- */
- public void visit(Intersection description) {
- if(description.getChild(0) instanceof Thing ){
- logger.trace("Intersection with TOP");
- description.getChild(1).accept(this);
- }else if(description.getChild(1) instanceof Thing ){
- logger.trace("Intersection with TOP");
- description.getChild(0).accept(this);
- }else{
- logger.trace("Intersection");
- description.getChild(0).accept(this);
- query += ". ";
- description.getChild(1).accept(this);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
- * .Union)
- */
- public void visit(Union description) {
-
- if(description.getChild(0) instanceof Thing ){
- logger.trace("Union with TOP");
- description.getChild(1).accept(this);
- }else if(description.getChild(1) instanceof Thing ){
- logger.trace("Union with TOP");
- description.getChild(0).accept(this);
- }else{
- logger.trace("Union");
- query += "{";
- description.getChild(0).accept(this);
- query += "} UNION {";
- description.getChild(1).accept(this);
- query += "}";
- }
-
-
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
- * .ObjectMinCardinalityRestriction)
- */
- public void visit(ObjectMinCardinalityRestriction description) {
- logger.trace("ObjectMinCardinalityRestriction");
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
- * .ObjectExactCardinalityRestriction)
- */
- public void visit(ObjectExactCardinalityRestriction description) {
- logger.trace("ObjectExactCardinalityRestriction");
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
- * .ObjectMaxCardinalityRestriction)
- */
- public void visit(ObjectMaxCardinalityRestriction description) {
- logger.trace("ObjectMaxCardinalityRestriction");
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
- * .ObjectValueRestriction)
- */
- public void visit(ObjectValueRestriction description) {
- ObjectProperty op = (ObjectProperty) description.getRestrictedPropertyExpression();
- Individual ind = description.getIndividual();
- query += "\n?" + stack.peek() + " <" + op.getName() + "> <" + ind.getName() + "> ";
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
- * .DatatypeValueRestriction)
- */
- public void visit(DatatypeValueRestriction description) {
- logger.trace("DatatypeValueRestriction");
- query += "\n?" + stack.peek() + " <" + description.getRestrictedPropertyExpression() + "> \""+description.getValue().getLiteral()+"\" ";
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
- * .NamedClass)
- */
- public void visit(NamedClass description) {
- logger.trace("NamedClass");
- query += "\n?" + stack.peek() + " a <" + description.getName() + "> ";
- foundNamedClasses.add(description.getName());
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.algorithms
- * .gp.ADC)
- */
- public void visit(ADC description) {
- logger.trace("ADC");
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
- * .DatatypeMinCardinalityRestriction)
- */
- public void visit(DatatypeMinCardinalityRestriction description) {
- logger.trace("DatatypeMinCardinalityRestriction");
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
- * .DatatypeExactCardinalityRestriction)
- */
- public void visit(DatatypeExactCardinalityRestriction description) {
- logger.trace("DatatypeExactCardinalityRestriction");
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
- * .DatatypeMaxCardinalityRestriction)
- */
- public void visit(DatatypeMaxCardinalityRestriction description) {
- logger.trace("DatatypeMaxCardinalityRestriction");
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
- * .DatatypeSomeRestriction)
- */
- public void visit(DatatypeSomeRestriction description) {
- logger.trace("DatatypeSomeRestriction");
- }
-
- @Override
- public void visit(ObjectOneOf description) {
- logger.trace("ObjectOneOf");
-
- }
-
-
-
+
+ private static Logger logger = Logger.getLogger(ComponentManager.class);
+
+ private int limit = 5;
+ private int offset = -1;
+ private boolean labels = false;
+ private boolean distinct = false;
+ private boolean count = false;
+ private String customFilter = null;
+
+ private SortedSet<String> transitiveProperties = null;
+ private Map<String, Set<String>> subclassMap = null;
+
+ private Stack<String> stack = new Stack<String>();
+ private String query = "";
+ private int currentObject = 0;
+ private List<String> foundNamedClasses = new ArrayList<String>();
+
+ /**
+ * resets internal variables
+ */
+ private void reset() {
+ currentObject = 0;
+ stack = new Stack<String>();
+ stack.push("subject");
+ query = "";
+ foundNamedClasses = new ArrayList<String>();
+ }
+
+ public SparqlQueryDescriptionConvertVisitor() {
+ stack.push("subject");
+ }
+
+ /**
+ * @param descriptionKBSyntax
+ * description which is parsed and passed to getSparqlQuery(
+ * Description description)
+ * @return
+ * @throws ParseException
+ */
+ public String getSparqlQuery(String descriptionKBSyntax) throws ParseException {
+ Description description = KBParser.parseConcept(descriptionKBSyntax);
+ return getSparqlQuery(description);
+ }
+
+ /**
+ * takes a description and transforms it into SPARQL
+ *
+ * @param description
+ * @return
+ */
+ public String getSparqlQuery(Description description) {
+ description.accept(this);
+ expandSubclasses();
+ String ret = "";
+ String customFilterTmp = pointalize(customFilter);
+ query = pointalize(query);
+ if (count) {
+ ret = "SELECT count(distinct(?subject)) as ?count { " + query + " \n"
+ + customFilterTmp + " \n } ";
+ } else {
+ ret = "SELECT " + distinct() + "?subject " + ((labels) ? "?label" : "") + " { "
+ + labels() + query + " \n" + customFilterTmp + "\n } " + limit();
+ }
+ reset();
+ return ret;
+ }
+
+ /**
+ * finalizes the patterns with a point
+ *
+ * @param toBePointed
+ * @return
+ */
+ private static String pointalize(String toBePointed) {
+ if (toBePointed == null) {
+ return "";
+ }
+ return (toBePointed.trim().endsWith(".")) ? toBePointed : toBePointed + " . ";
+ }
+
+ private void expandSubclasses() {
+ if (subclassMap == null) {
+ return;
+ }
+ int counter = 0;
+ int index = 0;
+ String var = "";
+ String uriPattern = "";
+ StringBuffer tmp;
+ StringBuffer filter = new StringBuffer();
+ Set<String> subClasses;
+ for (String nc : foundNamedClasses) {
+ index = query.indexOf("<" + nc + ">");
+ subClasses = subclassMap.get(nc);
+ if (index == -1) {
+ logger.error("named class was found before, but is not in query any more?? " + nc);
+ } else if (subClasses != null) {
+ var = "?expanded" + counter;
+ uriPattern = "<" + nc + ">";
+ tmp = new StringBuffer();
+ tmp.append(query.substring(0, index));
+ tmp.append(var);
+ tmp.append(query.substring(index + (uriPattern.length())));
+ query = tmp.toString();
+ filter.append(makeFilter(var, subClasses, nc));
+ } else {
+ logger.debug("no mapping found (" + nc + ") " + this.getClass().getSimpleName());
+ }
+
+ counter++;
+ }
+ query += filter.toString();
+ }
+
+ private String makeFilter(String var, Set<String> classes, String superClassUri) {
+ StringBuffer buf = new StringBuffer("\nFILTER ( " + var + " IN ( ");
+ for (String string : classes) {
+ buf.append("<" + string + ">, ");
+ }
+ buf.append("<" + superClassUri + "> ) ). ");
+ return buf.toString();
+ }
+
+ private String limit() {
+ if (limit > 0 && offset > 0) {
+ return " LIMIT " + limit + " OFFSET " + offset + " ";
+ } else if (limit > 0) {
+ return " LIMIT " + limit + " ";
+ } else {
+ return "";
+ }
+ }
+
+ private String labels() {
+ return (labels) ? "\n?subject rdfs:label ?label . " : "";
+ }
+
+ private String distinct() {
+ return (distinct) ? "DISTINCT " : "";
+ }
+
+ /**
+ * @param limit
+ * <= 0 means no limit
+ */
+ public void setLimit(int limit) {
+ this.limit = limit;
+ }
+
+ public void noLimit() {
+ this.limit = -1;
+ }
+
+ /**
+ * also retrieve labels (untested)
+ *
+ * @param labels
+ */
+ public void setLabels(boolean labels) {
+ this.labels = labels;
+ }
+
+ /**
+ * result is distinct
+ *
+ * @param distinct
+ */
+ public void setDistinct(boolean distinct) {
+ this.distinct = distinct;
+ }
+
+ /**
+ * virtuoso optimisation for transitive properties
+ *
+ * @param transitiveProperties
+ */
+ public void setTransitiveProperties(SortedSet<String> transitiveProperties) {
+ this.transitiveProperties = transitiveProperties;
+ }
+
+ /**
+ * needed for expanding subclasses, if store does no reasoning
+ *
+ * @param subclassMap
+ */
+ public void setSubclassMap(Map<String, Set<String>> subclassMap) {
+ this.subclassMap = subclassMap;
+ }
+
+ public void setCount(boolean count) {
+ this.count = count;
+ }
+
+ public void setOffset(int offset) {
+ this.offset = offset;
+ }
+
+ public void setCustomFilter(String customFilter) {
+ this.customFilter = customFilter;
+ }
+
+ public static String getSparqlQuery(String descriptionKBSyntax, int limit, boolean labels,
+ boolean distinct) throws ParseException {
+ Description d = KBParser.parseConcept(descriptionKBSyntax);
+ return getSparqlQuery(d, limit, labels, distinct);
+ }
+
+ public static String getSparqlQuery(Description description, int limit, boolean labels,
+ boolean distinct) {
+ SparqlQueryDescriptionConvertVisitor visitor = new SparqlQueryDescriptionConvertVisitor();
+ visitor.setDistinct(distinct);
+ visitor.setLabels(labels);
+ visitor.setLimit(limit);
+ return visitor.getSparqlQuery(description);
+ }
+
+ /**
+ * COMMENT: write some more includes subclasses, costly function, because
+ * subclasses have to be received first. TODO mentioned method cannot be
+ * found by Javadoc tool conceptRewrite(String descriptionKBSyntax,
+ * SparqlEndpoint se, Cache c, boolean simple)
+ *
+ * @param descriptionKBSyntax
+ * @see #getSparqlQuery(Description description, int limit)
+ * @param resultLimit
+ * @see #getSparqlQuery(Description description, int limit)
+ * @param maxDepth
+ * @throws ParseException
+ */
+
+ public static String getSparqlQueryIncludingSubclasses(String descriptionKBSyntax,
+ int resultLimit, SPARQLTasks st, int maxDepth) throws ParseException {
+ String rewritten = SparqlQueryDescriptionConvertRDFS.conceptRewrite(descriptionKBSyntax,
+ st, maxDepth);
+
+ return getSparqlQuery(rewritten, resultLimit, false, false);
+
+ }
+
+ public static void testHasValue() throws Exception {
+ // String ttt =
+ // "(\"http://dbpedia.org/ontology/Plant\" AND (\"http://dbpedia.org/ontology/kingdom\" hasValue \"http://dbpedia.org/resource/Plantae\" OR EXISTS \"http://dbpedia.org/ontology/family\".\"http://dbpedia.org/ontology/FloweringPlant\"))";
+ String ttt = "(\"http://dbpedia.org/ontology/Plant\" AND ((\"http://dbpedia.org/ontology/kingdom\" HASVALUE \"http://dbpedia.org/resource/Plantae\") OR EXISTS \"http://dbpedia.org/ontology/family\".\"http://dbpedia.org/ontology/FloweringPlant\"))";
+ SparqlQueryDescriptionConvertVisitor testVisitor = new SparqlQueryDescriptionConvertVisitor();
+ String q = testVisitor.getSparqlQuery(ttt);
+ System.out.println(q);
+ Description description = KBParser.parseConcept(ttt);
+ System.out.println(description.toString());
+ System.out.println(description.toKBSyntaxString());
+ System.out.println(description.toKBSyntaxString(null, null));
+ if (true) {
+ System.exit(0);
+ }
+
+ }
+
+ public static void testTrans() throws Exception {
+ // String ttt =
+ // "(\"http://dbpedia.org/ontology/Plant\" AND (\"http://dbpedia.org/ontology/kingdom\" hasValue \"http://dbpedia.org/resource/Plantae\" OR EXISTS \"http://dbpedia.org/ontology/family\".\"http://dbpedia.org/ontology/FloweringPlant\"))";
+ // String ttt =
+ // "(\"http://dbpedia.org/ontology/Plant\" AND ((\"http://dbpedia.org/ontology/kingdom\" HASVALUE \"http://dbpedia.org/resource/Plantae\") OR EXISTS \"http://dbpedia.org/ontology/family\".\"http://dbpedia.org/ontology/FloweringPlant\"))";
+ String ttt = "EXISTS \"http://dbpedia.org/ontology/kingdom\".\"http://dbpedia.org/resource/Plantae\"";
+ SparqlQueryDescriptionConvertVisitor testVisitor = new SparqlQueryDescriptionConvertVisitor();
+ testVisitor.setTransitiveProperties(new TreeSet<String>(Arrays
+ .asList(new String[] { "http://dbpedia.org/ontology/kingdom" })));
+ String q = testVisitor.getSparqlQuery(ttt);
+ System.out.println(q);
+ Description description = KBParser.parseConcept(ttt);
+ System.out.println(description.toString());
+ System.out.println(description.toKBSyntaxString());
+ System.out.println(description.toKBSyntaxString(null, null));
+ if (true) {
+ System.exit(0);
+ }
+
+ }
+
+ /**
+ * Used for testing the Sparql Query converter.
+ *
+ * @param args
+ */
+ public static void main(String[] args) throws Exception {
+
+ try {
+ // testTrans();
+ testHasValue();
+
+ // SparqlQueryConverter.test();
+
+ SortedSet<String> s = new TreeSet<String>();
+ HashMap<String, String> result = new HashMap<String, String>();
+ HashMap<String, String> subclassMap = new HashMap<String, String>();
+ subclassMap.put("http://nlp2rdf.org/ontology/Sentence",
+ "<http://nlp2rdf.org/ontology/Subsentence>");
+ String conj = "(\"http://dbpedia.org/class/yago/Person100007846\" AND \"http://dbpedia.org/class/yago/Head110162991\")";
+
+ s.add("EXISTS \"http://dbpedia.org/property/disambiguates\".TOP");
+ s.add("EXISTS \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
+ s.add("EXISTS \"http://dbpedia.org/property/successor\"." + conj);
+ s.add("ALL \"http://dbpedia.org/property/disambiguates\".TOP");
+ s.add("ALL \"http://dbpedia.org/property/successor\".\"http://dbpedia.org/class/yago/Person100007846\"");
+ s.add("\"http://dbpedia.org/class/yago/Person100007846\"");
+ s.add(conj);
+ s.add("(\"http://dbpedia.org/class/yago/Person100007846\" OR \"http://dbpedia.org/class/yago/Head110162991\")");
+ s.add("NOT \"http://dbpedia.org/class/yago/Person100007846\"");
+ s.add("(\"http://dbpedia.org/class/yago/HeadOfState110164747\" AND (\"http://dbpedia.org/class/yago/Negotiator110351874\" AND \"http://dbpedia.org/class/yago/Representative110522035\"))");
+
+ s.clear();
+ // s.add("(\"http://nlp2rdf.org/ontology/Sentence\" AND (EXISTS \"http://nlp2rdf.org/ontology/syntaxTreeHasPart\".\"http://nachhalt.sfb632.uni-potsdam.de/owl/stts.owl#Pronoun\" AND EXISTS \"http://nlp2rdf.org/ontology/syntaxTreeHasPart\".\"http://nlp2rdf.org/ontology/sentencefinalpunctuation_tag\"))");
+ // s.add("(\"http://nlp2rdf.org/ontology/Sentence\" AND (\"http://nlp2rdf.org/ontology/hasLemma\" VALUE \"test\" )");
+
+ String prefix = "http://nlp2rdf.org/ontology/";
+ String test = "(\"Sentence\" AND (EXISTS \"syntaxTreeHasPart\".\"VVPP\" AND EXISTS \"syntaxTreeHasPart\".(\"stts:AuxilliaryVerb\" AND \"hasLemma\" = werden)))";
+
+ ObjectProperty stp = new ObjectProperty(prefix + "syntaxTreeHasPart");
+ DatatypeProperty dtp = new DatatypeProperty(prefix + "hasLemma");
+ StringValueRestriction svr = new StringValueRestriction(dtp, "werden");
+ Intersection inner = new Intersection(new NamedClass(prefix + "Auxillary"), svr);
+ Intersection middle = new Intersection(new ObjectSomeRestriction(stp, new NamedClass(
+ prefix + "VVPP")), new ObjectSomeRestriction(stp, inner));
+ Intersection outer = new Intersection(new NamedClass(prefix + "Sentence"), middle);
+
+ System.out.println(outer.toKBSyntaxString(null, null));
+ System.out.println(test);
+
+ Map<String, Set<String>> testMap = new HashMap<String, Set<String>>();
+ testMap.put(prefix + "Sentence",
+ new HashSet<String>(Arrays.asList(new String[] { "whatever", "loser" })));
+ // s.add(outer.toKBSyntaxString(null,null));
+ SparqlQueryDescriptionConvertVisitor testVisitor = new SparqlQueryDescriptionConvertVisitor();
+ testVisitor.setSubclassMap(testMap);
+ String q = testVisitor.getSparqlQuery(outer.toKBSyntaxString());
+ System.out.println(q);
+ if (true) {
+ System.exit(0);
+ }
+ // <http://nlp2rdf.org/ontology/sentencefinalpunctuation_tag>
+ String query = "";
+ SparqlQueryDescriptionConvertVisitor visit = new SparqlQueryDescriptionConvertVisitor();
+ visit.setLabels(false);
+ visit.setDistinct(false);
+ // visit.setClassToSubclassesVirtuoso(subclassMap);
+
+ for (String kbsyntax : s) {
+ query = visit.getSparqlQuery(kbsyntax);
+ result.put(kbsyntax, query);
+ }
+ System.out.println("************************");
+ for (String string : result.keySet()) {
+ System.out.println("KBSyntayString: " + string);
+ System.out.println("Query:\n" + result.get(string));
+ System.out.println("************************");
+ }
+ System.out.println("Finished");
+ } catch (ParseException e) {
+ e.printStackTrace();
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
+ * .Negation)
+ */
+ public void visit(Negation description) {
+ logger.trace("Negation");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
+ * .ObjectAllRestriction)
+ */
+ public void visit(ObjectAllRestriction description) {
+ logger.trace("ObjectAllRestriction");
+ query+="\n ?"+stack.peek()+ " <"+description.getRole()+"> ?object"+currentObject;
+ customFilter += "\n FILTERS NOT EXISTS { ?object a ?object" + currentObject++
+ + " FILTER (?object" + currentObject + " != <"
+ + description.getChild(0) + "> ) }";
+ currentObject++;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
+ * .ObjectSomeRestriction)
+ */
+ public void visit(ObjectSomeRestriction description) {
+ logger.trace("ObjectSomeRestriction");
+ String option = "";
+ if (transitiveProperties != null
+ && transitiveProperties.contains(description.getRole().toString())) {
+ option = " OPTION (TRANSITIVE , t_in(?" + stack.peek() + "), t_out(?object"
+ + currentObject + "), T_MIN(0), T_MAX(6), T_DIRECTION 1 , T_NO_CYCLES) ";
+ }
+
+ if (description.getChild(0) instanceof Thing) {
+ // I removed a point here at the end
+ query += "\n?" + stack.peek() + " <" + description.getRole() + "> [] " + option + " ";
+ } else {
+ query += "\n?" + stack.peek() + " <" + description.getRole() + "> ?object"
+ + currentObject + option + " . ";
+ stack.push("object" + currentObject);
+ currentObject++;
+ description.getChild(0).accept(this);
+ stack.pop();
+ }
+
+ logger.trace(description.getRole().toString());
+ logger.trace(description.getChild(0).toString());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
+ * .Nothing)
+ */
+ public void visit(Nothing description) {
+ logger.trace("Nothing");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
+ * .Thing)
+ */
+ public void visit(Thing description) {
+ logger.trace("Thing");
+
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
+ * .Intersection)
+ */
+ public void visit(Intersection description) {
+ if (description.getChild(0) instanceof Thing) {
+ logger.trace("Intersection with TOP");
+ description.getChild(1).accept(this);
+ } else if (description.getChild(1) instanceof Thing) {
+ logger.trace("Intersection with TOP");
+ description.getChild(0).accept(this);
+ } else {
+ logger.trace("Intersection");
+ description.getChild(0).accept(this);
+ query += ". ";
+ description.getChild(1).accept(this);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
+ * .Union)
+ */
+ public void visit(Union description) {
+
+ if (description.getChild(0) instanceof Thing) {
+ logger.trace("Union with TOP");
+ description.getChild(1).accept(this);
+ } else if (description.getChild(1) instanceof Thing) {
+ logger.trace("Union with TOP");
+ description.getChild(0).accept(this);
+ } else {
+ logger.trace("Union");
+ query += "{";
+ description.getChild(0).accept(this);
+ query += "} UNION {";
+ description.getChild(1).accept(this);
+ query += "}";
+ }
+
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
+ * .ObjectMinCardinalityRestriction)
+ */
+ public void visit(ObjectMinCardinalityRestriction description) {
+ logger.trace("ObjectMinCardinalityRestriction");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
+ * .ObjectExactCardinalityRestriction)
+ */
+ public void visit(ObjectExactCardinalityRestriction description) {
+ logger.trace("ObjectExactCardinalityRestriction");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
+ * .ObjectMaxCardinalityRestriction)
+ */
+ public void visit(ObjectMaxCardinalityRestriction description) {
+ logger.trace("ObjectMaxCardinalityRestriction");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
+ * .ObjectValueRestriction)
+ */
+ public void visit(ObjectValueRestriction description) {
+ ObjectProperty op = (ObjectProperty) description.getRestrictedPropertyExpression();
+ Individual ind = description.getIndividual();
+ query += "\n?" + stack.peek() + " <" + op.getName() + "> <" + ind.getName() + "> ";
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
+ * .DatatypeValueRestriction)
+ */
+ public void visit(DatatypeValueRestriction description) {
+ logger.trace("DatatypeValueRestriction");
+ query += "\n?" + stack.peek() + " <" + description.getRestrictedPropertyExpression()
+ + "> \"" + description.getValue().getLiteral() + "\" ";
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
+ * .NamedClass)
+ */
+ public void visit(NamedClass description) {
+ logger.trace("NamedClass");
+ query += "\n?" + stack.peek() + " a <" + description.getName() + "> ";
+ foundNamedClasses.add(description.getName());
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.algorithms
+ * .gp.ADC)
+ */
+ public void visit(ADC description) {
+ logger.trace("ADC");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
+ * .DatatypeMinCardinalityRestriction)
+ */
+ public void visit(DatatypeMinCardinalityRestriction description) {
+ logger.trace("DatatypeMinCardinalityRestriction");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
+ * .DatatypeExactCardinalityRestriction)
+ */
+ public void visit(DatatypeExactCardinalityRestriction description) {
+ logger.trace("DatatypeExactCardinalityRestriction");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
+ * .DatatypeMaxCardinalityRestriction)
+ */
+ public void visit(DatatypeMaxCardinalityRestriction description) {
+ logger.trace("DatatypeMaxCardinalityRestriction");
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * org.dllearner.core.owl.DescriptionVisitor#visit(org.dllearner.core.owl
+ * .DatatypeSomeRestriction)
+ */
+ public void visit(DatatypeSomeRestriction description) {
+ logger.trace("DatatypeSomeRestriction");
+ }
+
+ @Override
+ public void visit(ObjectOneOf description) {
+ logger.trace("ObjectOneOf");
+
+ }
+
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-06-13 13:36:51
|
Revision: 3996
http://sourceforge.net/p/dl-learner/code/3996
Author: lorenz_b
Date: 2013-06-13 13:36:48 +0000 (Thu, 13 Jun 2013)
Log Message:
-----------
Improved enrichment.
Modified Paths:
--------------
trunk/interfaces/pom.xml
trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
Modified: trunk/interfaces/pom.xml
===================================================================
--- trunk/interfaces/pom.xml 2013-06-13 13:34:00 UTC (rev 3995)
+++ trunk/interfaces/pom.xml 2013-06-13 13:36:48 UTC (rev 3996)
@@ -521,6 +521,10 @@
<!-- Exclude Project-D from Project-B -->
<artifactId>slf4j-log4j12</artifactId>
</exclusion>
+ <exclusion>
+ <groupId>net.sourceforge</groupId>
+ <artifactId>owlapi</artifactId>
+ </exclusion>
</exclusions>
</dependency>
<dependency>
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2013-06-13 13:34:00 UTC (rev 3995)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2013-06-13 13:36:48 UTC (rev 3996)
@@ -67,6 +67,7 @@
import org.aksw.commons.jena_owlapi.Conversion;
import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
+import org.apache.jena.riot.Lang;
import org.apache.jena.riot.checker.CheckerLiterals;
import org.apache.jena.riot.system.ErrorHandlerFactory;
import org.apache.log4j.ConsoleAppender;
@@ -345,7 +346,7 @@
// loop over all entities and call appropriate algorithms
Set<NamedClass> classes = reasoner.getTypes();//st.getAllClasses();
- filterByNamespaces(classes);//classes = Sets.newHashSet(new NamedClass("http://dbpedia.org/ontology/AdministrativeRegion"));
+ filterByNamespaces(classes);//classes = Sets.newHashSet(new NamedClass("http://dbpedia.org/ontology/Arachnid"));
int entities = 0;
for(NamedClass nc : classes) {
try {
@@ -856,16 +857,14 @@
model.write(fos, "TURTLE", null);
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
OWLOntology ontology = man.loadOntologyFromOntologyDocument(new ByteArrayInputStream(baos.toByteArray()));
- try {
- man.saveOntology(ontology, new TurtleOntologyFormat(), new FileOutputStream("error.owl"));
- } catch (OWLOntologyStorageException e) {
- e.printStackTrace();
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- }
return ontology;
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
+ try {
+ model.write(new FileOutputStream("parse-error.ttl"), "TURTLE", null);
+ } catch (FileNotFoundException e1) {
+ e1.printStackTrace();
+ }
}
return null;
}
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|
|
From: <lor...@us...> - 2013-06-13 13:34:03
|
Revision: 3995
http://sourceforge.net/p/dl-learner/code/3995
Author: lorenz_b
Date: 2013-06-13 13:34:00 +0000 (Thu, 13 Jun 2013)
Log Message:
-----------
Cleaned up pom. Optimzed cache usage.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/kb/OWLAPIOntology.java
trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/SimpleOntologyToByteConverter.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2013-06-13 10:28:10 UTC (rev 3994)
+++ trunk/components-core/pom.xml 2013-06-13 13:34:00 UTC (rev 3995)
@@ -102,37 +102,8 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-distribution</artifactId>
- <type>pom</type>
+ <version>3.4.4</version>
</dependency>
- <dependency>
- <groupId>net.sourceforge.owlapi</groupId>
- <artifactId>owlapi-dlsyntax</artifactId>
- <version>3.3</version>
- </dependency>
- <dependency>
- <groupId>net.sourceforge.owlapi</groupId>
- <artifactId>owlapi-functional</artifactId>
- <version>3.3</version>
- </dependency>
-
- <dependency>
- <groupId>net.sourceforge.owlapi</groupId>
- <artifactId>owlapi-reasoner</artifactId>
-</dependency>
-<dependency>
- <groupId>net.sourceforge.owlapi</groupId>
- <artifactId>owlapi-debugging</artifactId>
- <version>3.3</version>
-</dependency>
-<dependency>
- <groupId>net.sourceforge.owlapi</groupId>
- <artifactId>owlapi-modularity</artifactId>
- <version>3.3</version>
-</dependency>
-<dependency>
- <groupId>net.sourceforge.owlapi</groupId>
- <artifactId>owlapi-util</artifactId>
- </dependency>
<!-- THIS IS FROM THE UNIBAS REPO -->
<dependency>
Modified: trunk/components-core/src/main/java/org/dllearner/kb/OWLAPIOntology.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/OWLAPIOntology.java 2013-06-13 10:28:10 UTC (rev 3994)
+++ trunk/components-core/src/main/java/org/dllearner/kb/OWLAPIOntology.java 2013-06-13 13:34:00 UTC (rev 3995)
@@ -21,6 +21,7 @@
import java.io.File;
import java.net.URI;
+import java.util.Collections;
import org.dllearner.core.AbstractKnowledgeSource;
import org.dllearner.core.OntologyFormat;
@@ -39,10 +40,12 @@
private byte[] ontologyBytes;
private OntologyToByteConverter converter = new SimpleOntologyToByteConverter();
+ private OWLOntology ontology;
- public OWLAPIOntology(OWLOntology onto) {
- ontologyBytes = converter.convert(onto);
+ public OWLAPIOntology(OWLOntology ontology) {
+ this.ontology = ontology;
+// ontologyBytes = converter.convert(ontology);
}
public static String getName() {
@@ -51,7 +54,20 @@
@Override
public OWLOntology createOWLOntology(OWLOntologyManager manager) {
- return converter.convert(ontologyBytes, manager);
+ OWLOntology copy = null;
+ try {
+ IRI iri;
+ if(ontology.getOntologyID().isAnonymous()){
+ iri = IRI.generateDocumentIRI();
+ } else {
+ iri = ontology.getOntologyID().getOntologyIRI();
+ }
+ copy = manager.createOntology(iri, Collections.singleton(ontology));
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ }
+// return converter.convert(ontologyBytes, manager);
+ return copy;
}
@Override
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java 2013-06-13 10:28:10 UTC (rev 3994)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java 2013-06-13 13:34:00 UTC (rev 3995)
@@ -11,7 +11,6 @@
import org.aksw.jena_sparql_api.cache.extra.CacheEx;
import org.aksw.jena_sparql_api.cache.extra.CacheExImpl;
import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
-//import org.aksw.jena_sparql_api.http.QueryExecutionFactoryHttp;
import org.aksw.jena_sparql_api.model.QueryExecutionFactoryModel;
import org.aksw.jena_sparql_api.pagination.core.QueryExecutionFactoryPaginated;
import org.apache.log4j.Level;
@@ -19,6 +18,7 @@
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.rdf.model.Model;
+//import org.aksw.jena_sparql_api.http.QueryExecutionFactoryHttp;
//import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
public class ConciseBoundedDescriptionGeneratorImpl implements ConciseBoundedDescriptionGenerator{
@@ -27,34 +27,42 @@
private int chunkSize = 0;
- private ExtractionDBCache cache;
- private SparqlEndpoint endpoint;
private Model baseModel;
private List<String> namespaces;
+ private static final int MAX_RECURSION_DEPTH_DEFAULT = 1;
private int maxRecursionDepth = 1;
- private String cacheDir;
+ private QueryExecutionFactory qef;
public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, ExtractionDBCache cache) {
- this.endpoint = endpoint;
- this.cache = cache;
+ this(endpoint, cache, MAX_RECURSION_DEPTH_DEFAULT);
}
public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, ExtractionDBCache cache, int maxRecursionDepth) {
- this.endpoint = endpoint;
- this.cache = cache;
- this.maxRecursionDepth = maxRecursionDepth;
+ this(endpoint, cache.getCacheDirectory(), maxRecursionDepth);
}
public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, String cacheDir, int maxRecursionDepth) {
- this.endpoint = endpoint;
- this.cacheDir = cacheDir;
this.maxRecursionDepth = maxRecursionDepth;
+
+ qef = new QueryExecutionFactoryHttp(endpoint.getURL().toString(), endpoint.getDefaultGraphURIs());
+ if(cacheDir != null){
+ try {
+ long timeToLive = TimeUnit.DAYS.toMillis(30);
+ CacheCoreEx cacheBackend = CacheCoreH2.create(cacheDir, timeToLive, true);
+ CacheEx cacheFrontend = new CacheExImpl(cacheBackend);
+ qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
+ } catch (ClassNotFoundException e) {
+ e.printStackTrace();
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ }
+ qef = new QueryExecutionFactoryPaginated(qef, 10000);
}
public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, String cacheDir) {
- this.endpoint = endpoint;
- this.cacheDir = cacheDir;
+ this(endpoint, cacheDir, MAX_RECURSION_DEPTH_DEFAULT);
}
public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint) {
@@ -63,6 +71,8 @@
public ConciseBoundedDescriptionGeneratorImpl(Model model) {
this.baseModel = model;
+
+ qef = new QueryExecutionFactoryModel(baseModel);
}
public Model getConciseBoundedDescription(String resourceURI){
@@ -79,25 +89,6 @@
private Model getModelChunked(String resource, int depth){
String query = makeConstructQueryOptional(resource, chunkSize, 0, depth);
- QueryExecutionFactory qef;
- if(endpoint != null){
- qef = new QueryExecutionFactoryHttp(endpoint.getURL().toString(), endpoint.getDefaultGraphURIs());
- if(cacheDir != null){
- try {
- long timeToLive = TimeUnit.DAYS.toMillis(30);
- CacheCoreEx cacheBackend = CacheCoreH2.create(cacheDir, timeToLive, true);
- CacheEx cacheFrontend = new CacheExImpl(cacheBackend);
- qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
- } catch (ClassNotFoundException e) {
- e.printStackTrace();
- } catch (SQLException e) {
- e.printStackTrace();
- }
- }
- qef = new QueryExecutionFactoryPaginated(qef, 10000);
- } else {
- qef = new QueryExecutionFactoryModel(baseModel);
- }
QueryExecution qe = qef.createQueryExecution(query);
Model model = qe.execConstruct();
return model;
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-06-13 10:28:10 UTC (rev 3994)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-06-13 13:34:00 UTC (rev 3995)
@@ -19,7 +19,6 @@
package org.dllearner.reasoning;
-import java.net.SocketTimeoutException;
import java.net.URL;
import java.sql.SQLException;
import java.util.ArrayList;
@@ -41,6 +40,7 @@
import org.aksw.jena_sparql_api.cache.extra.CacheExImpl;
import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
import org.aksw.jena_sparql_api.http.QueryExecutionFactoryHttp;
+import org.aksw.jena_sparql_api.model.QueryExecutionFactoryModel;
import org.aksw.jena_sparql_api.pagination.core.QueryExecutionFactoryPaginated;
import org.dllearner.core.ComponentAnn;
import org.dllearner.core.IndividualReasoner;
@@ -81,9 +81,6 @@
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
-import com.hp.hpl.jena.sparql.engine.http.QueryExceptionHTTP;
-import com.hp.hpl.jena.sparql.resultset.ResultSetMem;
import com.hp.hpl.jena.vocabulary.OWL;
import com.hp.hpl.jena.vocabulary.OWL2;
import com.hp.hpl.jena.vocabulary.RDF;
@@ -98,6 +95,7 @@
private boolean useCache = true;
private ExtractionDBCache cache;
+ private QueryExecutionFactory qef;
private SparqlEndpointKS ks;
private ClassHierarchy hierarchy;
@@ -128,6 +126,27 @@
classPopularityMap = new HashMap<NamedClass, Integer>();
objectPropertyPopularityMap = new HashMap<ObjectProperty, Integer>();
+
+ if(ks.isRemote()){
+ SparqlEndpoint endpoint = ks.getEndpoint();
+ qef = new QueryExecutionFactoryHttp(endpoint.getURL().toString(), endpoint.getDefaultGraphURIs());
+ if(cache != null){
+ try {
+ long timeToLive = TimeUnit.DAYS.toMillis(30);
+ CacheCoreEx cacheBackend = CacheCoreH2.create(cache.getCacheDirectory(), timeToLive, true);
+ CacheEx cacheFrontend = new CacheExImpl(cacheBackend);
+ qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
+ } catch (ClassNotFoundException e) {
+ e.printStackTrace();
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ }
+ qef = new QueryExecutionFactoryPaginated(qef, 10000);
+
+ } else {
+ qef = new QueryExecutionFactoryModel(((LocalModelBasedSparqlEndpointKS)ks).getModel());
+ }
}
public SPARQLReasoner(OntModel model) {
@@ -1362,58 +1381,25 @@
private ResultSet executeSelectQuery(String query){
logger.debug("Sending query \n {}", query);
- ResultSet rs = null;
- if(ks.isRemote()){
- SparqlEndpoint endpoint = ks.getEndpoint();
- QueryExecutionFactory qef = new QueryExecutionFactoryHttp(endpoint.getURL().toString(), endpoint.getDefaultGraphURIs());
- if(cache != null){
- try {
- long timeToLive = TimeUnit.DAYS.toMillis(30);
- CacheCoreEx cacheBackend = CacheCoreH2.create(cache.getCacheDirectory(), timeToLive, true);
- CacheEx cacheFrontend = new CacheExImpl(cacheBackend);
- qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
- } catch (ClassNotFoundException e) {
- e.printStackTrace();
- } catch (SQLException e) {
- e.printStackTrace();
- }
- }
- qef = new QueryExecutionFactoryPaginated(qef, 10000);
- QueryExecution qe = qef.createQueryExecution(query);
- rs = qe.execSelect();
- } else {
- QueryExecution qExec = com.hp.hpl.jena.query.QueryExecutionFactory.create(query, ((LocalModelBasedSparqlEndpointKS)ks).getModel());
- rs = qExec.execSelect();
- }
+ QueryExecution qe = qef.createQueryExecution(query);
+ ResultSet rs = qe.execSelect();
return rs;
}
private ResultSet executeSelectQuery(String query, long timeout){
logger.debug("Sending query \n {}", query);
- ResultSet rs = null;
- if(ks.isRemote()){
- SparqlEndpoint endpoint = ((SparqlEndpointKS) ks).getEndpoint();
- QueryEngineHTTP queryExecution = new QueryEngineHTTP(endpoint.getURL().toString(),
- query);
- queryExecution.setTimeout(timeout);
- queryExecution.setDefaultGraphURIs(endpoint.getDefaultGraphURIs());
- queryExecution.setNamedGraphURIs(endpoint.getNamedGraphURIs());
- try {
- rs = queryExecution.execSelect();
- } catch (QueryExceptionHTTP e) {
- if(e.getCause() instanceof SocketTimeoutException){
- logger.warn("Got timeout");
- } else {
- logger.error("Exception executing query", e);
- }
- rs = new ResultSetMem();
- }
- } else {
- QueryExecution qExec = com.hp.hpl.jena.query.QueryExecutionFactory.create(query, ((LocalModelBasedSparqlEndpointKS)ks).getModel());
- rs = qExec.execSelect();
- }
+ QueryExecution qe = qef.createQueryExecution(query);
+ qe.setTimeout(timeout);
+ ResultSet rs = qe.execSelect();
return rs;
}
+
+ private boolean executeAskQuery(String query){
+ logger.debug("Sending query \n {}", query);
+ QueryExecution qe = qef.createQueryExecution(query);
+ boolean ret = qe.execAsk();
+ return ret;
+ }
/**
* Returns TRUE if the class hierarchy was computed before.
@@ -1431,27 +1417,6 @@
this.useCache = useCache;
}
- private boolean executeAskQuery(String query){
- boolean ret;
- if(ks.isRemote()){
- QueryEngineHTTP queryExecution = new QueryEngineHTTP(ks.getEndpoint().getURL().toString(), query);
- for (String dgu : ks.getEndpoint().getDefaultGraphURIs()) {
- queryExecution.addDefaultGraph(dgu);
- }
- for (String ngu : ks.getEndpoint().getNamedGraphURIs()) {
- queryExecution.addNamedGraph(ngu);
- }
- ret = queryExecution.execAsk();
-
- } else {
- QueryExecution qExec = com.hp.hpl.jena.query.QueryExecutionFactory.create(query, ((LocalModelBasedSparqlEndpointKS)ks).getModel());
- ret = qExec.execAsk();
- }
-
- return ret;
- }
-
-
public static void main(String[] args) throws Exception{
// QueryEngineHTTP e = new QueryEngineHTTP("http://bibleontology.com/sparql/index.jsp",
// "SELECT DISTINCT ?type WHERE {?s a ?type) LIMIT 10");
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/owl/SimpleOntologyToByteConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/SimpleOntologyToByteConverter.java 2013-06-13 10:28:10 UTC (rev 3994)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/SimpleOntologyToByteConverter.java 2013-06-13 13:34:00 UTC (rev 3995)
@@ -1,5 +1,8 @@
package org.dllearner.utilities.owl;
+import org.coode.owlapi.turtle.TurtleOntologyFormat;
+import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
+import org.semanticweb.owlapi.model.OWLNamedIndividual;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
@@ -7,7 +10,9 @@
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
+import java.io.FileOutputStream;
import java.io.IOException;
+import java.util.Set;
/**
* Created by IntelliJ IDEA.
@@ -26,7 +31,7 @@
OWLOntologyManager manager = ontology.getOWLOntologyManager();
try {
- manager.saveOntology(ontology,baos);
+ manager.saveOntology(ontology, baos);
baos.close();
} catch (OWLOntologyStorageException e) {
throw new RuntimeException(e);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jen...@us...> - 2013-06-13 10:28:13
|
Revision: 3994
http://sourceforge.net/p/dl-learner/code/3994
Author: jenslehmann
Date: 2013-06-13 10:28:10 +0000 (Thu, 13 Jun 2013)
Log Message:
-----------
configurable semantics for all quantor in fast instance checker
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java 2013-06-13 07:46:18 UTC (rev 3993)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java 2013-06-13 10:28:10 UTC (rev 3994)
@@ -137,8 +137,10 @@
"to return all those which do not have an r-filler not in C. The domain semantics is to use those" +
"which are in the domain of r and do not have an r-filler not in C. The forallExists semantics is to"+
"use those which have at least one r-filler and do not have an r-filler not in C.",defaultValue = "standard",propertyEditorClass = StringTrimmerEditor.class)
- private String forAllSemantics;
+ private ForallSemantics forallSemantics = ForallSemantics.Standard;
+ public enum ForallSemantics { Standard, SomeOnly }
+
/**
* Creates an instance of the fast instance checker.
*/
@@ -400,7 +402,11 @@
}
SortedSet<Individual> roleFillers = opPos.get(op).get(individual);
if (roleFillers == null) {
- return true;
+ if(forallSemantics == ForallSemantics.Standard) {
+ return true;
+ } else {
+ return false;
+ }
}
for (Individual roleFiller : roleFillers) {
if (!hasTypeImpl(child, roleFiller)) {
@@ -1124,11 +1130,13 @@
this.defaultNegation = defaultNegation;
}
- public String getForAllSemantics() {
- return forAllSemantics;
- }
+ public ForallSemantics getForAllSemantics() {
+ return forallSemantics;
+ }
- public void setForAllSemantics(String forAllSemantics) {
- this.forAllSemantics = forAllSemantics;
- }
+ public void setForAllSemantics(ForallSemantics forallSemantics) {
+ this.forallSemantics = forallSemantics;
+ }
+
+
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-06-13 07:46:21
|
Revision: 3993
http://sourceforge.net/p/dl-learner/code/3993
Author: lorenz_b
Date: 2013-06-13 07:46:18 +0000 (Thu, 13 Jun 2013)
Log Message:
-----------
Updated SPARQL API.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/NBR.java
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
trunk/pom.xml
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2013-06-12 09:13:43 UTC (rev 3992)
+++ trunk/components-core/pom.xml 2013-06-13 07:46:18 UTC (rev 3993)
@@ -91,28 +91,6 @@
<dependencies>
<dependency>
- <groupId>org.aksw.commons</groupId>
- <artifactId>sparql</artifactId>
- <exclusions>
- <exclusion>
- <artifactId>slf4j-api</artifactId>
- <groupId>org.slf4j</groupId>
- </exclusion>
- <exclusion>
- <artifactId>arq</artifactId>
- <groupId>com.hp.hpl.jena</groupId>
- </exclusion>
- <exclusion>
- <artifactId>xercesImpl</artifactId>
- <groupId>xerces</groupId>
- </exclusion>
- <exclusion>
- <artifactId>any23-core</artifactId>
- <groupId>org.deri.any23</groupId>
- </exclusion>
- </exclusions>
- </dependency>
- <dependency>
<groupId>org.ini4j</groupId>
<artifactId>ini4j</artifactId>
</dependency>
@@ -323,7 +301,7 @@
<dependency>
<groupId>org.aksw.jena-sparql-api</groupId>
<artifactId>jena-sparql-api-core</artifactId>
- <version>2.10.0-3</version>
+ <version>2.10.0-4-SNAPSHOT</version>
</dependency>
</dependencies>
<dependencyManagement>
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/NBR.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/NBR.java 2013-06-12 09:13:43 UTC (rev 3992)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/NBR.java 2013-06-13 07:46:18 UTC (rev 3993)
@@ -18,7 +18,6 @@
import javax.xml.ws.http.HTTPException;
-import org.aksw.commons.jena.ExtendedQueryEngineHTTP;
import org.apache.log4j.Logger;
import org.dllearner.algorithms.qtl.datastructures.QueryTree;
import org.dllearner.algorithms.qtl.datastructures.impl.GeneralisedQueryTree;
@@ -41,6 +40,7 @@
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.RDFNode;
+import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
import com.hp.hpl.jena.sparql.expr.E_Equals;
import com.hp.hpl.jena.sparql.expr.E_LogicalNot;
import com.hp.hpl.jena.sparql.expr.ExprVar;
@@ -1401,8 +1401,8 @@
private ResultSet executeSelectQuery(String query){
ResultSet rs;
if(model == null){
- ExtendedQueryEngineHTTP queryExecution = new ExtendedQueryEngineHTTP(endpoint.getURL().toString(), query);
- queryExecution.setTimeOut(maxExecutionTimeInSeconds * 1000);
+ QueryEngineHTTP queryExecution = new QueryEngineHTTP(endpoint.getURL().toString(), query);
+ queryExecution.setTimeout(maxExecutionTimeInSeconds * 1000);
for (String dgu : endpoint.getDefaultGraphURIs()) {
queryExecution.addDefaultGraph(dgu);
}
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-06-12 09:13:43 UTC (rev 3992)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-06-13 07:46:18 UTC (rev 3993)
@@ -21,8 +21,8 @@
import java.net.SocketTimeoutException;
import java.net.URL;
+import java.sql.SQLException;
import java.util.ArrayList;
-import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
@@ -31,11 +31,17 @@
import java.util.SortedSet;
import java.util.TreeMap;
import java.util.TreeSet;
+import java.util.concurrent.TimeUnit;
-import org.aksw.commons.sparql.api.core.QueryExecutionFactory;
-import org.aksw.commons.sparql.api.http.QueryExecutionFactoryHttp;
-import org.aksw.commons.sparql.api.pagination.core.QueryExecutionFactoryPaginated;
import org.aksw.commons.util.strings.StringUtils;
+import org.aksw.jena_sparql_api.cache.core.QueryExecutionFactoryCacheEx;
+import org.aksw.jena_sparql_api.cache.extra.CacheCoreEx;
+import org.aksw.jena_sparql_api.cache.extra.CacheCoreH2;
+import org.aksw.jena_sparql_api.cache.extra.CacheEx;
+import org.aksw.jena_sparql_api.cache.extra.CacheExImpl;
+import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
+import org.aksw.jena_sparql_api.http.QueryExecutionFactoryHttp;
+import org.aksw.jena_sparql_api.pagination.core.QueryExecutionFactoryPaginated;
import org.dllearner.core.ComponentAnn;
import org.dllearner.core.IndividualReasoner;
import org.dllearner.core.SchemaReasoner;
@@ -61,7 +67,6 @@
import org.dllearner.kb.sparql.ExtractionDBCache;
import org.dllearner.kb.sparql.SPARQLTasks;
import org.dllearner.kb.sparql.SparqlEndpoint;
-import org.dllearner.kb.sparql.SparqlQuery;
import org.dllearner.utilities.datastructures.SortedSetTuple;
import org.dllearner.utilities.owl.ConceptComparator;
import org.slf4j.Logger;
@@ -73,7 +78,6 @@
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.query.ResultSetFormatter;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Resource;
@@ -1360,22 +1364,26 @@
logger.debug("Sending query \n {}", query);
ResultSet rs = null;
if(ks.isRemote()){
- if(useCache && cache != null){
- rs = SparqlQuery.convertJSONtoResultSet(cache.executeSelectQuery(ks.getEndpoint(), query));
- } else {
- QueryEngineHTTP queryExecution = new QueryEngineHTTP(ks.getEndpoint().getURL().toString(), query);
- for (String dgu : ks.getEndpoint().getDefaultGraphURIs()) {
- queryExecution.addDefaultGraph(dgu);
+ SparqlEndpoint endpoint = ks.getEndpoint();
+ QueryExecutionFactory qef = new QueryExecutionFactoryHttp(endpoint.getURL().toString(), endpoint.getDefaultGraphURIs());
+ if(cache != null){
+ try {
+ long timeToLive = TimeUnit.DAYS.toMillis(30);
+ CacheCoreEx cacheBackend = CacheCoreH2.create(cache.getCacheDirectory(), timeToLive, true);
+ CacheEx cacheFrontend = new CacheExImpl(cacheBackend);
+ qef = new QueryExecutionFactoryCacheEx(qef, cacheFrontend);
+ } catch (ClassNotFoundException e) {
+ e.printStackTrace();
+ } catch (SQLException e) {
+ e.printStackTrace();
}
- for (String ngu : ks.getEndpoint().getNamedGraphURIs()) {
- queryExecution.addNamedGraph(ngu);
- }
- rs = queryExecution.execSelect();
}
+ qef = new QueryExecutionFactoryPaginated(qef, 10000);
+ QueryExecution qe = qef.createQueryExecution(query);
+ rs = qe.execSelect();
} else {
QueryExecution qExec = com.hp.hpl.jena.query.QueryExecutionFactory.create(query, ((LocalModelBasedSparqlEndpointKS)ks).getModel());
rs = qExec.execSelect();
-
}
return rs;
}
Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml 2013-06-12 09:13:43 UTC (rev 3992)
+++ trunk/pom.xml 2013-06-13 07:46:18 UTC (rev 3993)
@@ -123,7 +123,7 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-distribution</artifactId>
- <version>3.4.3</version>
+ <version>3.4.4</version>
<type>pom</type>
</dependency>
<dependency>
@@ -133,6 +133,11 @@
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
+ <artifactId>owlapi-debugging</artifactId>
+ <version>3.3</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-util</artifactId>
<version>3.3</version>
</dependency>
@@ -524,6 +529,12 @@
<url>http://elk-reasoner.googlecode.com/svn/m2/releases</url>
<releases/>
</repository>
+ <repository>
+ <id>central</id>
+ <url>http://oss.sonatype.org</url>
+ <releases><enabled>true</enabled></releases>
+ <snapshots><enabled>true</enabled></snapshots>
+ </repository>
</repositories>
<distributionManagement>
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-06-12 09:13:43 UTC (rev 3992)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-06-13 07:46:18 UTC (rev 3993)
@@ -225,7 +225,7 @@
Collections.shuffle(classesList, new Random(123));
classesList = classesList.subList(0, maxNrOfTestedClasses);
classes = classesList;
- //classes = Collections.singleton(new NamedClass("http://dbpedia.org/ontology/ChristianBishop"));
+ classes = Collections.singleton(new NamedClass("http://dbpedia.org/ontology/BaseballPlayer"));
//get the maximum modal depth in the pattern axioms
int maxModalDepth = maxModalDepth(patterns);
@@ -1147,7 +1147,7 @@
//compute recall
double recall = wald(subClassCnt, overlap);
//if recall is too low we can skip the computation of the precision
- if(recall < 0.2){
+ if(recall < 0.3){
logger.warn("Recall(" + recall + ") too low. Skipping precision computation.");
continue;
}
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|
|
From: <lor...@us...> - 2013-06-12 09:13:46
|
Revision: 3992
http://sourceforge.net/p/dl-learner/code/3992
Author: lorenz_b
Date: 2013-06-12 09:13:43 +0000 (Wed, 12 Jun 2013)
Log Message:
-----------
Added Maven exec plugin.
Modified Paths:
--------------
trunk/interfaces/pom.xml
Modified: trunk/interfaces/pom.xml
===================================================================
--- trunk/interfaces/pom.xml 2013-06-12 09:00:36 UTC (rev 3991)
+++ trunk/interfaces/pom.xml 2013-06-12 09:13:43 UTC (rev 3992)
@@ -447,8 +447,26 @@
</excludes>
</configuration>
</plugin>
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>exec-maven-plugin</artifactId>
+ <version>1.2</version>
+ <executions>
+ <execution>
+ <goals>
+ <goal>exec</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <executable>java</executable>
+ <arguments>
+ <argument>-Xms512m</argument>
+ <argument>-Xmx4000m</argument>
+ </arguments>
+ </configuration>
+ </plugin>
-
</plugins>
</build>
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|
|
From: <lor...@us...> - 2013-06-12 09:00:39
|
Revision: 3991
http://sourceforge.net/p/dl-learner/code/3991
Author: lorenz_b
Date: 2013-06-12 09:00:36 +0000 (Wed, 12 Jun 2013)
Log Message:
-----------
Added methods to export class hierarchy as set of axioms.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java
Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java 2013-06-12 08:59:59 UTC (rev 3990)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java 2013-06-12 09:00:36 UTC (rev 3991)
@@ -28,6 +28,8 @@
import org.apache.log4j.Logger;
import org.dllearner.utilities.owl.ConceptComparator;
+import org.dllearner.utilities.owl.OWLAPIConverter;
+import org.semanticweb.owlapi.model.OWLAxiom;
/**
* Represents a subsumption hierarchy (ignoring equivalent concepts).
@@ -381,6 +383,31 @@
return new ClassHierarchy(subsumptionHierarchyUpNew, subsumptionHierarchyDownNew);
}
+ public Set<Axiom> toAxioms(){
+ return toAxioms(Thing.instance);
+ }
+
+ public Set<OWLAxiom> toOWLAPIAxioms(){
+ Set<OWLAxiom> owlAxioms = new HashSet<OWLAxiom>();
+ Set<Axiom> axioms = toAxioms();
+ for(Axiom axiom : axioms){
+ owlAxioms.add(OWLAPIConverter.getOWLAPIAxiom(axiom));
+ }
+ return owlAxioms;
+ }
+
+ public Set<Axiom> toAxioms(Description concept){
+ Set<Axiom> axioms = new HashSet<Axiom>();
+ Set<Description> subConcepts = subsumptionHierarchyDown.get(concept);
+ if (subConcepts != null) {
+ for (Description sub : subConcepts){
+ axioms.add(new SubClassAxiom(sub, concept));
+ axioms.addAll(toAxioms(sub));
+ }
+ }
+ return axioms;
+ }
+
/**
* Checks whether the description is contained in the hierarchy.
* @param description
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|
|
From: <lor...@us...> - 2013-06-12 09:00:02
|
Revision: 3990
http://sourceforge.net/p/dl-learner/code/3990
Author: lorenz_b
Date: 2013-06-12 08:59:59 +0000 (Wed, 12 Jun 2013)
Log Message:
-----------
Improved equivalence learning in enrichment script.
Modified Paths:
--------------
trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2013-06-12 07:34:30 UTC (rev 3989)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2013-06-12 08:59:59 UTC (rev 3990)
@@ -226,7 +226,7 @@
// restrict tested number of entities per type (only for testing purposes);
// should be set to -1 in production mode
- int maxEntitiesPerType = 5;
+ int maxEntitiesPerType = -1;
// number of axioms which will be learned/considered (only applies to
// some learners)
@@ -345,7 +345,7 @@
// loop over all entities and call appropriate algorithms
Set<NamedClass> classes = reasoner.getTypes();//st.getAllClasses();
- filterByNamespaces(classes);//classes = Sets.newHashSet(new NamedClass("http://dbpedia.org/ontology/GrandPrix"));
+ filterByNamespaces(classes);//classes = Sets.newHashSet(new NamedClass("http://dbpedia.org/ontology/AdministrativeRegion"));
int entities = 0;
for(NamedClass nc : classes) {
try {
@@ -425,7 +425,7 @@
Property predicate = st.getPredicate();
RDFNode object = st.getObject();
boolean startsWithAllowedNamespace = false;
- if(predicate.equals(RDF.type)){
+ if(predicate.equals(RDF.type) || predicate.equals(OWL.equivalentClass)){
if(object.isURIResource()){
for (String ns : allowedNamespaces) {
if(object.asResource().getURI().startsWith(ns)){
@@ -517,11 +517,14 @@
runTime = System.currentTimeMillis() - startTime;
System.out.println("done (" + model.size()+ " triples found in " + runTime + " ms)");
OWLOntology ontology = asOWLOntology(model);
+ if(reasoner.getClassHierarchy() != null){
+ ontology.getOWLOntologyManager().addAxioms(ontology, reasoner.getClassHierarchy().toOWLAPIAxioms());
+ }
ksFragment = new OWLAPIOntology(ontology);
// ksFragment.init();
rc = new FastInstanceChecker(ksFragment);
rc.init();
- rc.setSubsumptionHierarchy(reasoner.getClassHierarchy());
+// rc.setSubsumptionHierarchy(reasoner.getClassHierarchy());
ksCached = ksFragment;
rcCached = rc;
// for (Individual ind : posExamples) {
@@ -616,7 +619,7 @@
futures.add(threadPool.submit(new Callable<Model>() {
@Override
public Model call() throws Exception {
- ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(ks.getEndpoint(), cache, 2);
+ ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(ks.getEndpoint(), "enrichment-cache", 2);
return cbdGen.getConciseBoundedDescription(ind.getName());
}
}));
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|
|
From: <lor...@us...> - 2013-06-12 07:34:34
|
Revision: 3989
http://sourceforge.net/p/dl-learner/code/3989
Author: lorenz_b
Date: 2013-06-12 07:34:30 +0000 (Wed, 12 Jun 2013)
Log Message:
-----------
Added class for query execution.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java
trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
Added Paths:
-----------
trunk/components-core/src/main/java/org/dllearner/kb/sparql/QueryExecutionFactoryHttp.java
Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java 2013-06-11 13:07:42 UTC (rev 3988)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java 2013-06-12 07:34:30 UTC (rev 3989)
@@ -71,6 +71,8 @@
}
public SortedSet<Description> getSubClasses(Description concept) {
+ String s= concept.toString();
+
SortedSet<Description> result = subsumptionHierarchyDown.get(concept);
if(result == null) {
logger.error("Query for sub class of " + concept + " in subsumption hierarchy, but the class is not contained in the (downward) hierarchy, e.g. because the class does not exist or is ignored. Returning empty result instead.");
Added: trunk/components-core/src/main/java/org/dllearner/kb/sparql/QueryExecutionFactoryHttp.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/QueryExecutionFactoryHttp.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/QueryExecutionFactoryHttp.java 2013-06-12 07:34:30 UTC (rev 3989)
@@ -0,0 +1,60 @@
+package org.dllearner.kb.sparql;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+
+import org.aksw.jena_sparql_api.core.QueryExecutionFactoryBackString;
+
+import com.google.common.base.Joiner;
+import com.hp.hpl.jena.query.QueryExecution;
+
+/**
+ * @author Claus Stadler
+ * <p/>
+ * Date: 7/23/11
+ * Time: 9:47 PM
+ */
+public class QueryExecutionFactoryHttp
+ extends QueryExecutionFactoryBackString
+{
+ private String service;
+
+ private List<String> defaultGraphs = new ArrayList<String>();
+
+ public QueryExecutionFactoryHttp(String service) {
+ this(service, Collections.<String>emptySet());
+ }
+
+ public QueryExecutionFactoryHttp(String service, String defaultGraphName) {
+ this(service, Collections.singleton(defaultGraphName));
+ }
+
+ public QueryExecutionFactoryHttp(String service, Collection<String> defaultGraphs) {
+ this.service = service;
+ this.defaultGraphs = new ArrayList<String>(defaultGraphs);
+ Collections.sort(this.defaultGraphs);
+ }
+
+ @Override
+ public String getId() {
+ return service;
+ }
+
+ @Override
+ public String getState() {
+ return Joiner.on("|").join(defaultGraphs);
+ }
+
+ @Override
+ public QueryExecution createQueryExecution(String queryString) {
+ QueryEngineHTTP result = new QueryEngineHTTP(service, queryString);
+ result.setDefaultGraphURIs(defaultGraphs);
+
+ //QueryExecution result = QueryExecutionWrapper.wrap(engine);
+
+ return result;
+ }
+}
+
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java 2013-06-11 13:07:42 UTC (rev 3988)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/FastInstanceChecker.java 2013-06-12 07:34:30 UTC (rev 3989)
@@ -310,6 +310,9 @@
// System.out.println("FIC: " + description + " " + individual);
if (description instanceof NamedClass) {
+ if(((NamedClass) description).getURI().equals(Thing.instance.getURI())){
+ return true;
+ } else
if(!atomicConcepts.contains(description)) {
throw new ReasoningMethodUnsupportedException("Class " + description + " is not contained in knowledge base.");
}
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-06-11 13:07:42 UTC (rev 3988)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-06-12 07:34:30 UTC (rev 3989)
@@ -104,6 +104,8 @@
private Map<DatatypeProperty, Integer> dataPropertyPopularityMap;
private boolean prepared = false;
+
+ private ConceptComparator conceptComparator = new ConceptComparator();
public SPARQLReasoner(SparqlEndpointKS ks) {
@@ -602,7 +604,6 @@
if(limit != 0) {
query += " LIMIT " + limit;
}
- System.out.println("query: "+query);
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
@@ -1149,16 +1150,22 @@
if(description instanceof Nothing){
description = new NamedClass("http://www.w3.org/2002/07/owl#Nothing");
}
- SortedSet<Description> superClasses = new TreeSet<Description>();
+ SortedSet<Description> superClasses = new TreeSet<Description>(conceptComparator);
String query = String.format("SELECT ?sup {<%s> <%s> ?sup. FILTER(isIRI(?sup))}",
((NamedClass)description).getURI().toString(),
RDFS.subClassOf.getURI()
);
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
+ String uri = null;
while(rs.hasNext()){
qs = rs.next();
- superClasses.add(new NamedClass(qs.getResource("sup").getURI()));
+ uri = qs.getResource("sup").getURI();
+ if(uri.equals(Thing.instance.getURI().toString())){
+ superClasses.add(Thing.instance);
+ } else {
+ superClasses.add(new NamedClass(uri));
+ }
}
superClasses.remove(description);
return superClasses;
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|
|
From: <lor...@us...> - 2013-06-11 13:07:45
|
Revision: 3988
http://sourceforge.net/p/dl-learner/code/3988
Author: lorenz_b
Date: 2013-06-11 13:07:42 +0000 (Tue, 11 Jun 2013)
Log Message:
-----------
Added QueryExecutionFactory using TURTLE for CONSTRUCT queries.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/SetManipulation.java
trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLEntityTypeAdder.java
Modified: trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java 2013-06-11 13:06:13 UTC (rev 3987)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java 2013-06-11 13:07:42 UTC (rev 3988)
@@ -11,7 +11,7 @@
import org.aksw.jena_sparql_api.cache.extra.CacheEx;
import org.aksw.jena_sparql_api.cache.extra.CacheExImpl;
import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
-import org.aksw.jena_sparql_api.http.QueryExecutionFactoryHttp;
+//import org.aksw.jena_sparql_api.http.QueryExecutionFactoryHttp;
import org.aksw.jena_sparql_api.model.QueryExecutionFactoryModel;
import org.aksw.jena_sparql_api.pagination.core.QueryExecutionFactoryPaginated;
import org.apache.log4j.Level;
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-06-11 13:06:13 UTC (rev 3987)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-06-11 13:07:42 UTC (rev 3988)
@@ -492,7 +492,7 @@
* @return
*/
public Set<NamedClass> getSiblingClasses(NamedClass cls) {
- Set<NamedClass> siblings = new HashSet<NamedClass>();
+ Set<NamedClass> siblings = new TreeSet<NamedClass>();
String query = "SELECT ?sub WHERE { <" + cls.getName() + "> <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?super .";
query += "?sub <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?super .";
query += "FILTER( !SAMETERM(?sub, <" + cls.getName() + ">)) . }";System.out.println(query);
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/SetManipulation.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/SetManipulation.java 2013-06-11 13:06:13 UTC (rev 3987)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/SetManipulation.java 2013-06-11 13:07:42 UTC (rev 3988)
@@ -90,27 +90,25 @@
}
return ret;
}
-
+
/**
* shrinks a set to the limit takes the first elements up to limit
*
* @param set
* @param limit
*/
- public static SortedSet<String> stableShrink(SortedSet<String> set,
+ public static <T> SortedSet<T> stableShrink(SortedSet<T> set,
int limit) {
if (set.size() <= limit) {
return set;
}
- SortedSet<String> ret = new TreeSet<String>();
+ SortedSet<T> ret = new TreeSet<T>();
- for (String oneInd : set) {
+ for (T oneInd : set) {
ret.add(oneInd);
if (ret.size() >= limit)
break;
-
}
-
return ret;
}
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java 2013-06-11 13:06:13 UTC (rev 3987)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java 2013-06-11 13:07:42 UTC (rev 3988)
@@ -196,7 +196,7 @@
siblingNegativeExamples.addAll(sr.getIndividualsExcluding(siblingClass, nc, limit));
}
}
- siblingNegativeExamples = SetManipulation.fuzzyShrink(siblingNegativeExamples, strategyLimit);
+ siblingNegativeExamples = SetManipulation.stableShrink(siblingNegativeExamples, strategyLimit);
negativeExamples.addAll(siblingNegativeExamples);
} else if(strategy == SUPERCLASS){//get super class based examples
SortedSet<Individual> superClassNegativeExamples = new TreeSet<Individual>();
@@ -214,7 +214,7 @@
superClassNegativeExamples.addAll(sr.getIndividualsExcluding(superClass, nc, limit));
}
}
- superClassNegativeExamples = SetManipulation.fuzzyShrink(superClassNegativeExamples, strategyLimit);
+ superClassNegativeExamples = SetManipulation.stableShrink(superClassNegativeExamples, strategyLimit);
negativeExamples.addAll(superClassNegativeExamples);
} else if(strategy == RANDOM){//get some random examples
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLEntityTypeAdder.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLEntityTypeAdder.java 2013-06-11 13:06:13 UTC (rev 3987)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLEntityTypeAdder.java 2013-06-11 13:07:42 UTC (rev 3988)
@@ -38,6 +38,16 @@
}
}
iterator.close();
+ for (Property property : dataPropertyPredicates) {
+ if(!objectPropertyPredicates.contains(property)){
+ model.add(property, RDF.type, OWL.DatatypeProperty);
+ }
+ }
+ for (Property property : objectPropertyPredicates) {
+ if(!dataPropertyPredicates.contains(property)){
+ model.add(property, RDF.type, OWL.ObjectProperty);
+ }
+ }
}
}
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|
|
From: <lor...@us...> - 2013-06-11 13:06:16
|
Revision: 3987
http://sourceforge.net/p/dl-learner/code/3987
Author: lorenz_b
Date: 2013-06-11 13:06:13 +0000 (Tue, 11 Jun 2013)
Log Message:
-----------
Improved enrichment script.
Modified Paths:
--------------
trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2013-06-10 10:07:42 UTC (rev 3986)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2013-06-11 13:06:13 UTC (rev 3987)
@@ -52,6 +52,11 @@
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
import java.util.Set;
import java.util.SortedSet;
@@ -61,6 +66,7 @@
import joptsimple.OptionSpec;
import org.aksw.commons.jena_owlapi.Conversion;
+import org.aksw.jena_sparql_api.core.QueryExecutionFactory;
import org.apache.jena.riot.checker.CheckerLiterals;
import org.apache.jena.riot.system.ErrorHandlerFactory;
import org.apache.log4j.ConsoleAppender;
@@ -123,10 +129,10 @@
import org.dllearner.learningproblems.Heuristics.HeuristicType;
import org.dllearner.reasoning.FastInstanceChecker;
import org.dllearner.reasoning.SPARQLReasoner;
+import org.dllearner.refinementoperators.RhoDRDown;
import org.dllearner.utilities.EnrichmentVocabulary;
import org.dllearner.utilities.Helper;
import org.dllearner.utilities.PrefixCCMap;
-import org.dllearner.utilities.datastructures.SetManipulation;
import org.dllearner.utilities.datastructures.SortedSetTuple;
import org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2;
import org.dllearner.utilities.owl.OWLAPIAxiomConvertVisitor;
@@ -151,13 +157,17 @@
import com.clarkparsia.owlapiv3.XSD;
import com.google.common.collect.Sets;
+import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.query.ResultSetFormatter;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.Statement;
+import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.sparql.engine.http.QueryExceptionHTTP;
import com.hp.hpl.jena.vocabulary.OWL;
import com.hp.hpl.jena.vocabulary.RDF;
@@ -225,6 +235,8 @@
private int chunksize = 1000;
private boolean omitExistingAxioms;
private List<String> allowedNamespaces = new ArrayList<String>();
+ private int maxNrOfPositiveExamples = 20;
+ private int maxNrOfNegativeExamples = 20;
private boolean useInference;
private SPARQLReasoner reasoner;
@@ -333,7 +345,7 @@
// loop over all entities and call appropriate algorithms
Set<NamedClass> classes = reasoner.getTypes();//st.getAllClasses();
- filterByNamespaces(classes);
+ filterByNamespaces(classes);//classes = Sets.newHashSet(new NamedClass("http://dbpedia.org/ontology/GrandPrix"));
int entities = 0;
for(NamedClass nc : classes) {
try {
@@ -406,6 +418,39 @@
}
}
+ private void filterByNamespaces(Model model){
+ if(allowedNamespaces != null && !allowedNamespaces.isEmpty()){
+ for (StmtIterator iterator = model.listStatements(); iterator.hasNext();) {
+ Statement st = iterator.next();
+ Property predicate = st.getPredicate();
+ RDFNode object = st.getObject();
+ boolean startsWithAllowedNamespace = false;
+ if(predicate.equals(RDF.type)){
+ if(object.isURIResource()){
+ for (String ns : allowedNamespaces) {
+ if(object.asResource().getURI().startsWith(ns)){
+ startsWithAllowedNamespace = true;
+ break;
+ }
+ }
+ } else {
+ startsWithAllowedNamespace = true;
+ }
+ } else {
+ for (String ns : allowedNamespaces) {
+ if(predicate.getURI().startsWith(ns)){
+ startsWithAllowedNamespace = true;
+ break;
+ }
+ }
+ }
+ if(!startsWithAllowedNamespace){
+ iterator.remove();
+ }
+ }
+ }
+ }
+
@SuppressWarnings("unchecked")
private void runClassLearningAlgorithms(SparqlEndpointKS ks, NamedClass nc) throws ComponentInitException {
System.out.println("Running algorithms for class " + nc);
@@ -435,12 +480,10 @@
}
private List<EvaluatedAxiom> applyCELOE(SparqlEndpointKS ks, NamedClass nc, boolean equivalence, boolean reuseKnowledgeSource) throws ComponentInitException {
-
// get instances of class as positive examples
- SPARQLReasoner sr = new SPARQLReasoner(ks);
System.out.print("finding positives ... ");
long startTime = System.currentTimeMillis();
- SortedSet<Individual> posExamples = sr.getIndividuals(nc, 20);
+ SortedSet<Individual> posExamples = reasoner.getIndividuals(nc, maxNrOfPositiveExamples);
long runTime = System.currentTimeMillis() - startTime;
if(posExamples.isEmpty()){
System.out.println("Skipping CELOE because class " + nc.toString() + " is empty.");
@@ -452,13 +495,11 @@
// use own implementation of negative example finder
System.out.print("finding negatives ... ");
startTime = System.currentTimeMillis();
- AutomaticNegativeExampleFinderSPARQL2 finder = new AutomaticNegativeExampleFinderSPARQL2(ks.getEndpoint());
- SortedSet<String> negExStr = finder.getNegativeExamples(nc.getName(), posExStr);
- negExStr = SetManipulation.stableShrink(negExStr, 20);
- SortedSet<Individual> negExamples = Helper.getIndividualSet(negExStr);
+ AutomaticNegativeExampleFinderSPARQL2 finder = new AutomaticNegativeExampleFinderSPARQL2(reasoner, "http://dbpedia.org/ontology");
+ SortedSet<Individual> negExamples = finder.getNegativeExamples(nc, posExamples, maxNrOfNegativeExamples);
SortedSetTuple<Individual> examples = new SortedSetTuple<Individual>(posExamples, negExamples);
runTime = System.currentTimeMillis() - startTime;
- System.out.println("done (" + negExStr.size()+ " examples found in " + runTime + " ms)");
+ System.out.println("done (" + negExamples.size()+ " examples found in " + runTime + " ms)");
AbstractReasonerComponent rc;
KnowledgeSource ksFragment;
@@ -468,14 +509,11 @@
} else {
System.out.print("extracting fragment ... ");//com.hp.hpl.jena.shared.impl.JenaParameters.enableEagerLiteralValidation = true;
startTime = System.currentTimeMillis();
- ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(ks.getEndpoint(), cache, 2);
- Model model = ModelFactory.createDefaultModel();
- for(Individual example : Sets.union(posExamples, negExamples)){
- Model cbd = cbdGen.getConciseBoundedDescription(example.getName());
- model.add(cbd);
- }
+ Model model = getFragmentMultithreaded(ks, Sets.union(posExamples, negExamples));
filter(model);
+ filterByNamespaces(model);
OWLEntityTypeAdder.addEntityTypes(model);
+
runTime = System.currentTimeMillis() - startTime;
System.out.println("done (" + model.size()+ " triples found in " + runTime + " ms)");
OWLOntology ontology = asOWLOntology(model);
@@ -483,8 +521,12 @@
// ksFragment.init();
rc = new FastInstanceChecker(ksFragment);
rc.init();
+ rc.setSubsumptionHierarchy(reasoner.getClassHierarchy());
ksCached = ksFragment;
rcCached = rc;
+// for (Individual ind : posExamples) {
+// System.out.println(ResultSetFormatter.asText(com.hp.hpl.jena.query.QueryExecutionFactory.create("SELECT * WHERE {<" + ind.getName() + "> ?p ?o. OPTIONAL{?o a ?o_type}}",model).execSelect()));
+// }
}
/*//old way to get SPARQL fragment
@@ -516,7 +558,7 @@
ksCached = ks2;
rcCached = rc;
}*/
-
+
ClassLearningProblem lp = new ClassLearningProblem(rc);
lp.setClassToDescribe(nc);
lp.setEquivalence(equivalence);
@@ -528,7 +570,9 @@
CELOE la = new CELOE(lp, rc);
la.setMaxExecutionTimeInSeconds(10);
la.setNoisePercentage(25);
+ la.setMaxNrOfResults(100);
la.init();
+ ((RhoDRDown)la.getOperator()).setUseNegation(false);
startTime = System.currentTimeMillis();
System.out.print("running CELOE (for " + (equivalence ? "equivalent classes" : "sub classes") + ") ... ");
la.start();
@@ -554,6 +598,42 @@
return learnedAxioms;
}
+ private Model getFragment(SparqlEndpointKS ks, Set<Individual> individuals){
+ ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(ks.getEndpoint(), cache, 2);
+ Model model = ModelFactory.createDefaultModel();
+ for(Individual ind : individuals){
+ Model cbd = cbdGen.getConciseBoundedDescription(ind.getName());
+ model.add(cbd);
+ }
+ return model;
+ }
+
+ private Model getFragmentMultithreaded(final SparqlEndpointKS ks, Set<Individual> individuals){
+ Model model = ModelFactory.createDefaultModel();
+ ExecutorService threadPool = Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors());
+ List<Future<Model>> futures = new ArrayList<Future<Model>>();
+ for (final Individual ind : individuals) {
+ futures.add(threadPool.submit(new Callable<Model>() {
+ @Override
+ public Model call() throws Exception {
+ ConciseBoundedDescriptionGenerator cbdGen = new ConciseBoundedDescriptionGeneratorImpl(ks.getEndpoint(), cache, 2);
+ return cbdGen.getConciseBoundedDescription(ind.getName());
+ }
+ }));
+ }
+ for (Future<Model> future : futures) {
+ try {
+ model.add(future.get());
+ } catch (InterruptedException e) {
+ e.printStackTrace();
+ } catch (ExecutionException e) {
+ e.printStackTrace();
+ }
+ }
+ threadPool.shutdown();
+ return model;
+ }
+
private List<EvaluatedAxiom> applyLearningAlgorithm(Class<? extends AxiomLearningAlgorithm> algorithmClass, SparqlEndpointKS ks, Entity entity) throws ComponentInitException {
AxiomLearningAlgorithm learner = null;
try {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-06-10 10:07:45
|
Revision: 3986
http://sourceforge.net/p/dl-learner/code/3986
Author: lorenz_b
Date: 2013-06-10 10:07:42 +0000 (Mon, 10 Jun 2013)
Log Message:
-----------
Added class for mapping from URI to variable.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/NoiseSensitiveLGG.java
trunk/components-core/src/main/java/org/dllearner/core/AbstractReasonerComponent.java
trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java
trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/SetManipulation.java
trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java
Added Paths:
-----------
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLAxiomToSPARQLConverter.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/VariablesMapping.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/NoiseSensitiveLGG.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/NoiseSensitiveLGG.java 2013-06-06 13:32:30 UTC (rev 3985)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/NoiseSensitiveLGG.java 2013-06-10 10:07:42 UTC (rev 3986)
@@ -9,6 +9,7 @@
import java.util.TreeSet;
import org.dllearner.algorithms.qtl.datastructures.QueryTree;
+import org.dllearner.learningproblems.Heuristics;
import com.jamonapi.Monitor;
import com.jamonapi.MonitorFactory;
@@ -48,7 +49,7 @@
}
}
//compute score
- double score = (trees.size() - uncoveredExamples.size()) / (double)trees.size();
+ double score = Heuristics.getConfidenceInterval95WaldAverage(trees.size(), trees.size() - uncoveredExamples.size());
//add to todo list, if not already contained in todo list or solution list
EvaluatedQueryTree<N> solution = new EvaluatedQueryTree<N>(lgg, uncoveredExamples, score);
todo(solution);
Modified: trunk/components-core/src/main/java/org/dllearner/core/AbstractReasonerComponent.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/AbstractReasonerComponent.java 2013-06-06 13:32:30 UTC (rev 3985)
+++ trunk/components-core/src/main/java/org/dllearner/core/AbstractReasonerComponent.java 2013-06-10 10:07:42 UTC (rev 3986)
@@ -1158,6 +1158,10 @@
}
}
+
+ public void setSubsumptionHierarchy(ClassHierarchy subsumptionHierarchy) {
+ this.subsumptionHierarchy = subsumptionHierarchy;
+ }
public List<ObjectProperty> getAtomicRolesList() {
if (atomicRolesList == null)
Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java 2013-06-06 13:32:30 UTC (rev 3985)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/ClassHierarchy.java 2013-06-10 10:07:42 UTC (rev 3986)
@@ -346,7 +346,9 @@
// case 2: it is not allowed, so we try its super classes
} else {
Set<Description> tmp = subsumptionHierarchyUp.get(d);
- superClasses.addAll(tmp);
+ if(tmp != null){
+ superClasses.addAll(tmp);
+ }
}
}
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/SetManipulation.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/SetManipulation.java 2013-06-06 13:32:30 UTC (rev 3985)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/SetManipulation.java 2013-06-10 10:07:42 UTC (rev 3986)
@@ -38,11 +38,11 @@
* @param set
* @param limit
*/
- public static SortedSet<String> fuzzyShrink(SortedSet<String> set, int limit) {
+ public static <T> SortedSet<T> fuzzyShrink(SortedSet<T> set, int limit) {
if (set.size() <= limit) {
return set;
}
- SortedSet<String> ret = new TreeSet<String>();
+ SortedSet<T> ret = new TreeSet<T>();
Random r = new Random();
double treshold = ((double) limit) / set.size();
// System.out.println("treshold"+howmany);
@@ -50,7 +50,7 @@
// System.out.println("treshold"+treshold);
while (ret.size() < limit) {
- for (String oneInd : set) {
+ for (T oneInd : set) {
if (r.nextDouble() < treshold) {
ret.add(oneInd);
if (ret.size() >= limit)
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java 2013-06-06 13:32:30 UTC (rev 3985)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/examples/AutomaticNegativeExampleFinderSPARQL2.java 2013-06-10 10:07:42 UTC (rev 3986)
@@ -36,16 +36,21 @@
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Individual;
import org.dllearner.core.owl.NamedClass;
+import org.dllearner.core.owl.Thing;
import org.dllearner.kb.SparqlEndpointKS;
import org.dllearner.kb.sparql.SPARQLTasks;
import org.dllearner.kb.sparql.SparqlEndpoint;
import org.dllearner.reasoning.SPARQLReasoner;
import org.dllearner.utilities.datastructures.Datastructures;
+import org.dllearner.utilities.datastructures.SetManipulation;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import com.google.common.base.Predicate;
import com.google.common.collect.HashMultiset;
import com.google.common.collect.Multiset;
import com.google.common.collect.Multisets;
+import com.google.common.collect.Sets;
/**
*
* Utility class for automatically retrieving negative examples from a
@@ -57,6 +62,8 @@
*/
public class AutomaticNegativeExampleFinderSPARQL2 {
+ private static final Logger logger = LoggerFactory.getLogger(AutomaticNegativeExampleFinderSPARQL2.class.getSimpleName());
+
public enum Strategy{
SUPERCLASS, SIBLING, RANDOM;
}
@@ -113,6 +120,27 @@
return negEx;
}
+ public SortedSet<Individual> getNegativeExamples(NamedClass classToDescribe, Set<Individual> positiveExamples, int limit) {
+ return getNegativeExamples(classToDescribe, positiveExamples, Arrays.asList(SUPERCLASS, SIBLING, RANDOM), limit);
+ }
+
+ public SortedSet<Individual> getNegativeExamples(NamedClass classToDescribe, Set<Individual> positiveExamples, Collection<Strategy> strategies, int limit) {
+ Map<Strategy, Double> strategiesWithWeight = new HashMap<Strategy, Double>();
+ double weight = 1d/strategies.size();
+ for (Strategy strategy : strategies) {
+ strategiesWithWeight.put(strategy, weight);
+ }
+ return getNegativeExamples(classToDescribe, positiveExamples, strategiesWithWeight, limit);
+ }
+
+ public SortedSet<Individual> getNegativeExamples(NamedClass classToDescribe, Set<Individual> positiveExamples, Map<Strategy, Double> strategiesWithWeight, int maxNrOfReturnedInstances) {
+ //set class to describe as the type for each instance
+ Multiset<NamedClass> types = HashMultiset.create();
+ types.add(classToDescribe);
+
+ return computeNegativeExamples(types, strategiesWithWeight, maxNrOfReturnedInstances);
+ }
+
public SortedSet<Individual> getNegativeExamples(Set<Individual> positiveExamples, int limit) {
return getNegativeExamples(positiveExamples, Arrays.asList(SUPERCLASS, SIBLING, RANDOM), limit);
}
@@ -127,8 +155,6 @@
}
public SortedSet<Individual> getNegativeExamples(Set<Individual> positiveExamples, Map<Strategy, Double> strategiesWithWeight, int maxNrOfReturnedInstances) {
- SortedSet<Individual> negEx = new TreeSet<Individual>();
-
//get the types for each instance
Multiset<NamedClass> types = HashMultiset.create();
for (Individual ex : positiveExamples) {
@@ -136,56 +162,89 @@
}
//remove types that do not have the given namespace
- if(namespace != null){
- types = Multisets.filter(types, new Predicate<NamedClass>() {
- public boolean apply(NamedClass input){
- return input.getName().startsWith(namespace);
- }
- });
- }
+ types = filterByNamespace(types);
//keep the most specific types
keepMostSpecificClasses(types);
+ return computeNegativeExamples(types, strategiesWithWeight, maxNrOfReturnedInstances);
+ }
+
+ private SortedSet<Individual> computeNegativeExamples(Multiset<NamedClass> positiveExamplesTypes, Map<Strategy, Double> strategiesWithWeight, int maxNrOfReturnedInstances) {
+ SortedSet<Individual> negativeExamples = new TreeSet<Individual>();
for (Entry<Strategy, Double> entry : strategiesWithWeight.entrySet()) {
Strategy strategy = entry.getKey();
Double weight = entry.getValue();
//the max number of instances returned by the current strategy
- int limit = (int)(weight * maxNrOfReturnedInstances);
+ int strategyLimit = (int)(weight * maxNrOfReturnedInstances);
//the highest frequency value
- int maxFrequency = types.entrySet().iterator().next().getCount();
- if(strategy == SIBLING){
- System.out.println("Sibling Classes Strategy");
- for (NamedClass nc : types.elementSet()) {
- int frequency = types.count(nc);
+ int maxFrequency = positiveExamplesTypes.entrySet().iterator().next().getCount();
+
+ if(strategy == SIBLING){//get sibling class based examples
+ SortedSet<Individual> siblingNegativeExamples = new TreeSet<Individual>();
+ //for each type of the positive examples
+ for (NamedClass nc : positiveExamplesTypes.elementSet()) {
+ int frequency = positiveExamplesTypes.count(nc);
//get sibling classes
Set<NamedClass> siblingClasses = sr.getSiblingClasses(nc);
- int nrOfSiblings = siblingClasses.size();
- int v = (int)Math.ceil(((double)frequency / types.size()) / nrOfSiblings * limit); System.out.println(nc + ": " + v);
+ siblingClasses = filterByNamespace(siblingClasses);
+ System.out.println("Sibling classes: " + siblingClasses);
+
+ int limit = (int)Math.ceil(((double)frequency / positiveExamplesTypes.size()) / siblingClasses.size() * strategyLimit);
+ //get instances for each sibling class
for (NamedClass siblingClass : siblingClasses) {
- negEx.addAll(sr.getIndividualsExcluding(siblingClass, nc, v));
+ siblingNegativeExamples.addAll(sr.getIndividualsExcluding(siblingClass, nc, limit));
}
+ }
+ siblingNegativeExamples = SetManipulation.fuzzyShrink(siblingNegativeExamples, strategyLimit);
+ negativeExamples.addAll(siblingNegativeExamples);
+ } else if(strategy == SUPERCLASS){//get super class based examples
+ SortedSet<Individual> superClassNegativeExamples = new TreeSet<Individual>();
+ //for each type of the positive examples
+ for (NamedClass nc : positiveExamplesTypes.elementSet()) {
+ int frequency = positiveExamplesTypes.count(nc);
+ //get super classes
+ Set<Description> superClasses = sr.getSuperClasses(nc);
+ superClasses.remove(new NamedClass(Thing.instance.getURI()));
+ superClasses = filterByNamespace(superClasses);
- }
- } else if(strategy == SUPERCLASS){
- System.out.println("Super Classes Strategy");
- for (NamedClass nc : types.elementSet()) {
- int frequency = types.count(nc);
- //get sibling classes
- Set<Description> superClasses = sr.getSuperClasses(nc);System.out.println(superClasses);
- int nrOfSuperClasses = superClasses.size();
- int v = (int)Math.ceil(((double)frequency / types.size()) / nrOfSuperClasses * limit); System.out.println(nc + ": " + v);
+ int limit = (int)Math.ceil(((double)frequency / positiveExamplesTypes.size()) / superClasses.size() * strategyLimit);
+ //get instances for each super class
for (Description superClass : superClasses) {
- negEx.addAll(sr.getIndividualsExcluding(superClass, nc, v));
+ superClassNegativeExamples.addAll(sr.getIndividualsExcluding(superClass, nc, limit));
}
}
- } else if(strategy == RANDOM){
+ superClassNegativeExamples = SetManipulation.fuzzyShrink(superClassNegativeExamples, strategyLimit);
+ negativeExamples.addAll(superClassNegativeExamples);
+ } else if(strategy == RANDOM){//get some random examples
}
}
- return negEx;
+ return negativeExamples;
}
+ private <T extends Description> Set<T> filterByNamespace(Set<T> classes){
+ if(namespace != null){
+ return Sets.filter(classes, new Predicate<T>() {
+ public boolean apply(T input){
+ return input.toString().startsWith(namespace);
+ }
+ });
+ }
+ return classes;
+ }
+
+ private Multiset<NamedClass> filterByNamespace(Multiset<NamedClass> classes){
+ if(namespace != null){
+ return Multisets.filter(classes, new Predicate<NamedClass>() {
+ public boolean apply(NamedClass input){
+ return input.getName().startsWith(namespace);
+ }
+ });
+ }
+ return classes;
+ }
+
private void keepMostSpecificClasses(Multiset<NamedClass> classes){
HashMultiset<NamedClass> copy = HashMultiset.create(classes);
final ClassHierarchy hierarchy = sr.getClassHierarchy();
Added: trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLAxiomToSPARQLConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLAxiomToSPARQLConverter.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLAxiomToSPARQLConverter.java 2013-06-10 10:07:42 UTC (rev 3986)
@@ -0,0 +1,324 @@
+package org.dllearner.utilities.owl;
+
+
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.ToStringRenderer;
+import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
+import org.semanticweb.owlapi.model.OWLAnnotationPropertyDomainAxiom;
+import org.semanticweb.owlapi.model.OWLAnnotationPropertyRangeAxiom;
+import org.semanticweb.owlapi.model.OWLAsymmetricObjectPropertyAxiom;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLAxiomVisitor;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassAssertionAxiom;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLDataProperty;
+import org.semanticweb.owlapi.model.OWLDataPropertyAssertionAxiom;
+import org.semanticweb.owlapi.model.OWLDataPropertyDomainAxiom;
+import org.semanticweb.owlapi.model.OWLDataPropertyRangeAxiom;
+import org.semanticweb.owlapi.model.OWLDataRange;
+import org.semanticweb.owlapi.model.OWLDatatypeDefinitionAxiom;
+import org.semanticweb.owlapi.model.OWLDeclarationAxiom;
+import org.semanticweb.owlapi.model.OWLDifferentIndividualsAxiom;
+import org.semanticweb.owlapi.model.OWLDisjointClassesAxiom;
+import org.semanticweb.owlapi.model.OWLDisjointDataPropertiesAxiom;
+import org.semanticweb.owlapi.model.OWLDisjointObjectPropertiesAxiom;
+import org.semanticweb.owlapi.model.OWLDisjointUnionAxiom;
+import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
+import org.semanticweb.owlapi.model.OWLEquivalentDataPropertiesAxiom;
+import org.semanticweb.owlapi.model.OWLEquivalentObjectPropertiesAxiom;
+import org.semanticweb.owlapi.model.OWLFunctionalDataPropertyAxiom;
+import org.semanticweb.owlapi.model.OWLFunctionalObjectPropertyAxiom;
+import org.semanticweb.owlapi.model.OWLHasKeyAxiom;
+import org.semanticweb.owlapi.model.OWLIndividual;
+import org.semanticweb.owlapi.model.OWLInverseFunctionalObjectPropertyAxiom;
+import org.semanticweb.owlapi.model.OWLInverseObjectPropertiesAxiom;
+import org.semanticweb.owlapi.model.OWLIrreflexiveObjectPropertyAxiom;
+import org.semanticweb.owlapi.model.OWLLiteral;
+import org.semanticweb.owlapi.model.OWLNegativeDataPropertyAssertionAxiom;
+import org.semanticweb.owlapi.model.OWLNegativeObjectPropertyAssertionAxiom;
+import org.semanticweb.owlapi.model.OWLObjectIntersectionOf;
+import org.semanticweb.owlapi.model.OWLObjectProperty;
+import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom;
+import org.semanticweb.owlapi.model.OWLObjectPropertyDomainAxiom;
+import org.semanticweb.owlapi.model.OWLObjectPropertyRangeAxiom;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.model.OWLReflexiveObjectPropertyAxiom;
+import org.semanticweb.owlapi.model.OWLSameIndividualAxiom;
+import org.semanticweb.owlapi.model.OWLSubAnnotationPropertyOfAxiom;
+import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
+import org.semanticweb.owlapi.model.OWLSubDataPropertyOfAxiom;
+import org.semanticweb.owlapi.model.OWLSubObjectPropertyOfAxiom;
+import org.semanticweb.owlapi.model.OWLSubPropertyChainOfAxiom;
+import org.semanticweb.owlapi.model.OWLSymmetricObjectPropertyAxiom;
+import org.semanticweb.owlapi.model.OWLTransitiveObjectPropertyAxiom;
+import org.semanticweb.owlapi.model.PrefixManager;
+import org.semanticweb.owlapi.model.SWRLRule;
+import org.semanticweb.owlapi.util.DefaultPrefixManager;
+
+import uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxObjectRenderer;
+
+import com.hp.hpl.jena.query.Query;
+import com.hp.hpl.jena.query.QueryFactory;
+import com.hp.hpl.jena.query.Syntax;
+
+public class OWLAxiomToSPARQLConverter implements OWLAxiomVisitor{
+
+ private String root = "?x";
+ private String sparql;
+ private OWLClassExpressionToSPARQLConverter expressionConverter;
+
+ public String convert(String rootVariable, OWLAxiom axiom){
+ this.root = rootVariable;
+ sparql = "";
+ expressionConverter = new OWLClassExpressionToSPARQLConverter();
+ axiom.accept(this);
+ return sparql;
+ }
+
+ public Query asQuery(String rootVariable, OWLAxiom axiom){
+ String queryString = "SELECT DISTINCT " + rootVariable + " WHERE {";
+ queryString += convert(rootVariable, axiom);
+ queryString += "}";
+ return QueryFactory.create(queryString, Syntax.syntaxARQ);
+ }
+
+ @Override
+ public void visit(OWLAnnotationAssertionAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLSubAnnotationPropertyOfAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLAnnotationPropertyDomainAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLAnnotationPropertyRangeAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDeclarationAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLSubClassOfAxiom axiom) {
+ OWLClassExpression subClass = axiom.getSubClass();
+ String subClassPattern = expressionConverter.convert(root, subClass);
+ sparql += subClassPattern;
+
+ OWLClassExpression superClass = axiom.getSuperClass();
+ String superClassPattern = expressionConverter.convert(root, superClass);
+ sparql += superClassPattern;
+ }
+
+ @Override
+ public void visit(OWLNegativeObjectPropertyAssertionAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLAsymmetricObjectPropertyAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLReflexiveObjectPropertyAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDisjointClassesAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDataPropertyDomainAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLObjectPropertyDomainAxiom axiom) {
+ OWLSubClassOfAxiom subClassOfAxiom = axiom.asOWLSubClassOfAxiom();
+ }
+
+ @Override
+ public void visit(OWLEquivalentObjectPropertiesAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLNegativeDataPropertyAssertionAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDifferentIndividualsAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDisjointDataPropertiesAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDisjointObjectPropertiesAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLObjectPropertyRangeAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLObjectPropertyAssertionAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLFunctionalObjectPropertyAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLSubObjectPropertyOfAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDisjointUnionAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLSymmetricObjectPropertyAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDataPropertyRangeAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLFunctionalDataPropertyAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLEquivalentDataPropertiesAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLClassAssertionAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLEquivalentClassesAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDataPropertyAssertionAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLTransitiveObjectPropertyAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLIrreflexiveObjectPropertyAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLSubDataPropertyOfAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLInverseFunctionalObjectPropertyAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLSameIndividualAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLSubPropertyChainOfAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLInverseObjectPropertiesAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLHasKeyAxiom axiom) {
+ }
+
+ @Override
+ public void visit(OWLDatatypeDefinitionAxiom axiom) {
+ }
+
+ @Override
+ public void visit(SWRLRule rule) {
+ }
+
+ public static void main(String[] args) throws Exception {
+ ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
+ OWLAxiomToSPARQLConverter converter = new OWLAxiomToSPARQLConverter();
+
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ OWLDataFactory df = man.getOWLDataFactory();
+ PrefixManager pm = new DefaultPrefixManager("http://dbpedia.org/ontology/");
+
+ OWLClass clsA = df.getOWLClass("A", pm);
+ OWLClass clsB = df.getOWLClass("B", pm);
+ OWLClass clsC = df.getOWLClass("C", pm);
+
+ OWLObjectProperty propR = df.getOWLObjectProperty("r", pm);
+ OWLObjectProperty propS = df.getOWLObjectProperty("s", pm);
+
+ OWLDataProperty dpT = df.getOWLDataProperty("t", pm);
+ OWLDataRange booleanRange = df.getBooleanOWLDatatype();
+ OWLLiteral lit = df.getOWLLiteral(1);
+
+ OWLIndividual indA = df.getOWLNamedIndividual("a", pm);
+ OWLIndividual indB = df.getOWLNamedIndividual("b", pm);
+
+ String rootVar = "?x";
+ //NAMEDCLASS
+ OWLClassExpression subClass = clsA;
+ OWLClassExpression superClass = clsB;
+ OWLAxiom axiom = df.getOWLSubClassOfAxiom(subClass, superClass);
+ String query = converter.asQuery(rootVar, axiom).toString();
+ System.out.println(axiom + "\n" + query);
+ //EXISTENTIAL RESTRICTION
+ superClass = df.getOWLObjectSomeValuesFrom(propR, clsB);
+ axiom = df.getOWLSubClassOfAxiom(subClass, superClass);
+ query = converter.asQuery(rootVar, axiom).toString();
+ System.out.println(axiom + "\n" + query);
+ //INTERSECTION
+ superClass = df.getOWLObjectIntersectionOf(
+ df.getOWLObjectSomeValuesFrom(propR, clsB),
+ clsB);
+ axiom = df.getOWLSubClassOfAxiom(subClass, superClass);
+ query = converter.asQuery(rootVar, axiom).toString();
+ System.out.println(axiom + "\n" + query);
+ //UNION
+ superClass = df.getOWLObjectUnionOf(
+ clsB,
+ clsC);
+ axiom = df.getOWLSubClassOfAxiom(subClass, superClass);
+ query = converter.asQuery(rootVar, axiom).toString();
+ System.out.println(axiom + "\n" + query);
+ //HAS VALUE
+ superClass = df.getOWLObjectHasValue(propR, indA);
+ axiom = df.getOWLSubClassOfAxiom(subClass, superClass);
+ query = converter.asQuery(rootVar, axiom).toString();
+ System.out.println(axiom + "\n" + query);
+ //UNIVERSAL RESTRICTION
+ superClass = df.getOWLObjectAllValuesFrom(propR, clsB);
+ axiom = df.getOWLSubClassOfAxiom(subClass, superClass);
+ query = converter.asQuery(rootVar, axiom).toString();
+ System.out.println(axiom + "\n" + query);
+ // ONE OF
+ superClass = df.getOWLObjectOneOf(indA, indB);
+ axiom = df.getOWLSubClassOfAxiom(subClass, superClass);
+ query = converter.asQuery(rootVar, axiom).toString();
+ System.out.println(axiom + "\n" + query);
+ //existential restriction with one of filler
+ superClass = df.getOWLObjectSomeValuesFrom(propR, df.getOWLObjectOneOf(indA, indB));
+ axiom = df.getOWLSubClassOfAxiom(subClass, superClass);
+ query = converter.asQuery(rootVar, axiom).toString();
+ System.out.println(axiom + "\n" + query);
+
+
+
+ }
+
+}
Added: trunk/components-core/src/main/java/org/dllearner/utilities/owl/VariablesMapping.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/VariablesMapping.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/VariablesMapping.java 2013-06-10 10:07:42 UTC (rev 3986)
@@ -0,0 +1,38 @@
+package org.dllearner.utilities.owl;
+
+import java.util.HashMap;
+
+import org.semanticweb.owlapi.model.OWLEntity;
+
+public class VariablesMapping extends HashMap<OWLEntity, String>{
+
+ private int classCnt = 0;
+ private int propCnt = 0;
+ private int indCnt = 0;
+
+ public String getVariable(OWLEntity entity){
+ String var = get(entity);
+ if(var == null){
+ if(entity.isOWLClass()){
+ var = "?cls" + classCnt++;
+ } else if(entity.isOWLObjectProperty() || entity.isOWLDataProperty()){
+ var = "?p" + propCnt++;
+ } else if(entity.isOWLNamedIndividual()){
+ var = "?s" + indCnt++;
+ }
+ put(entity, var);
+ }
+ return var;
+ }
+
+ public String newIndividualVariable(){
+ return "?s" + indCnt++;
+ }
+
+ public void reset(){
+ clear();
+ classCnt = 0;
+ propCnt = 0;
+ indCnt = 0;
+ }
+}
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