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From: <lor...@us...> - 2013-05-08 16:37:55
|
Revision: 3960
http://sourceforge.net/p/dl-learner/code/3960
Author: lorenz_b
Date: 2013-05-08 16:37:49 +0000 (Wed, 08 May 2013)
Log Message:
-----------
Refactored pattern eval.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-08 15:05:35 UTC (rev 3959)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-08 16:37:49 UTC (rev 3960)
@@ -91,6 +91,7 @@
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.vocabulary.RDF;
public class OWLAxiomPatternUsageEvaluation {
@@ -118,7 +119,7 @@
private double threshold = 0.6;
private OWLAnnotationProperty confidenceProperty = df.getOWLAnnotationProperty(IRI.create("http://dl-learner.org/pattern/confidence"));
- private long maxFragmentExtractionTime = TimeUnit.SECONDS.toMillis(60);
+ private long maxFragmentExtractionTime = TimeUnit.SECONDS.toMillis(10);
private OWLClassExpressionToSPARQLConverter converter = new OWLClassExpressionToSPARQLConverter();
private long maxExecutionTime = TimeUnit.SECONDS.toMillis(20);
private int queryLimit = 10000;
@@ -321,7 +322,7 @@
long startTime = System.currentTimeMillis();
int offset = 0;
boolean hasMoreResults = true;
- while(hasMoreResults && (System.currentTimeMillis() - startTime)<= maxExecutionTime){
+ while(hasMoreResults && (System.currentTimeMillis() - startTime)<= maxFragmentExtractionTime){
query.setOffset(offset);System.out.println(query);
Model m = executeConstructQuery(query);
fragment.add(m);
@@ -563,26 +564,38 @@
qs = rs.next();
// get the IRIs for each variable
Map<OWLEntity, IRI> entity2IRIMap = new HashMap<OWLEntity, IRI>();
- entity2IRIMap.put(patternSubClass.asOWLClass(), cls.getIRI());
+ entity2IRIMap.put(pattern.getSubClass().asOWLClass(), cls.getIRI());
+ boolean skip = false;
for (OWLEntity entity : signature) {
String var = variablesMapping.get(entity);
+ if(qs.get(var).isLiteral()){
+ skip = true;
+ break;
+ }
Resource resource = qs.getResource(var);
+ if(entity.isOWLObjectProperty() && resource.hasURI(RDF.type.getURI())){
+ skip = true;
+ break;
+ }
entity2IRIMap.put(entity, IRI.create(resource.getURI()));
}
- // instantiate the pattern
- OWLObjectDuplicator duplicator = new OWLObjectDuplicator(entity2IRIMap, df);
- OWLAxiom patternInstantiation = duplicator.duplicateObject(pattern);
- int patternInstantiationCnt = qs.getLiteral("cnt").getInt();
- // compute score
- Score score;
- try {
- score = computeScore(subClassCnt, patternInstantiationCnt);
- axioms2Score.put(patternInstantiation, score);
- } catch (IllegalArgumentException e) {
- // sometimes Virtuosos returns 'wrong' cnt values such that the
- // success number as bigger than the total number of instances
- e.printStackTrace();
+ if(!skip){
+ // instantiate the pattern
+ OWLObjectDuplicator duplicator = new OWLObjectDuplicator(entity2IRIMap, df);
+ OWLAxiom patternInstantiation = duplicator.duplicateObject(pattern);
+ int patternInstantiationCnt = qs.getLiteral("cnt").getInt();
+ // compute score
+ Score score;
+ try {
+ score = computeScore(subClassCnt, patternInstantiationCnt);
+ axioms2Score.put(patternInstantiation, score);
+ } catch (IllegalArgumentException e) {
+ // sometimes Virtuosos returns 'wrong' cnt values such that the
+ // success number as bigger than the total number of instances
+ e.printStackTrace();
+ }
}
+
}
return axioms2Score;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-05-08 15:06:02
|
Revision: 3959
http://sourceforge.net/p/dl-learner/code/3959
Author: lorenz_b
Date: 2013-05-08 15:05:35 +0000 (Wed, 08 May 2013)
Log Message:
-----------
Refactored pattern eval.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-08 12:59:45 UTC (rev 3958)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-08 15:05:35 UTC (rev 3959)
@@ -107,7 +107,9 @@
private Connection conn;
private ExtractionDBCache cache = new ExtractionDBCache("pattern-cache");
- private SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpedia(), cache);//new LocalModelBasedSparqlEndpointKS(model);
+ private SparqlEndpoint endpoint = SparqlEndpoint.getEndpointDBpedia();
+
+ private SparqlEndpointKS ks = new SparqlEndpointKS(endpoint, cache);//new LocalModelBasedSparqlEndpointKS(model);
private String ns = "http://dbpedia.org/ontology/";
private boolean fancyLatex = false;
@@ -298,10 +300,12 @@
if (negation) {
modalDepth--;
}
+ System.out.println(modalDepth + ": " + pattern);
maxModalDepth = Math.max(modalDepth, maxModalDepth);
}
}
- return maxModalDepth;
+ return 3;
+// return maxModalDepth;
}
private Map<NamedClass, Model> extractFragments(Collection<NamedClass> classes, int depth){
@@ -455,15 +459,15 @@
Map<OWLAxiom, Score> axioms2Score = new HashMap<OWLAxiom, Score>();
OWLClassExpression patternSubClass = ((OWLSubClassOfAxiom)pattern).getSubClass();
- OWLClassExpression superClass = ((OWLSubClassOfAxiom)pattern).getSuperClass();
+ OWLClassExpression patternSuperClass = ((OWLSubClassOfAxiom)pattern).getSuperClass();
//set the subclass as a class from the KB
- OWLClass subClass = df.getOWLClass(IRI.create(cls.getName()));
+ patternSubClass = df.getOWLClass(IRI.create(cls.getName()));
//check if pattern is negation of something
- boolean negation = superClass instanceof OWLObjectComplementOf;
+ boolean negation = patternSuperClass instanceof OWLObjectComplementOf;
//build the query
- Description d = DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(superClass);
+ Description d = DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(patternSuperClass);
int modalDepth = d.getDepth();
if(negation){
modalDepth--;
@@ -495,13 +499,13 @@
logger.info("...got " + fragment.size() + " triples.");
//2. execute SPARQL query on local model
- query = QueryFactory.create("SELECT (COUNT(DISTINCT ?x) AS ?cnt) WHERE {" + converter.convert("?x", subClass) + "}",Syntax.syntaxARQ);
+ query = QueryFactory.create("SELECT (COUNT(DISTINCT ?x) AS ?cnt) WHERE {" + converter.convert("?x", patternSubClass) + "}",Syntax.syntaxARQ);
int subClassCnt = QueryExecutionFactory.create(query, fragment).execSelect().next().getLiteral("cnt").getInt();
System.out.println(subClassCnt);
- Set<OWLEntity> signature = superClass.getSignature();
- signature.remove(subClass);
- query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(subClass, superClass), signature, true);
+ Set<OWLEntity> signature = patternSuperClass.getSignature();
+ signature.remove(patternSubClass);
+ query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(patternSubClass, patternSuperClass), signature, true);
Map<OWLEntity, String> variablesMapping = converter.getVariablesMapping();
com.hp.hpl.jena.query.ResultSet rs = QueryExecutionFactory.create(query, fragment).execSelect();
QuerySolution qs;
@@ -509,7 +513,7 @@
qs = rs.next();
//get the IRIs for each variable
Map<OWLEntity, IRI> entity2IRIMap = new HashMap<OWLEntity, IRI>();
- entity2IRIMap.put(patternSubClass.asOWLClass(), subClass.getIRI());
+ entity2IRIMap.put(patternSubClass.asOWLClass(), patternSubClass.asOWLClass().getIRI());
for (OWLEntity entity : signature) {
String var = variablesMapping.get(entity);
Resource resource = qs.getResource(var);
@@ -539,6 +543,8 @@
OWLClassExpression patternSubClass = pattern.getSubClass();
OWLClassExpression patternSuperClass = pattern.getSuperClass();
+ patternSubClass = cls;
+
// 2. execute SPARQL query on local model
Query query = QueryFactory.create(
"SELECT (COUNT(DISTINCT ?x) AS ?cnt) WHERE {" + converter.convert("?x", patternSubClass) + "}",
@@ -549,6 +555,7 @@
Set<OWLEntity> signature = patternSuperClass.getSignature();
signature.remove(patternSubClass);
query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(patternSubClass, patternSuperClass), signature, true);
+ System.out.println(query);
Map<OWLEntity, String> variablesMapping = converter.getVariablesMapping();
com.hp.hpl.jena.query.ResultSet rs = QueryExecutionFactory.create(query, fragment).execSelect();
QuerySolution qs;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-05-08 12:59:48
|
Revision: 3958
http://sourceforge.net/p/dl-learner/code/3958
Author: lorenz_b
Date: 2013-05-08 12:59:45 +0000 (Wed, 08 May 2013)
Log Message:
-----------
Continued pattern eval.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/LatexObjectVisitor.java
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/LatexObjectVisitor.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/LatexObjectVisitor.java 2013-05-07 20:50:56 UTC (rev 3957)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/LatexObjectVisitor.java 2013-05-08 12:59:45 UTC (rev 3958)
@@ -579,7 +579,6 @@
writeSpace();
write(EQUIV);
writeSpace();
- write(axiom.getSecondProperty());
axiom.getSecondProperty().accept(this);
write("\\ensuremath{^-}");
}
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-07 20:50:56 UTC (rev 3957)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-08 12:59:45 UTC (rev 3958)
@@ -7,6 +7,7 @@
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
+import java.io.UnsupportedEncodingException;
import java.net.SocketTimeoutException;
import java.net.URI;
import java.net.URL;
@@ -33,13 +34,12 @@
import joptsimple.OptionParser;
import joptsimple.OptionSet;
-import org.apache.commons.lang.text.StrTokenizer;
+import org.aksw.commons.collections.diff.ModelDiff;
import org.apache.log4j.Logger;
-import org.coode.owlapi.functionalparser.OWLFunctionalSyntaxOWLParser;
import org.coode.owlapi.turtle.TurtleOntologyFormat;
import org.dllearner.core.EvaluatedAxiom;
import org.dllearner.core.Score;
-import org.dllearner.core.owl.EquivalentClassesAxiom;
+import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.kb.LocalModelBasedSparqlEndpointKS;
import org.dllearner.kb.SparqlEndpointKS;
@@ -49,13 +49,12 @@
import org.dllearner.learningproblems.AxiomScore;
import org.dllearner.learningproblems.Heuristics;
import org.dllearner.reasoning.SPARQLReasoner;
+import org.dllearner.utilities.owl.DLLearnerDescriptionConvertVisitor;
import org.dllearner.utilities.owl.OWLClassExpressionToSPARQLConverter;
import org.ini4j.IniPreferences;
import org.ini4j.InvalidFileFormatException;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.OWLObjectRenderer;
-import org.semanticweb.owlapi.io.OWLParserException;
-import org.semanticweb.owlapi.io.StringDocumentSource;
import org.semanticweb.owlapi.io.ToStringRenderer;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
@@ -66,30 +65,29 @@
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
+import org.semanticweb.owlapi.model.OWLObjectComplementOf;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLOntologyStorageException;
import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
-import org.semanticweb.owlapi.model.UnloadableImportException;
import org.semanticweb.owlapi.util.OWLObjectDuplicator;
import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
import uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxObjectRenderer;
-import com.google.common.base.Charsets;
import com.google.common.collect.HashMultiset;
import com.google.common.collect.Multiset;
-import com.google.common.hash.HashCode;
-import com.google.common.hash.HashFunction;
-import com.google.common.hash.Hashing;
+import com.hp.hpl.jena.query.ParameterizedSparqlString;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.Syntax;
+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;
@@ -109,7 +107,7 @@
private Connection conn;
private ExtractionDBCache cache = new ExtractionDBCache("pattern-cache");
- private SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpediaLiveAKSW(), cache);//new LocalModelBasedSparqlEndpointKS(model);
+ private SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpedia(), cache);//new LocalModelBasedSparqlEndpointKS(model);
private String ns = "http://dbpedia.org/ontology/";
private boolean fancyLatex = false;
@@ -118,6 +116,7 @@
private double threshold = 0.6;
private OWLAnnotationProperty confidenceProperty = df.getOWLAnnotationProperty(IRI.create("http://dl-learner.org/pattern/confidence"));
+ private long maxFragmentExtractionTime = TimeUnit.SECONDS.toMillis(60);
private OWLClassExpressionToSPARQLConverter converter = new OWLClassExpressionToSPARQLConverter();
private long maxExecutionTime = TimeUnit.SECONDS.toMillis(20);
private int queryLimit = 10000;
@@ -185,7 +184,8 @@
for (NamedClass cls : classes) {
logger.info("Processing " + cls + "...");
- Map<OWLAxiom, Score> result = evaluate2(pattern, cls);
+ Map<OWLAxiom, Score> result = evaluateUsingFragmentExtraction(pattern, cls);
+ axioms2Score.putAll(result);
for (Entry<OWLAxiom, Score> entry : result.entrySet()) {
OWLAxiom axiom = entry.getKey();
@@ -208,6 +208,135 @@
}
}
+ public void runUsingFragmentExtraction(SparqlEndpoint endpoint, OWLOntology ontology, 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(ontology);
+
+ //get all classes in KB
+ Collection<NamedClass> classes = reasoner.getTypes(ns);
+
+ //randomize and extract a chunk
+ List<NamedClass> classesList = new ArrayList<NamedClass>(classes);
+ Collections.shuffle(classesList, new Random(123));
+ classesList = classesList.subList(0, maxNrOfTestedClasses);
+ classes = classesList;
+
+ //get the maximum modal depth in the pattern axioms
+ int maxModalDepth = maxModalDepth(patterns);
+
+ //extract fragment for each class only once
+ Map<NamedClass, Model> class2Fragment = extractFragments(classes, maxModalDepth);
+
+ //for each pattern
+ for (OWLAxiom pattern : patterns) {
+ logger.info("Applying pattern " + pattern + "...");
+ //if pattern is equivalent classes axiom, we need to get the subclass axiom where the named class is the subclass
+ if(pattern.isOfType(AxiomType.EQUIVALENT_CLASSES)){
+ Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom)pattern).asOWLSubClassOfAxioms();
+ for (OWLSubClassOfAxiom axiom : subClassOfAxioms) {
+ if(!axiom.getSubClass().isAnonymous()){
+ pattern = axiom;
+ break;
+ }
+ }
+ }
+ if(pattern.isOfType(AxiomType.SUBCLASS_OF)){
+ Map<OWLAxiom, Score> axioms2Score = new LinkedHashMap<OWLAxiom, Score>();
+ //for each class
+ int i = 1;
+ for (NamedClass cls : classes) {
+ logger.info("...on class " + cls + "...");
+ Model fragment = class2Fragment.get(cls);
+ Map<OWLAxiom, Score> result = applyPattern((OWLSubClassOfAxiom) pattern, df.getOWLClass(IRI.create(cls.getName())), fragment);
+ axioms2Score.putAll(result);
+
+ for (Entry<OWLAxiom, Score> entry : result.entrySet()) {
+ OWLAxiom axiom = entry.getKey();
+ Score score = entry.getValue();
+ if(score.getAccuracy() >= threshold){
+ logger.info(axiom + "(" + format.format(score.getAccuracy()) + ")");
+ }
+ }
+
+ //wait some time to avoid flooding of endpoint
+ try {
+ Thread.sleep(waitingTime);
+ } catch (InterruptedException e) {
+ e.printStackTrace();
+ }
+// if(i++ == 3) break;
+ }
+ save(pattern, axioms2Score);
+ }
+ }
+ }
+
+ private int maxModalDepth(List<OWLAxiom> patterns) {
+ int maxModalDepth = 1;
+ for (OWLAxiom pattern : patterns) {
+ // get the superclass of the pattern
+ if (pattern.isOfType(AxiomType.EQUIVALENT_CLASSES)) {
+ Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom) pattern)
+ .asOWLSubClassOfAxioms();
+ for (OWLSubClassOfAxiom axiom : subClassOfAxioms) {
+ if (!axiom.getSubClass().isAnonymous()) {
+ pattern = axiom;
+ break;
+ }
+ }
+ }
+ if (pattern.isOfType(AxiomType.SUBCLASS_OF)) {
+ OWLClassExpression superClass = ((OWLSubClassOfAxiom) pattern).getSuperClass();
+ // check if pattern is negation of something
+ boolean negation = superClass instanceof OWLObjectComplementOf;
+ // build the query
+ Description d = DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(superClass);
+ int modalDepth = d.getDepth();
+ if (negation) {
+ modalDepth--;
+ }
+ maxModalDepth = Math.max(modalDepth, maxModalDepth);
+ }
+ }
+ return maxModalDepth;
+ }
+
+ 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
+ for (NamedClass cls : classes) {
+ logger.info("Extracting fragment for " + cls + "...");
+ Model fragment = ModelFactory.createDefaultModel();
+ //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)<= maxExecutionTime){
+ query.setOffset(offset);System.out.println(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.");
+ class2Fragment.put(cls, fragment);
+ }
+ return class2Fragment;
+ }
+
private Map<OWLAxiom, Score> evaluate1(OWLAxiom pattern, NamedClass cls){
Map<OWLAxiom, Score> axioms2Score = new HashMap<OWLAxiom, Score>();
@@ -322,7 +451,7 @@
return axioms2Score;
}
- private Map<OWLAxiom, Score> evaluate3(OWLAxiom pattern, NamedClass cls){
+ private Map<OWLAxiom, Score> evaluateUsingFragmentExtraction(OWLAxiom pattern, NamedClass cls){
Map<OWLAxiom, Score> axioms2Score = new HashMap<OWLAxiom, Score>();
OWLClassExpression patternSubClass = ((OWLSubClassOfAxiom)pattern).getSubClass();
@@ -331,18 +460,51 @@
//set the subclass as a class from the KB
OWLClass subClass = df.getOWLClass(IRI.create(cls.getName()));
- //1. count number of instances in subclass expression
- Query query = QueryFactory.create("SELECT (COUNT(DISTINCT ?x) AS ?cnt) WHERE {" + converter.convert("?x", subClass) + "}",Syntax.syntaxARQ);
- int subClassCnt = executeSelectQuery(query).next().getLiteral("cnt").getInt();
+ //check if pattern is negation of something
+ boolean negation = superClass instanceof OWLObjectComplementOf;
+ //build the query
+ Description d = DLLearnerDescriptionConvertVisitor.getDLLearnerDescription(superClass);
+ int modalDepth = d.getDepth();
+ if(negation){
+ modalDepth--;
+ }
+ //depending on the modal depth, we have to get triples
+ Query query = buildConstructQuery(cls, modalDepth);
+ query.setLimit(queryLimit);
- //2. get result
+ //1. get fragment until time elapsed
+ logger.info("Extracting fragment...");
+ Model fragment = ModelFactory.createDefaultModel();
+ long startTime = System.currentTimeMillis();
+ int offset = 0;
+ boolean hasMoreResults = true;
+ while(hasMoreResults && (System.currentTimeMillis() - startTime)<= maxExecutionTime){
+ query.setOffset(offset);
+ 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.");
+
+ //2. execute SPARQL query on local model
+ query = QueryFactory.create("SELECT (COUNT(DISTINCT ?x) AS ?cnt) WHERE {" + converter.convert("?x", subClass) + "}",Syntax.syntaxARQ);
+ int subClassCnt = QueryExecutionFactory.create(query, fragment).execSelect().next().getLiteral("cnt").getInt();
+ System.out.println(subClassCnt);
+
Set<OWLEntity> signature = superClass.getSignature();
signature.remove(subClass);
- query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(subClass, superClass), signature);
+ query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(subClass, superClass), signature, true);
Map<OWLEntity, String> variablesMapping = converter.getVariablesMapping();
- com.hp.hpl.jena.query.ResultSet rs = executeSelectQuery(query);
+ com.hp.hpl.jena.query.ResultSet rs = QueryExecutionFactory.create(query, fragment).execSelect();
QuerySolution qs;
- Multiset<OWLAxiom> instantiations = HashMultiset.create();
while(rs.hasNext()){
qs = rs.next();
//get the IRIs for each variable
@@ -356,19 +518,98 @@
//instantiate the pattern
OWLObjectDuplicator duplicator = new OWLObjectDuplicator(entity2IRIMap, df);
OWLAxiom patternInstantiation = duplicator.duplicateObject(pattern);
-
- instantiations.add(patternInstantiation);
+ int patternInstantiationCnt = qs.getLiteral("cnt").getInt();
+ //compute score
+ Score score;
+ try {
+ score = computeScore(subClassCnt, patternInstantiationCnt);//System.out.println(patternInstantiation + "(" + score.getAccuracy() + ")");
+ axioms2Score.put(patternInstantiation, score);
+ } catch (IllegalArgumentException e) {
+ //sometimes Virtuosos returns 'wrong' cnt values such that the success number as bigger than the total number of instances
+ e.printStackTrace();
+ }
}
- //compute the score
- for (OWLAxiom axiom : instantiations.elementSet()) {
- int frequency = instantiations.count(axiom);
- Score score = new AxiomScore(frequency);
- axioms2Score.put(axiom, score);
- }
return axioms2Score;
}
+ private Map<OWLAxiom, Score> applyPattern(OWLSubClassOfAxiom pattern, OWLClass cls, Model fragment) {
+ Map<OWLAxiom, Score> axioms2Score = new HashMap<OWLAxiom, Score>();
+
+ OWLClassExpression patternSubClass = pattern.getSubClass();
+ OWLClassExpression patternSuperClass = pattern.getSuperClass();
+
+ // 2. execute SPARQL query on local model
+ Query query = QueryFactory.create(
+ "SELECT (COUNT(DISTINCT ?x) AS ?cnt) WHERE {" + converter.convert("?x", patternSubClass) + "}",
+ Syntax.syntaxARQ);
+ int subClassCnt = QueryExecutionFactory.create(query, fragment).execSelect().next().getLiteral("cnt").getInt();
+ System.out.println(subClassCnt);
+
+ Set<OWLEntity> signature = patternSuperClass.getSignature();
+ signature.remove(patternSubClass);
+ query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(patternSubClass, patternSuperClass), signature, true);
+ Map<OWLEntity, String> variablesMapping = converter.getVariablesMapping();
+ com.hp.hpl.jena.query.ResultSet rs = QueryExecutionFactory.create(query, fragment).execSelect();
+ QuerySolution qs;
+ while (rs.hasNext()) {
+ qs = rs.next();
+ // get the IRIs for each variable
+ Map<OWLEntity, IRI> entity2IRIMap = new HashMap<OWLEntity, IRI>();
+ entity2IRIMap.put(patternSubClass.asOWLClass(), cls.getIRI());
+ for (OWLEntity entity : signature) {
+ String var = variablesMapping.get(entity);
+ Resource resource = qs.getResource(var);
+ entity2IRIMap.put(entity, IRI.create(resource.getURI()));
+ }
+ // instantiate the pattern
+ OWLObjectDuplicator duplicator = new OWLObjectDuplicator(entity2IRIMap, df);
+ OWLAxiom patternInstantiation = duplicator.duplicateObject(pattern);
+ int patternInstantiationCnt = qs.getLiteral("cnt").getInt();
+ // compute score
+ Score score;
+ try {
+ score = computeScore(subClassCnt, patternInstantiationCnt);
+ axioms2Score.put(patternInstantiation, score);
+ } catch (IllegalArgumentException e) {
+ // sometimes Virtuosos returns 'wrong' cnt values such that the
+ // success number as bigger than the total number of instances
+ e.printStackTrace();
+ }
+ }
+
+ return axioms2Score;
+ }
+
+ private Query buildConstructQuery(NamedClass cls, int depth){
+ StringBuilder sb = new StringBuilder();
+ int maxVarCnt = 0;
+ sb.append("CONSTRUCT {\n");
+ sb.append("?s").append("?p0 ").append("?o0").append(".\n");
+ for(int i = 1; i < depth-1; i++){
+ sb.append("?o").append(i-1).append(" ").append("?p").append(i).append(" ").append("?o").append(i).append(".\n");
+ maxVarCnt++;
+ }
+ sb.append("?o").append(maxVarCnt).append(" a ?type.\n");
+ sb.append("}\n");
+ sb.append("WHERE {\n");
+ sb.append("?s a ?cls.");
+ sb.append("?s").append("?p0 ").append("?o0").append(".\n");
+ for(int i = 1; i < depth-1; i++){
+ sb.append("OPTIONAL{\n");
+ sb.append("?o").append(i-1).append(" ").append("?p").append(i).append(" ").append("?o").append(i).append(".\n");
+ }
+ sb.append("OPTIONAL{?o").append(maxVarCnt).append(" a ?type}.\n");
+ for(int i = 1; i < depth-1; i++){
+ sb.append("}");
+ }
+
+ sb.append("}\n");
+ ParameterizedSparqlString template = new ParameterizedSparqlString(sb.toString());
+ template.setIri("cls", cls.getName());
+ return template.asQuery();
+ }
+
private void save(OWLAxiom pattern, Map<OWLAxiom, Score> axioms2Score){
try {
Set<OWLAxiom> annotatedAxioms = new HashSet<OWLAxiom>();
@@ -382,11 +623,8 @@
}
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
OWLOntology ontology = man.createOntology(annotatedAxioms);
- HashFunction hf = Hashing.md5();
- HashCode hc = hf.newHasher()
- .putString(pattern.toString(), Charsets.UTF_8)
- .hash();
- man.saveOntology(ontology, new TurtleOntologyFormat(), new FileOutputStream(hc.toString() + "-pattern-instantiations.ttl"));
+ String filename = axiomRenderer.render(pattern).replace(" ", "_");
+ man.saveOntology(ontology, new TurtleOntologyFormat(), new FileOutputStream(filename + "-instantiations.ttl"));
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
} catch (OWLOntologyStorageException e) {
@@ -484,6 +722,44 @@
return rs;
}
+ protected Model executeConstructQuery(Query query) {
+ if(ks.isRemote()){
+ SparqlEndpoint endpoint = ((SparqlEndpointKS) ks).getEndpoint();
+ ExtractionDBCache cache = ks.getCache();
+ Model model = null;
+ try {
+ if(cache != null){
+ try {
+ model = cache.executeConstructQuery(endpoint, query.toString());
+ } catch (UnsupportedEncodingException e) {
+ e.printStackTrace();
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ } else {
+ QueryEngineHTTP queryExecution = new QueryEngineHTTP(endpoint.getURL().toString(),
+ query);
+ queryExecution.setDefaultGraphURIs(endpoint.getDefaultGraphURIs());
+ queryExecution.setNamedGraphURIs(endpoint.getNamedGraphURIs());
+ model = queryExecution.execConstruct();
+ }
+ logger.debug("Got " + model.size() + " triples.");
+ return model;
+ } catch (QueryExceptionHTTP e) {
+ if(e.getCause() instanceof SocketTimeoutException){
+ logger.warn("Got timeout");
+ } else {
+ logger.error("Exception executing query", e);
+ }
+ return ModelFactory.createDefaultModel();
+ }
+ } else {
+ QueryExecution queryExecution = QueryExecutionFactory.create(query, ((LocalModelBasedSparqlEndpointKS)ks).getModel());
+ Model model = queryExecution.execConstruct();
+ return model;
+ }
+ }
+
private Score computeScore(int total, int success){
double[] confidenceInterval = Heuristics.getConfidenceInterval95Wald(total, success);
@@ -573,7 +849,7 @@
System.exit(0);
}
int maxNrOfTestedClasses = (Integer) options.valueOf("limit");
- new OWLAxiomPatternUsageEvaluation().run(endpoint, patternsOntology, outputFile, maxNrOfTestedClasses);
+ new OWLAxiomPatternUsageEvaluation().runUsingFragmentExtraction(endpoint, patternsOntology, outputFile, maxNrOfTestedClasses);
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-05-07 20:50:59
|
Revision: 3957
http://sourceforge.net/p/dl-learner/code/3957
Author: lorenz_b
Date: 2013-05-07 20:50:56 +0000 (Tue, 07 May 2013)
Log Message:
-----------
Added option to set a maximum number of tested classes for each pattern.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/LatexObjectVisitor.java
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.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 2013-05-07 06:24:03 UTC (rev 3956)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java 2013-05-07 20:50:56 UTC (rev 3957)
@@ -24,7 +24,7 @@
private Model baseModel;
private List<String> namespaces;
- private int maxRecursionDepth = 3;
+ private int maxRecursionDepth = 1;
public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, ExtractionDBCache cache) {
this.endpoint = endpoint;
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java 2013-05-07 06:24:03 UTC (rev 3956)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java 2013-05-07 20:50:56 UTC (rev 3957)
@@ -103,6 +103,10 @@
}
public Query asQuery(String rootVariable, OWLClassExpression expr, Set<? extends OWLEntity> variableEntities){
+ return asQuery(rootVariable, expr, variableEntities, false);
+ }
+
+ public Query asQuery(String rootVariable, OWLClassExpression expr, Set<? extends OWLEntity> variableEntities, boolean count){
this.variableEntities = variableEntities;
String queryString = "SELECT DISTINCT ";
String triplePattern = convert(rootVariable, expr);
@@ -113,18 +117,25 @@
String var = variablesMapping.get(owlEntity);
queryString += var + " ";
}
- queryString += "(COUNT(DISTINCT " + rootVariable + ") AS ?cnt) WHERE {";
+ if(count){
+ queryString += "(COUNT(DISTINCT " + rootVariable + ") AS ?cnt)";
+ } else {
+ queryString += rootVariable;
+ }
+ queryString += " WHERE {";
}
queryString += triplePattern;
queryString += "}";
if(!variableEntities.isEmpty()){
- queryString += "GROUP BY ";
- for (OWLEntity owlEntity : variableEntities) {
- String var = variablesMapping.get(owlEntity);
- queryString += var;
+ if(count){
+ queryString += "GROUP BY ";
+ for (OWLEntity owlEntity : variableEntities) {
+ String var = variablesMapping.get(owlEntity);
+ queryString += var;
+ }
+ queryString += " ORDER BY DESC(?cnt)";
}
- queryString += " ORDER BY DESC(?cnt)";
}
return QueryFactory.create(queryString, Syntax.syntaxARQ);
}
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/LatexObjectVisitor.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/LatexObjectVisitor.java 2013-05-07 06:24:03 UTC (rev 3956)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/LatexObjectVisitor.java 2013-05-07 20:50:56 UTC (rev 3957)
@@ -248,7 +248,8 @@
write(SOME);
writeSpace();
node.getProperty().accept(this);
- writeSpace();
+// writeSpace();
+ writeDot();
writeOpenBrace();
node.getValue().accept(this);
writeCloseBrace();
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java 2013-05-07 06:24:03 UTC (rev 3956)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java 2013-05-07 20:50:56 UTC (rev 3957)
@@ -378,7 +378,7 @@
}
if(formatNumbers){
- latexTable += i + " & " + axiomColumn + " & " + "\\num{" + frequency + "} & " + df;
+ latexTable += i + ". & " + axiomColumn + " & " + "\\num{" + frequency + "} & " + df;
for (OntologyRepository repository : repositories) {
int rank = 0;
boolean contained = false;
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-07 06:24:03 UTC (rev 3956)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-07 20:50:56 UTC (rev 3957)
@@ -12,11 +12,10 @@
import java.net.URL;
import java.sql.Connection;
import java.sql.DriverManager;
-import java.sql.PreparedStatement;
-import java.sql.ResultSet;
import java.sql.SQLException;
import java.text.DecimalFormat;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
@@ -25,6 +24,7 @@
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
+import java.util.Random;
import java.util.Set;
import java.util.concurrent.TimeUnit;
import java.util.prefs.Preferences;
@@ -33,12 +33,13 @@
import joptsimple.OptionParser;
import joptsimple.OptionSet;
-import org.aksw.commons.util.Pair;
+import org.apache.commons.lang.text.StrTokenizer;
import org.apache.log4j.Logger;
import org.coode.owlapi.functionalparser.OWLFunctionalSyntaxOWLParser;
import org.coode.owlapi.turtle.TurtleOntologyFormat;
import org.dllearner.core.EvaluatedAxiom;
import org.dllearner.core.Score;
+import org.dllearner.core.owl.EquivalentClassesAxiom;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.kb.LocalModelBasedSparqlEndpointKS;
import org.dllearner.kb.SparqlEndpointKS;
@@ -64,6 +65,7 @@
import org.semanticweb.owlapi.model.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLEntity;
+import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
@@ -77,6 +79,8 @@
import uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxObjectRenderer;
import com.google.common.base.Charsets;
+import com.google.common.collect.HashMultiset;
+import com.google.common.collect.Multiset;
import com.google.common.hash.HashCode;
import com.google.common.hash.HashFunction;
import com.google.common.hash.Hashing;
@@ -105,7 +109,7 @@
private Connection conn;
private ExtractionDBCache cache = new ExtractionDBCache("pattern-cache");
- private SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpedia(), cache);//new LocalModelBasedSparqlEndpointKS(model);
+ private SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpediaLiveAKSW(), cache);//new LocalModelBasedSparqlEndpointKS(model);
private String ns = "http://dbpedia.org/ontology/";
private boolean fancyLatex = false;
@@ -113,6 +117,10 @@
private long waitingTime = TimeUnit.SECONDS.toMillis(3);
private double threshold = 0.6;
private OWLAnnotationProperty confidenceProperty = df.getOWLAnnotationProperty(IRI.create("http://dl-learner.org/pattern/confidence"));
+
+ private OWLClassExpressionToSPARQLConverter converter = new OWLClassExpressionToSPARQLConverter();
+ private long maxExecutionTime = TimeUnit.SECONDS.toMillis(20);
+ private int queryLimit = 10000;
public OWLAxiomPatternUsageEvaluation() {
initDBConnection();
@@ -143,83 +151,50 @@
}
}
- public void run(SparqlEndpoint endpoint, OWLOntology ontology, File outputFile){
- ks = new SparqlEndpointKS(endpoint);
+ public void run(SparqlEndpoint endpoint, OWLOntology ontology, File outputFile, int maxNrOfTestedClasses){
+ ks = new SparqlEndpointKS(endpoint, cache);
SPARQLReasoner reasoner = new SPARQLReasoner(ks, cache);
- OWLClassExpressionToSPARQLConverter converter = new OWLClassExpressionToSPARQLConverter();
-
//get the axiom patterns to evaluate
- List<OWLAxiom> patterns = getPatternsToEvaluate();
+ List<OWLAxiom> patterns = getPatternsToEvaluate(ontology);
//get all classes in KB
- Set<NamedClass> classes = reasoner.getTypes(ns);
+ Collection<NamedClass> classes = reasoner.getTypes(ns);
+ List<NamedClass> classesList = new ArrayList<NamedClass>(classes);
+ Collections.shuffle(classesList, new Random(123));
+ classesList = classesList.subList(0, maxNrOfTestedClasses);
+ classes = classesList;
//for each pattern
for (OWLAxiom pattern : patterns) {
+ //if pattern is equivalent classes axiom, we need to get the subclass axiom where the named class is the subclass
+ if(pattern.isOfType(AxiomType.EQUIVALENT_CLASSES)){
+ Set<OWLSubClassOfAxiom> subClassOfAxioms = ((OWLEquivalentClassesAxiom)pattern).asOWLSubClassOfAxioms();
+ for (OWLSubClassOfAxiom axiom : subClassOfAxioms) {
+ if(!axiom.getSubClass().isAnonymous()){
+ pattern = axiom;
+ break;
+ }
+ }
+ }
if(pattern.isOfType(AxiomType.SUBCLASS_OF)){
logger.info("Processing " + pattern + "...");
- Set<EvaluatedAxiom> evaluatedAxioms = new HashSet<EvaluatedAxiom>();
Map<OWLAxiom, Score> axioms2Score = new LinkedHashMap<OWLAxiom, Score>();
- OWLClassExpression patternSubClass = ((OWLSubClassOfAxiom)pattern).getSubClass();
- OWLClassExpression superClass = ((OWLSubClassOfAxiom)pattern).getSuperClass();
//for each class
int i = 1;
for (NamedClass cls : classes) {
logger.info("Processing " + cls + "...");
- //set the subclass as a class from the KB
- OWLClass subClass = df.getOWLClass(IRI.create(cls.getName()));
- //1. count number of instances in subclass expression
- Query query = QueryFactory.create("SELECT (COUNT(DISTINCT ?x) AS ?cnt) WHERE {" + converter.convert("?x", subClass) + "}",Syntax.syntaxARQ);
- int subClassCnt = executeSelectQuery(query).next().getLiteral("cnt").getInt();
+ Map<OWLAxiom, Score> result = evaluate2(pattern, cls);
- //2. count number of instances in subclass AND superclass expression
- //we have 2 options here to evaluate the whole axiom pattern:
- //a) we replace all entities in the signature of the super class expression(except the subclass) with variables
- //and GROUP BY them
- //b) we replace only 1 entity with a variable, thus we have to try it for several combinations
-// for (OWLEntity entity : signature) {
-// //replace current entity with variable and for the rest use existing entities in KB
-// query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(subClass, superClass), signature);
-// }
- Set<OWLEntity> signature = superClass.getSignature();
- signature.remove(subClass);
- query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(subClass, superClass), signature);
- query.setLimit(100);
- Map<OWLEntity, String> variablesMapping = converter.getVariablesMapping();System.out.println(query);
- com.hp.hpl.jena.query.ResultSet rs = executeSelectQuery(query);
- QuerySolution qs;
- while(rs.hasNext()){
- qs = rs.next();
- //get the IRIs for each variable
- Map<OWLEntity, IRI> entity2IRIMap = new HashMap<OWLEntity, IRI>();
- entity2IRIMap.put(patternSubClass.asOWLClass(), subClass.getIRI());
- for (OWLEntity entity : signature) {
- String var = variablesMapping.get(entity);
- Resource resource = qs.getResource(var);
- entity2IRIMap.put(entity, IRI.create(resource.getURI()));
+ for (Entry<OWLAxiom, Score> entry : result.entrySet()) {
+ OWLAxiom axiom = entry.getKey();
+ Score score = entry.getValue();
+ if(score.getAccuracy() >= threshold){
+ logger.info(axiom + "(" + format.format(score.getAccuracy()) + ")");
}
- //instantiate the pattern
- OWLObjectDuplicator duplicator = new OWLObjectDuplicator(entity2IRIMap, df);
- OWLAxiom patternInstantiation = duplicator.duplicateObject(pattern);
- int patternInstantiationCnt = qs.getLiteral("cnt").getInt();
- //compute score
- Score score;
- try {
- score = computeScore(subClassCnt, patternInstantiationCnt);
- axioms2Score.put(patternInstantiation, score);
- logger.info(patternInstantiation + "(" + format.format(score.getAccuracy()) + ")");
- } catch (IllegalArgumentException e) {
- //sometimes Virtuosos returns 'wrong' cnt values such that the success number as bigger than the total number of instances
- e.printStackTrace();
- }
-
-// //convert into EvaluatedAxiom such we can serialize it as RDF with accuracy value as annotation
-// EvaluatedAxiom evaluatedAxiom = new EvaluatedAxiom(DLLearnerAxiomConvertVisitor.getDLLearnerAxiom(patternInstantiation), score);
-// evaluatedAxioms.add(evaluatedAxiom);
-
}
+
//wait some time to avoid flooding of endpoint
try {
Thread.sleep(waitingTime);
@@ -233,6 +208,167 @@
}
}
+ private Map<OWLAxiom, Score> evaluate1(OWLAxiom pattern, NamedClass cls){
+ Map<OWLAxiom, Score> axioms2Score = new HashMap<OWLAxiom, Score>();
+
+ OWLClassExpression patternSubClass = ((OWLSubClassOfAxiom)pattern).getSubClass();
+ OWLClassExpression superClass = ((OWLSubClassOfAxiom)pattern).getSuperClass();
+
+ //set the subclass as a class from the KB
+ OWLClass subClass = df.getOWLClass(IRI.create(cls.getName()));
+
+ //1. count number of instances in subclass expression
+ Query query = QueryFactory.create("SELECT (COUNT(DISTINCT ?x) AS ?cnt) WHERE {" + converter.convert("?x", subClass) + "}",Syntax.syntaxARQ);
+ int subClassCnt = executeSelectQuery(query).next().getLiteral("cnt").getInt();
+
+ //2. replace all entities which are not the subclass, GROUP BY and COUNT
+ Set<OWLEntity> signature = superClass.getSignature();
+ signature.remove(subClass);
+ query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(subClass, superClass), signature, true);
+ Map<OWLEntity, String> variablesMapping = converter.getVariablesMapping();
+ com.hp.hpl.jena.query.ResultSet rs = executeSelectQuery(query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ //get the IRIs for each variable
+ Map<OWLEntity, IRI> entity2IRIMap = new HashMap<OWLEntity, IRI>();
+ entity2IRIMap.put(patternSubClass.asOWLClass(), subClass.getIRI());
+ for (OWLEntity entity : signature) {
+ String var = variablesMapping.get(entity);
+ Resource resource = qs.getResource(var);
+ entity2IRIMap.put(entity, IRI.create(resource.getURI()));
+ }
+ //instantiate the pattern
+ OWLObjectDuplicator duplicator = new OWLObjectDuplicator(entity2IRIMap, df);
+ OWLAxiom patternInstantiation = duplicator.duplicateObject(pattern);
+ int patternInstantiationCnt = qs.getLiteral("cnt").getInt();
+ //compute score
+ Score score;
+ try {
+ score = computeScore(subClassCnt, patternInstantiationCnt);
+ axioms2Score.put(patternInstantiation, score);
+ } catch (IllegalArgumentException e) {
+ //sometimes Virtuosos returns 'wrong' cnt values such that the success number as bigger than the total number of instances
+ e.printStackTrace();
+ }
+ }
+
+ return axioms2Score;
+ }
+
+ private Map<OWLAxiom, Score> evaluate2(OWLAxiom pattern, NamedClass cls){
+ Map<OWLAxiom, Score> axioms2Score = new HashMap<OWLAxiom, Score>();
+
+ OWLClassExpression patternSubClass = ((OWLSubClassOfAxiom)pattern).getSubClass();
+ OWLClassExpression superClass = ((OWLSubClassOfAxiom)pattern).getSuperClass();
+
+ //set the subclass as a class from the KB
+ OWLClass subClass = df.getOWLClass(IRI.create(cls.getName()));
+
+ //1. convert class expression, replace non-subclass entities and get result
+ Set<OWLEntity> signature = superClass.getSignature();
+ signature.remove(subClass);
+
+ Query query;
+ Multiset<OWLAxiom> instantiations = HashMultiset.create();
+ Set<String> resources = new HashSet<String>();//we need the number of distinct resources (?x) to compute the score
+ long startTime = System.currentTimeMillis();
+ int offset = 0;
+ boolean hasMoreResults = true;
+ while(hasMoreResults && (System.currentTimeMillis() - startTime)<= maxExecutionTime){
+ query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(subClass, superClass), signature);
+ query.setLimit(queryLimit);
+ query.setOffset(offset);
+ System.out.println(query);
+ Map<OWLEntity, String> variablesMapping = converter.getVariablesMapping();
+ com.hp.hpl.jena.query.ResultSet rs = executeSelectQuery(query);
+ QuerySolution qs;
+ if(!rs.hasNext()){
+ hasMoreResults = false;
+ }
+ while(rs.hasNext()){
+ qs = rs.next();
+ resources.add(qs.getResource("x").getURI());
+ //get the IRIs for each variable
+ Map<OWLEntity, IRI> entity2IRIMap = new HashMap<OWLEntity, IRI>();
+ entity2IRIMap.put(patternSubClass.asOWLClass(), subClass.getIRI());
+ for (OWLEntity entity : signature) {
+ String var = variablesMapping.get(entity);
+ Resource resource = qs.getResource(var);
+ entity2IRIMap.put(entity, IRI.create(resource.getURI()));
+ }
+ //instantiate the pattern
+ OWLObjectDuplicator duplicator = new OWLObjectDuplicator(entity2IRIMap, df);
+ OWLAxiom patternInstantiation = duplicator.duplicateObject(pattern);
+
+ instantiations.add(patternInstantiation);
+ }
+ offset += queryLimit;
+ try {
+ Thread.sleep(300);
+ } catch (InterruptedException e) {
+ e.printStackTrace();
+ }
+ }
+
+ //compute the score
+ int total = resources.size();
+ for (OWLAxiom axiom : instantiations.elementSet()) {
+ int frequency = instantiations.count(axiom);
+ Score score = computeScore(total, Math.min(total, frequency));
+ axioms2Score.put(axiom, score);
+ }
+
+ return axioms2Score;
+ }
+
+ private Map<OWLAxiom, Score> evaluate3(OWLAxiom pattern, NamedClass cls){
+ Map<OWLAxiom, Score> axioms2Score = new HashMap<OWLAxiom, Score>();
+
+ OWLClassExpression patternSubClass = ((OWLSubClassOfAxiom)pattern).getSubClass();
+ OWLClassExpression superClass = ((OWLSubClassOfAxiom)pattern).getSuperClass();
+
+ //set the subclass as a class from the KB
+ OWLClass subClass = df.getOWLClass(IRI.create(cls.getName()));
+
+ //1. count number of instances in subclass expression
+ Query query = QueryFactory.create("SELECT (COUNT(DISTINCT ?x) AS ?cnt) WHERE {" + converter.convert("?x", subClass) + "}",Syntax.syntaxARQ);
+ int subClassCnt = executeSelectQuery(query).next().getLiteral("cnt").getInt();
+
+ //2. get result
+ Set<OWLEntity> signature = superClass.getSignature();
+ signature.remove(subClass);
+ query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(subClass, superClass), signature);
+ Map<OWLEntity, String> variablesMapping = converter.getVariablesMapping();
+ com.hp.hpl.jena.query.ResultSet rs = executeSelectQuery(query);
+ QuerySolution qs;
+ Multiset<OWLAxiom> instantiations = HashMultiset.create();
+ while(rs.hasNext()){
+ qs = rs.next();
+ //get the IRIs for each variable
+ Map<OWLEntity, IRI> entity2IRIMap = new HashMap<OWLEntity, IRI>();
+ entity2IRIMap.put(patternSubClass.asOWLClass(), subClass.getIRI());
+ for (OWLEntity entity : signature) {
+ String var = variablesMapping.get(entity);
+ Resource resource = qs.getResource(var);
+ entity2IRIMap.put(entity, IRI.create(resource.getURI()));
+ }
+ //instantiate the pattern
+ OWLObjectDuplicator duplicator = new OWLObjectDuplicator(entity2IRIMap, df);
+ OWLAxiom patternInstantiation = duplicator.duplicateObject(pattern);
+
+ instantiations.add(patternInstantiation);
+ }
+ //compute the score
+ for (OWLAxiom axiom : instantiations.elementSet()) {
+ int frequency = instantiations.count(axiom);
+ Score score = new AxiomScore(frequency);
+ axioms2Score.put(axiom, score);
+ }
+
+ return axioms2Score;
+ }
+
private void save(OWLAxiom pattern, Map<OWLAxiom, Score> axioms2Score){
try {
Set<OWLAxiom> annotatedAxioms = new HashSet<OWLAxiom>();
@@ -278,15 +414,6 @@
}
}
- public List<OWLAxiom> getPatternsToEvaluate(){
- List<OWLAxiom> axiomPatterns = new ArrayList<OWLAxiom>();
-
- Map<OWLAxiom, Pair<Integer, Integer>> topNAxiomPatterns = getTopNAxiomPatterns(AxiomTypeCategory.TBox, 10);
- axiomPatterns.addAll(topNAxiomPatterns.keySet());
-
- return axiomPatterns;
- }
-
public List<OWLAxiom> getPatternsToEvaluate(OWLOntology ontology){
List<OWLAxiom> axiomPatterns = new ArrayList<OWLAxiom>();
@@ -295,53 +422,6 @@
return axiomPatterns;
}
-
- private String asLatex(String title, Map<OWLAxiom, Pair<Integer, Integer>> topN){
- String latexTable = "\\begin{table}\n";
- latexTable += "\\begin{tabular}{lrr}\n";
- latexTable += "\\toprule\n";
- latexTable += "Pattern & Frequency & \\#Ontologies\\\\\\midrule\n";
-
- for (Entry<OWLAxiom, Pair<Integer, Integer>> entry : topN.entrySet()) {
- OWLAxiom axiom = entry.getKey();
- Integer frequency = entry.getValue().getKey();
- Integer idf = entry.getValue().getValue();
-
- if(axiom != null){
- String axiomColumn = axiomRenderer.render(axiom);
- if(fancyLatex){
- axiomColumn = "\\begin{lstlisting}[language=manchester]" + axiomColumn + "\\end{lstlisting}";
- }
- latexTable += axiomColumn + " & " + frequency + " & " + idf + "\\\\\n";
- }
- }
- latexTable += "\\bottomrule\n\\end{tabular}\n";
- latexTable += "\\caption{" + title + "}\n";
- latexTable += "\\end{table}\n";
- return latexTable;
- }
-
- private Map<OWLAxiom, Pair<Integer, Integer>> getTopNAxiomPatterns(AxiomTypeCategory axiomType, int n){
- Map<OWLAxiom, Pair<Integer, Integer>> topN = new LinkedHashMap<OWLAxiom, Pair<Integer, Integer>>();
- PreparedStatement ps;
- ResultSet rs;
- try {
- ps = conn.prepareStatement("SELECT pattern,SUM(occurrences),COUNT(ontology_id) FROM " +
- "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
- "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND P.axiom_type=?) " +
- "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
- ps.setString(1, axiomType.name());
- ps.setInt(2, n);
- rs = ps.executeQuery();
- while(rs.next()){
- topN.put(asOWLAxiom(rs.getString(1)), new Pair<Integer, Integer>(rs.getInt(2), rs.getInt(3)));
- }
- } catch(SQLException e){
- e.printStackTrace();
- }
- return topN;
- }
-
protected com.hp.hpl.jena.query.ResultSet executeSelectQuery(Query query) {
com.hp.hpl.jena.query.ResultSet rs = null;
if(ks.isRemote()){
@@ -414,27 +494,6 @@
return new AxiomScore(accuracy, confidence, total, success, total-success);
}
- private OWLAxiom asOWLAxiom(String functionalSyntaxAxiomString){
- try {
- StringDocumentSource s = new StringDocumentSource("Ontology(<http://www.pattern.org> " + functionalSyntaxAxiomString + ")");
- OWLFunctionalSyntaxOWLParser p = new OWLFunctionalSyntaxOWLParser();
- OWLOntology newOntology = OWLManager.createOWLOntologyManager().createOntology();
- p.parse(s, newOntology);
- if(!newOntology.getLogicalAxioms().isEmpty()){
- return newOntology.getLogicalAxioms().iterator().next();
- }
- } catch (UnloadableImportException e) {
- e.printStackTrace();
- } catch (OWLOntologyCreationException e) {
- e.printStackTrace();
- } catch (OWLParserException e) {
- System.err.println("Parsing failed for axiom " + functionalSyntaxAxiomString);
- } catch (IOException e) {
- e.printStackTrace();
- }
- return null;
- }
-
public static void main(String[] args) throws Exception {
ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
@@ -450,6 +509,8 @@
"The ontology file which contains the patterns.").withOptionalArg().ofType(File.class);
parser.acceptsAll(asList("o", "output"), "Specify a file where the output can be written.")
.withOptionalArg().ofType(File.class);
+ parser.acceptsAll(asList("l", "limit"), "Specify the maximum number of classes tested for each pattern.")
+ .withRequiredArg().ofType(Integer.class);
// parse options and display a message for the user in case of problems
OptionSet options = null;
@@ -503,7 +564,7 @@
System.out.println("The specified ontology patterns file can not be found.");
System.exit(0);
}
- OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(patternsFile);
+ OWLOntology patternsOntology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(patternsFile);
File outputFile = null;
try {
outputFile = (File) options.valueOf("output");
@@ -511,7 +572,8 @@
System.out.println("The specified output file can not be found.");
System.exit(0);
}
- new OWLAxiomPatternUsageEvaluation().run(endpoint, ontology, outputFile);
+ int maxNrOfTestedClasses = (Integer) options.valueOf("limit");
+ new OWLAxiomPatternUsageEvaluation().run(endpoint, patternsOntology, outputFile, maxNrOfTestedClasses);
}
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-05-07 06:24:07
|
Revision: 3956
http://sourceforge.net/p/dl-learner/code/3956
Author: lorenz_b
Date: 2013-05-07 06:24:03 +0000 (Tue, 07 May 2013)
Log Message:
-----------
Added Latex DLSyntax renderer.
Added Paths:
-----------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/LatexObjectVisitor.java
Added: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/LatexObjectVisitor.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/LatexObjectVisitor.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/LatexObjectVisitor.java 2013-05-07 06:24:03 UTC (rev 3956)
@@ -0,0 +1,938 @@
+/*
+ * This file is part of the OWL API.
+ *
+ * The contents of this file are subject to the LGPL License, Version 3.0.
+ *
+ * Copyright (C) 2011, The University of Manchester
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see http://www.gnu.org/licenses/.
+ *
+ *
+ * Alternatively, the contents of this file may be used under the terms of the Apache License, Version 2.0
+ * in which case, the provisions of the Apache License Version 2.0 are applicable instead of those above.
+ *
+ * Copyright 2011, University of Manchester
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.dllearner.scripts.pattern;
+
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Set;
+
+import org.coode.owlapi.latex.LatexBracketChecker;
+import org.coode.owlapi.latex.LatexWriter;
+import org.semanticweb.owlapi.model.*;
+import org.semanticweb.owlapi.util.CollectionFactory;
+import org.semanticweb.owlapi.util.ShortFormProvider;
+import org.semanticweb.owlapi.util.SimpleShortFormProvider;
+
+/**
+ * Author: Matthew Horridge<br>
+ * The University Of Manchester<br>
+ * Medical Informatics Group<br>
+ * Date: 15-Jun-2006<br>
+ * <br>
+ *
+ * NOTE: this class was not designed as a general purpose renderer, i.e.,
+ * some ontologies might be misrepresented in the output. Please report
+ * any formatting error you find to the bug tracker or the mailing list.
+ */
+@SuppressWarnings({"unused","javadoc"})
+public class LatexObjectVisitor implements OWLObjectVisitor {
+ public static final String AND = "\\ensuremath{\\sqcap}";
+ public static final String OR = "\\ensuremath{\\sqcup}";
+ public static final String NOT = "\\ensuremath{\\lnot}";
+ public static final String ALL = "\\ensuremath{\\forall}";
+ public static final String SOME = "\\ensuremath{\\exists}";
+ public static final String HASVALUE = "\\ensuremath{hasValue}";
+ public static final String MIN = "\\ensuremath{\\geq}";
+ public static final String MAX = "\\ensuremath{\\leq}";
+ public static final String EQUAL = "\\ensuremath{=}";
+ public static final String SUBCLASS = "\\ensuremath{\\sqsubseteq}";
+ public static final String EQUIV = "\\ensuremath{\\equiv}";
+ public static final String NOT_EQUIV = "\\ensuremath{\\not\\equiv}";
+ public static final String TOP = "\\ensuremath{\\top}";
+ public static final String BOTTOM = "\\ensuremath{\\bot}";
+ public static final String SELF = "\\ensuremath{\\Self}";
+ public static final String CIRC = "\\ensuremath{\\circ}";
+ private OWLObject subject;
+ private LatexWriter writer;
+ private boolean prettyPrint = true;
+ private OWLDataFactory df;
+ private ShortFormProvider shortFormProvider;
+
+ public LatexObjectVisitor(LatexWriter writer, OWLDataFactory df) {
+ this.writer = writer;
+ this.df = df;
+ shortFormProvider = new SimpleShortFormProvider();
+ subject = df.getOWLThing();
+ }
+
+ public void setSubject(OWLObject subject) {
+ this.subject = subject;
+ }
+
+ public void setShortFormProvider(ShortFormProvider shortFormProvder) {
+ this.shortFormProvider = shortFormProvder;
+ }
+
+ private void writeSpace() {
+ writer.writeSpace();
+ }
+
+ private void writeDot() {
+ writer.write(".");
+ }
+
+ private void write(Object o) {
+ writer.write(o);
+ }
+
+ private void writeOpenBrace() {
+ writer.writeOpenBrace();
+ }
+
+ private void writeCloseBrace() {
+ writer.writeCloseBrace();
+ }
+
+ public boolean isPrettyPrint() {
+ return prettyPrint;
+ }
+
+ public void setPrettyPrint(boolean prettyPrint) {
+ this.prettyPrint = prettyPrint;
+ }
+
+ //
+ // private void beginTabbing() {
+ // write("\\begin{tabbing}\n");
+ // }
+ //
+ // private void endTabbing() {
+ // write("\\end{tabbing}\n");
+ // }
+ public void visit(OWLObjectIntersectionOf node) {
+ for (Iterator<OWLClassExpression> it = node.getOperands().iterator(); it
+ .hasNext();) {
+ it.next().accept(this);
+ if (it.hasNext()) {
+ writeSpace();
+ write(AND);
+ writeSpace();
+ }
+ }
+ }
+
+ public void visit(OWLDataAllValuesFrom node) {
+ write(ALL);
+ writeSpace();
+ node.getProperty().accept(this);
+ writeSpace();
+ node.getFiller().accept(this);
+ }
+
+ public void visit(OWLDataExactCardinality desc) {
+ write(EQUAL);
+ writeSpace();
+ desc.getProperty().accept(this);
+ }
+
+ public void visit(OWLDataMaxCardinality desc) {
+ write(MAX);
+ writeSpace();
+ write(desc.getCardinality());
+ writeSpace();
+ desc.getProperty().accept(this);
+ }
+
+ public void visit(OWLDataMinCardinality desc) {
+ write(MIN);
+ writeSpace();
+ write(desc.getCardinality());
+ writeSpace();
+ desc.getProperty().accept(this);
+ }
+
+ public void visit(OWLDataSomeValuesFrom node) {
+ write(SOME);
+ writeSpace();
+ node.getProperty().accept(this);
+// writeSpace();
+ writeDot();
+ node.getFiller().accept(this);
+ }
+
+ public void visit(OWLDataHasValue node) {
+ write(HASVALUE);
+ writeSpace();
+ node.getProperty().accept(this);
+// writeSpace();
+ writeDot();
+ node.getValue().accept(this);
+ }
+
+ public void visit(OWLObjectAllValuesFrom node) {
+ write(ALL);
+ writeSpace();
+ node.getProperty().accept(this);
+// writeSpace();
+ writeDot();
+ writeNested(node.getFiller());
+ }
+
+ public void visit(OWLObjectExactCardinality desc) {
+ write(EQUAL);
+ writeSpace();
+ desc.getProperty().accept(this);
+// writeSpace();
+ writeDot();
+ writeNested(desc.getFiller());
+ }
+
+ public void visit(OWLObjectMaxCardinality desc) {
+ write(MAX);
+ writeSpace();
+ write(desc.getCardinality());
+ writeSpace();
+ desc.getProperty().accept(this);
+// writeSpace();
+ writeDot();
+ writeNested(desc.getFiller());
+ }
+
+ public void visit(OWLObjectMinCardinality desc) {
+ write(MIN);
+ writeSpace();
+ write(desc.getCardinality());
+ writeSpace();
+ desc.getProperty().accept(this);
+// writeSpace();
+ writeDot();
+ writeNested(desc.getFiller());
+ }
+
+ public void visit(OWLObjectSomeValuesFrom node) {
+ write(SOME);
+ writeSpace();
+ node.getProperty().accept(this);
+// writeSpace();
+ writeDot();
+ writeNested(node.getFiller());
+ }
+
+ public void visit(OWLObjectHasValue node) {
+ write(SOME);
+ writeSpace();
+ node.getProperty().accept(this);
+ writeSpace();
+ writeOpenBrace();
+ node.getValue().accept(this);
+ writeCloseBrace();
+ }
+
+ public void visit(OWLObjectComplementOf node) {
+ write(NOT);
+ writeNested(node.getOperand());
+ }
+
+ public void visit(OWLObjectUnionOf node) {
+ for (Iterator<OWLClassExpression> it = node.getOperands().iterator(); it
+ .hasNext();) {
+ it.next().accept(this);
+ if (it.hasNext()) {
+ writeSpace();
+ write(OR);
+ writeSpace();
+ }
+ }
+ }
+
+ public void visit(OWLClass node) {
+ write(escapeName(shortFormProvider.getShortForm(node)));
+ }
+
+ public void visit(OWLObjectOneOf node) {
+ for (Iterator<OWLIndividual> it = node.getIndividuals().iterator(); it
+ .hasNext();) {
+ writeOpenBrace();
+ it.next().accept(this);
+ writeCloseBrace();
+ if (it.hasNext()) {
+ writeSpace();
+ write(OR);
+ writeSpace();
+ }
+ }
+ }
+
+ public void visit(OWLDataProperty entity) {
+ write(escapeName(shortFormProvider.getShortForm(entity)));
+ }
+
+ public void visit(OWLObjectProperty entity) {
+ write(escapeName(shortFormProvider.getShortForm(entity)));
+ }
+
+ public void visit(OWLNamedIndividual entity) {
+ write(escapeName(shortFormProvider.getShortForm(entity)));
+ }
+
+ public void visit(OWLObjectHasSelf desc) {
+ write(SOME);
+ writeSpace();
+ desc.getProperty().accept(this);
+ writeSpace();
+ write(SELF);
+ }
+
+ public void visit(OWLDisjointClassesAxiom axiom) {
+ if (axiom.getClassExpressions().size() != 2) {
+ for (OWLClassExpression left : axiom.getClassExpressions()) {
+ for (OWLClassExpression right : axiom.getClassExpressions()) {
+ if (left != right) {
+ if (left.equals(subject)) {
+ left.accept(this);
+ writeSpace();
+ write(SUBCLASS);
+ writeSpace();
+ write(NOT);
+ writeSpace();
+ right.accept(this);
+ } else {
+ right.accept(this);
+ writeSpace();
+ write(SUBCLASS);
+ writeSpace();
+ write(NOT);
+ writeSpace();
+ left.accept(this);
+ }
+ writer.writeNewLine();
+ }
+ }
+ }
+ } else {
+ Iterator<OWLClassExpression> it = axiom.getClassExpressions()
+ .iterator();
+ OWLClassExpression descA = it.next();
+ OWLClassExpression descB = it.next();
+ OWLClassExpression lhs;
+ OWLClassExpression rhs;
+ if (descA.equals(subject)) {
+ lhs = descA;
+ rhs = descB;
+ } else {
+ lhs = descB;
+ rhs = descA;
+ }
+ lhs.accept(this);
+ writeSpace();
+ write(SUBCLASS);
+ writeSpace();
+ write(NOT);
+ writeSpace();
+ rhs.accept(this);
+ }
+ }
+
+ public void visit(OWLEquivalentClassesAxiom axiom) {
+ if (axiom.getClassExpressions().size() > 2) {
+ Set<Set<OWLClassExpression>> rendered = new HashSet<Set<OWLClassExpression>>();
+ for (OWLClassExpression left : axiom.getClassExpressions()) {
+ for (OWLClassExpression right : axiom.getClassExpressions()) {
+ if (left != right) {
+ Set<OWLClassExpression> cur = CollectionFactory
+ .createSet(left, right);
+ if (!rendered.contains(cur)) {
+ rendered.add(cur);
+ left.accept(this);
+ writeSpace();
+ write(EQUIV);
+ writeSpace();
+ right.accept(this);
+ }
+ }
+ }
+ }
+ } else if (axiom.getClassExpressions().size() == 2) {
+ Iterator<OWLClassExpression> it = axiom.getClassExpressions()
+ .iterator();
+ OWLClassExpression descA = it.next();
+ OWLClassExpression descB = it.next();
+ OWLClassExpression lhs;
+ OWLClassExpression rhs;
+ if (subject.equals(descA)) {
+ lhs = descA;
+ rhs = descB;
+ } else {
+ lhs = descB;
+ rhs = descA;
+ }
+ rhs.accept(this);
+ writeSpace();
+ write(EQUIV);
+ writeSpace();
+ lhs.accept(this);
+ }
+ }
+
+ public void visit(OWLSubClassOfAxiom axiom) {
+ this.setPrettyPrint(false);
+ axiom.getSubClass().accept(this);
+ writeSpace();
+ write(SUBCLASS);
+ writeSpace();
+ axiom.getSuperClass().accept(this);
+ writeSpace();
+ this.setPrettyPrint(true);
+ }
+
+ public void visit(OWLClassAssertionAxiom axiom) {
+ axiom.getIndividual().accept(this);
+ writeSpace();
+ write(":");
+ writeSpace();
+ axiom.getClassExpression().accept(this);
+ }
+
+ public void visit(OWLAsymmetricObjectPropertyAxiom axiom) {
+ write("AsymmetricProperty");
+ axiom.getProperty().accept(this);
+ }
+
+ public void visit(OWLDataPropertyAssertionAxiom axiom) {
+ axiom.getProperty().accept(this);
+ writeSpace();
+ write("(");
+ axiom.getSubject().accept(this);
+ writeSpace();
+ axiom.getObject().accept(this);
+ write(")");
+ }
+
+ public void visit(OWLDataPropertyDomainAxiom axiom) {
+ df.getOWLDataSomeValuesFrom(axiom.getProperty(), df.getTopDatatype())
+ .accept(this);
+ writeSpace();
+ write(SUBCLASS);
+ writeSpace();
+ axiom.getDomain().accept(this);
+ }
+
+ public void visit(OWLDataPropertyRangeAxiom axiom) {
+ write(TOP);
+ writeSpace();
+ write(SUBCLASS);
+ writeSpace();
+ df.getOWLDataAllValuesFrom(axiom.getProperty(), axiom.getRange())
+ .accept(this);
+ }
+
+ public void visit(OWLSubDataPropertyOfAxiom axiom) {
+ axiom.getSubProperty();
+ writeSpace();
+ write(SUBCLASS);
+ writeSpace();
+ axiom.getSuperProperty().accept(this);
+ }
+
+ public void visit(OWLDeclarationAxiom axiom) {
+ write("Declaration");
+ axiom.getEntity().accept(this);
+ }
+
+ public void visit(OWLDifferentIndividualsAxiom axiom) {
+ for (Iterator<OWLIndividual> it = axiom.getIndividuals().iterator(); it
+ .hasNext();) {
+ write("\\{");
+ it.next().accept(this);
+ write("\\}");
+ if (it.hasNext()) {
+ writeSpace();
+ write(NOT_EQUIV);
+ writeSpace();
+ }
+ }
+ }
+
+ public void visit(OWLDisjointDataPropertiesAxiom axiom) {
+ for (Iterator<OWLDataPropertyExpression> it = axiom.getProperties()
+ .iterator(); it.hasNext();) {
+ it.next().accept(this);
+ if (it.hasNext()) {
+ writeSpace();
+ write(NOT_EQUIV);
+ writeSpace();
+ }
+ }
+ }
+
+ public void visit(OWLDisjointObjectPropertiesAxiom axiom) {
+ write("DisjointObjectProperties");
+ writeSpace();
+ for (OWLObjectPropertyExpression p : axiom.getProperties()) {
+ p.accept(this);
+ writeSpace();
+ }
+ }
+
+ public void visit(OWLDisjointUnionAxiom axiom) {
+ write("DisjointUnion");
+ writeSpace();
+ for (OWLClassExpression p : axiom.getClassExpressions()) {
+ p.accept(this);
+ writeSpace();
+ }
+ }
+
+ public void visit(OWLAnnotationAssertionAxiom axiom) {
+ write("Annotation");
+ axiom.getSubject().accept(this);
+ writeSpace();
+ axiom.getProperty().accept(this);
+ writeSpace();
+ axiom.getValue().accept(this);
+ }
+
+ public void visit(OWLEquivalentDataPropertiesAxiom axiom) {
+ for (Iterator<OWLDataPropertyExpression> it = axiom.getProperties()
+ .iterator(); it.hasNext();) {
+ it.next().accept(this);
+ if (it.hasNext()) {
+ writeSpace();
+ write(NOT_EQUIV);
+ writeSpace();
+ }
+ }
+ }
+
+ public void visit(OWLEquivalentObjectPropertiesAxiom axiom) {
+ for (Iterator<OWLObjectPropertyExpression> it = axiom.getProperties()
+ .iterator(); it.hasNext();) {
+ it.next().accept(this);
+ if (it.hasNext()) {
+ writeSpace();
+ write(EQUIV);
+ writeSpace();
+ }
+ }
+ }
+
+ public void visit(OWLFunctionalDataPropertyAxiom axiom) {
+ write(TOP);
+ writeSpace();
+ write(SUBCLASS);
+ writeSpace();
+ df.getOWLDataMaxCardinality(1, axiom.getProperty()).accept(this);
+ }
+
+ public void visit(OWLFunctionalObjectPropertyAxiom axiom) {
+ write(TOP);
+ writeSpace();
+ write(SUBCLASS);
+ writeSpace();
+ df.getOWLObjectMaxCardinality(1, axiom.getProperty()).accept(this);
+ }
+
+ public void visit(OWLImportsDeclaration axiom) {
+ write("ImportsDeclaration");
+ axiom.getIRI().accept(this);
+ }
+
+ public void visit(OWLInverseFunctionalObjectPropertyAxiom axiom) {
+ write(TOP);
+ writeSpace();
+ write(SUBCLASS);
+ writeSpace();
+ OWLObjectPropertyExpression prop = df.getOWLObjectInverseOf(axiom
+ .getProperty());
+ df.getOWLObjectMaxCardinality(1, prop).accept(this);
+ }
+
+ public void visit(OWLInverseObjectPropertiesAxiom axiom) {
+ axiom.getFirstProperty().accept(this);
+ writeSpace();
+ write(EQUIV);
+ writeSpace();
+ write(axiom.getSecondProperty());
+ axiom.getSecondProperty().accept(this);
+ write("\\ensuremath{^-}");
+ }
+
+ public void visit(OWLIrreflexiveObjectPropertyAxiom axiom) {
+ write("IrreflexiveObjectProperty");
+ axiom.getProperty().accept(this);
+ }
+
+ public void visit(OWLNegativeDataPropertyAssertionAxiom axiom) {
+ write(NOT);
+ axiom.getProperty().accept(this);
+ write("(");
+ axiom.getSubject().accept(this);
+ write(", ");
+ axiom.getObject().accept(this);
+ write(")");
+ }
+
+ public void visit(OWLNegativeObjectPropertyAssertionAxiom axiom) {
+ write(NOT);
+ axiom.getProperty().accept(this);
+ write("(");
+ axiom.getSubject().accept(this);
+ write(", ");
+ axiom.getObject().accept(this);
+ write(")");
+ }
+
+ public void visit(OWLObjectPropertyAssertionAxiom axiom) {
+ axiom.getProperty().accept(this);
+ write("(");
+ axiom.getSubject().accept(this);
+ write(", ");
+ axiom.getObject().accept(this);
+ write(")");
+ }
+
+ public void visit(OWLSubPropertyChainOfAxiom axiom) {
+ for (Iterator<OWLObjectPropertyExpression> it = axiom
+ .getPropertyChain().iterator(); it.hasNext();) {
+ it.next().accept(this);
+ if (it.hasNext()) {
+ writeSpace();
+ write(CIRC);
+ writeSpace();
+ }
+ }
+ writeSpace();
+ write(SUBCLASS);
+ writeSpace();
+ axiom.getSuperProperty().accept(this);
+ }
+
+ public void visit(OWLObjectPropertyDomainAxiom axiom) {
+ df.getOWLObjectSomeValuesFrom(axiom.getProperty(), df.getOWLThing())
+ .accept(this);
+ writeSpace();
+ write(SUBCLASS);
+ writeSpace();
+ axiom.getDomain().accept(this);
+ }
+
+ public void visit(OWLObjectPropertyRangeAxiom axiom) {
+ write(TOP);
+ writeSpace();
+ write(SUBCLASS);
+ writeSpace();
+ df.getOWLObjectAllValuesFrom(axiom.getProperty(), axiom.getRange())
+ .accept(this);
+ }
+
+ public void visit(OWLSubObjectPropertyOfAxiom axiom) {
+ axiom.getSubProperty();
+ writeSpace();
+ write(SUBCLASS);
+ writeSpace();
+ axiom.getSuperProperty().accept(this);
+ }
+
+ public void visit(OWLReflexiveObjectPropertyAxiom axiom) {
+ write("ReflexiveProperty");
+ axiom.getProperty().accept(this);
+ }
+
+ public void visit(OWLSameIndividualAxiom axiom) {
+ for (Iterator<OWLIndividual> it = axiom.getIndividuals().iterator(); it
+ .hasNext();) {
+ write("\\{");
+ it.next().accept(this);
+ write("\\}");
+ if (it.hasNext()) {
+ writeSpace();
+ write(EQUIV);
+ writeSpace();
+ }
+ }
+ }
+
+ public void visit(OWLSymmetricObjectPropertyAxiom axiom) {
+ axiom.getProperty().accept(this);
+ writeSpace();
+ write(EQUIV);
+ writeSpace();
+ axiom.getProperty().accept(this);
+ write("\\ensuremath{^-}");
+ }
+
+ public void visit(OWLDatatypeDefinitionAxiom axiom) {
+ write("Datatype(");
+ axiom.getDatatype().accept(this);
+ write(EQUIV);
+ axiom.getDataRange().accept(this);
+ }
+
+ public void visit(OWLTransitiveObjectPropertyAxiom axiom) {
+ write("TransitiveProperty");
+ writer.writeSpace();
+ axiom.getProperty().accept(this);
+ }
+
+ public void visit(SWRLRule rule) {
+ write("SWRLRule");
+ for (SWRLAtom a : rule.getHead()) {
+ a.accept(this);
+ }
+ write("\\rightarrow");
+ for (SWRLAtom a : rule.getBody()) {
+ a.accept(this);
+ }
+ }
+
+ public void visit(SWRLVariable node) {
+ write(node.getIRI());
+ }
+
+ private void writeNested(OWLClassExpression classExpression) {
+ openBracket(classExpression);
+ classExpression.accept(this);
+ closeBracket(classExpression);
+ }
+
+ private void writeNested(OWLObject expression) {
+ expression.accept(this);
+ }
+
+ private void openBracket(OWLClassExpression classExpression) {
+ if (LatexBracketChecker.requiresBracket(classExpression)) {
+ write("(");
+ }
+ }
+
+ private void closeBracket(OWLClassExpression classExpression) {
+ if (LatexBracketChecker.requiresBracket(classExpression)) {
+ write(")");
+ }
+ }
+
+ private String escapeName(String name) {
+ return name.replace("_", "\\_");
+ }
+
+ public void visit(OWLOntology ontology) {
+ }
+
+ public void visit(OWLObjectInverseOf property) {
+ property.getInverse().accept(this);
+ write("\\ensuremath{^-}");
+ }
+
+ //////////////////////////////////////////////////////////////////////////////////////////////////
+ public void visit(OWLDataComplementOf node) {
+ write(NOT);
+ writeNested(node.getDataRange());
+ }
+
+ public void visit(OWLDataOneOf node) {
+ for (Iterator<OWLLiteral> it = node.getValues().iterator(); it
+ .hasNext();) {
+ writeOpenBrace();
+ it.next().accept(this);
+ writeCloseBrace();
+ if (it.hasNext()) {
+ writeSpace();
+ write(OR);
+ writeSpace();
+ }
+ }
+ }
+
+ public void visit(OWLFacetRestriction node) {
+ write("Facet");
+ write(node.getFacet());
+ node.getFacetValue().accept(this);
+ }
+
+ public void visit(OWLDatatypeRestriction node) {
+ write("DatatypeRestriction");
+ node.getDatatype().accept(this);
+ for (OWLFacetRestriction r : node.getFacetRestrictions()) {
+ writeSpace();
+ r.accept(this);
+ }
+ }
+
+ public void visit(OWLDatatype node) {
+ write("Datatype");
+// write(node.getIRI());
+ writer.writeOpenBrace();
+ write(escapeName(shortFormProvider.getShortForm(node)));
+ writer.writeCloseBrace();
+ }
+
+ public void visit(OWLLiteral node) {
+ write("\"");
+ write(node.getLiteral());
+ write("\"\\^\\^");
+ write(node.getDatatype().getIRI());
+ }
+
+ //////////////////////////////////////////////////////////////////////////////////////////////
+ public void visit(SWRLLiteralArgument node) {
+ node.getLiteral().accept(this);
+ }
+
+ public void visit(SWRLIndividualArgument node) {
+ node.getIndividual().accept(this);
+ }
+
+ public void visit(SWRLBuiltInAtom node) {
+ node.getPredicate().accept(this);
+ for (SWRLDArgument d : node.getArguments()) {
+ writeSpace();
+ d.accept(this);
+ }
+ }
+
+ public void visit(SWRLClassAtom node) {
+ node.getArgument().accept(this);
+ }
+
+ public void visit(SWRLDataRangeAtom node) {
+ node.getPredicate().accept(this);
+ }
+
+ public void visit(SWRLDataPropertyAtom node) {
+ node.getPredicate().accept(this);
+ }
+
+ public void visit(SWRLDifferentIndividualsAtom node) {
+ for (SWRLArgument a : node.getAllArguments()) {
+ writeSpace();
+ a.accept(this);
+ }
+ }
+
+ public void visit(SWRLObjectPropertyAtom node) {
+ node.getPredicate().accept(this);
+ }
+
+ public void visit(SWRLSameIndividualAtom node) {
+ for (SWRLArgument a : node.getAllArguments()) {
+ writeSpace();
+ a.accept(this);
+ }
+ }
+
+ public void visit(OWLAnnotationProperty property) {
+ write("AnnotationProperty");
+ property.getIRI().accept(this);
+ }
+
+ public void visit(OWLAnnotation annotation) {
+ write("Annotation");
+ annotation.getProperty().getIRI().accept(this);
+ annotation.getValue().accept(this);
+ }
+
+ public void visit(OWLAnnotationPropertyDomainAxiom axiom) {
+ write("Domain");
+ axiom.getProperty().getIRI().accept(this);
+ writeSpace();
+ axiom.getDomain().accept(this);
+ }
+
+ public void visit(OWLAnnotationPropertyRangeAxiom axiom) {
+ write("Range");
+ axiom.getProperty().getIRI().accept(this);
+ writeSpace();
+ axiom.getRange().accept(this);
+ }
+
+ public void visit(OWLSubAnnotationPropertyOfAxiom axiom) {
+ axiom.getSubProperty();
+ writeSpace();
+ write(SUBCLASS);
+ writeSpace();
+ axiom.getSuperProperty().accept(this);
+ }
+
+ public void visit(OWLAnnotationValue value) {
+ value.accept(new OWLAnnotationValueVisitor() {
+ public void visit(IRI iri) {
+ iri.accept(LatexObjectVisitor.this);
+ }
+
+ public void visit(OWLAnonymousIndividual individual) {
+ individual.accept(LatexObjectVisitor.this);
+ }
+
+ public void visit(OWLLiteral literal) {
+ literal.accept(LatexObjectVisitor.this);
+ }
+ });
+ }
+
+ public void visit(OWLHasKeyAxiom axiom) {
+ write("HasKey");
+ axiom.getClassExpression().accept(this);
+ for (OWLPropertyExpression<?, ?> p : axiom.getPropertyExpressions()) {
+ writeSpace();
+ p.accept(this);
+ }
+ }
+
+ public void visit(OWLDataIntersectionOf node) {
+ for (Iterator<OWLDataRange> it = node.getOperands().iterator(); it
+ .hasNext();) {
+ it.next().accept(this);
+ if (it.hasNext()) {
+ writeSpace();
+ write(AND);
+ writeSpace();
+ }
+ }
+ }
+
+ public void visit(OWLDataUnionOf node) {
+ for (Iterator<OWLDataRange> it = node.getOperands().iterator(); it
+ .hasNext();) {
+ it.next().accept(this);
+ if (it.hasNext()) {
+ writeSpace();
+ write(OR);
+ writeSpace();
+ }
+ }
+ }
+
+ public void visit(OWLAnonymousIndividual individual) {
+ write(individual.getID().toString());
+ }
+
+ public void visit(IRI iri) {
+ write(iri.getFragment());
+ }
+}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-05-07 06:23:02
|
Revision: 3955
http://sourceforge.net/p/dl-learner/code/3955
Author: lorenz_b
Date: 2013-05-07 06:22:59 +0000 (Tue, 07 May 2013)
Log Message:
-----------
Improved Latex output.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java 2013-05-06 21:02:45 UTC (rev 3954)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java 2013-05-07 06:22:59 UTC (rev 3955)
@@ -13,45 +13,32 @@
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
-import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
-import java.util.Set;
import java.util.prefs.Preferences;
import org.aksw.commons.util.Pair;
import org.coode.owlapi.functionalparser.OWLFunctionalSyntaxOWLParser;
-import org.coode.owlapi.latex.LatexObjectVisitor;
import org.coode.owlapi.latex.LatexWriter;
import org.dllearner.algorithms.pattern.OWLAxiomPatternFinder;
-import org.dllearner.core.owl.NamedClass;
-import org.dllearner.kb.SparqlEndpointKS;
import org.dllearner.kb.repository.OntologyRepository;
import org.dllearner.kb.repository.bioportal.BioPortalRepository;
import org.dllearner.kb.repository.oxford.OxfordRepository;
import org.dllearner.kb.repository.tones.TONESRepository;
-import org.dllearner.kb.sparql.SparqlEndpoint;
-import org.dllearner.reasoning.SPARQLReasoner;
-import org.dllearner.utilities.owl.OWLClassExpressionToSPARQLConverter;
import org.ini4j.IniPreferences;
import org.ini4j.InvalidFileFormatException;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.OWLObjectRenderer;
import org.semanticweb.owlapi.io.OWLParserException;
import org.semanticweb.owlapi.io.StringDocumentSource;
-import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.OWLAxiom;
-import org.semanticweb.owlapi.model.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
-import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
import org.semanticweb.owlapi.model.UnloadableImportException;
-import com.hp.hpl.jena.query.Query;
-
import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
@@ -66,7 +53,7 @@
private Connection conn;
private boolean fancyLatex = false;
- private boolean dlSyntax = false;
+ private boolean dlSyntax = true;
private boolean formatNumbers = true;
private int numberOfRowsPerTable = 25;
@@ -338,7 +325,8 @@
}
if(dlSyntax){
axiom.accept(renderer);
- axiomColumn = sw.toString();sw.getBuffer().setLength(0);
+ axiomColumn = sw.toString();
+ sw.getBuffer().setLength(0);
}
if(formatNumbers){
@@ -393,14 +381,16 @@
latexTable += i + " & " + axiomColumn + " & " + "\\num{" + frequency + "} & " + df;
for (OntologyRepository repository : repositories) {
int rank = 0;
+ boolean contained = false;
Map<Integer, Map<OWLAxiom, Pair<Integer, Integer>>> topNAxiomPatternsWithId = getTopNAxiomPatternsWithId(repository, axiomTypeCategory, 100);
for (Entry<Integer, Map<OWLAxiom, Pair<Integer, Integer>>> entry2 : topNAxiomPatternsWithId.entrySet()) {
rank++;
if(entry2.getKey() == patternId){
+ contained = true;
break;
}
}
- latexTable += " & " + rank;
+ latexTable += " & " + (contained ? rank : "n/a");
}
latexTable += "\\\\\n";
} else {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-05-06 21:02:48
|
Revision: 3954
http://sourceforge.net/p/dl-learner/code/3954
Author: lorenz_b
Date: 2013-05-06 21:02:45 +0000 (Mon, 06 May 2013)
Log Message:
-----------
Improved Latex output.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.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 2013-05-06 10:40:57 UTC (rev 3953)
+++ trunk/components-core/src/main/java/org/dllearner/kb/sparql/ConciseBoundedDescriptionGeneratorImpl.java 2013-05-06 21:02:45 UTC (rev 3954)
@@ -24,7 +24,7 @@
private Model baseModel;
private List<String> namespaces;
- private int maxRecursionDepth = 2;
+ private int maxRecursionDepth = 3;
public ConciseBoundedDescriptionGeneratorImpl(SparqlEndpoint endpoint, ExtractionDBCache cache) {
this.endpoint = endpoint;
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java 2013-05-06 10:40:57 UTC (rev 3953)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java 2013-05-06 21:02:45 UTC (rev 3954)
@@ -13,6 +13,7 @@
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
+import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
@@ -67,6 +68,8 @@
private boolean fancyLatex = false;
private boolean dlSyntax = false;
private boolean formatNumbers = true;
+
+ private int numberOfRowsPerTable = 25;
public OWLAxiomPatternDetectionEvaluation() {
initDBConnection();
@@ -107,7 +110,7 @@
makeRepositoryStatistics(repositories);
//get top n TBox, RBox and ABox patterns
- makePatternStatistics(repositories);
+ makePatternStatisticsSingleTable(repositories);
}
public void run(Collection<OntologyRepository> repositories){
@@ -132,7 +135,7 @@
}
private void makePatternStatistics(Collection<OntologyRepository> repositories){
- int n = 10;
+ int n = numberOfRowsPerTable;
String latex = "";
@@ -158,6 +161,26 @@
}
}
+ private void makePatternStatisticsSingleTable(Collection<OntologyRepository> repositories){
+ int n = numberOfRowsPerTable;
+
+ String latex = "";
+
+ //total pattern statistics
+ for (AxiomTypeCategory axiomTypeCategory : AxiomTypeCategory.values()) {
+ Map<Integer, Map<OWLAxiom, Pair<Integer, Integer>>> topNAxiomPatterns = getTopNAxiomPatternsWithId(axiomTypeCategory, n);
+ latex += asLatexWithId(axiomTypeCategory, topNAxiomPatterns, repositories, n) + "\n\n";
+ }
+
+ try {
+ new FileOutputStream("pattern-statistics.tex").write(latex.getBytes());
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
private void makeRepositoryStatistics(Collection<OntologyRepository> repositories){
String latexTable = "\\begin{tabular}{lrr|rrr|rrr|rrr|rrr}";
latexTable += "\\toprule\n";
@@ -331,6 +354,66 @@
return latexTable;
}
+ private String asLatexWithId(AxiomTypeCategory axiomTypeCategory, Map<Integer, Map<OWLAxiom, Pair<Integer, Integer>>> topNAxiomPatterns, Collection<OntologyRepository> repositories, int n){
+ StringWriter sw = new StringWriter();
+ LatexWriter w = new LatexWriter(sw);
+ LatexObjectVisitor renderer = new LatexObjectVisitor(w, df);
+ String latexTable = "\\begin{table}\n";
+ latexTable += "\\begin{tabular}{rlrr";
+ for (int i = 0; i < repositories.size(); i++) {
+ latexTable += "r";
+ }
+ latexTable += "}\n";
+ latexTable += "\\toprule\n";
+ latexTable += " & Pattern & Frequency & \\#Ontologies";
+ for (OntologyRepository repository : repositories) {
+ latexTable += " & " + repository.getName();
+ }
+ latexTable += "\\\\\\midrule\n";
+
+ int i = 0;
+ for (Entry<Integer, Map<OWLAxiom, Pair<Integer, Integer>>> entry : topNAxiomPatterns.entrySet()) {
+ i++;
+ int patternId = entry.getKey();
+ OWLAxiom axiom = entry.getValue().keySet().iterator().next();
+ Integer frequency = entry.getValue().values().iterator().next().getKey();
+ Integer df = entry.getValue().values().iterator().next().getValue();
+
+ if(axiom != null){
+ String axiomColumn = axiomRenderer.render(axiom);
+ if(fancyLatex){
+ axiomColumn = "\\begin{lstlisting}[language=manchester]" + axiomColumn + "\\end{lstlisting}";
+ }
+ if(dlSyntax){
+ axiom.accept(renderer);
+ axiomColumn = sw.toString();sw.getBuffer().setLength(0);
+
+ }
+ if(formatNumbers){
+ latexTable += i + " & " + axiomColumn + " & " + "\\num{" + frequency + "} & " + df;
+ for (OntologyRepository repository : repositories) {
+ int rank = 0;
+ Map<Integer, Map<OWLAxiom, Pair<Integer, Integer>>> topNAxiomPatternsWithId = getTopNAxiomPatternsWithId(repository, axiomTypeCategory, 100);
+ for (Entry<Integer, Map<OWLAxiom, Pair<Integer, Integer>>> entry2 : topNAxiomPatternsWithId.entrySet()) {
+ rank++;
+ if(entry2.getKey() == patternId){
+ break;
+ }
+ }
+ latexTable += " & " + rank;
+ }
+ latexTable += "\\\\\n";
+ } else {
+ latexTable += axiomColumn + " & " + frequency + " & " + df + "\\\\\n";
+ }
+ }
+ }
+ latexTable += "\\bottomrule\n\\end{tabular}\n";
+ latexTable += "\\caption{" + "Top " + n + " " + axiomTypeCategory.name() + " axiom patterns." + "}\n";
+ latexTable += "\\end{table}\n";
+ return latexTable;
+ }
+
private Map<OWLAxiom, Pair<Integer, Integer>> getTopNAxiomPatterns(AxiomTypeCategory axiomType, int n){
Map<OWLAxiom, Pair<Integer, Integer>> topN = new LinkedHashMap<OWLAxiom, Pair<Integer, Integer>>();
PreparedStatement ps;
@@ -352,6 +435,53 @@
return topN;
}
+ private Map<Integer, Map<OWLAxiom, Pair<Integer, Integer>>> getTopNAxiomPatternsWithId(AxiomTypeCategory axiomType, int n){
+ Map<Integer, Map<OWLAxiom, Pair<Integer, Integer>>> topN = new LinkedHashMap<Integer, Map<OWLAxiom, Pair<Integer, Integer>>>();
+ PreparedStatement ps;
+ ResultSet rs;
+ try {
+ ps = conn.prepareStatement("SELECT P.id, pattern,SUM(occurrences),COUNT(ontology_id) FROM " +
+ "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
+ "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND P.axiom_type=?) " +
+ "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
+ ps.setString(1, axiomType.name());
+ ps.setInt(2, n);
+ rs = ps.executeQuery();
+ while(rs.next()){
+ Map<OWLAxiom, Pair<Integer, Integer>> m = new LinkedHashMap<OWLAxiom, Pair<Integer,Integer>>();
+ m.put(asOWLAxiom(rs.getString(2)), new Pair<Integer, Integer>(rs.getInt(3), rs.getInt(4)));
+ topN.put(rs.getInt(1), m);
+ }
+ } catch(SQLException e){
+ e.printStackTrace();
+ }
+ return topN;
+ }
+
+ private Map<Integer, Map<OWLAxiom, Pair<Integer, Integer>>> getTopNAxiomPatternsWithId(OntologyRepository repository, AxiomTypeCategory axiomType, int n){
+ Map<Integer, Map<OWLAxiom, Pair<Integer, Integer>>> topN = new LinkedHashMap<Integer, Map<OWLAxiom, Pair<Integer, Integer>>>();
+ PreparedStatement ps;
+ ResultSet rs;
+ try {
+ ps = conn.prepareStatement("SELECT P.id, pattern,SUM(occurrences),COUNT(ontology_id) FROM " +
+ "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
+ "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND P.axiom_type=? AND O.repository=?) " +
+ "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
+ ps.setString(1, axiomType.name());
+ ps.setString(2, repository.getName());
+ ps.setInt(3, n);
+ rs = ps.executeQuery();
+ while(rs.next()){
+ Map<OWLAxiom, Pair<Integer, Integer>> m = new LinkedHashMap<OWLAxiom, Pair<Integer,Integer>>();
+ m.put(asOWLAxiom(rs.getString(2)), new Pair<Integer, Integer>(rs.getInt(3), rs.getInt(4)));
+ topN.put(rs.getInt(1), m);
+ }
+ } catch(SQLException e){
+ e.printStackTrace();
+ }
+ return topN;
+ }
+
private Map<OWLAxiom, Pair<Integer, Integer>> getTopNAxiomPatterns(OntologyRepository repository, AxiomTypeCategory axiomType, int n){
Map<OWLAxiom, Pair<Integer, Integer>> topN = new LinkedHashMap<OWLAxiom, Pair<Integer, Integer>>();
PreparedStatement ps;
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|
|
From: <lor...@us...> - 2013-05-06 10:41:00
|
Revision: 3953
http://sourceforge.net/p/dl-learner/code/3953
Author: lorenz_b
Date: 2013-05-06 10:40:57 +0000 (Mon, 06 May 2013)
Log Message:
-----------
Improved Latex output.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java 2013-05-06 10:34:52 UTC (rev 3952)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java 2013-05-06 10:40:57 UTC (rev 3953)
@@ -246,7 +246,7 @@
if(formatNumbers){
latexTable +=
- repository.getName() + "} & " +
+ repository.getName() + " & " +
"\\num{" + numberOfOntologies + "} & " +
"\\num{" + numberOfErrorOntologies + "} & " +
"\\num{" + minNumberOfLogicalAxioms + "} & " +
@@ -301,7 +301,7 @@
String latexTable = "\\begin{table}\n";
latexTable += "\\begin{tabular}{lrrr}\n";
latexTable += "\\toprule\n";
- latexTable += "Pattern & Frequency & \\#Ontologies & tf-idf \\\\\\midrule\n";
+ latexTable += "Pattern & Frequency & \\#Ontologies\\\\\\midrule\n";
for (Entry<OWLAxiom, Pair<Integer, Integer>> entry : topN.entrySet()) {
OWLAxiom axiom = entry.getKey();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-05-06 10:34:57
|
Revision: 3952
http://sourceforge.net/p/dl-learner/code/3952
Author: lorenz_b
Date: 2013-05-06 10:34:52 +0000 (Mon, 06 May 2013)
Log Message:
-----------
Improved Latex output.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/BioPortalRepository.java
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java
Modified: trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/BioPortalRepository.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/BioPortalRepository.java 2013-05-05 14:56:53 UTC (rev 3951)
+++ trunk/components-core/src/main/java/org/dllearner/kb/repository/bioportal/BioPortalRepository.java 2013-05-06 10:34:52 UTC (rev 3952)
@@ -26,6 +26,8 @@
private String apiKey = "8fadfa2c-47de-4487-a1f5-b7af7378d693";
private String serviceURL = "http://rest.bioontology.org/bioportal/ontologies";
+ private boolean initialized = false;
+
private List<OntologyRepositoryEntry> entries = new ArrayList<OntologyRepositoryEntry>();
@Override
@@ -41,6 +43,7 @@
@Override
public void initialize() {
refresh();
+ initialized = true;
}
@Override
@@ -90,6 +93,9 @@
@Override
public Collection<OntologyRepositoryEntry> getEntries() {
+ if(!initialized){
+ initialize();
+ }
return entries;
}
@@ -121,8 +127,6 @@
for(OntologyRepositoryEntry entry : entries){
System.out.println("Loading " + entry.getOntologyShortName());
System.out.println("From " + entry.getPhysicalURI());
- OWLOntology ont = OWLManager.createOWLOntologyManager().loadOntology(IRI.create(entry.getPhysicalURI()));
- System.out.println(ont.getAxiomCount());
}
}
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java 2013-05-05 14:56:53 UTC (rev 3951)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java 2013-05-06 10:34:52 UTC (rev 3952)
@@ -4,6 +4,7 @@
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
+import java.io.StringWriter;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.PreparedStatement;
@@ -21,6 +22,8 @@
import org.aksw.commons.util.Pair;
import org.coode.owlapi.functionalparser.OWLFunctionalSyntaxOWLParser;
+import org.coode.owlapi.latex.LatexObjectVisitor;
+import org.coode.owlapi.latex.LatexWriter;
import org.dllearner.algorithms.pattern.OWLAxiomPatternFinder;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.kb.SparqlEndpointKS;
@@ -62,6 +65,8 @@
private Connection conn;
private boolean fancyLatex = false;
+ private boolean dlSyntax = false;
+ private boolean formatNumbers = true;
public OWLAxiomPatternDetectionEvaluation() {
initDBConnection();
@@ -239,22 +244,41 @@
ps.setString(1, repository.getName());
avgNumberOfAboxAxioms = count(ps);
- latexTable +=
- repository.getName() + "&" +
- numberOfOntologies + "&" +
- numberOfErrorOntologies + "&" +
- minNumberOfLogicalAxioms + "&" +
- avgNumberOfLogicalAxioms + "&" +
- maxNumberOfLogicalAxioms + "&" +
- minNumberOfTboxAxioms + "&" +
- avgNumberOfTboxAxioms + "&" +
- maxNumberOfTboxAxioms + "&" +
- minNumberOfRboxAxioms + "&" +
- avgNumberOfRboxAxioms + "&" +
- maxNumberOfRboxAxioms + "&" +
- minNumberOfAboxAxioms + "&" +
- avgNumberOfAboxAxioms + "&" +
- maxNumberOfAboxAxioms + "\\\\\n";
+ if(formatNumbers){
+ latexTable +=
+ repository.getName() + "} & " +
+ "\\num{" + numberOfOntologies + "} & " +
+ "\\num{" + numberOfErrorOntologies + "} & " +
+ "\\num{" + minNumberOfLogicalAxioms + "} & " +
+ "\\num{" + avgNumberOfLogicalAxioms + "} & " +
+ "\\num{" + maxNumberOfLogicalAxioms + "} & " +
+ "\\num{" + minNumberOfTboxAxioms + "} & " +
+ "\\num{" + avgNumberOfTboxAxioms + "} & " +
+ "\\num{" + maxNumberOfTboxAxioms + "} & " +
+ "\\num{" + minNumberOfRboxAxioms + "} & " +
+ "\\num{" + avgNumberOfRboxAxioms + "} & " +
+ "\\num{" + maxNumberOfRboxAxioms + "} & " +
+ "\\num{" + minNumberOfAboxAxioms + "} & " +
+ "\\num{" + avgNumberOfAboxAxioms + "} & " +
+ "\\num{" + maxNumberOfAboxAxioms + "}\\\\\n";
+ } else {
+ latexTable +=
+ repository.getName() + " & " +
+ numberOfOntologies + " & " +
+ numberOfErrorOntologies + " & " +
+ minNumberOfLogicalAxioms + " & " +
+ avgNumberOfLogicalAxioms + " & " +
+ maxNumberOfLogicalAxioms + " & " +
+ minNumberOfTboxAxioms + " & " +
+ avgNumberOfTboxAxioms + " & " +
+ maxNumberOfTboxAxioms + " & " +
+ minNumberOfRboxAxioms + " & " +
+ avgNumberOfRboxAxioms + " & " +
+ maxNumberOfRboxAxioms + " & " +
+ minNumberOfAboxAxioms + " & " +
+ avgNumberOfAboxAxioms + " & " +
+ maxNumberOfAboxAxioms + "\\\\\n";
+ }
} catch (SQLException e) {
e.printStackTrace();
@@ -271,22 +295,34 @@
}
private String asLatex(String title, Map<OWLAxiom, Pair<Integer, Integer>> topN){
+ StringWriter sw = new StringWriter();
+ LatexWriter w = new LatexWriter(sw);
+ LatexObjectVisitor renderer = new LatexObjectVisitor(w, df);
String latexTable = "\\begin{table}\n";
- latexTable += "\\begin{tabular}{lrr}\n";
+ latexTable += "\\begin{tabular}{lrrr}\n";
latexTable += "\\toprule\n";
- latexTable += "Pattern & Frequency & \\#Ontologies\\\\\\midrule\n";
+ latexTable += "Pattern & Frequency & \\#Ontologies & tf-idf \\\\\\midrule\n";
for (Entry<OWLAxiom, Pair<Integer, Integer>> entry : topN.entrySet()) {
OWLAxiom axiom = entry.getKey();
Integer frequency = entry.getValue().getKey();
- Integer idf = entry.getValue().getValue();
+ Integer df = entry.getValue().getValue();
if(axiom != null){
String axiomColumn = axiomRenderer.render(axiom);
if(fancyLatex){
axiomColumn = "\\begin{lstlisting}[language=manchester]" + axiomColumn + "\\end{lstlisting}";
}
- latexTable += axiomColumn + " & " + frequency + " & " + idf + "\\\\\n";
+ if(dlSyntax){
+ axiom.accept(renderer);
+ axiomColumn = sw.toString();sw.getBuffer().setLength(0);
+
+ }
+ if(formatNumbers){
+ latexTable += axiomColumn + " & " + "\\num{" + frequency + "} & " + df + "\\\\\n";
+ } else {
+ latexTable += axiomColumn + " & " + frequency + " & " + df + "\\\\\n";
+ }
}
}
latexTable += "\\bottomrule\n\\end{tabular}\n";
@@ -394,6 +430,16 @@
return rs.getInt(1);
}
+ private double tf_idf(int nrOfOccurrences, int nrOfOntologies, int nrOfOntologiesWithAxiom){
+ double tf = nrOfOccurrences;
+ double idf = Math.log10(nrOfOntologies / nrOfOntologiesWithAxiom);
+ return tf * idf;
+ }
+
+ private double popularity(int totalNrOfOntologies, int patternFrequency, int nrOfOntologiesWithPattern){
+ return (double)Math.log10(patternFrequency) * (nrOfOntologiesWithPattern / (double)totalNrOfOntologies);
+ }
+
public static void main(String[] args) throws Exception {
// ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
boolean analyzeRepositories = true;
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|
|
From: <lor...@us...> - 2013-05-05 14:56:56
|
Revision: 3951
http://sourceforge.net/p/dl-learner/code/3951
Author: lorenz_b
Date: 2013-05-05 14:56:53 +0000 (Sun, 05 May 2013)
Log Message:
-----------
Continued script to evaluate patterns.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-05 14:24:32 UTC (rev 3950)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-05 14:56:53 UTC (rev 3951)
@@ -1,10 +1,15 @@
package org.dllearner.scripts.pattern;
+import static java.util.Arrays.asList;
+
+import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.net.SocketTimeoutException;
+import java.net.URI;
+import java.net.URL;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.PreparedStatement;
@@ -16,6 +21,7 @@
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashMap;
+import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
@@ -23,6 +29,10 @@
import java.util.concurrent.TimeUnit;
import java.util.prefs.Preferences;
+import joptsimple.OptionException;
+import joptsimple.OptionParser;
+import joptsimple.OptionSet;
+
import org.aksw.commons.util.Pair;
import org.apache.log4j.Logger;
import org.coode.owlapi.functionalparser.OWLFunctionalSyntaxOWLParser;
@@ -38,7 +48,6 @@
import org.dllearner.learningproblems.AxiomScore;
import org.dllearner.learningproblems.Heuristics;
import org.dllearner.reasoning.SPARQLReasoner;
-import org.dllearner.utilities.owl.DLLearnerAxiomConvertVisitor;
import org.dllearner.utilities.owl.OWLClassExpressionToSPARQLConverter;
import org.ini4j.IniPreferences;
import org.ini4j.InvalidFileFormatException;
@@ -67,6 +76,10 @@
import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
import uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxObjectRenderer;
+import com.google.common.base.Charsets;
+import com.google.common.hash.HashCode;
+import com.google.common.hash.HashFunction;
+import com.google.common.hash.Hashing;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
@@ -130,7 +143,8 @@
}
}
- public void run(){
+ public void run(SparqlEndpoint endpoint, OWLOntology ontology, File outputFile){
+ ks = new SparqlEndpointKS(endpoint);
SPARQLReasoner reasoner = new SPARQLReasoner(ks, cache);
OWLClassExpressionToSPARQLConverter converter = new OWLClassExpressionToSPARQLConverter();
@@ -214,12 +228,12 @@
}
// if(i++ == 3) break;
}
- save(axioms2Score);
+ save(pattern, axioms2Score);
}
}
}
- private void save(Map<OWLAxiom, Score> axioms2Score){
+ private void save(OWLAxiom pattern, Map<OWLAxiom, Score> axioms2Score){
try {
Set<OWLAxiom> annotatedAxioms = new HashSet<OWLAxiom>();
for (Entry<OWLAxiom, Score> entry : axioms2Score.entrySet()) {
@@ -232,7 +246,11 @@
}
OWLOntologyManager man = OWLManager.createOWLOntologyManager();
OWLOntology ontology = man.createOntology(annotatedAxioms);
- man.saveOntology(ontology, new TurtleOntologyFormat(), new FileOutputStream("pattern.ttl"));
+ HashFunction hf = Hashing.md5();
+ HashCode hc = hf.newHasher()
+ .putString(pattern.toString(), Charsets.UTF_8)
+ .hash();
+ man.saveOntology(ontology, new TurtleOntologyFormat(), new FileOutputStream(hc.toString() + "-pattern-instantiations.ttl"));
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
} catch (OWLOntologyStorageException e) {
@@ -269,7 +287,15 @@
return axiomPatterns;
}
+ public List<OWLAxiom> getPatternsToEvaluate(OWLOntology ontology){
+ List<OWLAxiom> axiomPatterns = new ArrayList<OWLAxiom>();
+
+ axiomPatterns.addAll(ontology.getLogicalAxioms());
+
+ return axiomPatterns;
+ }
+
private String asLatex(String title, Map<OWLAxiom, Pair<Integer, Integer>> topN){
String latexTable = "\\begin{table}\n";
latexTable += "\\begin{tabular}{lrr}\n";
@@ -411,8 +437,82 @@
public static void main(String[] args) throws Exception {
ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
- new OWLAxiomPatternUsageEvaluation().run();
+
+ OptionParser parser = new OptionParser();
+ parser.acceptsAll(asList("h", "?", "help"), "Show help.");
+// parser.acceptsAll(asList("v", "verbose"), "Verbosity level.").withOptionalArg().ofType(Boolean.class).defaultsTo(false);
+ parser.acceptsAll(asList("e", "endpoint"), "SPARQL endpoint URL to be used.")
+ .withRequiredArg().ofType(URL.class);
+ parser.acceptsAll(asList("g", "graph"),
+ "URI of default graph for queries on SPARQL endpoint.").withOptionalArg()
+ .ofType(URI.class);
+ parser.acceptsAll(asList("p", "patterns"),
+ "The ontology file which contains the patterns.").withOptionalArg().ofType(File.class);
+ parser.acceptsAll(asList("o", "output"), "Specify a file where the output can be written.")
+ .withOptionalArg().ofType(File.class);
+
+ // parse options and display a message for the user in case of problems
+ OptionSet options = null;
+ try {
+ options = parser.parse(args);
+ } catch (Exception e) {
+ System.out.println("Error: " + e.getMessage() + ". Use -? to get help.");
+ System.exit(0);
+ }
+ if (options.has("?")) {
+ parser.printHelpOn(System.out);
+ String addHelp = "Additional explanations: The resource specified should " +
+ "be a class, object \nproperty or data property. DL-Learner will try to " +
+ "automatically detect its \ntype. If no resource is specified, DL-Learner will " +
+ "generate enrichment \nsuggestions for all detected classes and properties in " +
+ "the given endpoint \nand graph. This can take several hours.";
+ System.out.println();
+ System.out.println(addHelp);
+ // main script
+ } else {
+ // check that endpoint was specified
+ if(!options.hasArgument("endpoint")) {
+ System.out.println("Please specify a SPARQL endpoint (using the -e option).");
+ System.exit(0);
+ }
+
+ // create SPARQL endpoint object (check that indeed a URL was given)
+ URL endpointURL = null;
+ try {
+ endpointURL = (URL) options.valueOf("endpoint");
+ } catch(OptionException e) {
+ System.out.println("The specified endpoint appears not be a proper URL.");
+ System.exit(0);
+ }
+ URI graph = null;
+ try {
+ graph = (URI) options.valueOf("graph");
+ } catch(OptionException e) {
+ System.out.println("The specified graph appears not be a proper URL.");
+ System.exit(0);
+ }
+ LinkedList<String> defaultGraphURIs = new LinkedList<String>();
+ if(graph != null) {
+ defaultGraphURIs.add(graph.toString());
+ }
+ SparqlEndpoint endpoint = new SparqlEndpoint(endpointURL, defaultGraphURIs, new LinkedList<String>());
+ File patternsFile = null;
+ try {
+ patternsFile = (File) options.valueOf("patterns");
+ } catch(OptionException e) {
+ System.out.println("The specified ontology patterns file can not be found.");
+ System.exit(0);
+ }
+ OWLOntology ontology = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(patternsFile);
+ File outputFile = null;
+ try {
+ outputFile = (File) options.valueOf("output");
+ } catch(OptionException e) {
+ System.out.println("The specified output file can not be found.");
+ System.exit(0);
+ }
+ new OWLAxiomPatternUsageEvaluation().run(endpoint, ontology, outputFile);
+ }
+
}
-
-
}
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|
|
From: <lor...@us...> - 2013-05-05 14:24:35
|
Revision: 3950
http://sourceforge.net/p/dl-learner/code/3950
Author: lorenz_b
Date: 2013-05-05 14:24:32 +0000 (Sun, 05 May 2013)
Log Message:
-----------
Added script to evaluate patterns.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/core/EvaluatedAxiom.java
trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
Added Paths:
-----------
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java
trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
Removed Paths:
-------------
trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
Modified: trunk/components-core/src/main/java/org/dllearner/core/EvaluatedAxiom.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/EvaluatedAxiom.java 2013-05-04 11:27:51 UTC (rev 3949)
+++ trunk/components-core/src/main/java/org/dllearner/core/EvaluatedAxiom.java 2013-05-05 14:24:32 UTC (rev 3950)
@@ -26,11 +26,14 @@
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import java.util.Set;
+import java.util.TreeSet;
import org.apache.commons.codec.digest.DigestUtils;
import org.dllearner.core.owl.Axiom;
import org.dllearner.utilities.EnrichmentVocabulary;
import org.dllearner.utilities.PrefixCCMap;
+import org.dllearner.utilities.owl.AxiomComparator;
import org.dllearner.utilities.owl.OWLAPIConverter;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotation;
@@ -44,9 +47,10 @@
import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxObjectRenderer;
import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxPrefixNameShortFormProvider;
-public class EvaluatedAxiom {
+public class EvaluatedAxiom implements Comparable<EvaluatedAxiom>{
private static DecimalFormat df = new DecimalFormat("##0.0");
+ private AxiomComparator axiomComparator = new AxiomComparator();
private Axiom axiom;
private Score score;
@@ -136,5 +140,38 @@
return str;
}
+ public static List<EvaluatedAxiom> getBestEvaluatedAxioms(Set<EvaluatedAxiom> evaluatedAxioms, int nrOfAxioms) {
+ return getBestEvaluatedAxioms(evaluatedAxioms, nrOfAxioms, 0.0);
+ }
+
+ public static List<EvaluatedAxiom> getBestEvaluatedAxioms(Set<EvaluatedAxiom> evaluatedAxioms, double accuracyThreshold) {
+ return getBestEvaluatedAxioms(evaluatedAxioms, Integer.MAX_VALUE, accuracyThreshold);
+ }
+ public static List<EvaluatedAxiom> getBestEvaluatedAxioms(Set<EvaluatedAxiom> evaluatedAxioms, int nrOfAxioms,
+ double accuracyThreshold) {
+ List<EvaluatedAxiom> returnList = new ArrayList<EvaluatedAxiom>();
+
+ //get the currently best evaluated axioms
+ Set<EvaluatedAxiom> orderedEvaluatedAxioms = new TreeSet<EvaluatedAxiom>(evaluatedAxioms);
+
+ for(EvaluatedAxiom evAx : orderedEvaluatedAxioms){
+ if(evAx.getScore().getAccuracy() >= accuracyThreshold && returnList.size() < nrOfAxioms){
+ returnList.add(evAx);
+ }
+ }
+
+ return returnList;
+ }
+
+ @Override
+ public int compareTo(EvaluatedAxiom other) {
+ int ret = Double.compare(score.getAccuracy(), other.getScore().getAccuracy());
+ if(ret == 0){
+ ret = axiomComparator.compare(axiom, other.getAxiom());
+ }
+ return ret;
+ }
+
+
}
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-05-04 11:27:51 UTC (rev 3949)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/SPARQLReasoner.java 2013-05-05 14:24:32 UTC (rev 3950)
@@ -450,8 +450,12 @@
}
public Set<NamedClass> getTypes() {
+ return getTypes((String)null);
+ }
+
+ public Set<NamedClass> getTypes(String namespace) {
Set<NamedClass> types = new TreeSet<NamedClass>();
- String query = String.format("SELECT DISTINCT ?class WHERE {[] a ?class.}");
+ String query = String.format("SELECT DISTINCT ?class WHERE {[] a ?class." + (namespace != null ? ("FILTER(REGEX(?class,'^" + namespace + "'))") : "") + "}");
ResultSet rs = executeSelectQuery(query);
QuerySolution qs;
while(rs.hasNext()){
Modified: trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java 2013-05-04 11:27:51 UTC (rev 3949)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/owl/OWLClassExpressionToSPARQLConverter.java 2013-05-05 14:24:32 UTC (rev 3950)
@@ -2,6 +2,7 @@
import java.util.Collections;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
@@ -74,7 +75,7 @@
private OWLDataFactory df = new OWLDataFactoryImpl();
private Map<Integer, Boolean> intersection;
- private Set<? extends OWLEntity> variableEntities;
+ private Set<? extends OWLEntity> variableEntities = new HashSet<OWLEntity>();
public OWLClassExpressionToSPARQLConverter() {
}
@@ -97,6 +98,10 @@
return asQuery(rootVariable, expr, Collections.<OWLEntity>emptySet());
}
+ public Query asQuery(String rootVariable, OWLClassExpression expr, boolean countQuery){
+ return asQuery(rootVariable, expr, Collections.<OWLEntity>emptySet());
+ }
+
public Query asQuery(String rootVariable, OWLClassExpression expr, Set<? extends OWLEntity> variableEntities){
this.variableEntities = variableEntities;
String queryString = "SELECT DISTINCT ";
@@ -108,7 +113,7 @@
String var = variablesMapping.get(owlEntity);
queryString += var + " ";
}
- queryString += "COUNT(" + rootVariable + ") WHERE {";
+ queryString += "(COUNT(DISTINCT " + rootVariable + ") AS ?cnt) WHERE {";
}
queryString += triplePattern;
@@ -119,10 +124,15 @@
String var = variablesMapping.get(owlEntity);
queryString += var;
}
+ queryString += " ORDER BY DESC(?cnt)";
}
return QueryFactory.create(queryString, Syntax.syntaxARQ);
}
+ public Map<OWLEntity, String> getVariablesMapping() {
+ return variablesMapping;
+ }
+
private void reset(){
variablesMapping.clear();
variables.clear();
Deleted: trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-04 11:27:51 UTC (rev 3949)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-05 14:24:32 UTC (rev 3950)
@@ -1,383 +0,0 @@
-package org.dllearner.scripts;
-
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.sql.Connection;
-import java.sql.DriverManager;
-import java.sql.PreparedStatement;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.LinkedHashMap;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.prefs.Preferences;
-
-import org.aksw.commons.util.Pair;
-import org.coode.owlapi.functionalparser.OWLFunctionalSyntaxOWLParser;
-import org.dllearner.algorithms.pattern.OWLAxiomPatternFinder;
-import org.dllearner.kb.repository.OntologyRepository;
-import org.dllearner.kb.repository.bioportal.BioPortalRepository;
-import org.dllearner.kb.repository.oxford.OxfordRepository;
-import org.dllearner.kb.repository.tones.TONESRepository;
-import org.ini4j.IniPreferences;
-import org.ini4j.InvalidFileFormatException;
-import org.semanticweb.owlapi.apibinding.OWLManager;
-import org.semanticweb.owlapi.io.OWLObjectRenderer;
-import org.semanticweb.owlapi.io.OWLParserException;
-import org.semanticweb.owlapi.io.StringDocumentSource;
-import org.semanticweb.owlapi.model.OWLAxiom;
-import org.semanticweb.owlapi.model.OWLOntology;
-import org.semanticweb.owlapi.model.OWLOntologyCreationException;
-import org.semanticweb.owlapi.model.UnloadableImportException;
-
-import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
-
-public class OWLAxiomPatternDetectionEvaluation {
-
- enum AxiomTypeCategory{
- TBox, RBox, ABox
- }
-
- private OWLObjectRenderer axiomRenderer = new ManchesterOWLSyntaxOWLObjectRendererImpl();
- private Connection conn;
-
- private boolean fancyLatex = false;
-
- public OWLAxiomPatternDetectionEvaluation() {
- initDBConnection();
- }
-
- private void initDBConnection() {
- try {
- InputStream is = this.getClass().getClassLoader().getResourceAsStream("db_settings.ini");
- Preferences prefs = new IniPreferences(is);
- String dbServer = prefs.node("database").get("server", null);
- String dbName = prefs.node("database").get("name", null);
- String dbUser = prefs.node("database").get("user", null);
- String dbPass = prefs.node("database").get("pass", null);
-
- Class.forName("com.mysql.jdbc.Driver");
- String url = "jdbc:mysql://" + dbServer + "/" + dbName;
- conn = DriverManager.getConnection(url, dbUser, dbPass);
- } catch (ClassNotFoundException e) {
- e.printStackTrace();
- } catch (SQLException e) {
- e.printStackTrace();
- } catch (InvalidFileFormatException e) {
- e.printStackTrace();
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- } catch (IOException e) {
- e.printStackTrace();
- }
- }
-
- public void run(boolean analyzeRepositories, Collection<OntologyRepository> repositories){
- //analyze repositories
- if(analyzeRepositories){
- analyze(repositories);
- }
-
- //create statistics for the repositories
- makeRepositoryStatistics(repositories);
-
- //get top n TBox, RBox and ABox patterns
- makePatternStatistics(repositories);
- }
-
- public void run(Collection<OntologyRepository> repositories){
- run(true, repositories);
- }
-
- private void analyze(Collection<OntologyRepository> repositories){
- for (OntologyRepository repository : repositories) {
- repository.initialize();
- OWLAxiomPatternFinder patternFinder = new OWLAxiomPatternFinder(repository, conn);
- patternFinder.start();
- }
- }
-
- private void makePatternStatistics(Collection<OntologyRepository> repositories){
- int n = 10;
-
- String latex = "";
-
- //total pattern statistics
- for (AxiomTypeCategory axiomTypeCategory : AxiomTypeCategory.values()) {
- Map<OWLAxiom, Pair<Integer, Integer>> topNAxiomPatterns = getTopNAxiomPatterns(axiomTypeCategory, n);
- latex += asLatex("Top " + n + " " + axiomTypeCategory.name() + " axiom patterns.", topNAxiomPatterns) + "\n\n";
- }
-
- //get top n TBox, RBox and ABox patterns by repository
- for (OntologyRepository repository : repositories) {
- for (AxiomTypeCategory axiomTypeCategory : AxiomTypeCategory.values()) {
- Map<OWLAxiom, Pair<Integer, Integer>> topNAxiomPatterns = getTopNAxiomPatterns(repository, axiomTypeCategory, n);
- latex += asLatex("Top " + n + " " + axiomTypeCategory.name() + " axiom patterns for " + repository.getName() + " repository.", topNAxiomPatterns) + "\n\n";
- }
- }
- try {
- new FileOutputStream("pattern-statistics.tex").write(latex.getBytes());
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- } catch (IOException e) {
- e.printStackTrace();
- }
- }
-
- private void makeRepositoryStatistics(Collection<OntologyRepository> repositories){
- String latexTable = "\\begin{tabular}{lrr|rrr|rrr|rrr|rrr}";
- latexTable += "\\toprule\n";
- latexTable += "Repository & \\multicolumn{2}{c}{\\#Ontologies} & \\multicolumn{12}{c}{\\#Axioms} \\\\\n";
- latexTable += "& Total & Error & \\multicolumn{3}{c}{Total} & \\multicolumn{3}{c}{Tbox} & \\multicolumn{3}{c}{RBox} & \\multicolumn{3}{c}{Abox} \\\\\\midrule\n";
- latexTable += "& & & Min & Avg & Max & Min & Avg & Max & Min & Avg & Max & Min & Avg & Max \\\\\\midrule\n";
-
-
- PreparedStatement ps;
- ResultSet rs;
-
- int numberOfOntologies;
- int numberOfErrorOntologies;
- int minNumberOfLogicalAxioms;
- int maxNumberOfLogicalAxioms;
- int avgNumberOfLogicalAxioms;
- int minNumberOfTboxAxioms;
- int maxNumberOfTboxAxioms;
- int avgNumberOfTboxAxioms;
- int minNumberOfRboxAxioms;
- int maxNumberOfRboxAxioms;
- int avgNumberOfRboxAxioms;
- int minNumberOfAboxAxioms;
- int maxNumberOfAboxAxioms;
- int avgNumberOfAboxAxioms;
-
- //for each repository
- for (OntologyRepository repository : repositories) {
- try {
- //get number of ontologies
- ps = conn.prepareStatement("SELECT COUNT(*) FROM Ontology WHERE repository=?");
- ps.setString(1, repository.getName());
- numberOfOntologies = count(ps);
- //get number of error causing ontologies
- ps = conn.prepareStatement("SELECT COUNT(*) FROM Ontology WHERE repository=? AND iri LIKE 'ERROR%'");
- ps.setString(1, repository.getName());
- numberOfErrorOntologies = count(ps);
- //get min number of logical axioms
- ps = conn.prepareStatement("SELECT MIN(logical_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
- ps.setString(1, repository.getName());
- minNumberOfLogicalAxioms = count(ps);
- //get max number of logical axioms
- ps = conn.prepareStatement("SELECT MAX(logical_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
- ps.setString(1, repository.getName());
- maxNumberOfLogicalAxioms = count(ps);
- //get avg number of logical axioms
- ps = conn.prepareStatement("SELECT AVG(logical_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
- ps.setString(1, repository.getName());
- avgNumberOfLogicalAxioms = count(ps);
- //get min number of tbox axioms
- ps = conn.prepareStatement("SELECT MIN(tbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
- ps.setString(1, repository.getName());
- minNumberOfTboxAxioms = count(ps);
- //get max number of tbox axioms
- ps = conn.prepareStatement("SELECT MAX(tbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
- ps.setString(1, repository.getName());
- maxNumberOfTboxAxioms = count(ps);
- //get avg number of tbox axioms
- ps = conn.prepareStatement("SELECT AVG(tbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
- ps.setString(1, repository.getName());
- avgNumberOfTboxAxioms = count(ps);
- //get min number of rbox axioms
- ps = conn.prepareStatement("SELECT MIN(rbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
- ps.setString(1, repository.getName());
- minNumberOfRboxAxioms = count(ps);
- //get max number of rbox axioms
- ps = conn.prepareStatement("SELECT MAX(rbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
- ps.setString(1, repository.getName());
- maxNumberOfRboxAxioms = count(ps);
- //get avg number of rbox axioms
- ps = conn.prepareStatement("SELECT AVG(rbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
- ps.setString(1, repository.getName());
- avgNumberOfRboxAxioms = count(ps);
- //get min number of abox axioms
- ps = conn.prepareStatement("SELECT MIN(abox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
- ps.setString(1, repository.getName());
- minNumberOfAboxAxioms = count(ps);
- //get max number of abox axioms
- ps = conn.prepareStatement("SELECT MAX(abox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
- ps.setString(1, repository.getName());
- maxNumberOfAboxAxioms = count(ps);
- //get avg number of abox axioms
- ps = conn.prepareStatement("SELECT AVG(abox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
- ps.setString(1, repository.getName());
- avgNumberOfAboxAxioms = count(ps);
-
- latexTable +=
- repository.getName() + "&" +
- numberOfOntologies + "&" +
- numberOfErrorOntologies + "&" +
- minNumberOfLogicalAxioms + "&" +
- avgNumberOfLogicalAxioms + "&" +
- maxNumberOfLogicalAxioms + "&" +
- minNumberOfTboxAxioms + "&" +
- avgNumberOfTboxAxioms + "&" +
- maxNumberOfTboxAxioms + "&" +
- minNumberOfRboxAxioms + "&" +
- avgNumberOfRboxAxioms + "&" +
- maxNumberOfRboxAxioms + "&" +
- minNumberOfAboxAxioms + "&" +
- avgNumberOfAboxAxioms + "&" +
- maxNumberOfAboxAxioms + "\\\\\n";
-
- } catch (SQLException e) {
- e.printStackTrace();
- }
- }
- latexTable += "\\bottomrule\\end{tabular}";
- try {
- new FileOutputStream("repository-statistics.tex").write(latexTable.getBytes());
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- } catch (IOException e) {
- e.printStackTrace();
- }
- }
-
- private String asLatex(String title, Map<OWLAxiom, Pair<Integer, Integer>> topN){
- String latexTable = "\\begin{table}\n";
- latexTable += "\\begin{tabular}{lrr}\n";
- latexTable += "\\toprule\n";
- latexTable += "Pattern & Frequency & \\#Ontologies\\\\\\midrule\n";
-
- for (Entry<OWLAxiom, Pair<Integer, Integer>> entry : topN.entrySet()) {
- OWLAxiom axiom = entry.getKey();
- Integer frequency = entry.getValue().getKey();
- Integer idf = entry.getValue().getValue();
-
- if(axiom != null){
- String axiomColumn = axiomRenderer.render(axiom);
- if(fancyLatex){
- axiomColumn = "\\begin{lstlisting}[language=manchester]" + axiomColumn + "\\end{lstlisting}";
- }
- latexTable += axiomColumn + " & " + frequency + " & " + idf + "\\\\\n";
- }
- }
- latexTable += "\\bottomrule\n\\end{tabular}\n";
- latexTable += "\\caption{" + title + "}\n";
- latexTable += "\\end{table}\n";
- return latexTable;
- }
-
- private Map<OWLAxiom, Pair<Integer, Integer>> getTopNAxiomPatterns(AxiomTypeCategory axiomType, int n){
- Map<OWLAxiom, Pair<Integer, Integer>> topN = new LinkedHashMap<OWLAxiom, Pair<Integer, Integer>>();
- PreparedStatement ps;
- ResultSet rs;
- try {
- ps = conn.prepareStatement("SELECT pattern,SUM(occurrences),COUNT(ontology_id) FROM " +
- "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
- "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND P.axiom_type=?) " +
- "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
- ps.setString(1, axiomType.name());
- ps.setInt(2, n);
- rs = ps.executeQuery();
- while(rs.next()){
- topN.put(asOWLAxiom(rs.getString(1)), new Pair<Integer, Integer>(rs.getInt(2), rs.getInt(3)));
- }
- } catch(SQLException e){
- e.printStackTrace();
- }
- return topN;
- }
-
- private Map<OWLAxiom, Pair<Integer, Integer>> getTopNAxiomPatterns(OntologyRepository repository, AxiomTypeCategory axiomType, int n){
- Map<OWLAxiom, Pair<Integer, Integer>> topN = new LinkedHashMap<OWLAxiom, Pair<Integer, Integer>>();
- PreparedStatement ps;
- ResultSet rs;
- try {
- //get number of ontologies
- ps = conn.prepareStatement("SELECT pattern,SUM(occurrences),COUNT(ontology_id) FROM " +
- "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
- "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND O.repository=? AND P.axiom_type=?) " +
- "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
- ps.setString(1, repository.getName());
- ps.setString(2, axiomType.name());
- ps.setInt(3, n);
- rs = ps.executeQuery();
- while(rs.next()){
- topN.put(asOWLAxiom(rs.getString(1)), new Pair<Integer, Integer>(rs.getInt(2), rs.getInt(3)));
- }
- } catch(SQLException e){
- e.printStackTrace();
- }
- return topN;
- }
-
- private Map<OntologyRepository, Map<OWLAxiom, Integer>> getTopNAxiomPatterns(Collection<OntologyRepository> repositories, AxiomTypeCategory axiomType, int n){
- Map<OntologyRepository, Map<OWLAxiom, Integer>> topNByRepository = new LinkedHashMap<OntologyRepository, Map<OWLAxiom,Integer>>();
- PreparedStatement ps;
- ResultSet rs;
- //for each repository
- for (OntologyRepository repository : repositories) {
- Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
- try {
- //get number of ontologies
- ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
- "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
- "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND O.repository=? AND P.axiom_type=?) " +
- "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
- ps.setString(1, repository.getName());
- ps.setString(2, "RBox");
- ps.setInt(3, n);
- rs = ps.executeQuery();
- while(rs.next()){
- topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
- }
- } catch(SQLException e){
- e.printStackTrace();
- }
- topNByRepository.put(repository, topN);
- }
- return topNByRepository;
- }
-
- private OWLAxiom asOWLAxiom(String functionalSyntaxAxiomString){
- try {
- StringDocumentSource s = new StringDocumentSource("Ontology(<http://www.pattern.org> " + functionalSyntaxAxiomString + ")");
- OWLFunctionalSyntaxOWLParser p = new OWLFunctionalSyntaxOWLParser();
- OWLOntology newOntology = OWLManager.createOWLOntologyManager().createOntology();
- p.parse(s, newOntology);
- if(!newOntology.getLogicalAxioms().isEmpty()){
- return newOntology.getLogicalAxioms().iterator().next();
- }
- } catch (UnloadableImportException e) {
- e.printStackTrace();
- } catch (OWLOntologyCreationException e) {
- e.printStackTrace();
- } catch (OWLParserException e) {
- System.err.println("Parsing failed for axiom " + functionalSyntaxAxiomString);
- } catch (IOException e) {
- e.printStackTrace();
- }
- return null;
- }
-
- private int count(PreparedStatement ps) throws SQLException{
- ResultSet rs = ps.executeQuery();
- rs.next();
- return rs.getInt(1);
- }
-
- public static void main(String[] args) throws Exception {
-// ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
- boolean analyzeRepositories = true;
- if(args.length == 1){
- analyzeRepositories = Boolean.parseBoolean(args[0]);
- }
- new OWLAxiomPatternDetectionEvaluation().run(analyzeRepositories, Arrays.asList(
- new TONESRepository(), new BioPortalRepository(), new OxfordRepository()));
- }
-
-
-}
Added: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternDetectionEvaluation.java 2013-05-05 14:24:32 UTC (rev 3950)
@@ -0,0 +1,408 @@
+package org.dllearner.scripts.pattern;
+
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.prefs.Preferences;
+
+import org.aksw.commons.util.Pair;
+import org.coode.owlapi.functionalparser.OWLFunctionalSyntaxOWLParser;
+import org.dllearner.algorithms.pattern.OWLAxiomPatternFinder;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.kb.SparqlEndpointKS;
+import org.dllearner.kb.repository.OntologyRepository;
+import org.dllearner.kb.repository.bioportal.BioPortalRepository;
+import org.dllearner.kb.repository.oxford.OxfordRepository;
+import org.dllearner.kb.repository.tones.TONESRepository;
+import org.dllearner.kb.sparql.SparqlEndpoint;
+import org.dllearner.reasoning.SPARQLReasoner;
+import org.dllearner.utilities.owl.OWLClassExpressionToSPARQLConverter;
+import org.ini4j.IniPreferences;
+import org.ini4j.InvalidFileFormatException;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.OWLObjectRenderer;
+import org.semanticweb.owlapi.io.OWLParserException;
+import org.semanticweb.owlapi.io.StringDocumentSource;
+import org.semanticweb.owlapi.model.AxiomType;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
+import org.semanticweb.owlapi.model.UnloadableImportException;
+
+import com.hp.hpl.jena.query.Query;
+
+import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
+import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
+
+public class OWLAxiomPatternDetectionEvaluation {
+
+ enum AxiomTypeCategory{
+ TBox, RBox, ABox
+ }
+
+ private OWLObjectRenderer axiomRenderer = new ManchesterOWLSyntaxOWLObjectRendererImpl();
+ private OWLDataFactory df = new OWLDataFactoryImpl();
+ private Connection conn;
+
+ private boolean fancyLatex = false;
+
+ public OWLAxiomPatternDetectionEvaluation() {
+ initDBConnection();
+ }
+
+ private void initDBConnection() {
+ try {
+ InputStream is = this.getClass().getClassLoader().getResourceAsStream("db_settings.ini");
+ Preferences prefs = new IniPreferences(is);
+ String dbServer = prefs.node("database").get("server", null);
+ String dbName = prefs.node("database").get("name", null);
+ String dbUser = prefs.node("database").get("user", null);
+ String dbPass = prefs.node("database").get("pass", null);
+
+ Class.forName("com.mysql.jdbc.Driver");
+ String url = "jdbc:mysql://" + dbServer + "/" + dbName;
+ conn = DriverManager.getConnection(url, dbUser, dbPass);
+ } catch (ClassNotFoundException e) {
+ e.printStackTrace();
+ } catch (SQLException e) {
+ e.printStackTrace();
+ } catch (InvalidFileFormatException e) {
+ e.printStackTrace();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ public void run(boolean analyzeRepositories, Collection<OntologyRepository> repositories){
+ //analyze repositories
+ if(analyzeRepositories){
+ analyze(repositories);
+ }
+
+ //create statistics for the repositories
+ makeRepositoryStatistics(repositories);
+
+ //get top n TBox, RBox and ABox patterns
+ makePatternStatistics(repositories);
+ }
+
+ public void run(Collection<OntologyRepository> repositories){
+ run(true, repositories);
+ }
+
+ public List<OWLAxiom> getPatternsToEvaluate(){
+ List<OWLAxiom> axiomPatterns = new ArrayList<OWLAxiom>();
+
+ Map<OWLAxiom, Pair<Integer, Integer>> topNAxiomPatterns = getTopNAxiomPatterns(AxiomTypeCategory.TBox, 10);
+ axiomPatterns.addAll(topNAxiomPatterns.keySet());
+
+ return axiomPatterns;
+ }
+
+ private void analyze(Collection<OntologyRepository> repositories){
+ for (OntologyRepository repository : repositories) {
+ repository.initialize();
+ OWLAxiomPatternFinder patternFinder = new OWLAxiomPatternFinder(repository, conn);
+ patternFinder.start();
+ }
+ }
+
+ private void makePatternStatistics(Collection<OntologyRepository> repositories){
+ int n = 10;
+
+ String latex = "";
+
+ //total pattern statistics
+ for (AxiomTypeCategory axiomTypeCategory : AxiomTypeCategory.values()) {
+ Map<OWLAxiom, Pair<Integer, Integer>> topNAxiomPatterns = getTopNAxiomPatterns(axiomTypeCategory, n);
+ latex += asLatex("Top " + n + " " + axiomTypeCategory.name() + " axiom patterns.", topNAxiomPatterns) + "\n\n";
+ }
+
+ //get top n TBox, RBox and ABox patterns by repository
+ for (OntologyRepository repository : repositories) {
+ for (AxiomTypeCategory axiomTypeCategory : AxiomTypeCategory.values()) {
+ Map<OWLAxiom, Pair<Integer, Integer>> topNAxiomPatterns = getTopNAxiomPatterns(repository, axiomTypeCategory, n);
+ latex += asLatex("Top " + n + " " + axiomTypeCategory.name() + " axiom patterns for " + repository.getName() + " repository.", topNAxiomPatterns) + "\n\n";
+ }
+ }
+ try {
+ new FileOutputStream("pattern-statistics.tex").write(latex.getBytes());
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ private void makeRepositoryStatistics(Collection<OntologyRepository> repositories){
+ String latexTable = "\\begin{tabular}{lrr|rrr|rrr|rrr|rrr}";
+ latexTable += "\\toprule\n";
+ latexTable += "Repository & \\multicolumn{2}{c}{\\#Ontologies} & \\multicolumn{12}{c}{\\#Axioms} \\\\\n";
+ latexTable += "& Total & Error & \\multicolumn{3}{c}{Total} & \\multicolumn{3}{c}{Tbox} & \\multicolumn{3}{c}{RBox} & \\multicolumn{3}{c}{Abox} \\\\\\midrule\n";
+ latexTable += "& & & Min & Avg & Max & Min & Avg & Max & Min & Avg & Max & Min & Avg & Max \\\\\\midrule\n";
+
+
+ PreparedStatement ps;
+ ResultSet rs;
+
+ int numberOfOntologies;
+ int numberOfErrorOntologies;
+ int minNumberOfLogicalAxioms;
+ int maxNumberOfLogicalAxioms;
+ int avgNumberOfLogicalAxioms;
+ int minNumberOfTboxAxioms;
+ int maxNumberOfTboxAxioms;
+ int avgNumberOfTboxAxioms;
+ int minNumberOfRboxAxioms;
+ int maxNumberOfRboxAxioms;
+ int avgNumberOfRboxAxioms;
+ int minNumberOfAboxAxioms;
+ int maxNumberOfAboxAxioms;
+ int avgNumberOfAboxAxioms;
+
+ //for each repository
+ for (OntologyRepository repository : repositories) {
+ try {
+ //get number of ontologies
+ ps = conn.prepareStatement("SELECT COUNT(*) FROM Ontology WHERE repository=?");
+ ps.setString(1, repository.getName());
+ numberOfOntologies = count(ps);
+ //get number of error causing ontologies
+ ps = conn.prepareStatement("SELECT COUNT(*) FROM Ontology WHERE repository=? AND iri LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ numberOfErrorOntologies = count(ps);
+ //get min number of logical axioms
+ ps = conn.prepareStatement("SELECT MIN(logical_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ minNumberOfLogicalAxioms = count(ps);
+ //get max number of logical axioms
+ ps = conn.prepareStatement("SELECT MAX(logical_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ maxNumberOfLogicalAxioms = count(ps);
+ //get avg number of logical axioms
+ ps = conn.prepareStatement("SELECT AVG(logical_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ avgNumberOfLogicalAxioms = count(ps);
+ //get min number of tbox axioms
+ ps = conn.prepareStatement("SELECT MIN(tbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ minNumberOfTboxAxioms = count(ps);
+ //get max number of tbox axioms
+ ps = conn.prepareStatement("SELECT MAX(tbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ maxNumberOfTboxAxioms = count(ps);
+ //get avg number of tbox axioms
+ ps = conn.prepareStatement("SELECT AVG(tbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ avgNumberOfTboxAxioms = count(ps);
+ //get min number of rbox axioms
+ ps = conn.prepareStatement("SELECT MIN(rbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ minNumberOfRboxAxioms = count(ps);
+ //get max number of rbox axioms
+ ps = conn.prepareStatement("SELECT MAX(rbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ maxNumberOfRboxAxioms = count(ps);
+ //get avg number of rbox axioms
+ ps = conn.prepareStatement("SELECT AVG(rbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ avgNumberOfRboxAxioms = count(ps);
+ //get min number of abox axioms
+ ps = conn.prepareStatement("SELECT MIN(abox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ minNumberOfAboxAxioms = count(ps);
+ //get max number of abox axioms
+ ps = conn.prepareStatement("SELECT MAX(abox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ maxNumberOfAboxAxioms = count(ps);
+ //get avg number of abox axioms
+ ps = conn.prepareStatement("SELECT AVG(abox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ avgNumberOfAboxAxioms = count(ps);
+
+ latexTable +=
+ repository.getName() + "&" +
+ numberOfOntologies + "&" +
+ numberOfErrorOntologies + "&" +
+ minNumberOfLogicalAxioms + "&" +
+ avgNumberOfLogicalAxioms + "&" +
+ maxNumberOfLogicalAxioms + "&" +
+ minNumberOfTboxAxioms + "&" +
+ avgNumberOfTboxAxioms + "&" +
+ maxNumberOfTboxAxioms + "&" +
+ minNumberOfRboxAxioms + "&" +
+ avgNumberOfRboxAxioms + "&" +
+ maxNumberOfRboxAxioms + "&" +
+ minNumberOfAboxAxioms + "&" +
+ avgNumberOfAboxAxioms + "&" +
+ maxNumberOfAboxAxioms + "\\\\\n";
+
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ }
+ latexTable += "\\bottomrule\\end{tabular}";
+ try {
+ new FileOutputStream("repository-statistics.tex").write(latexTable.getBytes());
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ private String asLatex(String title, Map<OWLAxiom, Pair<Integer, Integer>> topN){
+ String latexTable = "\\begin{table}\n";
+ latexTable += "\\begin{tabular}{lrr}\n";
+ latexTable += "\\toprule\n";
+ latexTable += "Pattern & Frequency & \\#Ontologies\\\\\\midrule\n";
+
+ for (Entry<OWLAxiom, Pair<Integer, Integer>> entry : topN.entrySet()) {
+ OWLAxiom axiom = entry.getKey();
+ Integer frequency = entry.getValue().getKey();
+ Integer idf = entry.getValue().getValue();
+
+ if(axiom != null){
+ String axiomColumn = axiomRenderer.render(axiom);
+ if(fancyLatex){
+ axiomColumn = "\\begin{lstlisting}[language=manchester]" + axiomColumn + "\\end{lstlisting}";
+ }
+ latexTable += axiomColumn + " & " + frequency + " & " + idf + "\\\\\n";
+ }
+ }
+ latexTable += "\\bottomrule\n\\end{tabular}\n";
+ latexTable += "\\caption{" + title + "}\n";
+ latexTable += "\\end{table}\n";
+ return latexTable;
+ }
+
+ private Map<OWLAxiom, Pair<Integer, Integer>> getTopNAxiomPatterns(AxiomTypeCategory axiomType, int n){
+ Map<OWLAxiom, Pair<Integer, Integer>> topN = new LinkedHashMap<OWLAxiom, Pair<Integer, Integer>>();
+ PreparedStatement ps;
+ ResultSet rs;
+ try {
+ ps = conn.prepareStatement("SELECT pattern,SUM(occurrences),COUNT(ontology_id) FROM " +
+ "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
+ "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND P.axiom_type=?) " +
+ "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
+ ps.setString(1, axiomType.name());
+ ps.setInt(2, n);
+ rs = ps.executeQuery();
+ while(rs.next()){
+ topN.put(asOWLAxiom(rs.getString(1)), new Pair<Integer, Integer>(rs.getInt(2), rs.getInt(3)));
+ }
+ } catch(SQLException e){
+ e.printStackTrace();
+ }
+ return topN;
+ }
+
+ private Map<OWLAxiom, Pair<Integer, Integer>> getTopNAxiomPatterns(OntologyRepository repository, AxiomTypeCategory axiomType, int n){
+ Map<OWLAxiom, Pair<Integer, Integer>> topN = new LinkedHashMap<OWLAxiom, Pair<Integer, Integer>>();
+ PreparedStatement ps;
+ ResultSet rs;
+ try {
+ //get number of ontologies
+ ps = conn.prepareStatement("SELECT pattern,SUM(occurrences),COUNT(ontology_id) FROM " +
+ "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
+ "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND O.repository=? AND P.axiom_type=?) " +
+ "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
+ ps.setString(1, repository.getName());
+ ps.setString(2, axiomType.name());
+ ps.setInt(3, n);
+ rs = ps.executeQuery();
+ while(rs.next()){
+ topN.put(asOWLAxiom(rs.getString(1)), new Pair<Integer, Integer>(rs.getInt(2), rs.getInt(3)));
+ }
+ } catch(SQLException e){
+ e.printStackTrace();
+ }
+ return topN;
+ }
+
+ private Map<OntologyRepository, Map<OWLAxiom, Integer>> getTopNAxiomPatterns(Collection<OntologyRepository> repositories, AxiomTypeCategory axiomType, int n){
+ Map<OntologyRepository, Map<OWLAxiom, Integer>> topNByRepository = new LinkedHashMap<OntologyRepository, Map<OWLAxiom,Integer>>();
+ PreparedStatement ps;
+ ResultSet rs;
+ //for each repository
+ for (OntologyRepository repository : repositories) {
+ Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
+ try {
+ //get number of ontologies
+ ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
+ "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
+ "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND O.repository=? AND P.axiom_type=?) " +
+ "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
+ ps.setString(1, repository.getName());
+ ps.setString(2, "RBox");
+ ps.setInt(3, n);
+ rs = ps.executeQuery();
+ while(rs.next()){
+ topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
+ }
+ } catch(SQLException e){
+ e.printStackTrace();
+ }
+ topNByRepository.put(repository, topN);
+ }
+ return topNByRepository;
+ }
+
+ private OWLAxiom asOWLAxiom(String functionalSyntaxAxiomString){
+ try {
+ StringDocumentSource s = new StringDocumentSource("Ontology(<http://www.pattern.org> " + functionalSyntaxAxiomString + ")");
+ OWLFunctionalSyntaxOWLParser p = new OWLFunctionalSyntaxOWLParser();
+ OWLOntology newOntology = OWLManager.createOWLOntologyManager().createOntology();
+ p.parse(s, newOntology);
+ if(!newOntology.getLogicalAxioms().isEmpty()){
+ return newOntology.getLogicalAxioms().iterator().next();
+ }
+ } catch (UnloadableImportException e) {
+ e.printStackTrace();
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ } catch (OWLParserException e) {
+ System.err.println("Parsing failed for axiom " + functionalSyntaxAxiomString);
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ private int count(PreparedStatement ps) throws SQLException{
+ ResultSet rs = ps.executeQuery();
+ rs.next();
+ return rs.getInt(1);
+ }
+
+ public static void main(String[] args) throws Exception {
+// ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
+ boolean analyzeRepositories = true;
+ if(args.length == 1){
+ analyzeRepositories = Boolean.parseBoolean(args[0]);
+ }
+ new OWLAxiomPatternDetectionEvaluation().run(analyzeRepositories, Arrays.asList(
+ new TONESRepository(), new BioPortalRepository(), new OxfordRepository()));
+ }
+
+
+}
Added: trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/pattern/OWLAxiomPatternUsageEvaluation.java 2013-05-05 14:24:32 UTC (rev 3950)
@@ -0,0 +1,418 @@
+package org.dllearner.scripts.pattern;
+
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.SocketTimeoutException;
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.text.DecimalFormat;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.concurrent.TimeUnit;
+import java.util.prefs.Preferences;
+
+import org.aksw.commons.util.Pair;
+import org.apache.log4j.Logger;
+import org.coode.owlapi.functionalparser.OWLFunctionalSyntaxOWLParser;
+import org.coode.owlapi.turtle.TurtleOntologyFormat;
+import org.dllearner.core.EvaluatedAxiom;
+import org.dllearner.core.Score;
+import org.dllearner.core.owl.NamedClass;
+import org.dllearner.kb.LocalModelBasedSparqlEndpointKS;
+import org.dllearner.kb.SparqlEndpointKS;
+import org.dllearner.kb.sparql.ExtractionDBCache;
+import org.dllearner.kb.sparql.SparqlEndpoint;
+import org.dllearner.kb.sparql.SparqlQuery;
+import org.dllearner.learningproblems.AxiomScore;
+import org.dllearner.learningproblems.Heuristics;
+import org.dllearner.reasoning.SPARQLReasoner;
+import org.dllearner.utilities.owl.DLLearnerAxiomConvertVisitor;
+import org.dllearner.utilities.owl.OWLClassExpressionToSPARQLConverter;
+import org.ini4j.IniPreferences;
+import org.ini4j.InvalidFileFormatException;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.OWLObjectRenderer;
+import org.semanticweb.owlapi.io.OWLParserException;
+import org.semanticweb.owlapi.io.StringDocumentSource;
+import org.semanticweb.owlapi.io.ToStringRenderer;
+import org.semanticweb.owlapi.model.AxiomType;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAnnotationProperty;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLEntity;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.model.OWLOntologyStorageException;
+import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
+import org.semanticweb.owlapi.model.UnloadableImportException;
+import org.semanticweb.owlapi.util.OWLObjectDuplicator;
+
+import uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
+import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
+import uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxObjectRenderer;
+
+import com.hp.hpl.jena.query.Query;
+import com.hp.hpl.jena.query.QueryExecution;
+import com.hp.hpl.jena.query.QueryExecutionFactory;
+import com.hp.hpl.jena.query.QueryFactory;
+import com.hp.hpl.jena.query.QuerySolution;
+import com.hp.hpl.jena.query.Syntax;
+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;
+
+public class OWLAxiomPatternUsageEvaluation {
+
+
+ private static final Logger logger = Logger.getLogger(OWLAxiomPatternUsageEvaluation.AxiomTypeCategory.class
+ .getName());
+
+ enum AxiomTypeCategory{
+ TBox, RBox, ABox
+ }
+
+ private OWLObjectRenderer axiomRenderer = new ManchesterOWLSyntaxOWLObjectRendererImpl();
+ private OWLDataFactory df = new OWLDataFactoryImpl();
+ private Connection conn;
+
+ private ExtractionDBCache cache = new ExtractionDBCache("pattern-cache");
+ private SparqlEndpointKS ks = new SparqlEndpointKS(SparqlEndpoint.getEndpointDBpedia(), cache);//new LocalModelBasedSparqlEndpointKS(model);
+ private String ns = "http://dbpedia.org/ontology/";
+
+ private boolean fancyLatex = false;
+ private DecimalFormat format = new DecimalFormat("00.0%");
+ private long waitingTime = TimeUnit.SECONDS.toMillis(3);
+ private double threshold = 0.6;
+ private OWLAnnotationProperty confidenceProperty = df.getOWLAnnotationProperty(IRI.create("http://dl-learner.org/pattern/confidence"));
+
+ public OWLAxiomPatternUsageEvaluation() {
+ initDBConnection();
+ }
+
+ private void initDBConnection() {
+ try {
+ InputStream is = this.getClass().getClassLoader().getResourceAsStream("db_settings.ini");
+ Preferences prefs = new IniPreferences(is);
+ String dbServer = prefs.node("database").get("server", null);
+ String dbName = prefs.node("database").get("name", null);
+ String dbUser = prefs.node("database").get("user", null);
+ String dbPass = prefs.node("database").get("pass", null);
+
+ Class.forName("com.mysql.jdbc.Driver");
+ String url = "jdbc:mysql://" + dbServer + "/" + dbName;
+ conn = DriverManager.getConnection(url, dbUser, dbPass);
+ } catch (ClassNotFoundException e) {
+ e.printStackTrace();
+ } catch (SQLException e) {
+ e.printStackTrace();
+ } catch (InvalidFileFormatException e) {
+ e.printStackTrace();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ public void run(){
+ SPARQLReasoner reasoner = new SPARQLReasoner(ks, cache);
+
+ OWLClassExpressionToSPARQLConverter converter = new OWLClassExpressionToSPARQLConverter();
+
+ //get the axiom patterns to evaluate
+ List<OWLAxiom> patterns = getPatternsToEvaluate();
+
+ //get all classes in KB
+ Set<NamedClass> classes = reasoner.getTypes(ns);
+
+ //for each pattern
+ for (OWLAxiom pattern : patterns) {
+ if(pattern.isOfType(AxiomType.SUBCLASS_OF)){
+ logger.info("Processing " + pattern + "...");
+ Set<EvaluatedAxiom> evaluatedAxioms = new HashSet<EvaluatedAxiom>();
+ Map<OWLAxiom, Score> axioms2Score = new LinkedHashMap<OWLAxiom, Score>();
+ OWLClassExpression patternSubClass = ((OWLSubClassOfAxiom)pattern).getSubClass();
+ OWLClassExpression superClass = ((OWLSubClassOfAxiom)pattern).getSuperClass();
+ //for each class
+ int i = 1;
+ for (NamedClass cls : classes) {
+ logger.info("Processing " + cls + "...");
+ //set the subclass as a class from the KB
+ OWLClass subClass = df.getOWLClass(IRI.create(cls.getName()));
+
+ //1. count number of instances in subclass expression
+ Query query = QueryFactory.create("SELECT (COUNT(DISTINCT ?x) AS ?cnt) WHERE {" + converter.convert("?x", subClass) + "}",Syntax.syntaxARQ);
+ int subClassCnt = executeSelectQuery(query).next().getLiteral("cnt").getInt();
+
+ //2. count number of instances in subclass AND superclass expression
+ //we have 2 options here to evaluate the whole axiom pattern:
+ //a) we replace all entities in the signature of the super class expression(except the subclass) with variables
+ //and GROUP BY them
+ //b) we replace only 1 entity with a variable, thus we have to try it for several combinations
+// for (OWLEntity entity : signature) {
+// //replace current entity with variable and for the rest use existing entities in KB
+// query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(subClass, superClass), signature);
+// }
+ Set<OWLEntity> signature = superClass.getSignature();
+ signature.remove(subClass);
+ query = converter.asQuery("?x", df.getOWLObjectIntersectionOf(subClass, superClass), signature);
+ query.setLimit(100);
+ Map<OWLEntity, String> variablesMapping = converter.getVariablesMapping();System.out.println(query);
+ com.hp.hpl.jena.query.ResultSet rs = executeSelectQuery(query);
+ QuerySolution qs;
+ while(rs.hasNext()){
+ qs = rs.next();
+ //get the IRIs for each variable
+ Map<OWLEntity, IRI> entity2IRIMap = new HashMap<OWLEntity, IRI>();
+ entity2IRIMap.put(patternSubClass.asOWLClass(), subClass.getIRI());
+ for (OWLEntity entity : signature) {
+ String var = variablesMapping.get(entity);
+ Resource resource = qs.getResource(var);
+ entity2IRIMap.put(entity, IRI.create(resource.getURI()));
+ }
+ //instantiate the pattern
+ OWLObjectDuplicator duplicator = new OWLObjectDuplicator(entity2IRIMap, df);
+ OWLAxiom patternInstantiation = duplicator.duplicateObject(pattern);
+ int patternInstantiationCnt = qs.getLiteral("cnt").getInt();
+ //compute score
+ Score score;
+ try {
+ score = computeScore(subClassCnt, patternInstantiationCnt);
+ axioms2Score.put(patternInstantiation, score);
+ logger.info(patternInstantiation + "(" + format.format(score.getAccuracy()) + ")");
+ } catch (IllegalArgumentException e) {
+ //sometimes Virtuosos returns 'wrong' cnt values such that the success number as bigger than the total number of instances
+ e.printStackTrace();
+ }
+
+// //convert into EvaluatedAxiom such we can serialize it as RDF with accuracy value as annotation
+// EvaluatedAxiom evaluatedAxiom = new EvaluatedAxiom(DLLearnerAxiomConvertVisitor.getDLLearnerAxiom(patternInstantiation), score);
+// evaluatedAxioms.add(evaluatedAxiom);
+
+ }
+ //wait some time to avoid flooding of endpoint
+ try {
+ Thread.sleep(waitingTime);
+ } catch (InterruptedException e) {
+ e.printStackTrace();
+ }
+// if(i++ == 3) break;
+ }
+ save(axioms2Score);
+ }
+ }
+ }
+
+ private void save(Map<OWLAxiom, Score> axioms2Score){
+ try {
+ Set<OWLAxiom> annotatedAxioms = new HashSet<OWLAxiom>();
+ for (Entry<OWLAxiom, Score> entry : axioms2Score.entrySet()) {
+ OWLAxiom axiom = entry.getKey();
+ Score score = entry.getValue();
+ if(score.getAccuracy() >= threshold){
+ annotatedAxioms.add(axiom.getAnnotatedAxiom(Collections.singleton(df.getOWLAnnotation(confidenceProperty, df.getOWLLiteral(score.getAccuracy())))));
+
+ }
+ }
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ OWLOntology ontology = man.createOntology(annotatedAxioms);
+ man.saveOntology(ontology, new TurtleOntologyFormat(), new FileOutputStream("pattern.ttl"));
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ } catch (OWLOntologyStorageException e) {
+ e.printStackTrace();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+ }
+
+ private void save(Set<EvaluatedAxiom> evaluatedAxioms){
+ try {
+ Set<OWLAxiom> axioms = new HashSet<OWLAxiom>();
+ for (EvaluatedAxiom evaluatedAxiom : EvaluatedAxiom.getBestEvaluatedAxioms(evaluatedAxioms, threshold)) {
+ axioms.addAll(evaluatedAxiom.toRDF("http://dl-learner.org/pattern/").values().iterator().next());
+ }
+ OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+ OWLOntology ontology = man.createOntology(axioms);
+ man.saveOntology(ontology, new TurtleOntologyFormat(), new FileOutputStream("pattern.ttl"));
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ } catch (OWLOntologyStorageException e) {
+ e.printStackTrace();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+ }
+
+ public List<OWLAxiom> getPatternsToEvaluate(){
+ List<OWLAxiom> axiomPatterns = new ArrayList<OWLAxiom>();
+
+ Map<OWLAxiom, Pair<Integer, Integer>> topNAxiomPatterns = getTopNAxiomPatterns(AxiomTypeCategory.TBox, 10);
+ axiomPatterns.addAll(topNAxiomPatterns.keySet());
+
+ return axiomPatterns;
+ }
+
+
+ private String asLatex(String title, Map<OWLAxiom, Pair<Integer, Integer>> topN){
+ String latexTable = "\\begin{table}\n";
+ latexTable += "\\begin{tabular}{lrr}\n";
+ latexTable += "\\toprule\n";
+ latexTable += "Pattern & Frequency & \\#Ontologies\\\\\\midrule\n";
+
+ for (Entry<OWLAxiom, Pair<Integer, Integer>> entry : topN.entrySet()) {
+ OWLAxiom axiom = entry.getKey();
+ Integer frequency = entry.getValue().getKey();
+ Integer idf = entry.getValue().getValue();
+
+ if(axiom != null){
+ String axiomColumn = axiomRenderer.render(axiom);
+ if(fancyLatex){
+ axiomColumn = "\\begin{lstlisting}[language=manchester]" + axiomColumn + "\\end{lstlisting}";
+ }
+ latexTable += axiomColumn + " & " + frequency + " & " + idf + "\\\\\n";
+ }
+ }
+ latexTable += "\\bottomrule\n\\end{tabular}\n";
+ latexTable += "\\caption{" + title + "}\n";
+ latexTable += "\\end{table}\n";
+ return latexTable;
+ }
+
+ private Map<OWLAxiom, Pair<Integer, Integer>> getTopNAxiomPatterns(AxiomTypeCategory axiomType, int n){
+ Map<OWLAxiom, Pair<Integer, Integer>> topN = new LinkedHashMap<OWLAxiom, Pair<Integer, Integer>>();
+ PreparedStatement ps;
+ ResultSet rs;
+ try {
+ ps = conn.prepareStatement("SELECT pattern,SUM(occurrences),COUNT(ontology_id) FROM " +
+ "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
+ "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND P.axiom_type=?) " +
+ "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
+ ps.setString(1, axiomType.name());
+ ps.setInt(2, n);
+ rs = ps.executeQuery();
+ while(rs.next()){
+ topN.put(asOWLAxiom(rs.getString(1)), new Pair<Integer, Integer>(rs.getInt(2), rs.getInt(3)));
+ }
+ } catch(SQLException e){
+ e.printStackTrace();
+ }
+ return topN;
+ }
+
+ protected com.hp.hpl.jena.query.ResultSet executeSelectQuery(Query query) {
+ com.hp.hpl.jena.query.ResultSet rs = null;
+ if(ks.isRemote()){
+ SparqlEndpoint endpoint = ((SparqlEndpointKS) ks).getEndpoint();
+ ExtractionDBCache cache = ks.getCache();
+ if(cache != null){
+ rs = SparqlQuery.convertJSONtoResultSet(cache.executeSelectQuery(endpoint, query.toString()));
+ } else {
+ QueryEngineHTTP queryExecution = new QueryEngineHTTP(endpoint.getURL().toString(),
+ query);
+ queryExecution.setDefaultGraphURIs(endpoint.getDefaultGraphURIs());
+ queryExecution.setNamedGraphURIs(endpoint.getNamedGraphURIs());
+ try {
+ rs = queryExecution.execSelect();
+ return rs;
+ } catch (QueryExceptionHTTP e) {
+ if(e.getCause() instanceof SocketTimeoutException){
+ logger.warn("Got timeout");
+ } else {
+ logger.error("Exception executing query", e);
+ }
+ }
+ }
+
+ } else {
+ QueryExecution queryExecution = QueryExecutionFactory.create(query, ((LocalModelBasedSparqlEndpointKS)ks).getModel());
+ rs = queryExecution.execSelect();
+ }
+ return rs;
+ }
+
+ protected com.hp.hpl.jena.query.ResultSet executeSelectQuery(Query query, boolean cached) {
+ com.hp.hpl.jena.query.ResultSet rs = null;
+ if(ks.isRemote()){
+ SparqlEndpoint endpoint = ((SparqlEndpointKS) ks).getEndpoint();
+ ExtractionDBCache cache = ks.getCache();
+ if(cache != null && cached){
+ rs = SparqlQuery.convertJSONtoResultSet(cache.executeSelectQuery(endpoint, query.toString()));
+ } else {
+ QueryEngineHTTP queryExecution = new QueryEngineHTTP(endpoint.getURL().toString(),
+ query);
+ queryExecution.setDefaultGraphURIs(endpoint.getDefaultGraphURIs());
+ queryExecution.setNamedGraphURIs(endpoint.getNamedGraphURIs());
+ try {
+ rs = queryExecution.execSelect();
+ return rs;
+ } catch (QueryExceptionHTTP e) {
+ if(e.getCause() instanceof SocketTimeoutException){
+ logger.warn("Got timeout");
+ } else {
+ logger.error("Exception executing query", e);
+ }
+ }
+ }
+
+ } else {
+ QueryExecution queryExecution = QueryExecutionFactory.create(query, ((LocalModelBasedSparqlEndpointKS)ks).getModel());
+ rs = queryExecution.execSelect();
+ }
+ return rs;
+ }
+
+ private Score computeScore(int total, int success){
+ double[] confidenceInterval = Heuristics.getConfidenceInterval95Wald(total, success);
+
+ double accuracy = (confidenceInterval[0] + confidenceInterval[1]) / 2;
+
+ double confidence = confidenceInterval[1] - confidenceInterval[0];
+
+ return new AxiomScore(accuracy, confidence, total, success, total-success);
+ }
+
+ private OWLAxiom asOWLAxiom(String functionalSyntaxAxiomString){
+ try {
+ StringDocumentSource s = new StringDocumentSource("Ontology(<http://www.pattern.org> " + functionalSyntaxAxiomString + ")");
+ OWLFunctionalSyntaxOWLParser p = new OWLFunctionalSyntaxOWLParser();
+ OWLOntology newOntology = OWLManager.createOWLOntologyManager().createOntology();
+ p.parse(s, newOntology);
+ if(!newOntology.getLogicalAxioms().isEmpty()){
+ return newOntology.getLogicalAxioms().iterator().next();
+ }
+ } catch (UnloadableImportException e) {
+ e.printStackTrace();
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ } catch (OWLParserException e) {
+ System.err.println("Parsing failed for axiom " + functionalSyntaxAxiomString);
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ public static void main(String[] args) throws Exception {
+ ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
+ new OWLAxiomPatternUsageEvaluation().run();
+ }
+
+
+}
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|
|
From: <lor...@us...> - 2013-05-04 11:27:54
|
Revision: 3949
http://sourceforge.net/p/dl-learner/code/3949
Author: lorenz_b
Date: 2013-05-04 11:27:51 +0000 (Sat, 04 May 2013)
Log Message:
-----------
Added Oxford Ontologies repository
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
Added Paths:
-----------
trunk/components-core/src/main/java/org/dllearner/kb/repository/oxford/
trunk/components-core/src/main/java/org/dllearner/kb/repository/oxford/OxfordRepository.java
Added: trunk/components-core/src/main/java/org/dllearner/kb/repository/oxford/OxfordRepository.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/repository/oxford/OxfordRepository.java (rev 0)
+++ trunk/components-core/src/main/java/org/dllearner/kb/repository/oxford/OxfordRepository.java 2013-05-04 11:27:51 UTC (rev 3949)
@@ -0,0 +1,125 @@
+package org.dllearner.kb.repository.oxford;
+
+import java.net.URI;
+import java.text.DecimalFormat;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.dllearner.kb.repository.OntologyRepository;
+import org.dllearner.kb.repository.OntologyRepositoryEntry;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.util.OntologyIRIShortFormProvider;
+
+public class OxfordRepository implements OntologyRepository{
+
+ private static final Logger log = Logger.getLogger(OxfordRepository.class);
+
+ private final String repositoryName = "Oxford";
+
+ private final URI repositoryLocation = URI.create("http://www.cs.ox.ac.uk/isg/ontologies/UID/");
+
+ private List<RepositoryEntry> entries;
+
+ int numberOfEntries = 793;
+
+ DecimalFormat df = new DecimalFormat("00000");
+
+
+ public OxfordRepository() {
+ entries = new ArrayList<RepositoryEntry>();
+ }
+
+ @Override
+ public void initialize() {
+ refresh();
+ }
+
+
+ public String getName() {
+ return repositoryName;
+ }
+
+
+ public String getLocation() {
+ return repositoryLocation.toString();
+ }
+
+
+ public void refresh() {
+ fillRepository();
+ }
+
+
+ public Collection<OntologyRepositoryEntry> getEntries() {
+ List<OntologyRepositoryEntry> ret = new ArrayList<OntologyRepositoryEntry>();
+ ret.addAll(entries);
+ return ret;
+ }
+
+
+ public List<Object> getMetaDataKeys() {
+ return Collections.emptyList();
+ }
+
+
+ public void dispose() throws Exception {
+ }
+
+ /////////////////////////////////////////////////////////////////////////////////////////////////
+ //
+ // Implementation details
+
+
+ private void fillRepository() {
+ entries.clear();
+ for(int i = 1; i <= numberOfEntries; i++){
+ entries.add(new RepositoryEntry(URI.create(repositoryLocation + df.format(i) + ".owl")));
+ }
+ log.info("Loaded " + entries.size() + " ontology entries from Oxford.");
+ }
+
+ private class RepositoryEntry implements OntologyRepositoryEntry {
+
+ private String shortName;
+
+ private URI ontologyURI;
+
+ private URI physicalURI;
+
+ public RepositoryEntry(URI ontologyIRI) {
+ this.ontologyURI = ontologyIRI;System.out.println(ontologyIRI);
+ OntologyIRIShortFormProvider sfp = new OntologyIRIShortFormProvider();
+ shortName = sfp.getShortForm(IRI.create(ontologyIRI));
+ physicalURI = ontologyIRI;
+ }
+
+
+ public String getOntologyShortName() {
+ return shortName;
+ }
+
+
+ public URI getOntologyURI() {
+ return ontologyURI;
+ }
+
+
+ public URI getPhysicalURI() {
+ return physicalURI;
+ }
+
+
+ public String getMetaData(Object key) {
+ return null;
+ }
+
+ }
+
+ public static void main(String[] args) throws Exception {
+ new OxfordRepository().fillRepository();
+ }
+
+}
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-04 11:13:37 UTC (rev 3948)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-04 11:27:51 UTC (rev 3949)
@@ -21,6 +21,7 @@
import org.dllearner.algorithms.pattern.OWLAxiomPatternFinder;
import org.dllearner.kb.repository.OntologyRepository;
import org.dllearner.kb.repository.bioportal.BioPortalRepository;
+import org.dllearner.kb.repository.oxford.OxfordRepository;
import org.dllearner.kb.repository.tones.TONESRepository;
import org.ini4j.IniPreferences;
import org.ini4j.InvalidFileFormatException;
@@ -375,7 +376,7 @@
analyzeRepositories = Boolean.parseBoolean(args[0]);
}
new OWLAxiomPatternDetectionEvaluation().run(analyzeRepositories, Arrays.asList(
- new TONESRepository(), new BioPortalRepository()));
+ new TONESRepository(), new BioPortalRepository(), new OxfordRepository()));
}
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|
|
From: <lor...@us...> - 2013-05-04 11:13:40
|
Revision: 3948
http://sourceforge.net/p/dl-learner/code/3948
Author: lorenz_b
Date: 2013-05-04 11:13:37 +0000 (Sat, 04 May 2013)
Log Message:
-----------
Added option to create only statistics.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-04 11:09:49 UTC (rev 3947)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-04 11:13:37 UTC (rev 3948)
@@ -77,7 +77,9 @@
public void run(boolean analyzeRepositories, Collection<OntologyRepository> repositories){
//analyze repositories
- analyze(repositories);
+ if(analyzeRepositories){
+ analyze(repositories);
+ }
//create statistics for the repositories
makeRepositoryStatistics(repositories);
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|
|
From: <lor...@us...> - 2013-05-04 11:09:52
|
Revision: 3947
http://sourceforge.net/p/dl-learner/code/3947
Author: lorenz_b
Date: 2013-05-04 11:09:49 +0000 (Sat, 04 May 2013)
Log Message:
-----------
Improved script Latex output.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-04 11:07:10 UTC (rev 3946)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-04 11:09:49 UTC (rev 3947)
@@ -75,7 +75,7 @@
}
}
- public void run(Collection<OntologyRepository> repositories){
+ public void run(boolean analyzeRepositories, Collection<OntologyRepository> repositories){
//analyze repositories
analyze(repositories);
@@ -86,6 +86,10 @@
makePatternStatistics(repositories);
}
+ public void run(Collection<OntologyRepository> repositories){
+ run(true, repositories);
+ }
+
private void analyze(Collection<OntologyRepository> repositories){
for (OntologyRepository repository : repositories) {
repository.initialize();
@@ -364,7 +368,11 @@
public static void main(String[] args) throws Exception {
// ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
- new OWLAxiomPatternDetectionEvaluation().run(Arrays.asList(
+ boolean analyzeRepositories = true;
+ if(args.length == 1){
+ analyzeRepositories = Boolean.parseBoolean(args[0]);
+ }
+ new OWLAxiomPatternDetectionEvaluation().run(analyzeRepositories, Arrays.asList(
new TONESRepository(), new BioPortalRepository()));
}
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|
|
From: <lor...@us...> - 2013-05-04 11:07:14
|
Revision: 3946
http://sourceforge.net/p/dl-learner/code/3946
Author: lorenz_b
Date: 2013-05-04 11:07:10 +0000 (Sat, 04 May 2013)
Log Message:
-----------
Improved script Latex output.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-04 10:59:43 UTC (rev 3945)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-04 11:07:10 UTC (rev 3946)
@@ -77,7 +77,7 @@
public void run(Collection<OntologyRepository> repositories){
//analyze repositories
-// analyze(repositories);
+ analyze(repositories);
//create statistics for the repositories
makeRepositoryStatistics(repositories);
@@ -295,7 +295,7 @@
"(P.id=OP.pattern_id AND O.id=OP.ontology_id AND O.repository=? AND P.axiom_type=?) " +
"GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
ps.setString(1, repository.getName());
- ps.setString(2, "RBox");
+ ps.setString(2, axiomType.name());
ps.setInt(3, n);
rs = ps.executeQuery();
while(rs.next()){
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|
|
From: <lor...@us...> - 2013-05-04 10:59:46
|
Revision: 3945
http://sourceforge.net/p/dl-learner/code/3945
Author: lorenz_b
Date: 2013-05-04 10:59:43 +0000 (Sat, 04 May 2013)
Log Message:
-----------
Improved script Latex output.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java
trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java 2013-05-04 10:20:34 UTC (rev 3944)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java 2013-05-04 10:59:43 UTC (rev 3945)
@@ -68,6 +68,7 @@
private OWLAxiom renamedAxiom;
private boolean normalizeABoxAxioms = true;
+ private boolean ignoreTrivialAxioms = true;//ignore Thing(a),SubClassOf(A,Thing),SubPropertyOf(A,TopProperty)
public OWLAxiomRenamer(OWLDataFactory df) {
this.df = df;
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-04 10:20:34 UTC (rev 3944)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-04 10:59:43 UTC (rev 3945)
@@ -16,6 +16,7 @@
import java.util.Map.Entry;
import java.util.prefs.Preferences;
+import org.aksw.commons.util.Pair;
import org.coode.owlapi.functionalparser.OWLFunctionalSyntaxOWLParser;
import org.dllearner.algorithms.pattern.OWLAxiomPatternFinder;
import org.dllearner.kb.repository.OntologyRepository;
@@ -42,6 +43,8 @@
private OWLObjectRenderer axiomRenderer = new ManchesterOWLSyntaxOWLObjectRendererImpl();
private Connection conn;
+
+ private boolean fancyLatex = false;
public OWLAxiomPatternDetectionEvaluation() {
initDBConnection();
@@ -98,14 +101,14 @@
//total pattern statistics
for (AxiomTypeCategory axiomTypeCategory : AxiomTypeCategory.values()) {
- Map<OWLAxiom, Integer> topNAxiomPatterns = getTopNAxiomPatterns(axiomTypeCategory, n);
+ Map<OWLAxiom, Pair<Integer, Integer>> topNAxiomPatterns = getTopNAxiomPatterns(axiomTypeCategory, n);
latex += asLatex("Top " + n + " " + axiomTypeCategory.name() + " axiom patterns.", topNAxiomPatterns) + "\n\n";
}
//get top n TBox, RBox and ABox patterns by repository
for (OntologyRepository repository : repositories) {
for (AxiomTypeCategory axiomTypeCategory : AxiomTypeCategory.values()) {
- Map<OWLAxiom, Integer> topNAxiomPatterns = getTopNAxiomPatterns(repository, axiomTypeCategory, n);
+ Map<OWLAxiom, Pair<Integer, Integer>> topNAxiomPatterns = getTopNAxiomPatterns(repository, axiomTypeCategory, n);
latex += asLatex("Top " + n + " " + axiomTypeCategory.name() + " axiom patterns for " + repository.getName() + " repository.", topNAxiomPatterns) + "\n\n";
}
}
@@ -235,32 +238,37 @@
}
}
- private String asLatex(String title, Map<OWLAxiom, Integer> topN){
+ private String asLatex(String title, Map<OWLAxiom, Pair<Integer, Integer>> topN){
String latexTable = "\\begin{table}\n";
- latexTable += "\\begin{tabular}{lr}\n";
+ latexTable += "\\begin{tabular}{lrr}\n";
latexTable += "\\toprule\n";
- latexTable += "Pattern & Frequency\\\\\\midrule\n";
+ latexTable += "Pattern & Frequency & \\#Ontologies\\\\\\midrule\n";
- for (Entry<OWLAxiom, Integer> entry : topN.entrySet()) {
+ for (Entry<OWLAxiom, Pair<Integer, Integer>> entry : topN.entrySet()) {
OWLAxiom axiom = entry.getKey();
- Integer frequency = entry.getValue();
+ Integer frequency = entry.getValue().getKey();
+ Integer idf = entry.getValue().getValue();
if(axiom != null){
- latexTable += axiomRenderer.render(axiom) + " & " + frequency + "\\\\\n";
+ String axiomColumn = axiomRenderer.render(axiom);
+ if(fancyLatex){
+ axiomColumn = "\\begin{lstlisting}[language=manchester]" + axiomColumn + "\\end{lstlisting}";
+ }
+ latexTable += axiomColumn + " & " + frequency + " & " + idf + "\\\\\n";
}
}
- latexTable += "\\bottomrule\\end{tabular}\n";
+ latexTable += "\\bottomrule\n\\end{tabular}\n";
latexTable += "\\caption{" + title + "}\n";
latexTable += "\\end{table}\n";
return latexTable;
}
- private Map<OWLAxiom, Integer> getTopNAxiomPatterns(AxiomTypeCategory axiomType, int n){
- Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
+ private Map<OWLAxiom, Pair<Integer, Integer>> getTopNAxiomPatterns(AxiomTypeCategory axiomType, int n){
+ Map<OWLAxiom, Pair<Integer, Integer>> topN = new LinkedHashMap<OWLAxiom, Pair<Integer, Integer>>();
PreparedStatement ps;
ResultSet rs;
try {
- ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
+ ps = conn.prepareStatement("SELECT pattern,SUM(occurrences),COUNT(ontology_id) FROM " +
"Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
"(P.id=OP.pattern_id AND O.id=OP.ontology_id AND P.axiom_type=?) " +
"GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
@@ -268,7 +276,7 @@
ps.setInt(2, n);
rs = ps.executeQuery();
while(rs.next()){
- topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
+ topN.put(asOWLAxiom(rs.getString(1)), new Pair<Integer, Integer>(rs.getInt(2), rs.getInt(3)));
}
} catch(SQLException e){
e.printStackTrace();
@@ -276,13 +284,13 @@
return topN;
}
- private Map<OWLAxiom, Integer> getTopNAxiomPatterns(OntologyRepository repository, AxiomTypeCategory axiomType, int n){
+ private Map<OWLAxiom, Pair<Integer, Integer>> getTopNAxiomPatterns(OntologyRepository repository, AxiomTypeCategory axiomType, int n){
+ Map<OWLAxiom, Pair<Integer, Integer>> topN = new LinkedHashMap<OWLAxiom, Pair<Integer, Integer>>();
PreparedStatement ps;
ResultSet rs;
- Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
try {
//get number of ontologies
- ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
+ ps = conn.prepareStatement("SELECT pattern,SUM(occurrences),COUNT(ontology_id) FROM " +
"Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
"(P.id=OP.pattern_id AND O.id=OP.ontology_id AND O.repository=? AND P.axiom_type=?) " +
"GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
@@ -291,7 +299,7 @@
ps.setInt(3, n);
rs = ps.executeQuery();
while(rs.next()){
- topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
+ topN.put(asOWLAxiom(rs.getString(1)), new Pair<Integer, Integer>(rs.getInt(2), rs.getInt(3)));
}
} catch(SQLException e){
e.printStackTrace();
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|
|
From: <lor...@us...> - 2013-05-04 10:20:37
|
Revision: 3944
http://sourceforge.net/p/dl-learner/code/3944
Author: lorenz_b
Date: 2013-05-04 10:20:34 +0000 (Sat, 04 May 2013)
Log Message:
-----------
Improved script Latex output.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-04 09:36:21 UTC (rev 3943)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-04 10:20:34 UTC (rev 3944)
@@ -27,17 +27,19 @@
import org.semanticweb.owlapi.io.OWLObjectRenderer;
import org.semanticweb.owlapi.io.OWLParserException;
import org.semanticweb.owlapi.io.StringDocumentSource;
-import org.semanticweb.owlapi.io.ToStringRenderer;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.UnloadableImportException;
import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
-import uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxObjectRenderer;
public class OWLAxiomPatternDetectionEvaluation {
+ enum AxiomTypeCategory{
+ TBox, RBox, ABox
+ }
+
private OWLObjectRenderer axiomRenderer = new ManchesterOWLSyntaxOWLObjectRendererImpl();
private Connection conn;
@@ -91,23 +93,21 @@
private void makePatternStatistics(Collection<OntologyRepository> repositories){
int n = 10;
+
String latex = "";
- Map<OWLAxiom, Integer> topNTBoxAxiomPatterns = getTopNTBoxAxiomPatterns(n);
- latex += asLatex("Total TBox", topNTBoxAxiomPatterns) + "\n\n";
- Map<OWLAxiom, Integer> topNRBoxAxiomPatterns = getTopNRBoxAxiomPatterns(n);
- latex += asLatex("Total RBox", topNRBoxAxiomPatterns) + "\n\n";
- Map<OWLAxiom, Integer> topNABoxAxiomPatterns = getTopNABoxAxiomPatterns(n);
- latex += asLatex("Total ABox", topNABoxAxiomPatterns) + "\n\n";
+ //total pattern statistics
+ for (AxiomTypeCategory axiomTypeCategory : AxiomTypeCategory.values()) {
+ Map<OWLAxiom, Integer> topNAxiomPatterns = getTopNAxiomPatterns(axiomTypeCategory, n);
+ latex += asLatex("Top " + n + " " + axiomTypeCategory.name() + " axiom patterns.", topNAxiomPatterns) + "\n\n";
+ }
+
//get top n TBox, RBox and ABox patterns by repository
-
- Map<OntologyRepository, Map<OWLAxiom, Integer>> topNTBoxAxiomPatternsByRepository = getTopNTBoxAxiomPatterns(repositories, n);
- Map<OntologyRepository, Map<OWLAxiom, Integer>> topNRBoxAxiomPatternsByRepository = getTopNRBoxAxiomPatterns(repositories, n);
- Map<OntologyRepository, Map<OWLAxiom, Integer>> topNABoxAxiomPatternsByRepository = getTopNABoxAxiomPatterns(repositories, n);
for (OntologyRepository repository : repositories) {
- latex += asLatex(repository.getName() + " TBox", topNTBoxAxiomPatternsByRepository.get(repository)) + "\n\n";
- latex += asLatex(repository.getName() + " RBox", topNRBoxAxiomPatternsByRepository.get(repository)) + "\n\n";
- latex += asLatex(repository.getName() + " ABox", topNABoxAxiomPatternsByRepository.get(repository)) + "\n\n";
+ for (AxiomTypeCategory axiomTypeCategory : AxiomTypeCategory.values()) {
+ Map<OWLAxiom, Integer> topNAxiomPatterns = getTopNAxiomPatterns(repository, axiomTypeCategory, n);
+ latex += asLatex("Top " + n + " " + axiomTypeCategory.name() + " axiom patterns for " + repository.getName() + " repository.", topNAxiomPatterns) + "\n\n";
+ }
}
try {
new FileOutputStream("pattern-statistics.tex").write(latex.getBytes());
@@ -255,7 +255,7 @@
return latexTable;
}
- private Map<OWLAxiom, Integer> getTopNTBoxAxiomPatterns(int n){
+ private Map<OWLAxiom, Integer> getTopNAxiomPatterns(AxiomTypeCategory axiomType, int n){
Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
PreparedStatement ps;
ResultSet rs;
@@ -264,7 +264,7 @@
"Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
"(P.id=OP.pattern_id AND O.id=OP.ontology_id AND P.axiom_type=?) " +
"GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
- ps.setString(1, "TBox");
+ ps.setString(1, axiomType.name());
ps.setInt(2, n);
rs = ps.executeQuery();
while(rs.next()){
@@ -276,45 +276,19 @@
return topN;
}
- private Map<OntologyRepository, Map<OWLAxiom, Integer>> getTopNTBoxAxiomPatterns(Collection<OntologyRepository> repositories, int n){
- Map<OntologyRepository, Map<OWLAxiom, Integer>> topNByRepository = new LinkedHashMap<OntologyRepository, Map<OWLAxiom,Integer>>();
+ private Map<OWLAxiom, Integer> getTopNAxiomPatterns(OntologyRepository repository, AxiomTypeCategory axiomType, int n){
PreparedStatement ps;
ResultSet rs;
- //for each repository
- for (OntologyRepository repository : repositories) {
- Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
- try {
- //get number of ontologies
- ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
- "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
- "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND O.repository=? AND P.axiom_type=?) " +
- "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
- ps.setString(1, repository.getName());
- ps.setString(2, "TBox");
- ps.setInt(3, n);
- rs = ps.executeQuery();
- while(rs.next()){
- topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
- }
- } catch(SQLException e){
- e.printStackTrace();
- }
- topNByRepository.put(repository, topN);
- }
- return topNByRepository;
- }
-
- private Map<OWLAxiom, Integer> getTopNRBoxAxiomPatterns(int n){
Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
- PreparedStatement ps;
- ResultSet rs;
try {
+ //get number of ontologies
ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
"Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
- "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND P.axiom_type=?) " +
+ "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND O.repository=? AND P.axiom_type=?) " +
"GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
- ps.setString(1, "RBox");
- ps.setInt(2, n);
+ ps.setString(1, repository.getName());
+ ps.setString(2, "RBox");
+ ps.setInt(3, n);
rs = ps.executeQuery();
while(rs.next()){
topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
@@ -325,7 +299,7 @@
return topN;
}
- private Map<OntologyRepository, Map<OWLAxiom, Integer>> getTopNRBoxAxiomPatterns(Collection<OntologyRepository> repositories, int n){
+ private Map<OntologyRepository, Map<OWLAxiom, Integer>> getTopNAxiomPatterns(Collection<OntologyRepository> repositories, AxiomTypeCategory axiomType, int n){
Map<OntologyRepository, Map<OWLAxiom, Integer>> topNByRepository = new LinkedHashMap<OntologyRepository, Map<OWLAxiom,Integer>>();
PreparedStatement ps;
ResultSet rs;
@@ -352,56 +326,7 @@
}
return topNByRepository;
}
-
- private Map<OWLAxiom, Integer> getTopNABoxAxiomPatterns(int n){
- Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
- PreparedStatement ps;
- ResultSet rs;
- try {
- ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
- "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
- "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND P.axiom_type=?) " +
- "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
- ps.setString(1, "ABox");
- ps.setInt(2, n);
- rs = ps.executeQuery();
- while(rs.next()){
- topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
- }
- } catch(SQLException e){
- e.printStackTrace();
- }
- return topN;
- }
- private Map<OntologyRepository, Map<OWLAxiom, Integer>> getTopNABoxAxiomPatterns(Collection<OntologyRepository> repositories, int n){
- Map<OntologyRepository, Map<OWLAxiom, Integer>> topNByRepository = new LinkedHashMap<OntologyRepository, Map<OWLAxiom,Integer>>();
- PreparedStatement ps;
- ResultSet rs;
- //for each repository
- for (OntologyRepository repository : repositories) {
- Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
- try {
- //get number of ontologies
- ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
- "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
- "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND O.repository=? AND P.axiom_type=?) " +
- "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
- ps.setString(1, repository.getName());
- ps.setString(2, "ABox");
- ps.setInt(3, n);
- rs = ps.executeQuery();
- while(rs.next()){
- topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
- }
- } catch(SQLException e){
- e.printStackTrace();
- }
- topNByRepository.put(repository, topN);
- }
- return topNByRepository;
- }
-
private OWLAxiom asOWLAxiom(String functionalSyntaxAxiomString){
try {
StringDocumentSource s = new StringDocumentSource("Ontology(<http://www.pattern.org> " + functionalSyntaxAxiomString + ")");
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-05-04 09:36:24
|
Revision: 3943
http://sourceforge.net/p/dl-learner/code/3943
Author: lorenz_b
Date: 2013-05-04 09:36:21 +0000 (Sat, 04 May 2013)
Log Message:
-----------
Ignore illegal axioms?
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java
trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java 2013-05-04 06:14:53 UTC (rev 3942)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java 2013-05-04 09:36:21 UTC (rev 3943)
@@ -8,6 +8,7 @@
import java.util.Set;
import java.util.TreeSet;
+import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
import org.semanticweb.owlapi.model.OWLAnnotationPropertyDomainAxiom;
import org.semanticweb.owlapi.model.OWLAnnotationPropertyRangeAxiom;
@@ -66,6 +67,8 @@
private OWLClassExpressionRenamer expressionRenamer;
private OWLAxiom renamedAxiom;
+ private boolean normalizeABoxAxioms = true;
+
public OWLAxiomRenamer(OWLDataFactory df) {
this.df = df;
}
@@ -163,8 +166,13 @@
@Override
public void visit(OWLDifferentIndividualsAxiom axiom) {
Set<OWLIndividual> renamedIndividuals = new HashSet<OWLIndividual>();
- for(OWLIndividual ind : axiom.getIndividuals()){
- renamedIndividuals.add(expressionRenamer.rename(ind));
+ if(normalizeABoxAxioms){
+ renamedIndividuals.add(df.getOWLNamedIndividual(IRI.create("http://dl-learner.org/pattern/a")));
+ renamedIndividuals.add(df.getOWLNamedIndividual(IRI.create("http://dl-learner.org/pattern/b")));
+ } else {
+ for(OWLIndividual ind : axiom.getIndividuals()){
+ renamedIndividuals.add(expressionRenamer.rename(ind));
+ }
}
renamedAxiom = df.getOWLDifferentIndividualsAxiom(renamedIndividuals);
}
@@ -333,8 +341,13 @@
@Override
public void visit(OWLSameIndividualAxiom axiom) {
Set<OWLIndividual> renamedIndividuals = new HashSet<OWLIndividual>();
- for(OWLIndividual ind : axiom.getIndividuals()){
- renamedIndividuals.add(expressionRenamer.rename(ind));
+ if(normalizeABoxAxioms){
+ renamedIndividuals.add(df.getOWLNamedIndividual(IRI.create("http://dl-learner.org/pattern/a")));
+ renamedIndividuals.add(df.getOWLNamedIndividual(IRI.create("http://dl-learner.org/pattern/b")));
+ } else {
+ for(OWLIndividual ind : axiom.getIndividuals()){
+ renamedIndividuals.add(expressionRenamer.rename(ind));
+ }
}
renamedAxiom = df.getOWLSameIndividualAxiom(renamedIndividuals);
}
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-04 06:14:53 UTC (rev 3942)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-04 09:36:21 UTC (rev 3943)
@@ -72,7 +72,7 @@
public void run(Collection<OntologyRepository> repositories){
//analyze repositories
- analyze(repositories);
+// analyze(repositories);
//create statistics for the repositories
makeRepositoryStatistics(repositories);
@@ -245,8 +245,9 @@
OWLAxiom axiom = entry.getKey();
Integer frequency = entry.getValue();
- latexTable += axiomRenderer.render(axiom) + " & " + frequency + "\\\\\n";
-
+ if(axiom != null){
+ latexTable += axiomRenderer.render(axiom) + " & " + frequency + "\\\\\n";
+ }
}
latexTable += "\\bottomrule\\end{tabular}\n";
latexTable += "\\caption{" + title + "}\n";
@@ -403,7 +404,7 @@
private OWLAxiom asOWLAxiom(String functionalSyntaxAxiomString){
try {
- StringDocumentSource s = new StringDocumentSource("Ontology(<http://www.pattern.org>" + functionalSyntaxAxiomString + ")");
+ StringDocumentSource s = new StringDocumentSource("Ontology(<http://www.pattern.org> " + functionalSyntaxAxiomString + ")");
OWLFunctionalSyntaxOWLParser p = new OWLFunctionalSyntaxOWLParser();
OWLOntology newOntology = OWLManager.createOWLOntologyManager().createOntology();
p.parse(s, newOntology);
@@ -415,7 +416,7 @@
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
} catch (OWLParserException e) {
- e.printStackTrace();
+ System.err.println("Parsing failed for axiom " + functionalSyntaxAxiomString);
} catch (IOException e) {
e.printStackTrace();
}
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|
|
From: <lor...@us...> - 2013-05-04 06:14:56
|
Revision: 3942
http://sourceforge.net/p/dl-learner/code/3942
Author: lorenz_b
Date: 2013-05-04 06:14:53 +0000 (Sat, 04 May 2013)
Log Message:
-----------
Some modifications in pattern detection script.
Modified Paths:
--------------
trunk/components-core/pom.xml
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
trunk/scripts/src/main/java/org/dllearner/scripts/OntologyMatching.java
Modified: trunk/components-core/pom.xml
===================================================================
--- trunk/components-core/pom.xml 2013-05-04 05:50:47 UTC (rev 3941)
+++ trunk/components-core/pom.xml 2013-05-04 06:14:53 UTC (rev 3942)
@@ -124,7 +124,7 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-distribution</artifactId>
- <version>3.4</version>
+ <type>pom</type>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-05-04 05:50:47 UTC (rev 3941)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-05-04 06:14:53 UTC (rev 3942)
@@ -36,7 +36,6 @@
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLFunctionalDataPropertyAxiom;
-import org.semanticweb.owlapi.model.OWLLogicalAxiom;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
@@ -46,7 +45,6 @@
import com.google.common.collect.HashMultiset;
import com.google.common.collect.Multiset;
-import com.google.common.collect.Multisets;
public class OWLAxiomPatternFinder {
@@ -363,19 +361,22 @@
Multiset<OWLAxiom> allAxiomPatterns = HashMultiset.create();
int i = 1;
for (OntologyRepositoryEntry entry : entries) {
- System.out.print(i + ": ");
+ System.out.print(i++ + ": ");
URI uri = entry.getPhysicalURI();
// if(uri.toString().startsWith("http://rest.bioontology.org/bioportal/ontologies/download/42764")){
if (!ontologyProcessed(uri)) {
- System.out.println("Loading \"" + entry.getOntologyShortName() + "\" from "+ uri);
+ System.out.print("Loading \"" + entry.getOntologyShortName() + "\" from "+ uri);
try {
manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = manager.loadOntology(IRI.create(uri));
Multiset<OWLAxiom> axiomPatterns = HashMultiset.create();
Set<OWLAxiom> logicalAxioms = new HashSet<OWLAxiom>();
for (AxiomType<?> type : AxiomType.AXIOM_TYPES) {
- logicalAxioms.addAll(ontology.getAxioms(type, true));
+ if(type.isLogical()){
+ logicalAxioms.addAll(ontology.getAxioms(type, true));
+ }
}
+ System.out.println(" (" + logicalAxioms.size() + " axioms)");
for (OWLAxiom axiom : logicalAxioms) {
OWLAxiom renamedAxiom = renamer.rename(axiom);
axiomPatterns.add(renamedAxiom);
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/OntologyMatching.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/OntologyMatching.java 2013-05-04 05:50:47 UTC (rev 3941)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/OntologyMatching.java 2013-05-04 06:14:53 UTC (rev 3942)
@@ -315,7 +315,7 @@
logger.info("Done.");
if(performCrossValidation){
- org.dllearner.cli.CrossValidation cv = new org.dllearner.cli.CrossValidation(la, lp, rc, 5, false);
+// org.dllearner.cli.CrossValidation cv = new org.dllearner.cli.CrossValidation(la, lp, rc, 5, false);
} else {
//apply the learning algorithm
logger.info("Running learning algorithm...");
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-05-04 05:50:52
|
Revision: 3941
http://sourceforge.net/p/dl-learner/code/3941
Author: lorenz_b
Date: 2013-05-04 05:50:47 +0000 (Sat, 04 May 2013)
Log Message:
-----------
Some modifications in pattern detection script.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java
trunk/components-core/src/main/java/org/dllearner/kb/repository/tones/TONESRepository.java
trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
trunk/pom.xml
trunk/scripts/pom.xml
trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-05-03 08:49:17 UTC (rev 3940)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-05-04 05:50:47 UTC (rev 3941)
@@ -21,6 +21,7 @@
import java.util.Set;
import java.util.prefs.Preferences;
+import org.coode.owlapi.functionalparser.OWLFunctionalSyntaxOWLParser;
import org.dllearner.kb.dataset.OWLOntologyDataset;
import org.dllearner.kb.repository.OntologyRepository;
import org.dllearner.kb.repository.OntologyRepositoryEntry;
@@ -28,6 +29,7 @@
import org.ini4j.InvalidFileFormatException;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.OWLObjectRenderer;
+import org.semanticweb.owlapi.io.StringDocumentSource;
import org.semanticweb.owlapi.io.UnparsableOntologyException;
import org.semanticweb.owlapi.model.AxiomType;
import org.semanticweb.owlapi.model.IRI;
@@ -359,7 +361,9 @@
entries = entryList;
}
Multiset<OWLAxiom> allAxiomPatterns = HashMultiset.create();
+ int i = 1;
for (OntologyRepositoryEntry entry : entries) {
+ System.out.print(i + ": ");
URI uri = entry.getPhysicalURI();
// if(uri.toString().startsWith("http://rest.bioontology.org/bioportal/ontologies/download/42764")){
if (!ontologyProcessed(uri)) {
@@ -368,15 +372,19 @@
manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = manager.loadOntology(IRI.create(uri));
Multiset<OWLAxiom> axiomPatterns = HashMultiset.create();
- for (OWLLogicalAxiom axiom : ontology.getLogicalAxioms()) {
+ Set<OWLAxiom> logicalAxioms = new HashSet<OWLAxiom>();
+ for (AxiomType<?> type : AxiomType.AXIOM_TYPES) {
+ logicalAxioms.addAll(ontology.getAxioms(type, true));
+ }
+ for (OWLAxiom axiom : logicalAxioms) {
OWLAxiom renamedAxiom = renamer.rename(axiom);
axiomPatterns.add(renamedAxiom);
}
allAxiomPatterns.addAll(axiomPatterns);
addOntologyPatterns(uri, ontology, axiomPatterns);
- for (OWLAxiom owlAxiom : Multisets.copyHighestCountFirst(allAxiomPatterns).elementSet()) {
+// for (OWLAxiom owlAxiom : Multisets.copyHighestCountFirst(allAxiomPatterns).elementSet()) {
// System.out.println(owlAxiom + ": " + allAxiomPatterns.count(owlAxiom));
- }
+// }
manager.removeOntology(ontology);
} catch (OWLOntologyAlreadyExistsException e) {
e.printStackTrace();
@@ -384,6 +392,8 @@
e.printStackTrace();
addOntologyError(uri, e);
}
+ } else {
+ System.out.println("Already processed.");
}
}
@@ -401,5 +411,11 @@
org.coode.owlapi.functionalrenderer.OWLObjectRenderer r = new org.coode.owlapi.functionalrenderer.OWLObjectRenderer(man, ontology, sw);
axiom.accept(r);
System.out.println(sw.toString());
+ StringDocumentSource s = new StringDocumentSource("Ontology(<http://www.pattern.org>" + sw.toString() + ")");
+ OWLFunctionalSyntaxOWLParser p = new OWLFunctionalSyntaxOWLParser();
+ OWLOntology newOntology = man.createOntology();
+ p.parse(s, newOntology);
+ System.out.println(newOntology.getLogicalAxioms());
+
}
}
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java 2013-05-03 08:49:17 UTC (rev 3940)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java 2013-05-04 05:50:47 UTC (rev 3941)
@@ -341,14 +341,13 @@
@Override
public void visit(OWLSubPropertyChainOfAxiom axiom) {
+ List<OWLObjectPropertyExpression> renamedSubPropertyChain = new ArrayList<OWLObjectPropertyExpression>();
+ for (OWLObjectPropertyExpression owlObjectPropertyExpression : axiom.getPropertyChain()) {
+ renamedSubPropertyChain.add(expressionRenamer.rename(owlObjectPropertyExpression));
+ }
OWLObjectPropertyExpression superProperty = axiom.getSuperProperty();
superProperty = expressionRenamer.rename(superProperty);
- List<OWLObjectPropertyExpression> subPropertyChain = axiom.getPropertyChain();
- List<OWLObjectPropertyExpression> renamedSubPropertyChain = axiom.getPropertyChain();
- for (OWLObjectPropertyExpression owlObjectPropertyExpression : subPropertyChain) {
- renamedSubPropertyChain.add(expressionRenamer.rename(owlObjectPropertyExpression));
- }
- renamedAxiom = df.getOWLSubPropertyChainOfAxiom(subPropertyChain, superProperty);
+ renamedAxiom = df.getOWLSubPropertyChainOfAxiom(renamedSubPropertyChain, superProperty);
}
@Override
Modified: trunk/components-core/src/main/java/org/dllearner/kb/repository/tones/TONESRepository.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/kb/repository/tones/TONESRepository.java 2013-05-03 08:49:17 UTC (rev 3940)
+++ trunk/components-core/src/main/java/org/dllearner/kb/repository/tones/TONESRepository.java 2013-05-04 05:50:47 UTC (rev 3941)
@@ -10,14 +10,18 @@
import java.util.Collections;
import java.util.List;
+import org.apache.log4j.Logger;
import org.dllearner.kb.repository.OntologyRepository;
import org.dllearner.kb.repository.OntologyRepositoryEntry;
+import org.dllearner.kb.repository.bioportal.BioPortalRepository;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLOntologyIRIMapper;
import org.semanticweb.owlapi.util.OntologyIRIShortFormProvider;
public class TONESRepository implements OntologyRepository{
+ private static final Logger log = Logger.getLogger(TONESRepository.class);
+
private final String repositoryName = "TONES";
private final URI repositoryLocation = URI.create("http://owl.cs.manchester.ac.uk/repository");
@@ -91,6 +95,7 @@
catch (IOException e) {
e.printStackTrace();
}
+ log.info("Loaded " + entries.size() + " ontology entries from TONES.");
}
private class RepositoryEntry implements OntologyRepositoryEntry {
Modified: trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java
===================================================================
--- trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2013-05-03 08:49:17 UTC (rev 3940)
+++ trunk/interfaces/src/main/java/org/dllearner/cli/Enrichment.java 2013-05-04 05:50:47 UTC (rev 3941)
@@ -61,11 +61,14 @@
import joptsimple.OptionSpec;
import org.aksw.commons.jena_owlapi.Conversion;
+import org.apache.jena.riot.checker.CheckerLiterals;
+import org.apache.jena.riot.system.ErrorHandlerFactory;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.Level;
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.celoe.CELOE;
import org.dllearner.algorithms.properties.AsymmetricObjectPropertyAxiomLearner;
import org.dllearner.algorithms.properties.DataPropertyDomainAxiomLearner;
@@ -127,6 +130,7 @@
import org.dllearner.utilities.datastructures.SortedSetTuple;
import org.dllearner.utilities.examples.AutomaticNegativeExampleFinderSPARQL2;
import org.dllearner.utilities.owl.OWLAPIAxiomConvertVisitor;
+import org.dllearner.utilities.owl.OWLEntityTypeAdder;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
import org.semanticweb.owlapi.io.SystemOutDocumentTarget;
@@ -212,7 +216,7 @@
// restrict tested number of entities per type (only for testing purposes);
// should be set to -1 in production mode
- int maxEntitiesPerType = -1;
+ int maxEntitiesPerType = 5;
// number of axioms which will be learned/considered (only applies to
// some learners)
@@ -462,7 +466,7 @@
ksFragment = ksCached;
rc = rcCached;
} else {
- System.out.print("extracting fragment ... ");
+ 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();
@@ -471,6 +475,7 @@
model.add(cbd);
}
filter(model);
+ OWLEntityTypeAdder.addEntityTypes(model);
runTime = System.currentTimeMillis() - startTime;
System.out.println("done (" + model.size()+ " triples found in " + runTime + " ms)");
OWLOntology ontology = asOWLOntology(model);
@@ -768,6 +773,13 @@
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();
@@ -797,6 +809,7 @@
// fix URIs with spaces
Resource newSubject = (Resource) subject;
RDFNode newObject = object;
+ boolean validTriple = true;
if (subject.isURIResource()) {
String uri = subject.asResource().getURI();
if (uri.contains(" ")) {
@@ -814,8 +827,11 @@
if (lit.getDatatype() == null || lit.getDatatype().equals(XSD.STRING)) {
newObject = model.createLiteral("shortened", "en");
}
+ validTriple = CheckerLiterals.checkLiteral(object.asNode(), ErrorHandlerFactory.errorHandlerNoLogging, 1l, 1l);
}
- statementsToAdd.add(model.createStatement(newSubject, st.getPredicate(), newObject));
+ if(validTriple){
+ statementsToAdd.add(model.createStatement(newSubject, st.getPredicate(), newObject));
+ }
statementsToRemove.add(st);
}
Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml 2013-05-03 08:49:17 UTC (rev 3940)
+++ trunk/pom.xml 2013-05-04 05:50:47 UTC (rev 3941)
@@ -123,7 +123,8 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-distribution</artifactId>
- <version>3.4.4</version>
+ <version>3.4.3</version>
+ <type>pom</type>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
@@ -379,7 +380,7 @@
<dependency>
<groupId>mysql</groupId>
<artifactId>mysql-connector-java</artifactId>
- <version>5.1.13</version>
+ <version>5.1.24</version>
</dependency>
<!--GWT Dependencies -->
Modified: trunk/scripts/pom.xml
===================================================================
--- trunk/scripts/pom.xml 2013-05-03 08:49:17 UTC (rev 3940)
+++ trunk/scripts/pom.xml 2013-05-04 05:50:47 UTC (rev 3941)
@@ -116,6 +116,7 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-distribution</artifactId>
+ <type>pom</type>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-03 08:49:17 UTC (rev 3940)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-04 05:50:47 UTC (rev 3941)
@@ -11,17 +11,34 @@
import java.sql.SQLException;
import java.util.Arrays;
import java.util.Collection;
+import java.util.LinkedHashMap;
+import java.util.Map;
+import java.util.Map.Entry;
import java.util.prefs.Preferences;
+import org.coode.owlapi.functionalparser.OWLFunctionalSyntaxOWLParser;
import org.dllearner.algorithms.pattern.OWLAxiomPatternFinder;
import org.dllearner.kb.repository.OntologyRepository;
import org.dllearner.kb.repository.bioportal.BioPortalRepository;
import org.dllearner.kb.repository.tones.TONESRepository;
import org.ini4j.IniPreferences;
import org.ini4j.InvalidFileFormatException;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.OWLObjectRenderer;
+import org.semanticweb.owlapi.io.OWLParserException;
+import org.semanticweb.owlapi.io.StringDocumentSource;
+import org.semanticweb.owlapi.io.ToStringRenderer;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.UnloadableImportException;
+import uk.ac.manchester.cs.owl.owlapi.mansyntaxrenderer.ManchesterOWLSyntaxOWLObjectRendererImpl;
+import uk.ac.manchester.cs.owlapi.dlsyntax.DLSyntaxObjectRenderer;
+
public class OWLAxiomPatternDetectionEvaluation {
+ private OWLObjectRenderer axiomRenderer = new ManchesterOWLSyntaxOWLObjectRendererImpl();
private Connection conn;
public OWLAxiomPatternDetectionEvaluation() {
@@ -59,6 +76,9 @@
//create statistics for the repositories
makeRepositoryStatistics(repositories);
+
+ //get top n TBox, RBox and ABox patterns
+ makePatternStatistics(repositories);
}
private void analyze(Collection<OntologyRepository> repositories){
@@ -69,6 +89,35 @@
}
}
+ private void makePatternStatistics(Collection<OntologyRepository> repositories){
+ int n = 10;
+ String latex = "";
+ Map<OWLAxiom, Integer> topNTBoxAxiomPatterns = getTopNTBoxAxiomPatterns(n);
+ latex += asLatex("Total TBox", topNTBoxAxiomPatterns) + "\n\n";
+ Map<OWLAxiom, Integer> topNRBoxAxiomPatterns = getTopNRBoxAxiomPatterns(n);
+ latex += asLatex("Total RBox", topNRBoxAxiomPatterns) + "\n\n";
+ Map<OWLAxiom, Integer> topNABoxAxiomPatterns = getTopNABoxAxiomPatterns(n);
+ latex += asLatex("Total ABox", topNABoxAxiomPatterns) + "\n\n";
+
+ //get top n TBox, RBox and ABox patterns by repository
+
+ Map<OntologyRepository, Map<OWLAxiom, Integer>> topNTBoxAxiomPatternsByRepository = getTopNTBoxAxiomPatterns(repositories, n);
+ Map<OntologyRepository, Map<OWLAxiom, Integer>> topNRBoxAxiomPatternsByRepository = getTopNRBoxAxiomPatterns(repositories, n);
+ Map<OntologyRepository, Map<OWLAxiom, Integer>> topNABoxAxiomPatternsByRepository = getTopNABoxAxiomPatterns(repositories, n);
+ for (OntologyRepository repository : repositories) {
+ latex += asLatex(repository.getName() + " TBox", topNTBoxAxiomPatternsByRepository.get(repository)) + "\n\n";
+ latex += asLatex(repository.getName() + " RBox", topNRBoxAxiomPatternsByRepository.get(repository)) + "\n\n";
+ latex += asLatex(repository.getName() + " ABox", topNABoxAxiomPatternsByRepository.get(repository)) + "\n\n";
+ }
+ try {
+ new FileOutputStream("pattern-statistics.tex").write(latex.getBytes());
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
private void makeRepositoryStatistics(Collection<OntologyRepository> repositories){
String latexTable = "\\begin{tabular}{lrr|rrr|rrr|rrr|rrr}";
latexTable += "\\toprule\n";
@@ -147,7 +196,7 @@
ps.setString(1, repository.getName());
minNumberOfAboxAxioms = count(ps);
//get max number of abox axioms
- ps = conn.prepareStatement("SELECT MAX(tbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps = conn.prepareStatement("SELECT MAX(abox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
ps.setString(1, repository.getName());
maxNumberOfAboxAxioms = count(ps);
//get avg number of abox axioms
@@ -186,6 +235,193 @@
}
}
+ private String asLatex(String title, Map<OWLAxiom, Integer> topN){
+ String latexTable = "\\begin{table}\n";
+ latexTable += "\\begin{tabular}{lr}\n";
+ latexTable += "\\toprule\n";
+ latexTable += "Pattern & Frequency\\\\\\midrule\n";
+
+ for (Entry<OWLAxiom, Integer> entry : topN.entrySet()) {
+ OWLAxiom axiom = entry.getKey();
+ Integer frequency = entry.getValue();
+
+ latexTable += axiomRenderer.render(axiom) + " & " + frequency + "\\\\\n";
+
+ }
+ latexTable += "\\bottomrule\\end{tabular}\n";
+ latexTable += "\\caption{" + title + "}\n";
+ latexTable += "\\end{table}\n";
+ return latexTable;
+ }
+
+ private Map<OWLAxiom, Integer> getTopNTBoxAxiomPatterns(int n){
+ Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
+ PreparedStatement ps;
+ ResultSet rs;
+ try {
+ ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
+ "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
+ "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND P.axiom_type=?) " +
+ "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
+ ps.setString(1, "TBox");
+ ps.setInt(2, n);
+ rs = ps.executeQuery();
+ while(rs.next()){
+ topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
+ }
+ } catch(SQLException e){
+ e.printStackTrace();
+ }
+ return topN;
+ }
+
+ private Map<OntologyRepository, Map<OWLAxiom, Integer>> getTopNTBoxAxiomPatterns(Collection<OntologyRepository> repositories, int n){
+ Map<OntologyRepository, Map<OWLAxiom, Integer>> topNByRepository = new LinkedHashMap<OntologyRepository, Map<OWLAxiom,Integer>>();
+ PreparedStatement ps;
+ ResultSet rs;
+ //for each repository
+ for (OntologyRepository repository : repositories) {
+ Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
+ try {
+ //get number of ontologies
+ ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
+ "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
+ "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND O.repository=? AND P.axiom_type=?) " +
+ "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
+ ps.setString(1, repository.getName());
+ ps.setString(2, "TBox");
+ ps.setInt(3, n);
+ rs = ps.executeQuery();
+ while(rs.next()){
+ topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
+ }
+ } catch(SQLException e){
+ e.printStackTrace();
+ }
+ topNByRepository.put(repository, topN);
+ }
+ return topNByRepository;
+ }
+
+ private Map<OWLAxiom, Integer> getTopNRBoxAxiomPatterns(int n){
+ Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
+ PreparedStatement ps;
+ ResultSet rs;
+ try {
+ ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
+ "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
+ "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND P.axiom_type=?) " +
+ "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
+ ps.setString(1, "RBox");
+ ps.setInt(2, n);
+ rs = ps.executeQuery();
+ while(rs.next()){
+ topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
+ }
+ } catch(SQLException e){
+ e.printStackTrace();
+ }
+ return topN;
+ }
+
+ private Map<OntologyRepository, Map<OWLAxiom, Integer>> getTopNRBoxAxiomPatterns(Collection<OntologyRepository> repositories, int n){
+ Map<OntologyRepository, Map<OWLAxiom, Integer>> topNByRepository = new LinkedHashMap<OntologyRepository, Map<OWLAxiom,Integer>>();
+ PreparedStatement ps;
+ ResultSet rs;
+ //for each repository
+ for (OntologyRepository repository : repositories) {
+ Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
+ try {
+ //get number of ontologies
+ ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
+ "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
+ "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND O.repository=? AND P.axiom_type=?) " +
+ "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
+ ps.setString(1, repository.getName());
+ ps.setString(2, "RBox");
+ ps.setInt(3, n);
+ rs = ps.executeQuery();
+ while(rs.next()){
+ topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
+ }
+ } catch(SQLException e){
+ e.printStackTrace();
+ }
+ topNByRepository.put(repository, topN);
+ }
+ return topNByRepository;
+ }
+
+ private Map<OWLAxiom, Integer> getTopNABoxAxiomPatterns(int n){
+ Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
+ PreparedStatement ps;
+ ResultSet rs;
+ try {
+ ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
+ "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
+ "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND P.axiom_type=?) " +
+ "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
+ ps.setString(1, "ABox");
+ ps.setInt(2, n);
+ rs = ps.executeQuery();
+ while(rs.next()){
+ topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
+ }
+ } catch(SQLException e){
+ e.printStackTrace();
+ }
+ return topN;
+ }
+
+ private Map<OntologyRepository, Map<OWLAxiom, Integer>> getTopNABoxAxiomPatterns(Collection<OntologyRepository> repositories, int n){
+ Map<OntologyRepository, Map<OWLAxiom, Integer>> topNByRepository = new LinkedHashMap<OntologyRepository, Map<OWLAxiom,Integer>>();
+ PreparedStatement ps;
+ ResultSet rs;
+ //for each repository
+ for (OntologyRepository repository : repositories) {
+ Map<OWLAxiom, Integer> topN = new LinkedHashMap<OWLAxiom, Integer>();
+ try {
+ //get number of ontologies
+ ps = conn.prepareStatement("SELECT pattern,SUM(occurrences) FROM " +
+ "Ontology_Pattern OP, Pattern P, Ontology O WHERE " +
+ "(P.id=OP.pattern_id AND O.id=OP.ontology_id AND O.repository=? AND P.axiom_type=?) " +
+ "GROUP BY P.id ORDER BY SUM(`OP`.`occurrences`) DESC LIMIT ?");
+ ps.setString(1, repository.getName());
+ ps.setString(2, "ABox");
+ ps.setInt(3, n);
+ rs = ps.executeQuery();
+ while(rs.next()){
+ topN.put(asOWLAxiom(rs.getString(1)), rs.getInt(2));
+ }
+ } catch(SQLException e){
+ e.printStackTrace();
+ }
+ topNByRepository.put(repository, topN);
+ }
+ return topNByRepository;
+ }
+
+ private OWLAxiom asOWLAxiom(String functionalSyntaxAxiomString){
+ try {
+ StringDocumentSource s = new StringDocumentSource("Ontology(<http://www.pattern.org>" + functionalSyntaxAxiomString + ")");
+ OWLFunctionalSyntaxOWLParser p = new OWLFunctionalSyntaxOWLParser();
+ OWLOntology newOntology = OWLManager.createOWLOntologyManager().createOntology();
+ p.parse(s, newOntology);
+ if(!newOntology.getLogicalAxioms().isEmpty()){
+ return newOntology.getLogicalAxioms().iterator().next();
+ }
+ } catch (UnloadableImportException e) {
+ e.printStackTrace();
+ } catch (OWLOntologyCreationException e) {
+ e.printStackTrace();
+ } catch (OWLParserException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ return null;
+ }
+
private int count(PreparedStatement ps) throws SQLException{
ResultSet rs = ps.executeQuery();
rs.next();
@@ -193,6 +429,7 @@
}
public static void main(String[] args) throws Exception {
+// ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
new OWLAxiomPatternDetectionEvaluation().run(Arrays.asList(
new TONESRepository(), new BioPortalRepository()));
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lor...@us...> - 2013-05-03 08:49:20
|
Revision: 3940
http://sourceforge.net/p/dl-learner/code/3940
Author: lorenz_b
Date: 2013-05-03 08:49:17 +0000 (Fri, 03 May 2013)
Log Message:
-----------
Added axiomtype column.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-05-03 08:48:11 UTC (rev 3939)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-05-03 08:49:17 UTC (rev 3940)
@@ -81,7 +81,7 @@
private OWLObjectRenderer axiomRenderer = new ManchesterOWLSyntaxOWLObjectRendererImpl();
- private boolean randomOrder = true;
+ private boolean randomOrder = false;
public OWLAxiomPatternFinder(OWLOntologyDataset dataset) {
@@ -113,7 +113,7 @@
", abox_axioms, classes, object_properties, data_properties, individuals) VALUES(?,?,?,?,?,?,?,?,?,?,?)");
insertOntologyErrorPs = conn.prepareStatement("INSERT INTO Ontology (url, iri, repository) VALUES(?,?,?)");
selectPatternIdPs = conn.prepareStatement("SELECT id FROM Pattern WHERE pattern=?");
- insertPatternIdPs = conn.prepareStatement("INSERT INTO Pattern (pattern,pattern_pretty) VALUES(?,?)");
+ insertPatternIdPs = conn.prepareStatement("INSERT INTO Pattern (pattern,pattern_pretty,axiom_type) VALUES(?,?,?)");
insertOntologyPatternPs = conn.prepareStatement("INSERT INTO Ontology_Pattern (ontology_id, pattern_id, occurrences) VALUES(?,?,?)");
} catch (SQLException e) {
e.printStackTrace();
@@ -168,6 +168,7 @@
+ "id MEDIUMINT NOT NULL AUTO_INCREMENT,"
+ "pattern TEXT NOT NULL,"
+ "pattern_pretty TEXT NOT NULL,"
+ + "axiom_type VARCHAR(15) NOT NULL,"
+ "PRIMARY KEY(id),"
+ "INDEX(pattern(8000))) DEFAULT CHARSET=utf8");
@@ -216,9 +217,10 @@
try {
insertPatternIdPs.setString(1, axiomString);
insertPatternIdPs.setString(2, axiomRenderer.render(axiom));
+ insertPatternIdPs.setString(3, getAxiomType(axiom));
insertPatternIdPs.execute();
} catch (SQLException e) {
- System.out.println(axiomString.length());
+ System.err.println("Pattern too long for database?" + axiomString.length());
e.printStackTrace();
}
//get the auto generated ID
@@ -234,6 +236,22 @@
return -1;
}
+ private String getAxiomType(OWLAxiom axiom){
+ AxiomType<?> type = axiom.getAxiomType();
+ String s;
+ if(AxiomType.TBoxAxiomTypes.contains(type)){
+ s = "TBox";
+ } else if(AxiomType.RBoxAxiomTypes.contains(type)){
+ s = "RBox";
+ } else if(AxiomType.ABoxAxiomTypes.contains(type)){
+ s = "ABox";
+ } else {System.out.println(axiom + "-" + type);
+ //should not happen
+ s="Non-Logical";
+ }
+ return s;
+ }
+
private boolean ontologyProcessed(URI uri){
//check if ontology was already processed
try {
@@ -287,13 +305,11 @@
insertOntologyPs.setString(1, url);
insertOntologyPs.setString(2, ontologyIRI);
insertOntologyPs.setString(3, repository.getName());
- Set<OWLAxiom> logicalAxioms = new HashSet<OWLAxiom>();
- logicalAxioms.addAll(ontology.getLogicalAxioms());
- Set<OWLAxiom> tbox = AxiomType.getAxiomsOfTypes(logicalAxioms, new ArrayList<AxiomType>(AxiomType.TBoxAxiomTypes).toArray(new AxiomType[AxiomType.TBoxAxiomTypes.size()]));
- Set<OWLAxiom> rbox = AxiomType.getAxiomsOfTypes(logicalAxioms, new ArrayList<AxiomType>(AxiomType.RBoxAxiomTypes).toArray(new AxiomType[AxiomType.RBoxAxiomTypes.size()]));
- Set<OWLAxiom> abox = AxiomType.getAxiomsOfTypes(logicalAxioms, new ArrayList<AxiomType>(AxiomType.ABoxAxiomTypes).toArray(new AxiomType[AxiomType.ABoxAxiomTypes.size()]));
+ Set<OWLAxiom> tbox = ontology.getTBoxAxioms(true);
+ Set<OWLAxiom> rbox = ontology.getRBoxAxioms(true);
+ Set<OWLAxiom> abox = ontology.getABoxAxioms(true);
- insertOntologyPs.setInt(4, ontology.getLogicalAxiomCount());
+ insertOntologyPs.setInt(4, tbox.size() + rbox.size() + abox.size());
insertOntologyPs.setInt(5, tbox.size());
insertOntologyPs.setInt(6, rbox.size());
insertOntologyPs.setInt(7, abox.size());
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java 2013-05-03 08:48:11 UTC (rev 3939)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomRenamer.java 2013-05-03 08:49:17 UTC (rev 3940)
@@ -48,6 +48,7 @@
import org.semanticweb.owlapi.model.OWLObjectPropertyDomainAxiom;
import org.semanticweb.owlapi.model.OWLObjectPropertyExpression;
import org.semanticweb.owlapi.model.OWLObjectPropertyRangeAxiom;
+import org.semanticweb.owlapi.model.OWLPropertyExpression;
import org.semanticweb.owlapi.model.OWLReflexiveObjectPropertyAxiom;
import org.semanticweb.owlapi.model.OWLSameIndividualAxiom;
import org.semanticweb.owlapi.model.OWLSubAnnotationPropertyOfAxiom;
@@ -86,27 +87,14 @@
}
@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(OWLNegativeObjectPropertyAssertionAxiom axiom) {
+ OWLObjectPropertyExpression property = axiom.getProperty();
+ property = expressionRenamer.rename(property);
+ OWLIndividual subject = axiom.getSubject();
+ subject = expressionRenamer.rename(subject);
+ OWLIndividual object = axiom.getObject();
+ object = expressionRenamer.rename(object);
+ renamedAxiom = df.getOWLNegativeObjectPropertyAssertionAxiom(property, subject, object);
}
@Override
@@ -163,7 +151,13 @@
@Override
public void visit(OWLNegativeDataPropertyAssertionAxiom axiom) {
-// axiom.
+ OWLDataPropertyExpression property = axiom.getProperty();
+ property = expressionRenamer.rename(property);
+ OWLIndividual subject = axiom.getSubject();
+ subject = expressionRenamer.rename(subject);
+ OWLLiteral object = axiom.getObject();
+ object = expressionRenamer.rename(object);
+ renamedAxiom = df.getOWLNegativeDataPropertyAssertionAxiom(property, subject, object);
}
@Override
@@ -347,6 +341,14 @@
@Override
public void visit(OWLSubPropertyChainOfAxiom axiom) {
+ OWLObjectPropertyExpression superProperty = axiom.getSuperProperty();
+ superProperty = expressionRenamer.rename(superProperty);
+ List<OWLObjectPropertyExpression> subPropertyChain = axiom.getPropertyChain();
+ List<OWLObjectPropertyExpression> renamedSubPropertyChain = axiom.getPropertyChain();
+ for (OWLObjectPropertyExpression owlObjectPropertyExpression : subPropertyChain) {
+ renamedSubPropertyChain.add(expressionRenamer.rename(owlObjectPropertyExpression));
+ }
+ renamedAxiom = df.getOWLSubPropertyChainOfAxiom(subPropertyChain, superProperty);
}
@Override
@@ -360,6 +362,14 @@
@Override
public void visit(OWLHasKeyAxiom axiom) {
+ OWLClassExpression classExpression = axiom.getClassExpression();
+ classExpression = expressionRenamer.rename(classExpression);
+ Set<OWLPropertyExpression<?, ?>> propertyExpressions = axiom.getPropertyExpressions();
+ Set<OWLPropertyExpression<?, ?>> renamedPropertyExpressions = new HashSet<OWLPropertyExpression<?,?>>();
+ for (OWLPropertyExpression<?, ?> owlPropertyExpression : propertyExpressions) {
+ renamedPropertyExpressions.add(expressionRenamer.rename(owlPropertyExpression));
+ }
+ renamedAxiom = df.getOWLHasKeyAxiom(classExpression, renamedPropertyExpressions);
}
@Override
@@ -370,6 +380,23 @@
public void visit(SWRLRule axiom) {
}
-
+ @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) {
+ }
}
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|
|
From: <lor...@us...> - 2013-05-03 08:48:20
|
Revision: 3939
http://sourceforge.net/p/dl-learner/code/3939
Author: lorenz_b
Date: 2013-05-03 08:48:11 +0000 (Fri, 03 May 2013)
Log Message:
-----------
Continued script.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-03 07:56:49 UTC (rev 3938)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-03 08:48:11 UTC (rev 3939)
@@ -71,10 +71,10 @@
private void makeRepositoryStatistics(Collection<OntologyRepository> repositories){
String latexTable = "\\begin{tabular}{lrr|rrr|rrr|rrr|rrr}";
- latexTable += "\\toprule";
- latexTable += "Repository & \\multicolumn{2}{c}{\\#Ontologies} & \\multicolumn{12}{c}{\\#Axioms} \\\\";
- latexTable += "& Total & Error & \\multicolumn{3}{c}{Total} & \\multicolumn{3}{c}{Tbox} & \\multicolumn{3}{c}{RBox} & \\multicolumn{3}{c}{Abox} \\\\\\midrule";
- latexTable += "& & & Min & Avg & Max & Min & Avg & Max & Min & Avg & Max & Min & Avg & Max \\\\\\midrule";
+ latexTable += "\\toprule\n";
+ latexTable += "Repository & \\multicolumn{2}{c}{\\#Ontologies} & \\multicolumn{12}{c}{\\#Axioms} \\\\\n";
+ latexTable += "& Total & Error & \\multicolumn{3}{c}{Total} & \\multicolumn{3}{c}{Tbox} & \\multicolumn{3}{c}{RBox} & \\multicolumn{3}{c}{Abox} \\\\\\midrule\n";
+ latexTable += "& & & Min & Avg & Max & Min & Avg & Max & Min & Avg & Max & Min & Avg & Max \\\\\\midrule\n";
PreparedStatement ps;
@@ -170,7 +170,7 @@
maxNumberOfRboxAxioms + "&" +
minNumberOfAboxAxioms + "&" +
avgNumberOfAboxAxioms + "&" +
- maxNumberOfAboxAxioms + "\\\\";
+ maxNumberOfAboxAxioms + "\\\\\n";
} catch (SQLException e) {
e.printStackTrace();
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|
|
From: <lor...@us...> - 2013-05-03 07:56:55
|
Revision: 3938
http://sourceforge.net/p/dl-learner/code/3938
Author: lorenz_b
Date: 2013-05-03 07:56:49 +0000 (Fri, 03 May 2013)
Log Message:
-----------
Updated script for pattern detection evaluation.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-03 07:32:44 UTC (rev 3937)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-03 07:56:49 UTC (rev 3938)
@@ -38,7 +38,7 @@
String dbPass = prefs.node("database").get("pass", null);
Class.forName("com.mysql.jdbc.Driver");
- String url = "jdbc:mysql://" + dbServer + "/" + dbName;System.out.println(url);
+ String url = "jdbc:mysql://" + dbServer + "/" + dbName;
conn = DriverManager.getConnection(url, dbUser, dbPass);
} catch (ClassNotFoundException e) {
e.printStackTrace();
@@ -101,73 +101,59 @@
//get number of ontologies
ps = conn.prepareStatement("SELECT COUNT(*) FROM Ontology WHERE repository=?");
ps.setString(1, repository.getName());
- rs = ps.executeQuery();
- numberOfOntologies = rs.getInt(1);
+ numberOfOntologies = count(ps);
//get number of error causing ontologies
ps = conn.prepareStatement("SELECT COUNT(*) FROM Ontology WHERE repository=? AND iri LIKE 'ERROR%'");
ps.setString(1, repository.getName());
- rs = ps.executeQuery();
- numberOfErrorOntologies = rs.getInt(1);
+ numberOfErrorOntologies = count(ps);
//get min number of logical axioms
ps = conn.prepareStatement("SELECT MIN(logical_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
ps.setString(1, repository.getName());
- rs = ps.executeQuery();
- minNumberOfLogicalAxioms = rs.getInt(1);
+ minNumberOfLogicalAxioms = count(ps);
//get max number of logical axioms
ps = conn.prepareStatement("SELECT MAX(logical_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
ps.setString(1, repository.getName());
- rs = ps.executeQuery();
- maxNumberOfLogicalAxioms = rs.getInt(1);
+ maxNumberOfLogicalAxioms = count(ps);
//get avg number of logical axioms
ps = conn.prepareStatement("SELECT AVG(logical_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
ps.setString(1, repository.getName());
- rs = ps.executeQuery();
- avgNumberOfLogicalAxioms = rs.getInt(1);
+ avgNumberOfLogicalAxioms = count(ps);
//get min number of tbox axioms
ps = conn.prepareStatement("SELECT MIN(tbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
ps.setString(1, repository.getName());
- rs = ps.executeQuery();
- minNumberOfTboxAxioms = rs.getInt(1);
+ minNumberOfTboxAxioms = count(ps);
//get max number of tbox axioms
ps = conn.prepareStatement("SELECT MAX(tbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
ps.setString(1, repository.getName());
- rs = ps.executeQuery();
- maxNumberOfTboxAxioms = rs.getInt(1);
+ maxNumberOfTboxAxioms = count(ps);
//get avg number of tbox axioms
ps = conn.prepareStatement("SELECT AVG(tbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
ps.setString(1, repository.getName());
- rs = ps.executeQuery();
- avgNumberOfTboxAxioms = rs.getInt(1);
+ avgNumberOfTboxAxioms = count(ps);
//get min number of rbox axioms
ps = conn.prepareStatement("SELECT MIN(rbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
ps.setString(1, repository.getName());
- rs = ps.executeQuery();
- minNumberOfRboxAxioms = rs.getInt(1);
+ minNumberOfRboxAxioms = count(ps);
//get max number of rbox axioms
ps = conn.prepareStatement("SELECT MAX(rbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
ps.setString(1, repository.getName());
- rs = ps.executeQuery();
- maxNumberOfRboxAxioms = rs.getInt(1);
+ maxNumberOfRboxAxioms = count(ps);
//get avg number of rbox axioms
ps = conn.prepareStatement("SELECT AVG(rbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
ps.setString(1, repository.getName());
- rs = ps.executeQuery();
- avgNumberOfRboxAxioms = rs.getInt(1);
+ avgNumberOfRboxAxioms = count(ps);
//get min number of abox axioms
ps = conn.prepareStatement("SELECT MIN(abox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
ps.setString(1, repository.getName());
- rs = ps.executeQuery();
- minNumberOfAboxAxioms = rs.getInt(1);
+ minNumberOfAboxAxioms = count(ps);
//get max number of abox axioms
ps = conn.prepareStatement("SELECT MAX(tbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
ps.setString(1, repository.getName());
- rs = ps.executeQuery();
- maxNumberOfAboxAxioms = rs.getInt(1);
+ maxNumberOfAboxAxioms = count(ps);
//get avg number of abox axioms
ps = conn.prepareStatement("SELECT AVG(abox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
ps.setString(1, repository.getName());
- rs = ps.executeQuery();
- avgNumberOfAboxAxioms = rs.getInt(1);
+ avgNumberOfAboxAxioms = count(ps);
latexTable +=
repository.getName() + "&" +
@@ -200,6 +186,12 @@
}
}
+ private int count(PreparedStatement ps) throws SQLException{
+ ResultSet rs = ps.executeQuery();
+ rs.next();
+ return rs.getInt(1);
+ }
+
public static void main(String[] args) throws Exception {
new OWLAxiomPatternDetectionEvaluation().run(Arrays.asList(
new TONESRepository(), new BioPortalRepository()));
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|
|
From: <lor...@us...> - 2013-05-03 07:32:48
|
Revision: 3937
http://sourceforge.net/p/dl-learner/code/3937
Author: lorenz_b
Date: 2013-05-03 07:32:44 +0000 (Fri, 03 May 2013)
Log Message:
-----------
Added script for pattern detection evaluation.
Added Paths:
-----------
trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
Added: trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/OWLAxiomPatternDetectionEvaluation.java 2013-05-03 07:32:44 UTC (rev 3937)
@@ -0,0 +1,209 @@
+package org.dllearner.scripts;
+
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.prefs.Preferences;
+
+import org.dllearner.algorithms.pattern.OWLAxiomPatternFinder;
+import org.dllearner.kb.repository.OntologyRepository;
+import org.dllearner.kb.repository.bioportal.BioPortalRepository;
+import org.dllearner.kb.repository.tones.TONESRepository;
+import org.ini4j.IniPreferences;
+import org.ini4j.InvalidFileFormatException;
+
+public class OWLAxiomPatternDetectionEvaluation {
+
+ private Connection conn;
+
+ public OWLAxiomPatternDetectionEvaluation() {
+ initDBConnection();
+ }
+
+ private void initDBConnection() {
+ try {
+ InputStream is = this.getClass().getClassLoader().getResourceAsStream("db_settings.ini");
+ Preferences prefs = new IniPreferences(is);
+ String dbServer = prefs.node("database").get("server", null);
+ String dbName = prefs.node("database").get("name", null);
+ String dbUser = prefs.node("database").get("user", null);
+ String dbPass = prefs.node("database").get("pass", null);
+
+ Class.forName("com.mysql.jdbc.Driver");
+ String url = "jdbc:mysql://" + dbServer + "/" + dbName;System.out.println(url);
+ conn = DriverManager.getConnection(url, dbUser, dbPass);
+ } catch (ClassNotFoundException e) {
+ e.printStackTrace();
+ } catch (SQLException e) {
+ e.printStackTrace();
+ } catch (InvalidFileFormatException e) {
+ e.printStackTrace();
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ public void run(Collection<OntologyRepository> repositories){
+ //analyze repositories
+ analyze(repositories);
+
+ //create statistics for the repositories
+ makeRepositoryStatistics(repositories);
+ }
+
+ private void analyze(Collection<OntologyRepository> repositories){
+ for (OntologyRepository repository : repositories) {
+ repository.initialize();
+ OWLAxiomPatternFinder patternFinder = new OWLAxiomPatternFinder(repository, conn);
+ patternFinder.start();
+ }
+ }
+
+ private void makeRepositoryStatistics(Collection<OntologyRepository> repositories){
+ String latexTable = "\\begin{tabular}{lrr|rrr|rrr|rrr|rrr}";
+ latexTable += "\\toprule";
+ latexTable += "Repository & \\multicolumn{2}{c}{\\#Ontologies} & \\multicolumn{12}{c}{\\#Axioms} \\\\";
+ latexTable += "& Total & Error & \\multicolumn{3}{c}{Total} & \\multicolumn{3}{c}{Tbox} & \\multicolumn{3}{c}{RBox} & \\multicolumn{3}{c}{Abox} \\\\\\midrule";
+ latexTable += "& & & Min & Avg & Max & Min & Avg & Max & Min & Avg & Max & Min & Avg & Max \\\\\\midrule";
+
+
+ PreparedStatement ps;
+ ResultSet rs;
+
+ int numberOfOntologies;
+ int numberOfErrorOntologies;
+ int minNumberOfLogicalAxioms;
+ int maxNumberOfLogicalAxioms;
+ int avgNumberOfLogicalAxioms;
+ int minNumberOfTboxAxioms;
+ int maxNumberOfTboxAxioms;
+ int avgNumberOfTboxAxioms;
+ int minNumberOfRboxAxioms;
+ int maxNumberOfRboxAxioms;
+ int avgNumberOfRboxAxioms;
+ int minNumberOfAboxAxioms;
+ int maxNumberOfAboxAxioms;
+ int avgNumberOfAboxAxioms;
+
+ //for each repository
+ for (OntologyRepository repository : repositories) {
+ try {
+ //get number of ontologies
+ ps = conn.prepareStatement("SELECT COUNT(*) FROM Ontology WHERE repository=?");
+ ps.setString(1, repository.getName());
+ rs = ps.executeQuery();
+ numberOfOntologies = rs.getInt(1);
+ //get number of error causing ontologies
+ ps = conn.prepareStatement("SELECT COUNT(*) FROM Ontology WHERE repository=? AND iri LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ rs = ps.executeQuery();
+ numberOfErrorOntologies = rs.getInt(1);
+ //get min number of logical axioms
+ ps = conn.prepareStatement("SELECT MIN(logical_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ rs = ps.executeQuery();
+ minNumberOfLogicalAxioms = rs.getInt(1);
+ //get max number of logical axioms
+ ps = conn.prepareStatement("SELECT MAX(logical_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ rs = ps.executeQuery();
+ maxNumberOfLogicalAxioms = rs.getInt(1);
+ //get avg number of logical axioms
+ ps = conn.prepareStatement("SELECT AVG(logical_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ rs = ps.executeQuery();
+ avgNumberOfLogicalAxioms = rs.getInt(1);
+ //get min number of tbox axioms
+ ps = conn.prepareStatement("SELECT MIN(tbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ rs = ps.executeQuery();
+ minNumberOfTboxAxioms = rs.getInt(1);
+ //get max number of tbox axioms
+ ps = conn.prepareStatement("SELECT MAX(tbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ rs = ps.executeQuery();
+ maxNumberOfTboxAxioms = rs.getInt(1);
+ //get avg number of tbox axioms
+ ps = conn.prepareStatement("SELECT AVG(tbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ rs = ps.executeQuery();
+ avgNumberOfTboxAxioms = rs.getInt(1);
+ //get min number of rbox axioms
+ ps = conn.prepareStatement("SELECT MIN(rbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ rs = ps.executeQuery();
+ minNumberOfRboxAxioms = rs.getInt(1);
+ //get max number of rbox axioms
+ ps = conn.prepareStatement("SELECT MAX(rbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ rs = ps.executeQuery();
+ maxNumberOfRboxAxioms = rs.getInt(1);
+ //get avg number of rbox axioms
+ ps = conn.prepareStatement("SELECT AVG(rbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ rs = ps.executeQuery();
+ avgNumberOfRboxAxioms = rs.getInt(1);
+ //get min number of abox axioms
+ ps = conn.prepareStatement("SELECT MIN(abox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ rs = ps.executeQuery();
+ minNumberOfAboxAxioms = rs.getInt(1);
+ //get max number of abox axioms
+ ps = conn.prepareStatement("SELECT MAX(tbox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ rs = ps.executeQuery();
+ maxNumberOfAboxAxioms = rs.getInt(1);
+ //get avg number of abox axioms
+ ps = conn.prepareStatement("SELECT AVG(abox_axioms) FROM Ontology WHERE repository=? AND iri NOT LIKE 'ERROR%'");
+ ps.setString(1, repository.getName());
+ rs = ps.executeQuery();
+ avgNumberOfAboxAxioms = rs.getInt(1);
+
+ latexTable +=
+ repository.getName() + "&" +
+ numberOfOntologies + "&" +
+ numberOfErrorOntologies + "&" +
+ minNumberOfLogicalAxioms + "&" +
+ avgNumberOfLogicalAxioms + "&" +
+ maxNumberOfLogicalAxioms + "&" +
+ minNumberOfTboxAxioms + "&" +
+ avgNumberOfTboxAxioms + "&" +
+ maxNumberOfTboxAxioms + "&" +
+ minNumberOfRboxAxioms + "&" +
+ avgNumberOfRboxAxioms + "&" +
+ maxNumberOfRboxAxioms + "&" +
+ minNumberOfAboxAxioms + "&" +
+ avgNumberOfAboxAxioms + "&" +
+ maxNumberOfAboxAxioms + "\\\\";
+
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ }
+ latexTable += "\\bottomrule\\end{tabular}";
+ try {
+ new FileOutputStream("repository-statistics.tex").write(latexTable.getBytes());
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ public static void main(String[] args) throws Exception {
+ new OWLAxiomPatternDetectionEvaluation().run(Arrays.asList(
+ new TONESRepository(), new BioPortalRepository()));
+ }
+
+
+}
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|
|
From: <lor...@us...> - 2013-05-03 07:31:42
|
Revision: 3936
http://sourceforge.net/p/dl-learner/code/3936
Author: lorenz_b
Date: 2013-05-03 07:31:37 +0000 (Fri, 03 May 2013)
Log Message:
-----------
Commented tests.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java
trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/SetManipulation.java
trunk/components-core/src/test/java/org/dllearner/algorithms/pattern/OWLPatternDetectionTest.java
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-05-02 10:57:42 UTC (rev 3935)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/pattern/OWLAxiomPatternFinder.java 2013-05-03 07:31:37 UTC (rev 3936)
@@ -93,6 +93,19 @@
dataFactory = manager.getOWLDataFactory();
initDBConnection();
+ prepare();
+ }
+
+ public OWLAxiomPatternFinder(OntologyRepository repository, Connection conn) {
+ this.repository = repository;
+ this.conn = conn;
+ manager = OWLManager.createOWLOntologyManager();
+ dataFactory = manager.getOWLDataFactory();
+
+ prepare();
+ }
+
+ private void prepare(){
createTables();
try {
selectOntologyIdPs = conn.prepareStatement("SELECT id FROM Ontology WHERE url=?");
Modified: trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java 2013-05-02 10:57:42 UTC (rev 3935)
+++ trunk/components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java 2013-05-03 07:31:37 UTC (rev 3936)
@@ -45,6 +45,7 @@
import org.dllearner.core.KnowledgeSource;
import org.dllearner.core.config.ConfigOption;
import org.dllearner.core.owl.Axiom;
+import org.dllearner.core.owl.ClassHierarchy;
import org.dllearner.core.owl.Constant;
import org.dllearner.core.owl.Datatype;
import org.dllearner.core.owl.DatatypeProperty;
@@ -59,6 +60,7 @@
import org.dllearner.core.owl.Thing;
import org.dllearner.core.owl.TypedConstant;
import org.dllearner.core.owl.UntypedConstant;
+import org.dllearner.kb.OWLAPIOntology;
import org.dllearner.kb.OWLOntologyKnowledgeSource;
import org.dllearner.utilities.owl.ConceptComparator;
import org.dllearner.utilities.owl.DLLearnerDescriptionConvertVisitor;
@@ -938,7 +940,11 @@
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
try {
OWLOntology ontology = manager.loadOntologyFromOntologyDocument(IRI.create(iri));
- ontology = manager.loadOntologyFromOntologyDocument(new File("../test/phaenotype/mp-equivalence-axioms-subq.owl"));
+ KnowledgeSource ks = new OWLAPIOntology(ontology);
+ OWLAPIReasoner reasoner = new OWLAPIReasoner(ks);
+ reasoner.init();
+ ClassHierarchy classHierarchy = reasoner.getClassHierarchy();
+ System.out.println(classHierarchy.toString(false));
// new PelletReasonerFactory().createReasoner(ontology);
System.out.println("Reasoner loaded succesfully.");
CelReasoner r = new CelReasoner(ontology);
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 2013-05-02 10:57:42 UTC (rev 3935)
+++ trunk/components-core/src/main/java/org/dllearner/utilities/datastructures/SetManipulation.java 2013-05-03 07:31:37 UTC (rev 3936)
@@ -19,6 +19,7 @@
package org.dllearner.utilities.datastructures;
+import java.util.Collection;
import java.util.List;
import java.util.Random;
import java.util.SortedSet;
@@ -160,6 +161,14 @@
return ret;
}
+ public static SortedSet<Individual> stringToInd(Collection<String> individualsAsString) {
+ SortedSet<Individual> ret = new TreeSet<Individual>();
+ for (String ind : individualsAsString) {
+ ret.add(new Individual(ind));
+ }
+ return ret;
+ }
+
public static SortedSet<String>indToString(SortedSet<Individual> set) {
SortedSet<String> ret = new TreeSet<String>();
for (Individual ind : set) {
Modified: trunk/components-core/src/test/java/org/dllearner/algorithms/pattern/OWLPatternDetectionTest.java
===================================================================
--- trunk/components-core/src/test/java/org/dllearner/algorithms/pattern/OWLPatternDetectionTest.java 2013-05-02 10:57:42 UTC (rev 3935)
+++ trunk/components-core/src/test/java/org/dllearner/algorithms/pattern/OWLPatternDetectionTest.java 2013-05-03 07:31:37 UTC (rev 3936)
@@ -17,7 +17,7 @@
ToStringRenderer.getInstance().setRenderer(new DLSyntaxObjectRenderer());
}
- @Test
+// @Test
public void testTONESRepository(){
OntologyRepository repository = new TONESRepository();
repository.initialize();
@@ -25,7 +25,7 @@
patternFinder.start();
}
- @Test
+// @Test
public void testBioPortalRepository(){
OntologyRepository repository = new BioPortalRepository();
repository.initialize();
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