Code improvements for release.

SmartDataAnalytics · Dec 30, 2015 · 8d65034 · 8d65034
1 parent aa7aaca
commit 8d65034
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diff --git a/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java b/components-core/src/main/java/org/dllearner/algorithms/celoe/PCELOE.java
@@ -19,35 +19,14 @@
 
 package org.dllearner.algorithms.celoe;
 
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.NavigableSet;
-import java.util.Set;
-import java.util.SortedSet;
-import java.util.TreeSet;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-import java.util.concurrent.Future;
-
+import com.google.common.collect.Sets;
+import com.jamonapi.Monitor;
+import com.jamonapi.MonitorFactory;
 import org.apache.log4j.FileAppender;
 import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
 import org.apache.log4j.PatternLayout;
-import org.dllearner.core.AbstractCELA;
-import org.dllearner.core.AbstractClassExpressionLearningProblem;
-import org.dllearner.core.AbstractHeuristic;
-import org.dllearner.core.AbstractKnowledgeSource;
-import org.dllearner.core.AbstractReasonerComponent;
-import org.dllearner.core.ComponentAnn;
-import org.dllearner.core.ComponentInitException;
-import org.dllearner.core.EvaluatedDescription;
-import org.dllearner.core.Score;
+import org.dllearner.core.*;
 import org.dllearner.core.config.ConfigOption;
 import org.dllearner.core.owl.ClassHierarchy;
 import org.dllearner.core.owl.DatatypePropertyHierarchy;
@@ -59,36 +38,23 @@
 import org.dllearner.learningproblems.PosOnlyLP;
 import org.dllearner.reasoning.ClosedWorldReasoner;
 import org.dllearner.reasoning.SPARQLReasoner;
-import org.dllearner.refinementoperators.CustomHierarchyRefinementOperator;
-import org.dllearner.refinementoperators.CustomStartRefinementOperator;
-import org.dllearner.refinementoperators.LengthLimitedRefinementOperator;
-import org.dllearner.refinementoperators.OperatorInverter;
-import org.dllearner.refinementoperators.ReasoningBasedRefinementOperator;
-import org.dllearner.refinementoperators.RhoDRDown;
-import org.dllearner.refinementoperators.SynchronizedRefinementOperator;
+import org.dllearner.refinementoperators.*;
 import org.dllearner.utilities.Files;
 import org.dllearner.utilities.Helper;
 import org.dllearner.utilities.OWLAPIUtils;
 import org.dllearner.utilities.TreeUtils;
 import org.dllearner.utilities.datastructures.SynchronizedSearchTree;
-import org.dllearner.utilities.owl.ConceptTransformation;
-import org.dllearner.utilities.owl.EvaluatedDescriptionSet;
-import org.dllearner.utilities.owl.OWLAPIRenderers;
-import org.dllearner.utilities.owl.OWLClassExpressionMinimizer;
-import org.dllearner.utilities.owl.OWLClassExpressionUtils;
-import org.dllearner.utilities.owl.PropertyContext;
-import org.semanticweb.owlapi.model.IRI;
-import org.semanticweb.owlapi.model.OWLClass;
-import org.semanticweb.owlapi.model.OWLClassExpression;
-import org.semanticweb.owlapi.model.OWLIndividual;
-import org.semanticweb.owlapi.model.OWLNaryBooleanClassExpression;
+import org.dllearner.utilities.owl.*;
+import org.semanticweb.owlapi.model.*;
 import org.springframework.beans.factory.annotation.Autowired;
-
 import uk.ac.manchester.cs.owl.owlapi.OWLClassImpl;
 
-import com.google.common.collect.Sets;
-import com.jamonapi.Monitor;
-import com.jamonapi.MonitorFactory;
+import java.io.File;
+import java.util.*;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
 
 /**
  * The PCELOE is an experimental, parallel implementation of the CELOE algorithm.

diff --git a/components-core/src/main/java/org/dllearner/algorithms/decisiontrees/utils/SetUtils.java b/components-core/src/main/java/org/dllearner/algorithms/decisiontrees/utils/SetUtils.java
@@ -87,10 +87,8 @@ public static <T> List<T> union(List<T> list1,List<T> list2){
 	 */
 	public static <T> boolean areEquals(List<T>l1, List<T> l2){
 		// due insiemi sono uguali se uno � incluso nell'altro
-		if (l1.containsAll(l2)&&l2.containsAll(l1))
-			return true;
-
-		return false;
+		return l1.containsAll(l2) && l2.containsAll(l1);
+
 	}
 
 	/**

diff --git a/components-core/src/main/java/org/dllearner/algorithms/hybridgp/Psi.java b/components-core/src/main/java/org/dllearner/algorithms/hybridgp/Psi.java
@@ -158,7 +158,7 @@ else if(downwardProbability<0)
 
 
 		// ein refinement zufällig auswählen
-		OWLClassExpression[] array = refinements.toArray(new OWLClassExpression[0]);
+		OWLClassExpression[] array = refinements.toArray(new OWLClassExpression[refinements.size()]);
 		// kein refinement gefunden
 		if(array.length==0) {
 			if(debug) {

diff --git a/components-core/src/main/java/org/dllearner/algorithms/ocel/ROLearner2.java b/components-core/src/main/java/org/dllearner/algorithms/ocel/ROLearner2.java
@@ -1253,10 +1253,11 @@ public ExampleBasedNode getStartNode() {
 	 * @return true if the algorithm should stop, this is mostly indepent of the question if a solution was found
 	 */
 	private boolean isTerminationCriteriaReached(){
+		// algorithm was stopped from outside
 		if(this.stop){
 			return true;
 		}
-//		System.out.println("ssssss");
+
 		long totalTimeNeeded = System.currentTimeMillis() - this.runtime;
 		long maxMilliSeconds = maxExecutionTimeInSeconds * 1000;
 		long minMilliSeconds = minExecutionTimeInSeconds * 1000;

diff --git a/components-core/src/main/java/org/dllearner/algorithms/properties/AxiomAlgorithms.java b/components-core/src/main/java/org/dllearner/algorithms/properties/AxiomAlgorithms.java
@@ -93,7 +93,7 @@ public class AxiomAlgorithms {
     /** set of tbox and rbox axiom types */
     public static final Set<AxiomType<? extends OWLAxiom>> TBoxAndRBoxAxiomTypes = tboxAndRbox();
 
-    private static final Set<AxiomType<? extends OWLAxiom>> tboxAndRbox() {
+    private static Set<AxiomType<? extends OWLAxiom>> tboxAndRbox() {
         Set<AxiomType<?>> axioms = new HashSet<>(TBoxAxiomTypes);
         axioms.addAll(RBoxAxiomTypes);
         return axioms;

diff --git a/.../main/java/org/dllearner/algorithms/qtl/datastructures/impl/EvaluatedRDFResourceTree.java b/.../main/java/org/dllearner/algorithms/qtl/datastructures/impl/EvaluatedRDFResourceTree.java
@@ -13,6 +13,7 @@
 import org.dllearner.learningproblems.QueryTreeScore;
 
 import com.google.common.collect.ComparisonChain;
+import org.jetbrains.annotations.NotNull;
 
 public class EvaluatedRDFResourceTree implements Comparable<EvaluatedRDFResourceTree>{
 
@@ -128,7 +129,7 @@ public QueryTreeScore getTreeScore() {
 	}
 
 	@Override
-	public int compareTo(EvaluatedRDFResourceTree other) {
+	public int compareTo(@NotNull EvaluatedRDFResourceTree other) {
 		return ComparisonChain.start()
 //		         .compare(this.getScore(), other.getScore())
 		         .compare(other.getScore(), this.getScore())

diff --git a/...onents-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/rendering/Edge.java b/...onents-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/rendering/Edge.java
@@ -40,9 +40,7 @@ public boolean equals(Object obj) {
 		if (getClass() != obj.getClass())
 			return false;
 		Edge other = (Edge) obj;
-		if (id != other.id)
-			return false;
-		return true;
+		return id == other.id;
 	}
 
 

diff --git a/...ents-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/rendering/Vertex.java b/...ents-core/src/main/java/org/dllearner/algorithms/qtl/datastructures/rendering/Vertex.java
@@ -40,8 +40,6 @@ public boolean equals(Object obj) {
 		if (getClass() != obj.getClass())
 			return false;
 		Vertex other = (Vertex) obj;
-		if (id != other.id)
-			return false;
-		return true;
+		return id == other.id;
 	}
 }
diff --git a/...re/src/main/java/org/dllearner/algorithms/qtl/filters/QuestionBasedStatementSelector.java b/...re/src/main/java/org/dllearner/algorithms/qtl/filters/QuestionBasedStatementSelector.java
@@ -34,11 +34,8 @@ public boolean test(Statement s) {
 		} else if(s.getObject().isLiteral()){
 			object = s.getObject().asLiteral().getLexicalForm();
 		}
-		if(isSimiliar2QuestionWord(object) || isSimiliar2QuestionWord(predicate)){
-			return true;
-		}
-
-		return false;
+		return isSimiliar2QuestionWord(object) || isSimiliar2QuestionWord(predicate);
+
 	}
 
 	private boolean isSimiliar2QuestionWord(String s){

diff --git a/...ts-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/EvaluatedQueryTree.java b/...ts-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/EvaluatedQueryTree.java
@@ -13,6 +13,7 @@
 import org.dllearner.learningproblems.QueryTreeScore;
 
 import com.google.common.collect.ComparisonChain;
+import org.jetbrains.annotations.NotNull;
 
 public class EvaluatedQueryTree<N> implements Comparable<EvaluatedQueryTree<N>>{
 
@@ -128,7 +129,7 @@ public QueryTreeScore getTreeScore() {
 	}
 
 	@Override
-	public int compareTo(EvaluatedQueryTree<N> other) {
+	public int compareTo(@NotNull EvaluatedQueryTree<N> other) {
 		return ComparisonChain.start()
 //		         .compare(this.getScore(), other.getScore())
 		         .compare(other.getScore(), this.getScore())

diff --git a/components-core/src/main/java/org/dllearner/algorithms/qtl/util/SPARQLEndpointEx.java b/components-core/src/main/java/org/dllearner/algorithms/qtl/util/SPARQLEndpointEx.java
@@ -63,15 +63,14 @@ public Set<String> getPredicateFilters(){
 
 	@Override
 	public String toString() {
-		StringBuilder sb = new StringBuilder();
-		sb.append("ENDPOINT\n");
-		sb.append("Label: ").append(getLabel()).append("\n");
-		sb.append("URL: ").append(getURL()).append("\n");
-		sb.append("Default Graph URI: ").append(getDefaultGraphURIs()).append("\n");
-		sb.append("Named Graph URI: ").append(getNamedGraphURIs()).append("\n");
-		sb.append("Predicate Filters: ").append(getPredicateFilters()).append("\n");
-
-		return sb.toString();
+		String sb = "ENDPOINT\n" +
+				"Label: " + getLabel() + "\n" +
+				"URL: " + getURL() + "\n" +
+				"Default Graph URI: " + getDefaultGraphURIs() + "\n" +
+				"Named Graph URI: " + getNamedGraphURIs() + "\n" +
+				"Predicate Filters: " + getPredicateFilters() + "\n";
+
+		return sb;
 	}
 
 	@Override

diff --git a/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java b/components-core/src/main/java/org/dllearner/core/AbstractAxiomLearningAlgorithm.java
@@ -532,8 +532,7 @@ protected long getRemainingRuntimeInMilliSeconds(){
 	}
 
 	protected boolean terminationCriteriaSatisfied(){
-		boolean timeLimitExceeded = maxExecutionTimeInSeconds == 0 ? false : getRemainingRuntimeInMilliSeconds() <= 0;
-		return  timeLimitExceeded ;
+		return maxExecutionTimeInSeconds != 0 && getRemainingRuntimeInMilliSeconds() <= 0;
 	}
 
 	protected List<Entry<OWLClassExpression, Integer>> sortByValues(Map<OWLClassExpression, Integer> map, final boolean useHierachy){

diff --git a/components-core/src/main/java/org/dllearner/core/AbstractCELA.java b/components-core/src/main/java/org/dllearner/core/AbstractCELA.java
@@ -380,7 +380,7 @@ protected String getSolutionString() {
 			if(learningProblem instanceof PosNegLP) {
 				Set<OWLIndividual> positiveExamples = ((PosNegLP)learningProblem).getPositiveExamples();
 				Set<OWLIndividual> negativeExamples = ((PosNegLP)learningProblem).getNegativeExamples();
-				ReasoningUtils reasoningUtil = ((PosNegLP)learningProblem).getReasoningUtil();
+				ReasoningUtils reasoningUtil = learningProblem.getReasoningUtil();
 
 				str += current + ": " + descriptionString + " (pred. acc.: "
 						+ dfPercent.format(reasoningUtil.getAccuracyOrTooWeak2(new AccMethodPredAcc(true), description, positiveExamples, negativeExamples, 1))

diff --git a/components-core/src/main/java/org/dllearner/core/EvaluatedHypothesis.java b/components-core/src/main/java/org/dllearner/core/EvaluatedHypothesis.java
@@ -22,6 +22,7 @@
 import java.io.Serializable;
 import java.text.DecimalFormat;
 
+import org.jetbrains.annotations.NotNull;
 import org.semanticweb.owlapi.model.OWLObject;
 
 import com.google.common.collect.ComparisonChain;
@@ -92,7 +93,7 @@ public String toString() {
 	 * @see java.lang.Comparable#compareTo(java.lang.Object)
 	 */
 	@Override
-	public int compareTo(EvaluatedHypothesis<T, S> o) {
+	public int compareTo(@NotNull EvaluatedHypothesis<T, S> o) {
 		return ComparisonChain.start()
 				.compare(score.getAccuracy(), o.score.getAccuracy())
 				.compare(hypothesis, o.getDescription())

diff --git a/components-core/src/main/java/org/dllearner/kb/aquisitors/SparqlTupleAquisitor.java b/components-core/src/main/java/org/dllearner/kb/aquisitors/SparqlTupleAquisitor.java
@@ -183,7 +183,6 @@ private void assignIds(int currentId, ResultSetRewindable rsw, int lastDepth){
 			// could be two different blank nodes here, but unlikely
 			if(!q.get("o0").isAnon()){
 				lastNodes.put(q.get("o0").toString(), currentId);
-				continue;
 			}else{
 
 				// remove the first node

diff --git a/components-core/src/main/java/org/dllearner/kb/dataset/AbstractOWLOntologyDataset.java b/components-core/src/main/java/org/dllearner/kb/dataset/AbstractOWLOntologyDataset.java
@@ -59,7 +59,7 @@ public abstract class AbstractOWLOntologyDataset implements OWLOntologyDataset{
 
 	protected Map<URL, String> ontologyURLs = new HashMap<>();
 
-	private final int nrOfThreads = 1;
+	private static final int nrOfThreads = 1;
 	private boolean analyze = false;
 
 	public AbstractOWLOntologyDataset(String name, boolean analyze) {
@@ -231,7 +231,7 @@ protected OWLOntology loadOWLOntology(URL url) {
 
 	private OWLOntology loadFromLocal(URL url){
 		String filename = getFilename(url);
-		for(File parent : Arrays.asList(directory)){
+		for(File parent : Collections.singletonList(directory)){
 			File file = new File(parent, filename);
 			if(file.exists()){
 				try {

diff --git a/components-core/src/main/java/org/dllearner/kb/extraction/InstanceNode.java b/components-core/src/main/java/org/dllearner/kb/extraction/InstanceNode.java
@@ -201,7 +201,7 @@ public void toOWLOntology( OWLAPIOntologyCollector owlAPIOntologyCollector){
 			if(one.getURIString().equals(OWLVocabulary.OWL_DIFFERENT_FROM)){
 				OWLIndividual o = factory.getOWLNamedIndividual(one.getBPart().getIRI());
 
-				ax = factory.getOWLDifferentIndividualsAxiom(new OWLIndividual[]{me,o});
+				ax = factory.getOWLDifferentIndividualsAxiom(me, o);
 			}else{
 
 				//create axiom

diff --git a/components-core/src/main/java/org/dllearner/kb/extraction/LiteralNode.java b/components-core/src/main/java/org/dllearner/kb/extraction/LiteralNode.java
@@ -104,79 +104,34 @@ public void toOWLOntology( OWLAPIOntologyCollector owlAPIOntologyCollector){
 
 	public boolean isDouble(){
 		try{
-			if(l.getDatatypeURI().contains("double")){return true;}
-			else{return false;}
-
-			//l.getFloat();
-
-			//l.getDouble();
-			//return true;
-		}catch (Exception e) {
-			return false;
-		}/*
-		try{
-			l.getDouble();
-			return true;
+			return l.getDatatypeURI() != null && l.getDatatypeURI().contains("double");
 		}catch (Exception e) {
 			return false;
-		}*/
+		}
 	}
 
 	public boolean isFloat(){
 		try{
-			if(l.getDatatypeURI().contains("float")){return true;}
-			else{return false;}
-
-			//l.getFloat();
-
-			//l.getDouble();
-			//return true;
+			return l.getDatatypeURI() != null && l.getDatatypeURI().contains("float");
 		}catch (Exception e) {
 			return false;
 		}
 	}
 
 	public boolean isInt(){
 		try{
-			if(l.getDatatypeURI().contains("int")){return true;}
-			else{return false;}
-
-			//l.getFloat();
-
-			//l.getDouble();
-			//return true;
+			return l.getDatatypeURI() != null && l.getDatatypeURI().contains("int");
 		}catch (Exception e) {
 			return false;
 		}
-
-
-	/*try{
-			l.getInt();
-			return true;
-		}catch (Exception e) {
-			return false;
-		}*/
 	}
 
 	public boolean isBoolean(){
 		try{
-			if(l.getDatatypeURI().contains("boolean")){return true;}
-			else{return false;}
-
-			//l.getFloat();
-
-			//l.getDouble();
-			//return true;
+			return l.getDatatypeURI() != null && l.getDatatypeURI().contains("boolean");
 		}catch (Exception e) {
 			return false;
 		}
-
-		/*try{
-			l.getBoolean();
-			return true;
-		}catch (Exception e) {
-			return false;
-		}*/
 	}
 
 	public boolean isString(){

diff --git a/components-core/src/main/java/org/dllearner/kb/repository/bioportal/BioPortalRepository.java b/components-core/src/main/java/org/dllearner/kb/repository/bioportal/BioPortalRepository.java
@@ -20,8 +20,8 @@ public class BioPortalRepository implements OntologyRepository {
 
 	private static final Logger log = Logger.getLogger(BioPortalRepository.class);
 
-	private String apiKey = "8fadfa2c-47de-4487-a1f5-b7af7378d693";
-	private String serviceURL = "http://rest.bioontology.org/bioportal/ontologies";
+	private static final String apiKey = "8fadfa2c-47de-4487-a1f5-b7af7378d693";
+	private static final String serviceURL = "http://rest.bioontology.org/bioportal/ontologies";
 
 	private boolean initialized = false;