Merge pull request #72 from SmartDataAnalytics/dependency-updates

Dependency updates

Author: SimonBin

components-core/pom.xml

@@ -61,7 +61,6 @@
 					<plugin>
 						<groupId>org.codehaus.mojo</groupId>
 						<artifactId>license-maven-plugin</artifactId>
-						<version>1.14</version>
 						<configuration>
 							<licenseName>gpl_v3</licenseName>
 							<organizationName>AKSW</organizationName>
@@ -114,7 +113,7 @@
 								/&gt;Copyright &amp;#169; 2007-2016 Jens Lehmann</bottom>
 							<encoding>ISO-8859-1</encoding>
 							<windowtitle>DL-Learner Javadoc</windowtitle>
-							<additionalparam>-Xdoclint:none</additionalparam>
+							<doclint>none</doclint>
 						</configuration>
 					</plugin>
 				</plugins>

components-core/src/main/java/org/dllearner/algorithms/qtl/filters/Filters.java

@@ -69,7 +69,7 @@ public static List<String> getFOAFFilterProperties(){
 		filters.add(FOAF.homepage.toString());
 		filters.add(FOAF.depiction.toString());
 		filters.add(FOAF.Image.toString());
-		filters.add(FOAF.surname.toString());
+		filters.add(FOAF.familyName.toString());
 		filters.add(FOAF.birthday.toString());
 		filters.add(FOAF.name.toString());
 		filters.add(FOAF.firstName.toString());

components-core/src/main/java/org/dllearner/algorithms/qtl/util/filters/PredicateExistenceFilterDBpedia.java

@@ -106,7 +106,7 @@ private void analyze() {
 			sb.append(p).append("\n");
 		}
 		try {
-			Files.write(sb.toString(), new File("dbpedia_meaningless_properties.txt"), Charsets.UTF_8);
+			Files.asCharSink(new File("dbpedia_meaningless_properties.txt"), Charsets.UTF_8).write(sb.toString());
 		} catch (IOException e) {
 			e.printStackTrace();
 		}

components-core/src/main/java/org/dllearner/kb/dataset/AbstractOWLOntologyDataset.java

@@ -294,11 +294,7 @@ protected File downloadFile(URL url){
 	}
 
 	private void add403Error(URL url){
-		try {
-			Files.append(url.toString() + "\n", new File(directory, "403.txt"), Charset.defaultCharset());
-		} catch (IOException e) {
-			e.printStackTrace();
-		}
+		org.dllearner.utilities.Files.appendToFile(new File(directory, "403.txt"), url.toString() + "\n");
 	}
 
 	@Override

components-core/src/main/java/org/dllearner/kb/repository/bioportal/BioPortalRepository.java

@@ -28,6 +28,7 @@
 import org.apache.log4j.Logger;
 import org.dllearner.kb.repository.OntologyRepository;
 import org.dllearner.kb.repository.OntologyRepositoryEntry;
+import org.dllearner.utilities.Files;
 import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.model.*;
 
@@ -236,10 +237,8 @@ public static void main(String[] args) throws Exception{
 						System.out.println(entry.getOntologyShortName() + ": " + FileUtils.byteCountToDisplaySize(f.length()));
 						map.put(entry.getOntologyShortName(), FileUtils.byteCountToDisplaySize(f.length()));
 					} catch (Exception e) {
-						com.google.common.io.Files.write(
-								ExceptionUtils.getMessage(e),
-								new File(downloadFailedDir, entry.getOntologyShortName() + ".txt"),
-								Charsets.UTF_8);
+						com.google.common.io.Files.asCharSink(new File(downloadFailedDir, entry.getOntologyShortName() + ".txt"),
+								Charsets.UTF_8).write(ExceptionUtils.getMessage(e));
 						return;
 					}
 				}
@@ -267,24 +266,24 @@ public static void main(String[] args) throws Exception{
 						OWLOntology ont = man.loadOntologyFromOntologyDocument(f);
 						System.out.println("#Axioms: " + ont.getLogicalAxiomCount());
 
-						com.google.common.io.Files.write(
+						com.google.common.io.Files.asCharSink(
+								new File(parsedSuccessfulDir, entry.getOntologyShortName() + ".txt"),
+								Charsets.UTF_8).write(
 								ont.getLogicalAxiomCount() + "\t" +
 										ont.getClassesInSignature().size() + "\t" +
 										ont.getObjectPropertiesInSignature().size() + "\t" +
 										ont.getDataPropertiesInSignature().size() + "\t" +
-										ont.getIndividualsInSignature().size(),
-								new File(parsedSuccessfulDir, entry.getOntologyShortName() + ".txt"),
-								Charsets.UTF_8);
+										ont.getIndividualsInSignature().size()
+						);
 
 						map.replace(entry.getOntologyShortName(), map.get(entry.getOntologyShortName()) + "||#Axioms: " + ont.getLogicalAxiomCount());
 						man.removeOntology(ont);
 					} catch (Exception e1) {
 						System.err.println("Failed to parse " + entry.getOntologyShortName());
 						map.replace(entry.getOntologyShortName(), map.get(entry.getOntologyShortName()) + "||Parse Error");
-						com.google.common.io.Files.write(
-								ExceptionUtils.getMessage(e1),
+						com.google.common.io.Files.asCharSink(
 								new File(parsedFailedDir, entry.getOntologyShortName() + ".txt"),
-								Charsets.UTF_8);
+								Charsets.UTF_8).write(ExceptionUtils.getMessage(e1));
 					}
 				}
 			} catch (Exception e) {

components-core/src/main/java/org/dllearner/kb/sparql/ClassBasedSampleGenerator.java

@@ -106,7 +106,7 @@ public void setMaxNrOfPosExamples(int maxNrOfPosExamples) {
 	public void setMaxNrOfNegExamples(int maxNrOfNegExamples) {
 		this.maxNrOfNegExamples = maxNrOfNegExamples;
 	}
-	
+
 	/**
 	 * @param useNegExamples whether to use negative examples or not
 	 */
@@ -138,7 +138,7 @@ public Set<OWLIndividual> getNegativeExamples() {
 	public void setSeed(long seed) {
 		rnd.setSeed(seed);
 	}
-	
+
 	private Set<OWLIndividual> computePosExamples(OWLClass cls) {
 		List<OWLIndividual> posExamples = new ArrayList<>();
 

components-core/src/main/java/org/dllearner/utilities/Files.java

@@ -30,10 +30,12 @@
 import java.io.ObjectInputStream;
 import java.io.ObjectOutputStream;
 import java.net.URL;
+import java.nio.charset.Charset;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.StringTokenizer;
 
+import com.google.common.io.FileWriteMode;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -171,7 +173,7 @@ public static void createFile(File file, String content) {
 		File parentFile = file.getParentFile();
 		if (parentFile != null) { parentFile.mkdirs(); }
 		try {
-			com.google.common.io.Files.write(content, file, Charsets.UTF_8);
+			com.google.common.io.Files.asCharSink(file, Charsets.UTF_8).write(content);
 		} catch (IOException e) {
 			logger.error("Failed to write content to file " + file, e);
 		}
@@ -187,11 +189,23 @@ public static void createFile(File file, String content) {
 	 */
 	public static void appendToFile(File file, String content) {
 		try {
-			com.google.common.io.Files.append(content, file, Charsets.UTF_8);
+			com.google.common.io.Files.asCharSink(file, Charsets.UTF_8, FileWriteMode.APPEND).write(content);
 		} catch (IOException e) {
 			logger.error("Failed to append content to file " + file, e);
 		}
 	}
+
+	/**
+	 * Write content to a file.
+	 *
+	 * @param file
+	 *            The file to create.
+	 * @param content
+	 *            Content of the file.
+	 */
+	public static void writeToFile(String content, File file) throws IOException {
+		java.nio.file.Files.write(file.toPath(), content.getBytes());
+	}
 
 	public static void clearFile(File file) {
 		try{

components-core/src/main/java/org/dllearner/utilities/QueryUtils.java

@@ -41,7 +41,6 @@
 import org.apache.jena.sparql.util.VarUtils;
 import org.apache.jena.vocabulary.RDF;
 import org.dllearner.kb.sparql.CBDStructureTree;
-import org.jgrapht.DirectedGraph;
 import org.jgrapht.ext.JGraphXAdapter;
 import org.jgrapht.graph.DefaultDirectedGraph;
 import org.jgrapht.graph.DefaultEdge;
@@ -722,12 +721,12 @@ public void filterOutGeneralTypes(QueryExecutionFactory qef, Query query){
 		}
 	}
 
-	public static DirectedGraph<Node, LabeledEdge> asJGraphT(Query query) {
+	public static DefaultDirectedGraph<Node, LabeledEdge> asJGraphT(Query query) {
 		QueryUtils utils = new QueryUtils();
 
 		Set<Triple> tps = utils.extractTriplePattern(query);
 
-		DirectedGraph<Node, LabeledEdge> g = new DefaultDirectedGraph<>(LabeledEdge.class);
+		DefaultDirectedGraph<Node, LabeledEdge> g = new DefaultDirectedGraph<>(LabeledEdge.class);
 
 		tps.forEach(tp -> {
 			g.addVertex(tp.getSubject());
@@ -739,7 +738,7 @@ public static DirectedGraph<Node, LabeledEdge> asJGraphT(Query query) {
 	}
 
 	public static void exportAsGraph(Query query, File file) {
-		DirectedGraph<Node, LabeledEdge> g = asJGraphT(query);
+		DefaultDirectedGraph<Node, LabeledEdge> g = asJGraphT(query);
 		System.out.println(g.edgeSet().size());
 
 		JGraphXAdapter adapter = new JGraphXAdapter(g);

components-core/src/main/java/org/dllearner/utilities/owl/OWL2SPARULConverter.java

@@ -31,6 +31,7 @@
 import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
+import java.util.Map;
 import java.util.concurrent.atomic.AtomicInteger;
 
 import static org.semanticweb.owlapi.util.OWLAPIPreconditions.checkNotNull;
@@ -47,13 +48,13 @@ public class OWL2SPARULConverter
 
 	public OWL2SPARULConverter(OWLOntologyManager manager,
 							   OWLOntology ontology, boolean useStrongTyping, IndividualAppearance individualAppearance,
-							   AxiomAppearance axiomAppearance, AtomicInteger nextNode) {
-		super(manager, ontology, useStrongTyping, individualAppearance, axiomAppearance, nextNode);
+							   AxiomAppearance axiomAppearance, AtomicInteger nextNode, Map<Object, Integer> blankNodeMap) {
+		super(manager, ontology, useStrongTyping, individualAppearance, axiomAppearance, nextNode, blankNodeMap);
 	}
 
 	public OWL2SPARULConverter(OWLOntology ontology, boolean useStrongTyping) {
 		this(ontology.getOWLOntologyManager(), ontology, useStrongTyping,
-			 new OWLAnonymousIndividualsWithMultipleOccurrences(), new AlwaysOutputId(), new AtomicInteger());
+			 new OWLAnonymousIndividualsWithMultipleOccurrences(), new AlwaysOutputId(), new AtomicInteger(), Collections.emptyMap());
 	}
 
 	/**

components-core/src/test/java/org/dllearner/algorithms/qtl/experiments/Diagrams.java

@@ -29,8 +29,6 @@
 import java.util.Properties;
 import java.util.TreeMap;
 
-import org.dllearner.learningproblems.Heuristics.HeuristicType;
-
 import com.google.common.base.Charsets;
 import com.google.common.base.Joiner;
 import com.google.common.collect.Maps;
@@ -42,6 +40,7 @@
 import com.panayotis.gnuplot.plot.DataSetPlot;
 import com.panayotis.gnuplot.style.PlotStyle;
 import com.panayotis.gnuplot.style.Style;
+import org.dllearner.learningproblems.Heuristics.HeuristicType;
 
 /**
  * @author Lorenz Buehmann
@@ -121,7 +120,7 @@ public static void main(String[] args) throws Exception {
 				}
 				 s += "\n";
 			}
-			Files.write(s, new File(dir, "examplesVsScore-" + noise + ".tsv"), Charsets.UTF_8);
+			org.dllearner.utilities.Files.writeToFile(s, new File(dir, "examplesVsScore-" + noise + ".tsv"));
 		}
 
 		// noise vs fscore