Merge remote-tracking branch 'fork/develop' into develop

# Conflicts:
#	interfaces-ext/pom.xml
#	interfaces/pom.xml

Author: LorenzBuehmann

components-core/pom.xml

@@ -220,7 +220,7 @@
 			<plugin>
 				<groupId>org.jacoco</groupId>
 				<artifactId>jacoco-maven-plugin</artifactId>
-				<version>0.7.6.201602180812</version>
+				<version>0.8.4</version>
 				<executions>
 					<execution>
 						<goals>
@@ -303,12 +303,12 @@
 		<dependency>
 			<groupId>javax.json</groupId>
 			<artifactId>javax.json-api</artifactId>
-			<version>1.1.2</version>
+			<version>1.1.4</version>
 		</dependency>
 		<dependency>
 			<groupId>org.glassfish</groupId>
 			<artifactId>javax.json</artifactId>
-			<version>1.1.2</version>
+			<version>1.1.4</version>
 		</dependency>
 
 		<!--
@@ -577,7 +577,18 @@
 			<artifactId>commons-collections4</artifactId>
 		</dependency>
 
-
+		<dependency>
+			<groupId>javax.annotation</groupId>
+			<artifactId>javax.annotation-api</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>javax.xml.bind</groupId>
+			<artifactId>jaxb-api</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>javax.xml.ws</groupId>
+			<artifactId>jaxws-api</artifactId>
+		</dependency>
 
 			<dependency>
 				<groupId>org.apache.logging.log4j</groupId>

components-core/src/main/java/org/dllearner/algorithms/CELOEWrapper.java

@@ -18,6 +18,7 @@
  */
 package org.dllearner.algorithms;
 
+import com.google.common.base.StandardSystemProperty;
 import com.google.common.collect.Sets;
 import org.apache.jena.query.ParameterizedSparqlString;
 import org.apache.jena.query.QueryExecution;
@@ -41,6 +42,7 @@
 import org.semanticweb.owlapi.model.*;
 import uk.ac.manchester.cs.owl.owlapi.OWLClassImpl;
 
+import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.util.Set;
@@ -113,7 +115,7 @@ protected void learnAxioms() {
 
 		OWLOntology fragment = buildFragment(posExamples, negExamples);
 		try {
-			fragment.getOWLOntologyManager().saveOntology(fragment, new RDFXMLDocumentFormat(), new FileOutputStream("/tmp/ont.owl"));
+			fragment.getOWLOntologyManager().saveOntology(fragment, new RDFXMLDocumentFormat(), new FileOutputStream(System.getProperty("java.io.tmpdir") + File.separator + "ont.owl"));
 		} catch (OWLOntologyStorageException | FileNotFoundException e1) {
 			// TODO Auto-generated catch block
 			e1.printStackTrace();

components-core/src/main/java/org/dllearner/algorithms/qtl/operations/lgg/LGGGeneratorRDFS.java

@@ -18,6 +18,7 @@
  */
 package org.dllearner.algorithms.qtl.operations.lgg;
 
+import com.google.common.base.StandardSystemProperty;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Sets;
 import org.aksw.jena_sparql_api.cache.h2.CacheUtilsH2;
@@ -49,6 +50,7 @@
 import org.dllearner.utilities.NonStandardReasoningServices;
 import org.semanticweb.owlapi.model.EntityType;
 
+import java.io.File;
 import java.util.*;
 import java.util.concurrent.TimeUnit;
 import java.util.function.Predicate;
@@ -214,7 +216,7 @@ public static void main(String[] args) throws Exception {
 		endpoint = SparqlEndpoint.create("http://sake.informatik.uni-leipzig.de:8890/sparql", "http://dbpedia.org");
 		QueryExecutionFactory qef = FluentQueryExecutionFactory
 				.http(endpoint.getURL().toString(), endpoint.getDefaultGraphURIs()).config()
-				.withCache(CacheUtilsH2.createCacheFrontend("/tmp/cache", false, TimeUnit.DAYS.toMillis(60)))
+				.withCache(CacheUtilsH2.createCacheFrontend(System.getProperty("java.io.tmpdir") + File.separator + "cache", false, TimeUnit.DAYS.toMillis(60)))
 				.withPagination(10000).withDelay(50, TimeUnit.MILLISECONDS).end().create();
 
 		// tree generation

components-core/src/main/java/org/dllearner/algorithms/qtl/operations/tuples/QTLTuples.java

@@ -8,6 +8,7 @@
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
+import com.google.common.base.StandardSystemProperty;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;
 import com.google.common.collect.Sets;
@@ -308,7 +309,7 @@ private Map<String, Map.Entry<RDFResourceTree, List<Node>>> connect(List<Node> t
                             });
                         });
                         log.debug("connected tree\n{}", tree::getStringRepresentation);
-                        QueryTreeUtils.asGraph(tree, baseIRI, pm, new File("/tmp/tree-" + FmtUtils.stringForNode(node, pm) + ".graphml"));
+                        QueryTreeUtils.asGraph(tree, baseIRI, pm, new File(System.getProperty("java.io.tmpdir") + File.separator + "tree-" + FmtUtils.stringForNode(node, pm) + ".graphml"));
                         result.put(key, Maps.immutableEntry(tree, new ArrayList<>(nodes2Project)));
                     };
 
@@ -729,7 +730,7 @@ public static void main(String[] args) throws Exception {
 
             Graph<Vertex, Edge> g = QueryTreeUtils.toGraph(tree, baseIRI, pm);
 
-            QueryTreeUtils.asGraph(tree, baseIRI, pm, new File("/tmp/lgg.graphml"));
+            QueryTreeUtils.asGraph(tree, baseIRI, pm, new File(System.getProperty("java.io.tmpdir") + File.separator + "lgg.graphml"));
 
         });
 

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

@@ -19,6 +19,7 @@
 package org.dllearner.kb.repository.bioportal;
 
 import com.google.common.base.Charsets;
+import com.google.common.base.StandardSystemProperty;
 import joptsimple.OptionParser;
 import joptsimple.OptionSet;
 import joptsimple.OptionSpec;
@@ -186,7 +187,7 @@ public static void main(String[] args) throws Exception{
 		// create Options object
 		OptionParser parser = new OptionParser();
 		OptionSpec<File> baseDir =
-				parser.accepts( "basedir" ).withRequiredArg().ofType( File.class ).defaultsTo(new File("/tmp/bioportal/"));
+				parser.accepts( "basedir" ).withRequiredArg().ofType( File.class ).defaultsTo(new File(System.getProperty("java.io.tmpdir") + File.separator + "bioportal" + File.separator));
 		OptionSpec<Void> downloadOption =
 				parser.accepts( "download" );
 		OptionSpec<Void> parseOption =

components-core/src/main/java/org/dllearner/reasoning/OWLAPIReasoner.java

@@ -21,6 +21,7 @@
 import com.clarkparsia.owlapi.explanation.PelletExplanation;
 import com.clarkparsia.owlapiv3.XSD;
 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
+import com.google.common.base.StandardSystemProperty;
 import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
 import org.dllearner.core.*;
@@ -1258,7 +1259,7 @@ public void setSynchronized() {
 	}
 
 	public static void main(String[] args) throws Exception{
-		OWLOntology o = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(new File("/tmp/test2.rdf"));
+		OWLOntology o = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(new File(System.getProperty("java.io.tmpdir") + File.separator + "test2.rdf"));
 		System.out.println(o.getClassesInSignature());
 		System.out.println(o.getDataPropertiesInSignature());
 		System.out.println(o.getIndividualsInSignature().size());

components-core/src/main/java/org/dllearner/reasoning/StructuralReasonerExtended.java

@@ -18,6 +18,7 @@
  */
 package org.dllearner.reasoning;
 
+import com.google.common.base.StandardSystemProperty;
 import org.dllearner.kb.OWLAPIOntology;
 import org.dllearner.kb.OWLOntologyKnowledgeSource;
 import org.joda.time.Period;
@@ -33,6 +34,7 @@
 import org.semanticweb.owlapi.util.Version;
 
 import javax.annotation.Nonnull;
+import java.io.File;
 import java.util.*;
 import java.util.stream.Stream;
 
@@ -1446,7 +1448,7 @@ public Collection<OWLDataProperty> getChildren(OWLDataProperty parent) {
     public static void main(String[] args) throws Exception {
         OWLOntologyManager man = OWLManager.createOWLOntologyManager();
         OWLOntology schema = //man.loadOntology(IRI.create("http://downloads.dbpedia.org/2016-10/dbpedia_2016-10.nt"));
-        man.loadOntology(IRI.create("file:///tmp/merged.ttl"));
+        man.loadOntology(IRI.create("file://" + System.getProperty("java.io.tmpdir") + "/merged.ttl"));
 
         OWLOntologyKnowledgeSource sampleKS = new OWLAPIOntology(schema);
         sampleKS.init();

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

@@ -18,10 +18,13 @@
  */
 package org.dllearner.utilities;
 
+import org.dllearner.algorithms.ocel.ExampleBasedNode;
 import org.dllearner.core.AbstractSearchTreeNode;
 import org.dllearner.core.Heuristic;
 import org.dllearner.utilities.datastructures.AbstractSearchTree;
 
+import javax.annotation.Nonnull;
+
 public class TreeUtils {
 
 	public static <T extends AbstractSearchTreeNode> String toTreeString(
@@ -49,7 +52,7 @@ private static <T extends AbstractSearchTreeNode> StringBuilder toTreeString(T n
 		if(depth!=0)
 			treeString.append("|--> ");
 		treeString.append(node.toString())
-				.append(heuristic != null ? ("[score: " + heuristic.getNodeScore(node) + "]") : "")
+				.append(addNodeScore(node, heuristic))
 				.append("\n");
 		for (Object child :
 		     node.getChildren()) {
@@ -58,4 +61,21 @@ private static <T extends AbstractSearchTreeNode> StringBuilder toTreeString(T n
 		return treeString;
 	}
 
+	@Nonnull
+	private static <T extends AbstractSearchTreeNode> String addNodeScore(T node, Heuristic<T> heuristic) {
+		if (heuristic == null)
+			return "";
+
+		if (node instanceof ExampleBasedNode) {
+			if (!((ExampleBasedNode) node).isQualityEvaluated()) {
+				return "";
+			}
+			if (((ExampleBasedNode) node).isTooWeak()) {
+				return "[score:too weak]";
+			}
+		}
+
+		return "[score: " + heuristic.getNodeScore(node) + "]";
+	}
+
 }

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

@@ -19,6 +19,7 @@
 package org.dllearner.algorithms.qtl;
 
 import com.google.common.base.Splitter;
+import com.google.common.base.StandardSystemProperty;
 import com.google.common.collect.Sets;
 import com.jamonapi.Monitor;
 import com.jamonapi.MonitorFactory;
@@ -218,7 +219,7 @@ public static void main(String[] args) throws Exception {
 		System.out.println(filter.apply(bestSolution).getStringRepresentation());
 		System.out.println(QueryTreeUtils.toSPARQLQueryString(filter.apply(bestSolution)));
 
-		QueryTreeUtils.asGraph(bestSolution, null, PrefixCCPrefixMapping.Full, new File("/tmp/tree.graphml"));
+		QueryTreeUtils.asGraph(bestSolution, null, PrefixCCPrefixMapping.Full, new File(System.getProperty("java.io.tmpdir") + File.separator + "tree.graphml"));
 	}
 
 	private static RDFResourceTree getQueryTree(String resource, CBDStructureTree cbdStructure,

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

@@ -1,5 +1,6 @@
 package org.dllearner.algorithms.qtl.experiments;
 
+import com.google.common.base.StandardSystemProperty;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Sets;
 import com.google.common.io.FileWriteMode;
@@ -61,7 +62,7 @@ public static void main(String[] args) throws Exception{
         SparqlEndpoint endpoint = SparqlEndpoint.getEndpointDBpedia();
         endpoint = SparqlEndpoint.create("http://localhost:7200/repositories/dbpedia?infer=false", Collections.emptyList());
         SparqlEndpointKS ks = new SparqlEndpointKS(endpoint);
-        ks.setCacheDir("/tmp/qtl/sparql-cache");
+        ks.setCacheDir(System.getProperty("java.io.tmpdir") + File.separator + "qtl" + File.separator + "sparql-cache");
         ks.init();
 
         QueryExecutionFactory qef = ks.getQueryExecutionFactory();
@@ -122,7 +123,7 @@ public boolean isMeaningless(Node predicate) {
 
         List<Query> queries = getQueries();
 
-        File out = new File("/tmp/qtl.out");
+        File out = new File(System.getProperty("java.io.tmpdir") + File.separator + "qtl.out");
 
         queries.forEach(query -> {
             try {