Bump org.apache.jena:apache-jena-libs from 4.10.0 to 5.2.0

admin-ui/src/main/java/eu/knowledge/engine/admin/AdminUI.java

@@ -9,7 +9,6 @@
 
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.Resource;
-import org.apache.jena.rdf.model.SimpleSelector;
 import org.apache.jena.shared.PrefixMapping;
 import org.apache.jena.sparql.graph.PrefixMappingMem;
 import org.apache.jena.sparql.lang.arq.ParseException;
@@ -184,9 +183,9 @@ public BindingSet handleChangedKnowledgeBaseKnowledge(ReactExchangeInfo ei) {
 			// - delete all old data about that knowledge base
 			// - insert the *new* data about that knowledge base
 
-			Resource kb = model.query(new SimpleSelector(null, RDF.type, Vocab.KNOWLEDGE_BASE)).listSubjects().next();
-			String query = String.format("DELETE { %s } WHERE { %s FILTER (?kb = <%s>) } ",
-					this.metaGraphPattern.getPattern(), this.metaGraphPattern.getPattern(), kb.toString());
+			Resource kb = model.listSubjectsWithProperty(RDF.type, Vocab.KNOWLEDGE_BASE).next();
+			String query = String.format("DELETE { %s } WHERE { %s FILTER (?kb = <%s>) } ", this.metaGraphPattern.getPattern(), this.metaGraphPattern.getPattern(), kb.toString());
+
 			UpdateRequest updateRequest = UpdateFactory.create(query);
 			UpdateAction.execute(updateRequest, this.model);
 
@@ -215,9 +214,9 @@ public BindingSet handleRemovedKnowledgeBaseKnowledge(ReactExchangeInfo ei) {
 			// - extract the knowledge base that this message is about
 			// - delete all old data about that knowledge base
 
-			Resource kb = model.query(new SimpleSelector(null, RDF.type, Vocab.KNOWLEDGE_BASE)).listSubjects().next();
-			String query = String.format("DELETE { %s } WHERE { %s FILTER (?kb = <%s>) } ",
-					this.metaGraphPattern.getPattern(), this.metaGraphPattern.getPattern(), kb.toString());
+			Resource kb = model.listSubjectsWithProperty(RDF.type, Vocab.KNOWLEDGE_BASE).next();
+			String query = String.format("DELETE { %s } WHERE { %s FILTER (?kb = <%s>) } ", this.metaGraphPattern.getPattern(), this.metaGraphPattern.getPattern(), kb.toString());
+
 			UpdateRequest updateRequest = UpdateFactory.create(query);
 			UpdateAction.execute(updateRequest, this.model);
 

pom.xml

@@ -82,7 +82,7 @@
 			<dependency>
 				<groupId>org.apache.jena</groupId>
 				<artifactId>apache-jena-libs</artifactId>
-				<version>4.10.0</version>
+				<version>5.2.0</version>
 				<type>pom</type>
 			</dependency>
 		</dependencies>

reasoner/src/main/java/eu/knowledge/engine/reasoner/api/Binding.java

@@ -4,30 +4,28 @@
 import java.util.Map;
 
 import org.apache.jena.graph.Node;
-import org.apache.jena.graph.Node_Concrete;
 
 import org.apache.jena.sparql.core.Var;
 import org.apache.jena.sparql.graph.PrefixMappingZero;
 import org.apache.jena.sparql.sse.SSE;
 import org.apache.jena.sparql.util.FmtUtils;
 
-import eu.knowledge.engine.reasoner.api.Binding;
 
-public class Binding extends HashMap<Var, Node_Concrete> {
+public class Binding extends HashMap<Var, Node> {
 
 	private static final long serialVersionUID = 2381462612239850018L;
 
 	public Binding() {
 		super();
 	}
 
-	public Binding(Var variable, Node_Concrete lit) {
+	public Binding(Var variable, Node lit) {
 		super();
 		this.put(variable, lit);
 	}
 
 	public Binding(String variable, String val) {
-		this(Var.alloc(variable), (Node_Concrete) SSE.parseNode(val));
+		this(Var.alloc(variable), (Node) SSE.parseNode(val));
 	}
 
 	public Binding(Binding b) {
@@ -48,13 +46,13 @@ public Node get(String variable) {
 	}
 
 	public Node put(String variable, String val) {
-		return this.put(Var.alloc(variable), (Node_Concrete) SSE.parseNode(val));
+		return this.put(Var.alloc(variable), (Node) SSE.parseNode(val));
 	}
 
 	public Map<String, String> toMap() {
 
 		Map<String, String> result = new HashMap<String, String>();
-		for (Map.Entry<Var, Node_Concrete> entry : this.entrySet()) {
+		for (Map.Entry<Var, Node> entry : this.entrySet()) {
 			// TODO: Util function that does the stringForNode without prefixes
 			result.put(entry.getKey().getName(), FmtUtils.stringForNode(entry.getValue(), new PrefixMappingZero()));
 		}

reasoner/src/main/java/eu/knowledge/engine/reasoner/api/TripleVarBinding.java

@@ -6,7 +6,6 @@
 import java.util.Set;
 
 import org.apache.jena.graph.Node;
-import org.apache.jena.graph.Node_Concrete;
 import org.apache.jena.sparql.core.Var;
 import org.apache.jena.sparql.graph.PrefixMappingZero;
 import org.apache.jena.sparql.sse.SSE;
@@ -20,7 +19,7 @@
  */
 public class TripleVarBinding {
 
-	private Map<TripleNode, Node_Concrete> tripleVarMapping;
+	private Map<TripleNode, Node> tripleVarMapping;
 
 	/**
 	 * Optimize the getVarValue method.
@@ -57,7 +56,7 @@ public TripleVarBinding(Set<TriplePattern> aGraphPattern, Binding aBinding) {
 
 	public TripleVarBinding(TripleVarBinding b) {
 		this();
-		for (Map.Entry<TripleNode, Node_Concrete> entry : b.tripleVarMapping.entrySet()) {
+		for (Map.Entry<TripleNode, Node> entry : b.tripleVarMapping.entrySet()) {
 			this.put(entry.getKey(), entry.getValue());
 		}
 
@@ -66,23 +65,23 @@ public TripleVarBinding(TripleVarBinding b) {
 		}
 	}
 
-	public Set<Map.Entry<TripleNode, Node_Concrete>> entrySet() {
+	public Set<Map.Entry<TripleNode, Node>> entrySet() {
 		return tripleVarMapping.entrySet();
 	}
 
 	public Set<TripleNode> getTripleVars() {
 		return tripleVarMapping.keySet();
 	}
 
-	public void put(TripleNode aTripleVar, Node_Concrete aLiteral) {
+	public void put(TripleNode aTripleVar, Node aLiteral) {
 		assert aTripleVar.node.isVariable();
 		tripleVarMapping.put(aTripleVar, aLiteral);
 		variableTripleVarMapping.put((Var) aTripleVar.node, aTripleVar);
 	}
 
 	public void put(TripleNode aTripleVar, String aLiteral) {
 		assert aTripleVar.node.isVariable();
-		tripleVarMapping.put(aTripleVar, (Node_Concrete) SSE.parseNode(aLiteral));
+		tripleVarMapping.put(aTripleVar, (Node) SSE.parseNode(aLiteral));
 		variableTripleVarMapping.put((Var) aTripleVar.node, aTripleVar);
 	}
 
@@ -97,7 +96,7 @@ public void put(TripleNode aTripleVar, String aLiteral) {
 	public Binding toBinding() {
 
 		Binding b = new Binding();
-		for (Map.Entry<TripleNode, Node_Concrete> entry : this.tripleVarMapping.entrySet()) {
+		for (Map.Entry<TripleNode, Node> entry : this.tripleVarMapping.entrySet()) {
 			assert entry.getKey().node.isVariable();
 			b.put((Var) entry.getKey().node, entry.getValue());
 		}
@@ -111,7 +110,7 @@ public Binding toBinding() {
 	public boolean isConflicting(TripleVarBinding tvb) {
 
 		Node l;
-		for (Map.Entry<TripleNode, Node_Concrete> e : this.tripleVarMapping.entrySet()) {
+		for (Map.Entry<TripleNode, Node> e : this.tripleVarMapping.entrySet()) {
 			assert e.getKey().node.isVariable();
 			l = tvb.getVarValue((Var) e.getKey().node);
 
@@ -126,15 +125,15 @@ public boolean isConflicting(TripleVarBinding tvb) {
 	 * We assume all occurrences of a var have the same literal, we just return the
 	 * first one found.
 	 * 
-	 * @param var
+	 * @param variable
 	 * @return
 	 */
-	public Node_Concrete getVarValue(Var variable) {
+	public Node getVarValue(Var variable) {
 		TripleNode tripleVar = this.variableTripleVarMapping.get(variable);
 		return this.get(tripleVar);
 	}
 
-	public Node_Concrete get(TripleNode key) {
+	public Node get(TripleNode key) {
 		return this.tripleVarMapping.get(key);
 	}
 
@@ -196,7 +195,7 @@ public String toString() {
 		StringBuilder sb = new StringBuilder();
 		String prefix = "";
 		sb.append("{");
-		for (Map.Entry<TripleNode, Node_Concrete> entry : this.tripleVarMapping.entrySet()) {
+		for (Map.Entry<TripleNode, Node> entry : this.tripleVarMapping.entrySet()) {
 			sb.append(prefix).append(entry.getKey().node).append("=")
 					.append(FmtUtils.stringForNode(entry.getValue(), new PrefixMappingZero()));
 			prefix = ",";
@@ -228,7 +227,7 @@ public TripleVarBinding merge(TripleVarBinding otherB) {
 		return b;
 	}
 
-	private void putAll(Map<TripleNode, Node_Concrete> aTripleVarMapping) {
+	private void putAll(Map<TripleNode, Node> aTripleVarMapping) {
 
 		for (TripleNode tv : aTripleVarMapping.keySet()) {
 			assert tv.node.isVariable();

reasoner/src/main/java/eu/knowledge/engine/reasoner/api/TripleVarBindingSet.java

@@ -8,7 +8,6 @@
 import java.util.concurrent.ConcurrentHashMap;
 
 import org.apache.jena.graph.Node;
-import org.apache.jena.graph.Node_Concrete;
 import org.apache.jena.sparql.core.Var;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -153,7 +152,7 @@ public String toString() {
 	/**
 	 * Simply the union between the two bindingsets. Does nothing complex for now.
 	 * 
-	 * @param gbs
+	 * @param aGraphBindingSet
 	 * @return
 	 */
 	public TripleVarBindingSet merge(TripleVarBindingSet aGraphBindingSet) {
@@ -232,18 +231,18 @@ public TripleVarBindingSet translate(Set<TriplePattern> graphPattern, Set<Match>
 									&& !fromB.get(fromTVar).equals(toBVarValue)) {
 								skip = true; // conflict, so skip
 							}
-						} else if (fromTNode.node instanceof Var && toTNode.node instanceof Node_Concrete) {
+						} else if (fromTNode.node instanceof Var && toTNode.node instanceof Node && toTNode.node.isConcrete() ) {
 							var fromTVar = new TripleNode(fromTriple, (Var) fromTNode.node, fromTNode.nodeIdx);
 							if (fromB.containsKey(fromTVar) && !fromB.get(fromTVar).equals(toTNode.node)) {
 								skip = true; // conflict, so skip
 							}
-						} else if (fromTNode.node instanceof Node_Concrete && toTNode.node instanceof Var) {
+						} else if (fromTNode.node instanceof Node && fromTNode.node.isConcrete() && toTNode.node instanceof Var) {
 							var toTVar = new TripleNode(toTriple, (Var) toTNode.node, toTNode.nodeIdx);
 							if (toB.containsVar((Var) toTVar.node)
 									&& !toB.getVarValue((Var) toTVar.node).equals(fromTNode.node)) {
 								skip = true;
 							} else if (!toB.containsVar((Var) toTVar.node)) {
-								toB.put(toTVar, (Node_Concrete) fromTNode.node);
+								toB.put(toTVar, (Node) fromTNode.node);
 							}
 						}
 					}
@@ -332,9 +331,9 @@ public void printDebuggingTable() {
 				Set<TripleNode> nodes = tvb.getTripleNodes(tp);
 				if (!nodes.isEmpty()) {
 
-					Node_Concrete subject = null;
-					Node_Concrete predicate = null;
-					Node_Concrete object = null;
+					Node subject = null;
+					Node predicate = null;
+					Node object = null;
 
 					for (TripleNode tn : nodes) {
 						if (tn.nodeIdx == 0) {

reasoner/src/main/java/eu/knowledge/engine/reasoner/rulenode/BindingSetStore.java

@@ -8,7 +8,6 @@
 import java.util.Set;
 
 import org.apache.jena.graph.Node;
-import org.apache.jena.graph.Node_Concrete;
 
 import eu.knowledge.engine.reasoner.BaseRule;
 import eu.knowledge.engine.reasoner.api.TripleNode;
@@ -160,9 +159,9 @@ public void printDebuggingTable() {
 						Set<TripleNode> nodes = tvb.getTripleNodes(tp);
 						if (!nodes.isEmpty()) {
 
-							Node_Concrete subject = null;
-							Node_Concrete predicate = null;
-							Node_Concrete object = null;
+							Node subject = null;
+							Node predicate = null;
+							Node object = null;
 
 							for (TripleNode tn : nodes) {
 								if (tn.nodeIdx == 0) {

reasoner/src/test/java/eu/knowledge/engine/reasoner/JenaRDFSRulesTest.java

@@ -91,7 +91,7 @@ public void test() throws InterruptedException, ExecutionException, ParseExcepti
 
 		Model m = ModelFactory.createDefaultModel();
 		for (Binding binding : results2) {
-			m.add(m.asStatement(new Triple(binding.get("s"), binding.get("p"), binding.get("o"))));
+			m.add(m.asStatement(Triple.create(binding.get("s"), binding.get("p"), binding.get("o"))));
 		}
 
 //		Model m = Util.generateModel(new TriplePattern(genericTriple), results2);

reasoner/src/test/java/eu/knowledge/engine/reasoner/api/BindingTest.java

@@ -8,18 +8,11 @@
 import java.util.Set;
 
 import org.apache.jena.graph.Node;
-import org.apache.jena.graph.Node_Concrete;
 import org.apache.jena.sparql.graph.PrefixMappingZero;
 import org.apache.jena.sparql.sse.SSE;
 import org.apache.jena.sparql.util.FmtUtils;
 import org.junit.jupiter.api.Test;
 
-import eu.knowledge.engine.reasoner.api.Binding;
-import eu.knowledge.engine.reasoner.api.BindingSet;
-import eu.knowledge.engine.reasoner.api.TriplePattern;
-import eu.knowledge.engine.reasoner.api.TripleNode;
-import eu.knowledge.engine.reasoner.api.TripleVarBinding;
-import eu.knowledge.engine.reasoner.api.TripleVarBindingSet;
 
 public class BindingTest {
 
@@ -28,7 +21,7 @@ public void testGraphPatternBindingSets() {
 		TriplePattern t1 = new TriplePattern("?a <type> <Sensor>");
 		TriplePattern t2 = new TriplePattern("?a <hasVal> ?b");
 		TripleVarBinding tb1 = new TripleVarBinding();
-		tb1.put(new TripleNode(t1, "?a", 0), (Node_Concrete) SSE.parseNode("<sensor1>"));
+		tb1.put(new TripleNode(t1, "?a", 0), (Node) SSE.parseNode("<sensor1>"));
 
 		TripleVarBinding tb2 = new TripleVarBinding();
 		tb2.put(new TripleNode(t2, "?b", 2), "22");

reasoner/src/test/java/eu/knowledge/engine/reasoner/api/Util.java

@@ -102,7 +102,7 @@ public static Model generateModel(TriplePattern tp, BindingSet variableBindings)
 				newNodes[i] = newN;
 			}
 
-			m.add(m.asStatement(new Triple(newNodes[0], newNodes[1], newNodes[2])));
+			m.add(m.asStatement(Triple.create(newNodes[0], newNodes[1], newNodes[2])));
 		}
 		return m;
 	}

smart-connector-api/src/main/java/eu/knowledge/engine/smartconnector/api/KnowledgeInteraction.java

@@ -1,6 +1,5 @@
 package eu.knowledge.engine.smartconnector.api;
 
-import com.fasterxml.jackson.core.format.MatchStrength;
 
 /**
  * A {@link KnowledgeInteraction} represents an agreement about the exchange of

smart-connector/src/main/java/eu/knowledge/engine/smartconnector/impl/ReasonerProcessor.java

@@ -10,7 +10,7 @@
 import java.util.concurrent.CompletableFuture;
 import java.util.concurrent.ConcurrentHashMap;
 
-import org.apache.jena.graph.Node_Concrete;
+import org.apache.jena.graph.Node;
 import org.apache.jena.sparql.core.TriplePath;
 import org.apache.jena.sparql.core.Var;
 import org.apache.jena.sparql.graph.PrefixMappingZero;
@@ -294,7 +294,7 @@ protected BindingSet translateBindingSetFrom(eu.knowledge.engine.reasoner.api.Bi
 
 		for (eu.knowledge.engine.reasoner.api.Binding b : bs) {
 			newB = new Binding();
-			for (Map.Entry<Var, Node_Concrete> entry : b.entrySet()) {
+			for (Map.Entry<Var, Node> entry : b.entrySet()) {
 				newB.put(entry.getKey().getName(), FmtUtils.stringForNode(entry.getValue(), context));
 			}
 			newBS.add(newB);
@@ -305,7 +305,7 @@ protected BindingSet translateBindingSetFrom(eu.knowledge.engine.reasoner.api.Bi
 	/**
 	 * Translate bindingset from the ke bindingset to the reasoner bindingset.
 	 * 
-	 * @param bs a ke bindingset
+	 * @param someBindings a ke bindingset
 	 * @return a reasoner bindingset
 	 */
 	protected eu.knowledge.engine.reasoner.api.BindingSet translateBindingSetTo(BindingSet someBindings) {

smart-connector/src/main/java/eu/knowledge/engine/smartconnector/impl/Util.java

@@ -100,7 +100,7 @@ public static Model generateModel(GraphPattern graphPattern, BindingSet variable
 					newNodes[i] = newN;
 				}
 
-				m.add(m.asStatement(new Triple(newNodes[0], newNodes[1], newNodes[2])));
+				m.add(m.asStatement(Triple.create(newNodes[0], newNodes[1], newNodes[2])));
 			}
 		}
 		return m;

smart-connector/src/test/java/eu/knowledge/engine/smartconnector/impl/TestBindingSetConversions.java

@@ -8,7 +8,7 @@
 import org.apache.jena.datatypes.xsd.XSDDatatype;
 import org.apache.jena.graph.Node;
 import org.apache.jena.graph.NodeFactory;
-import org.apache.jena.graph.Node_Concrete;
+import org.apache.jena.graph.Node;
 import org.apache.jena.sparql.core.Var;
 import org.junit.jupiter.api.Test;
 
@@ -41,7 +41,7 @@ void testTypedLiteral() {
 
 		eu.knowledge.engine.reasoner.api.BindingSet bsR = new eu.knowledge.engine.reasoner.api.BindingSet();
 		eu.knowledge.engine.reasoner.api.Binding bR = new eu.knowledge.engine.reasoner.api.Binding();
-		bR.put(varNodeVersion, (Node_Concrete) literalNodeVersion);
+		bR.put(varNodeVersion, (Node) literalNodeVersion);
 		bsR.add(bR);
 		BindingSet otherBS = rp.testerFrom(bsR);
 		assertEquals(literalStringVersion, otherBS.iterator().next().get(varStringVersion));