Upgrade to Apache Jena 6.0.0

.github/workflows/maven-test-pr.yml

@@ -10,7 +10,7 @@ jobs:
     strategy:
       matrix:
         distribution: [ "temurin", "corretto" ]
-        java: [ "17", "21" ]
+        java: [ "21", "25" ]
     name: Testing with Java ${{ matrix.java }} (${{ matrix.distribution }})
     steps:
       - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0

pom.xml

@@ -22,7 +22,7 @@
 
   <groupId>org.topbraid</groupId>
   <artifactId>shacl</artifactId>
-  <version>1.4.5-SNAPSHOT</version>
+  <version>1.5.0-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <name>TopBraid SHACL API</name>
@@ -68,11 +68,11 @@
 
   <properties>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-    <ver.jena>5.2.0</ver.jena>
+    <ver.jena>6.0.0</ver.jena>
     <ver.junit>4.13.2</ver.junit>
     <ver.slf4j>2.0.17</ver.slf4j>
     <ver.log4j2>2.25.2</ver.log4j2>
-    <java.version>17</java.version>
+    <java.version>21</java.version>
   </properties>
 
   <dependencies>

src/main/java/org/topbraid/jenax/functions/CurrentThreadFunctionRegistry.java

@@ -27,12 +27,12 @@
  * An ARQ FunctionRegistry that can be used to associate functions
  * with Threads, so that additional functions from a given Model can
  * be made visible depending on the SPARQL query thread.
- * 
+ *
  * <p>The contract of this class is very strict to prevent memory leaks:
  * Users always need to make sure that unregister is called as soon
  * as a query (block) ends, and to restore any old CurrentThreadFunctions
  * object that was registered before.  So a typical block would be:</p>
- * 
+ *
  * <code>
  * 	Model model = ... a Model with extra SHACL/SPIN functions
  * 	CurrentThreadFunctions old = CurrentThreadFunctionRegistry.register(model);
@@ -42,32 +42,32 @@
  * 	finally {
  * 		CurrentThreadFunctionRegistry.unregister(old);
  * 	}</code>
- * 
+ *
  * <p>In preparation of the above, the application should start up with code
  * such as</p>
- * 
+ *
  * <code>
  * 	FunctionRegistry oldFR = FunctionRegistry.get();
  *  CurrentThreadFunctionRegistry threadFR = new CurrentThreadFunctionRegistry(oldFR);
  *	FunctionRegistry.set(ARQ.getContext(), threadFR);
  * </code>
  *
  * <p>and (for SPIN) do the same for the SPINThreadPropertyFunctionRegistry.</p>
- * 
+ *
  * @author Holger Knublauch
  */
 public class CurrentThreadFunctionRegistry extends FunctionRegistry {
-	
+
 	private static ThreadLocal<CurrentThreadFunctions> localFunctions = new ThreadLocal<>();
-	
+
 	private static CurrentThreadFunctionRegistry singleton = new CurrentThreadFunctionRegistry(FunctionRegistry.get());
-	
-	
+
+
 	public static CurrentThreadFunctionRegistry get() {
 		return singleton;
 	}
 
-	
+
 	/**
 	 * Registers a set of extra SPIN functions from a given Model for the current
 	 * Thread.
@@ -92,8 +92,8 @@ public static Runnable register(Model model) {
 			};
 		}
 	}
-	
-	
+
+
 	/**
 	 * Unregisters the current Model for the current Thread.
 	 * @param old  the old functions that shall be restored or null
@@ -106,21 +106,21 @@ private static void unregister(CurrentThreadFunctions old) {
 			localFunctions.remove();
 		}
 	}
-	
+
 	public static CurrentThreadFunctions getFunctions() {
 		return localFunctions.get();
 	}
-	
+
 	private FunctionRegistry base;
-	
+
 	private CurrentThreadFunctionRegistry(FunctionRegistry base) {
 		this.base = base;
 	}
 
 
 	@Override
-	public FunctionFactory get(String uri) {
-		FunctionFactory b = base.get(uri);
+	public FunctionFactory getFunctionFactory(String uri) {
+		FunctionFactory b = base.getFunctionFactory(uri);
 		if(b != null) {
 			return b;
 		}
@@ -141,7 +141,7 @@ public boolean isRegistered(String uri) {
 			return true;
 		}
 		else {
-			return get(uri) != null;
+			return getFunctionFactory(uri) != null;
 		}
 	}
 
@@ -154,19 +154,21 @@ public Iterator<String> keys() {
 
 
 	@Override
-	public void put(String uri, Class<?> funcClass) {
+	public FunctionRegistry put(String uri, Class<?> funcClass) {
 		base.put(uri, funcClass);
+		return this;
 	}
 
 
 	@Override
-	public void put(String uri, FunctionFactory f) {
+	public FunctionRegistry put(String uri, FunctionFactory f) {
 		base.put(uri, f);
+		return this;
 	}
 
 
 	@Override
-	public FunctionFactory remove(String uri) {
-		return base.remove(uri);
+	public void remove(String uri) {
+	    base.remove(uri);
 	}
 }

src/main/java/org/topbraid/jenax/util/DiffGraph.java

@@ -149,7 +149,7 @@ public ExtendedIterator<Triple> find(Node s, Node p, Node o) {
 
     @Override
     public ExtendedIterator<Triple> find(Triple m) {
-        return find(m.getMatchSubject(), m.getMatchPredicate(), m.getMatchObject());
+        return find(m.getSubject(), m.getPredicate(), m.getObject());
     }
 
 

src/main/java/org/topbraid/jenax/util/ExceptionUtil.java

@@ -43,7 +43,7 @@ public static RuntimeException throwRootCauseUnchecked(Throwable t) {
 		return ExceptionUtil.throwDeepCauseChecked(t,RuntimeException.class);
 	}
 
-	
+
 	/**
 	 * Does not return:
 	 * throws an unchecked exception, based on <code>t</code>.
@@ -68,9 +68,9 @@ public static RuntimeException throwUnchecked(Throwable t) {
 		throw new RuntimeException(t);
 	}
 
-	
+
 	/**
-	 * Always 
+	 * Always
 	 * throw an exception; based on <code>t</code>.
 	 * The <code>getCause</code> chain of <code>t</code>
 	 * is analyzed, and then,
@@ -109,7 +109,7 @@ public static <EX extends Throwable> EX throwDeepCauseChecked(Throwable t, Class
 	    if (firstError!=null) { throw firstError; }
 	    if (firstEX!=null) { throw firstEX; }
 	    if (firstRTE!=null) { throw firstRTE; }
-	    
+
 	    // Wrap original problem in clazz.
 	    EX rslt = null;
 	    try {
@@ -138,11 +138,11 @@ public static <EX extends Throwable> EX throwDeepCauseChecked(Throwable t, Class
 	 * from its cause if the given throwable has no own message.
 	 * Will return null if no explicit message is provided
 	 * in the throwable or any of its causes.
-	 * 
+	 *
 	 * The intent is to get "The real message" instead of
 	 * "x.y.SomeException: The real message" when the throwable
 	 * bearing the real message is wrapped without a new message.
-	 * 
+	 *
 	 * @see Throwable#getMessage()
 	 * @see Throwable#getCause()
 	 */
@@ -164,7 +164,7 @@ public static String getDeepMessage(Throwable t) {
 		// It's a custom message, good!
 		return msg;
 	}
-	
+
 	public static String getStackTrace(Throwable t) {
 		if (t == null) return null;
 		StringWriter writer = new StringWriter();
@@ -181,21 +181,21 @@ private static <TT extends Throwable> TT chooseNonNullCorrectClass(Class<? exten
 
 	/**
 	 * True if the given throwable or one of its causes (via {@link Throwable#getCause()})
-	 * is an instance of the given class. 
+	 * is an instance of the given class.
 	 */
 	public static boolean hasDeepCause(Throwable t, Class<? extends Throwable> throwableClass) {
 		return t != null && getDeepCause(t, throwableClass) != null;
 	}
-	
+
 	@SuppressWarnings("unchecked")
 	public static <EX extends Throwable> EX getDeepCause(Throwable t, Class<? extends EX> clazz) {
 		if (t == null ) {
 		   throw new NullPointerException();
 	    }
 	    // Walk chain finding first item of each interesting class.
 	    for (Throwable tt=t;tt!=null;tt=tt.getCause()) {
-			if (clazz.isInstance(tt)) { 
-				return (EX)tt; 
+			if (clazz.isInstance(tt)) {
+				return (EX)tt;
 			}
 	    }
 		return null;
@@ -259,7 +259,6 @@ public static String shortenStackTraceForServletCall(String stackTrace) {
 	 *
 	 * @see #shortenStackTrace(String, String)
 	 */
-	@SuppressWarnings("serial")
 	public static Throwable withServletContainerStackOmitted(Throwable t) {
 		if (t == null) return null;
 		return new Throwable(t) {

src/main/java/org/topbraid/jenax/util/JenaUtil.java

@@ -1156,7 +1156,7 @@ private static Node invokeFunction(Resource function, ExprList args, Dataset dat
         DatasetGraph dsg = dataset.asDatasetGraph();
         Context cxt = ARQ.getContext().copy();
         cxt.set(ARQConstants.sysCurrentTime, NodeFactoryExtra.nowAsDateTime());
-        FunctionEnv env = new ExecutionContext(cxt, dsg.getDefaultGraph(), dsg, null);
+        FunctionEnv env = ExecutionContext.create(dsg, cxt);
         try {
             NodeValue r = expr.eval(BindingRoot.create(), env);
             if (r != null) {
@@ -1182,7 +1182,7 @@ public static Node invokeFunction3(Resource function, Node argument1, Node argum
      * @return a new Query with the bindings applied
      */
     public static Query queryWithSubstitutions(Query query, final Map<Var, Node> substitutions) {
-        Query result = QueryTransformOps.transform(query, substitutions);
+        Query result = QueryTransformOps.replaceVars(query, substitutions);
 
         // TODO: Replace this hack once there is a Jena patch
         if (result.hasHaving()) {

src/main/java/org/topbraid/jenax/util/JenaUtilHelper.java

@@ -20,7 +20,8 @@
 
 import org.apache.jena.graph.Graph;
 import org.apache.jena.graph.compose.MultiUnion;
-import org.apache.jena.mem.GraphMemBase;
+import org.apache.jena.mem.GraphMem;
+import org.apache.jena.memvalue.GraphMemValue;
 import org.apache.jena.ontology.OntModel;
 import org.apache.jena.ontology.OntModelSpec;
 import org.apache.jena.rdf.model.Model;
@@ -31,22 +32,22 @@
  * This is an extension point for the SPIN library
  * allowing modification of some low level utilities
  * that are exposed through {@link JenaUtil}.
- * 
+ *
  * Note: Unstable - should not be used outside of TopBraid.
- * 
+ *
  * @author Jeremy Carroll
  */
 public class JenaUtilHelper {
-	
+
 	/**
 	 * Return a multiunion.
 	 * @return the MultiUnion graph
 	 */
 	public MultiUnion createMultiUnion() {
 		return new MultiUnion();
 	}
-	
-	
+
+
 	/**
 	 * Return a multiunion, initialized with the given graphs.
 	 * @param graphs  the Graphs to convert
@@ -56,7 +57,7 @@ public MultiUnion createMultiUnion(Iterator<Graph> graphs) {
 		return new MultiUnion(graphs);
 	}
 
-	
+
 	/**
 	 * Return a multiunion, initialized with the given graphs.
 	 * @param graphs  the Graphs to convert
@@ -65,8 +66,8 @@ public MultiUnion createMultiUnion(Iterator<Graph> graphs) {
 	public MultiUnion createMultiUnion(Graph[] graphs) {
 		return new MultiUnion(graphs);
 	}
-	
-	
+
+
 	/**
 	 * A memory graph with no reification.
 	 * @return the default Graph
@@ -75,7 +76,7 @@ public Graph createDefaultGraph() {
 		return GraphFactory.createDefaultGraph();
 	}
 
-	
+
 	/**
 	 * Returns true if optimizations for faster graphs should
 	 * be applied; false if graph is slower. A typical fast graph
@@ -86,34 +87,35 @@ public Graph createDefaultGraph() {
 	 * @param graph A simple graph, not a {@link MultiUnion}
 	 * @return true if the graph is fast
 	 */
-	public boolean isMemoryGraph(Graph graph) {
-		return (graph instanceof GraphMemBase);
+	@SuppressWarnings("deprecation")
+    public boolean isMemoryGraph(Graph graph) {
+		return (graph instanceof GraphMem) || (graph instanceof GraphMemValue );
 	}
-	
-	
+
+
 	public Model asReadOnlyModel(Model m) {
 		return m;
 	}
-	
-	
+
+
 	public Graph asReadOnlyGraph(Graph g) {
 		return g;
 	}
-	
-	
+
+
 	public OntModel createOntologyModel(OntModelSpec spec, Model base) {
 		return ModelFactory.createOntologyModel(spec, base);
 	}
-	
-	
+
+
 	public Graph createConcurrentGraph() {
 		return createDefaultGraph();
 	}
-	
-	
+
+
 	public void setGraphReadOptimization(boolean b) {
 	}
-	
+
 	public Graph deepCloneReadOnlyGraph(Graph g) {
 		return asReadOnlyGraph(g);
 	}

src/main/java/org/topbraid/jenax/util/QueryExecutionFactoryFilter.java

@@ -60,7 +60,7 @@ public QueryExecution create(Query query, Model model, QuerySolution initialBind
         return QueryExecution.create()
                 .query(query)
                 .model(model)
-                .initialBinding(initialBinding)
+                .substitution(initialBinding)
                 .build();
     }