Merge branch 'shacl-1.4.0'

.settings/org.eclipse.jdt.core.prefs

@@ -1,5 +1,8 @@
 eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
-org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=11
+org.eclipse.jdt.core.compiler.compliance=11
+org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
 org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
-org.eclipse.jdt.core.compiler.source=1.8
+org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=ignore
+org.eclipse.jdt.core.compiler.release=enabled
+org.eclipse.jdt.core.compiler.source=11

README.md

@@ -10,13 +10,15 @@ This API also serves as a reference implementation of the SHACL spec.
 Coverage:
 * [SHACL Core and SHACL-SPARQL validation](https://www.w3.org/TR/shacl/)
 * [SHACL Advanced Features (Rules etc)](https://www.w3.org/TR/shacl-af/)
-* [SHACL JavaScript Extensions](https://www.w3.org/TR/shacl-js/)
 * [SHACL Compact Syntax](https://w3c.github.io/shacl/shacl-compact-syntax/)
 
+Former Coverage until version 1.3.2
+* [SHACL JavaScript Extensions](https://www.w3.org/TR/shacl-js/)
+
 The TopBraid SHACL API is internally used by the European Commission's generic [SHACL-based RDF validator](https://www.itb.ec.europa.eu/shacl/any/upload) (used to validate RDF content against SHACL shapes)
 and [SHACL shape validator](https://www.itb.ec.europa.eu/shacl/shacl/upload) (used to validate SHACL shapes themselves).
 
-The same code is used in the TopBraid products (currently aligned with the TopBraid 6.3 release).
+The same code is used in the TopBraid products (currently aligned with the TopBraid 7.1 release).
 
 Feedback and questions should become GitHub issues or sent to TopBraid Users mailing list:
 https://groups.google.com/forum/#!forum/topbraid-users

pom.xml

@@ -22,7 +22,7 @@
 
   <groupId>org.topbraid</groupId>
   <artifactId>shacl</artifactId>
-  <version>1.3.3-SNAPSHOT</version>
+  <version>1.4.0</version>
   <packaging>jar</packaging>
 
   <name>TopBraid SHACL API</name>
@@ -63,7 +63,7 @@
     <url>https://github.com/TopQuadrant/shacl</url>
     <connection>scm:git:https://github.com/TopQuadrant/shacl</connection>
     <developerConnection>scm:git:[email protected]:TopQuadrant/shacl.git</developerConnection>
-    <tag>shacl-1.3.2</tag>
+    <tag>shacl-1.4.0</tag>
   </scm>
 
   <properties>

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

@@ -18,6 +18,7 @@
 
 import java.util.Iterator;
 
+import org.apache.jena.query.ARQ;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.sparql.function.FunctionFactory;
 import org.apache.jena.sparql.function.FunctionRegistry;
@@ -59,26 +60,45 @@ 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.
 	 * @param model  the Model containing the SPIN functions
-	 * @return any old object that was registered for the current Thread, so that
-	 *         the old value can be restored when done.
+	 * @return a Runnable that must be called (in a finally block) when done to restore the previous state
 	 */
-	public static CurrentThreadFunctions register(Model model) {
+	public static Runnable register(Model model) {
 		CurrentThreadFunctions old = localFunctions.get();
 		CurrentThreadFunctions neo = new CurrentThreadFunctions(model);
 		localFunctions.set(neo);
-		return old;
+		FunctionRegistry oldFR = FunctionRegistry.get();
+		if(oldFR != singleton) {
+			FunctionRegistry.set(ARQ.getContext(), singleton);
+			return () -> {
+				unregister(old);
+				FunctionRegistry.set(ARQ.getContext(), oldFR);
+			};
+		}
+		else {
+			return () -> {
+				unregister(old);
+			};
+		}
 	}
 
 
 	/**
 	 * Unregisters the current Model for the current Thread.
 	 * @param old  the old functions that shall be restored or null
 	 */
-	public static void unregister(CurrentThreadFunctions old) {
+	private static void unregister(CurrentThreadFunctions old) {
 		if(old != null) {
 			localFunctions.set(old);
 		}
@@ -93,7 +113,7 @@ public static CurrentThreadFunctions getFunctions() {
 
 	private FunctionRegistry base;
 
-	public CurrentThreadFunctionRegistry(FunctionRegistry base) {
+	private CurrentThreadFunctionRegistry(FunctionRegistry base) {
 		this.base = base;
 	}
 

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

@@ -28,15 +28,15 @@
 import org.apache.jena.rdf.model.StmtIterator;
 import org.topbraid.jenax.util.JenaDatatypes;
 import org.topbraid.jenax.util.JenaUtil;
-import org.topbraid.shacl.arq.SHACLFunctionDriver;
+import org.topbraid.shacl.arq.functions.SHACLSPARQLFunctionDriver;
 import org.topbraid.shacl.vocabulary.DASH;
 import org.topbraid.shacl.vocabulary.SH;
 
 
 /**
  * The singleton that creates ARQ FunctionFactories from (SHACL, SPIN) function declarations.
  * Can be used by applications to install a different singleton with support
- * for different kinds of functions, such as SPINx.
+ * for different kinds of functions, such as SHACL-JS or Script-based functions.
  * 
  * @author Holger Knublauch
  */
@@ -58,9 +58,8 @@ public static void set(DeclarativeFunctionDrivers value) {
 	private Map<Property,DeclarativeFunctionDriver> drivers = new HashMap<>();
 
 	DeclarativeFunctionDrivers() {
-		register(SH.ask, new SHACLFunctionDriver());
-		register(SH.select, new SHACLFunctionDriver());
-		register(SH.jsLibrary, new SHACLFunctionDriver());
+		register(SH.ask, new SHACLSPARQLFunctionDriver());
+		register(SH.select, new SHACLSPARQLFunctionDriver());
 	}
 
 

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

@@ -93,12 +93,6 @@ public Iterator<Node> listGraphNodes() {
 
 
 	@Override
-    public PrefixMap prefixes() {
-        return Prefixes.adapt(dataset.getPrefixMapping());
-    }
-
-
-    @Override
 	public Iterator<Quad> find(Node g, Node s, Node p, Node o) {
 		// TODO Auto-generated method stub
 		throw new UnsupportedOperationException();
@@ -239,4 +233,14 @@ public void end() {
 	public boolean supportsTransactions() {
 		return dataset.supportsTransactions();
 	}
+
+
+	@Override
+	public PrefixMap prefixes() {
+		Model defaultModel = dataset.getDefaultModel();
+		if (defaultModel != null) {
+			return Prefixes.adapt(defaultModel);
+		}
+		return null;
+	}
 }

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

@@ -14,13 +14,21 @@
 import org.apache.jena.util.iterator.ExtendedIterator;
 
 
-// TODO: note this graph does not correctly implement GraphWithPerform and event notification contracts
 /**
  * A WrappedGraph that filters out deleted triples or adds added triples, without
  * modifying the underlying base graph.
  * 
- * Similar to BufferingGraph in TopBraid, but with minimal code dependencies
- * and simpler contracts that are just right for use in SPARQLMotion.
+ * This class is for single-threaded use only, typically used as temporary graph layer on top of an existing
+ * graph for the duration of some algorithm.
+ *   
+ * This runs in two modes, based on the updateBaseGraph flag.
+ * 
+ * By default/legacy (false) the system will only add triples that exist in none of the subgraphs of the delegate graph
+ * and claim to delete triples even if they exist in subgraphs only.
+ * 
+ * If true, the adds will always be applied even if one of the subgraphs already contains the triple.
+ * This is making sure that transformations will always produce all requested triples.
+ * Furthermore this mode is more correct w.r.t. deletes because it will only allow deleting triples from the editable graph.
  * 
  * @author Holger Knublauch
  */
@@ -32,16 +40,29 @@ public class DiffGraph extends TransparentWrappedGraph {
 	protected GraphWithPerform addedGraph = new GraphMem();
 
 	/**
-	 * This Set has triples that are in the delegate but are excluded
-	 * from the filtered graph.
+	 * This Set has triples that are in the delegate but are excluded from the filtered graph.
 	 */
-	protected Set<Triple> deletedTriples = new HashSet<Triple>();
+	protected Set<Triple> deletedTriples = new HashSet<>();
 
 	private PrefixMapping pm;
 
+	// The graph that the triples will be added to
+	private Graph updateableGraph;
+
 
-	public DiffGraph(Graph base) {
-		super(base);
+	public DiffGraph(Graph delegate) {
+		this(delegate, false);
+	}
+
+
+	public DiffGraph(Graph delegate, boolean updateBaseGraph) {
+		super(delegate);
+		if(updateBaseGraph) {
+			updateableGraph = JenaUtil.getBaseGraph(delegate);
+		}
+		else {
+			updateableGraph = delegate;
+		}
 	}
 
 
@@ -91,7 +112,7 @@ public boolean contains(Triple t) {
 	// but sameValueAs then this code is incorrect.
 	// Specifically we should be able to show bugs with TDB which does
 	// something different from either equals or sameValueAs.
-	protected boolean containsByEquals(Graph g,Triple t) {
+	protected boolean containsByEquals(Graph g, Triple t) {
 		ExtendedIterator<Triple> it = g.find(t);
 		try {
 			while (it.hasNext()) {
@@ -179,34 +200,21 @@ public boolean isIsomorphicWith(Graph g) {
 	public void performAdd(Triple t) {
     	if (deletedTriples.contains(t)) {
     		deletedTriples.remove(t);
-    		// getEventManager().notifyAddTriple(this, t);
     	}
-    	else if (containsByEquals(addedGraph,t) || containsByEquals(base, t) ) {
-    		// notify even unsuccessful adds - see javadoc for graphlistener
-    		// getEventManager().notifyAddTriple(this, t);
-        }
-    	else {
-    		// addedGraph does notification for us.
+    	else if(!containsByEquals(addedGraph, t) && !containsByEquals(updateableGraph, t)) {
     		addedGraph.add(t);
     	}
 	}
 
 
 	@Override
 	public void performDelete(Triple t) {
-		if( containsByEquals(addedGraph,t) ) {
-			// addedGraph does notification for us.
+		if(containsByEquals(addedGraph, t)) {
 			addedGraph.delete(t);
 		} 
-		else if ( containsByEquals(base, t) ) {
+		else if(containsByEquals(updateableGraph, t)) {
 			deletedTriples.add(t);
-			// getEventManager().notifyDeleteTriple(this, t);
 		} 
-		else {
-			// notify even unsuccessful deletes - see javadoc for graphlistener
-			// getEventManager().notifyDeleteTriple(this, t);
-			return;
-		}
 	}
 
 

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

@@ -117,7 +117,7 @@ public static <EX extends Throwable> EX throwDeepCauseChecked(Throwable t, Class
 		}
 		catch (Exception e) {
 			try {
-				rslt = clazz.newInstance();
+				rslt = clazz.getDeclaredConstructor().newInstance();
 				rslt.initCause(t);
 			}
 			catch (Exception e1) {
@@ -166,6 +166,7 @@ public static String getDeepMessage(Throwable t) {
 	}
 
 	public static String getStackTrace(Throwable t) {
+		if (t == null) return null;
 		StringWriter writer = new StringWriter();
 		t.printStackTrace(new PrintWriter(writer));
 		return writer.getBuffer().toString();

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

@@ -34,12 +34,12 @@ public class ExtraPrefixes {
 	private static Map<String,String> map = new HashMap<String,String>();
 
 	static {
-		map.put("afn",  "http://jena.apache.org/ARQ/function#");
-		map.put("fn",   "http://www.w3.org/2005/xpath-functions#");
-		map.put("jfn",  "java:org.apache.jena.sparql.function.library.");
+		map.put("afn", "http://jena.hpl.hp.com/ARQ/function#");
+		map.put("fn", "http://www.w3.org/2005/xpath-functions#");
+		map.put("jfn", "java:org.apache.jena.sparql.function.library.");
 		map.put("list", "http://jena.apache.org/ARQ/list#");
-		map.put("pf",   "http://jena.apache.org/ARQ/property#");
-		map.put("smf",  "http://topbraid.org/sparqlmotionfunctions#");
+		map.put("pf", "http://jena.hpl.hp.com/ARQ/property#");
+		map.put("smf", "http://topbraid.org/sparqlmotionfunctions#");
 		map.put("tops", "http://www.topbraid.org/tops#");
 	}
 

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

@@ -80,6 +80,7 @@
 import org.apache.jena.sparql.util.Context;
 import org.apache.jena.sparql.util.NodeFactoryExtra;
 import org.apache.jena.sparql.util.NodeUtils;
+import org.apache.jena.util.iterator.ExtendedIterator;
 import org.apache.jena.vocabulary.OWL;
 import org.apache.jena.vocabulary.RDF;
 import org.apache.jena.vocabulary.RDFS;
@@ -498,11 +499,12 @@ public static Literal getBestStringLiteral(Resource resource, List<String> langs
 	}
 
 
-	public static Literal getBestStringLiteral(Resource resource, List<String> langs, Iterable<Property> properties, BiFunction<Resource,Property,Iterator<Statement>> getter) {
+	public static Literal getBestStringLiteral(Resource resource, List<String> langs, Iterable<Property> properties, BiFunction<Resource,Property,ExtendedIterator<Statement>> getter) {
+		String prefLang = langs.isEmpty() ? null : langs.get(0);
 		Literal label = null;
 		int bestLang = -1;
 		for(Property predicate : properties) {
-			Iterator<Statement> it = getter.apply(resource, predicate);
+			ExtendedIterator<Statement> it = getter.apply(resource, predicate);
 			while(it.hasNext()) {
 				RDFNode object = it.next().getObject();
 				if(object.isLiteral()) {
@@ -511,18 +513,22 @@ public static Literal getBestStringLiteral(Resource resource, List<String> langs
 					if(lang.length() == 0 && label == null) {
 						label = literal;
 					}
+					else if(prefLang != null && prefLang.equalsIgnoreCase(lang)) {
+						it.close();
+						return literal;
+					}
 					else {
 						// 1) Never use a less suitable language
 						// 2) Never replace an already existing label (esp: skos:prefLabel) unless new lang is better
 						// 3) Fall back to more special languages if no other was found (e.g. use en-GB if only "en" is accepted)
 						int startLang = bestLang < 0 ? langs.size() - 1 : (label != null ? bestLang - 1 : bestLang);
-						for(int i = startLang; i >= 0; i--) {
+						for(int i = startLang; i > 0; i--) {
 							String langi = langs.get(i);
 							if(langi.equalsIgnoreCase(lang)) {
 								label = literal;
 								bestLang = i;
 							}
-							else if(lang.contains("-") && NodeFunctions.langMatches(lang, langi) && label == null) {
+							else if(label == null && lang.contains("-") && NodeFunctions.langMatches(lang, langi)) {
 								label = literal;
 							}
 						}

src/main/java/org/topbraid/shacl/arq/SHACLARQFunction.java

@@ -27,11 +27,11 @@
 import org.apache.jena.graph.Node;
 import org.apache.jena.graph.NodeFactory;
 import org.apache.jena.query.Dataset;
+import org.apache.jena.query.DatasetFactory;
 import org.apache.jena.query.QuerySolution;
 import org.apache.jena.query.QuerySolutionMap;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
-import org.apache.jena.sparql.core.DatasetImpl;
 import org.apache.jena.sparql.core.Substitute;
 import org.apache.jena.sparql.engine.binding.Binding;
 import org.apache.jena.sparql.expr.Expr;
@@ -43,8 +43,8 @@
 import org.apache.jena.sparql.sse.SSE;
 import org.apache.jena.sparql.util.ExprUtils;
 import org.apache.jena.sparql.util.FmtUtils;
-import org.topbraid.jenax.functions.OptionalArgsFunction;
 import org.topbraid.jenax.functions.DeclarativeFunctionFactory;
+import org.topbraid.jenax.functions.OptionalArgsFunction;
 import org.topbraid.jenax.statistics.ExecStatistics;
 import org.topbraid.jenax.statistics.ExecStatisticsManager;
 import org.topbraid.jenax.util.JenaDatatypes;
@@ -154,7 +154,7 @@ else if(!optional.get(i)) {
 			}
 		}
 
-		Dataset dataset = DatasetImpl.wrap(env.getDataset());
+		Dataset dataset = DatasetFactory.wrap(env.getDataset());
 
 		if(ExecStatisticsManager.get().isRecording() && ExecStatisticsManager.get().isRecordingDeclarativeFunctions()) {
 			StringBuffer sb = new StringBuffer();