Upgrade Jena to 3.11.0 (#119)

Resolves: https://jira.duraspace.org/browse/VIVO-1693

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/RDFServiceDataset.java

@@ -14,6 +14,7 @@ import org.apache.jena.graph.NodeFactory;
 import org.apache.jena.query.Dataset;
 import org.apache.jena.query.LabelExistsException;
 import org.apache.jena.query.ReadWrite;
+import org.apache.jena.query.TxnType;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.shared.Lock;
 import org.apache.jena.sparql.core.DatasetGraph;
@@ -86,7 +87,7 @@ public class RDFServiceDataset implements Dataset {
     }
 
 	@Override
-	public void addNamedModel(String uri, Model model)
+	public Dataset addNamedModel(String uri, Model model)
 			throws LabelExistsException {
 		Iterator<Node> graphNodes = g.listGraphNodes();
 		while (graphNodes.hasNext()) {
@@ -97,6 +98,7 @@ public class RDFServiceDataset implements Dataset {
 			}
 		}
 		g.addGraph(NodeFactory.createURI(uri), model.getGraph());
+		return this;
 	}
 
 	@Override
@@ -105,19 +107,22 @@ public class RDFServiceDataset implements Dataset {
 	}
 
 	@Override
-	public void removeNamedModel(String uri) {
+	public Dataset removeNamedModel(String uri) {
 		g.removeGraph(NodeFactory.createURI(uri));
+		return this;
 	}
 
 	@Override
-	public void replaceNamedModel(String uri, Model model) {
+	public Dataset replaceNamedModel(String uri, Model model) {
 		removeNamedModel(uri);
 		addNamedModel(uri, model);
+		return this;
 	}
 
 	@Override
-	public void setDefaultModel(Model model) {
+	public Dataset setDefaultModel(Model model) {
 		g.setDefaultGraph(model.getGraph());
+		return this;
 	}
 
 	@Override
@@ -173,4 +178,23 @@ public class RDFServiceDataset implements Dataset {
 		return g.isEmpty();
 	}
 
+	@Override
+	public TxnType transactionType() {
+		return g.transactionType();
+	}
+
+	@Override
+	public boolean promote(Promote promote) {
+		return g.promote(promote);
+	}
+
+	@Override
+	public ReadWrite transactionMode() {
+		return g.transactionMode();
+	}
+
+	@Override
+	public void begin(TxnType txnType) {
+		g.begin(txnType);
+	}
 }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/RDFServiceDatasetGraph.java

@@ -15,6 +15,7 @@ import org.apache.jena.graph.NodeFactory;
 import org.apache.jena.graph.Triple;
 import org.apache.jena.query.QuerySolution;
 import org.apache.jena.query.ReadWrite;
+import org.apache.jena.query.TxnType;
 import org.apache.jena.shared.Lock;
 import org.apache.jena.shared.LockMRSW;
 import org.apache.jena.sparql.core.DatasetGraph;
@@ -36,6 +37,7 @@ public class RDFServiceDatasetGraph implements DatasetGraph {
     private Context context = new Context() ;
     private Map<String, RDFServiceGraph> graphCache = new ConcurrentHashMap<String, RDFServiceGraph>();
     private ReadWrite transactionMode;
+    private TxnType transactionType;
 
     public RDFServiceDatasetGraph(RDFService rdfService) {
         this.rdfService = rdfService;
@@ -52,9 +54,16 @@ public class RDFServiceDatasetGraph implements DatasetGraph {
         graphCache.clear();
     }
 
+    @Override
+    public void begin(TxnType txnType) {
+        this.transactionType = txnType;
+        graphCache.clear();
+    }
+
     @Override
     public synchronized void commit() {
         this.transactionMode = null;
+        this.transactionType = null;
         if (supportsTransactions(defaultGraph)) {
             defaultGraph.getTransactionHandler().commit();
         }
@@ -88,6 +97,21 @@ public class RDFServiceDatasetGraph implements DatasetGraph {
 
     @Override
     public boolean isInTransaction() {
+        return transactionMode != null || transactionType != null;
+    }
+
+    @Override
+    public TxnType transactionType() {
+        return transactionType;
+    }
+
+    @Override
+    public ReadWrite transactionMode() {
+        return transactionMode;
+    }
+
+    @Override
+    public boolean promote(Promote promote) {
         return false;
     }
 
@@ -253,9 +277,11 @@ public class RDFServiceDatasetGraph implements DatasetGraph {
         } else {
             RDFServiceGraph graph = new RDFServiceGraph(rdfService, arg0.getURI());
             graphCache.put(graphURI, graph);
-            if(transactionMode != null && supportsTransactions(graph)) {
+            if (supportsTransactions(graph)) {
+                if(transactionMode != null || transactionType != null) {
                     graph.getTransactionHandler().begin();
                 }
+            }
             return graph;
         }
     }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/adapters/AbstractModelDecorator.java

@@ -266,27 +266,27 @@ public abstract class AbstractModelDecorator implements Model {
 	}
 
 	@Override
-	public PrefixMapping setNsPrefix(String prefix, String uri) {
+	public Model setNsPrefix(String prefix, String uri) {
 		return inner.setNsPrefix(prefix, uri);
 	}
 
 	@Override
-	public PrefixMapping removeNsPrefix(String prefix) {
+	public Model removeNsPrefix(String prefix) {
 		return inner.removeNsPrefix(prefix);
 	}
 
 	@Override
-	public PrefixMapping setNsPrefixes(PrefixMapping other) {
+	public Model setNsPrefixes(PrefixMapping other) {
 		return inner.setNsPrefixes(other);
 	}
 
 	@Override
-	public PrefixMapping setNsPrefixes(Map<String, String> map) {
+	public Model setNsPrefixes(Map<String, String> map) {
 		return inner.setNsPrefixes(map);
 	}
 
 	@Override
-	public PrefixMapping withDefaultMappings(PrefixMapping map) {
+	public Model withDefaultMappings(PrefixMapping map) {
 		return inner.withDefaultMappings(map);
 	}
 
@@ -1100,7 +1100,7 @@ public abstract class AbstractModelDecorator implements Model {
 	}
 
 	@Override
-	public PrefixMapping clearNsPrefixMap() {
+	public Model clearNsPrefixMap() {
 		return inner.clearNsPrefixMap();
 	}
 
@@ -1108,4 +1108,14 @@ public abstract class AbstractModelDecorator implements Model {
 	public int numPrefixes() {
 		return inner.numPrefixes();
 	}
+
+	@Override
+	public RDFList getList(String s) {
+		return inner.getList(s);
+	}
+
+	@Override
+	public RDFList getList(Resource resource) {
+		return inner.getList(resource);
+	}
 }

api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/adapters/AbstractOntModelDecorator.java

@@ -305,27 +305,27 @@ public abstract class AbstractOntModelDecorator implements OntModel {
 	}
 
 	@Override
-	public PrefixMapping setNsPrefix(String prefix, String uri) {
+	public Model setNsPrefix(String prefix, String uri) {
 		return inner.setNsPrefix(prefix, uri);
 	}
 
 	@Override
-	public PrefixMapping removeNsPrefix(String prefix) {
+	public Model removeNsPrefix(String prefix) {
 		return inner.removeNsPrefix(prefix);
 	}
 
 	@Override
-	public PrefixMapping setNsPrefixes(PrefixMapping other) {
+	public Model setNsPrefixes(PrefixMapping other) {
 		return inner.setNsPrefixes(other);
 	}
 
 	@Override
-	public PrefixMapping setNsPrefixes(Map<String, String> map) {
+	public Model setNsPrefixes(Map<String, String> map) {
 		return inner.setNsPrefixes(map);
 	}
 
 	@Override
-	public PrefixMapping withDefaultMappings(PrefixMapping map) {
+	public Model withDefaultMappings(PrefixMapping map) {
 		return inner.withDefaultMappings(map);
 	}
 
@@ -400,16 +400,19 @@ public abstract class AbstractOntModelDecorator implements OntModel {
 	}
 
 	@Override
+	@Deprecated
 	public String setReaderClassName(String lang, String className) {
 		return inner.setReaderClassName(lang, className);
 	}
 
 	@Override
+	@Deprecated
 	public void resetRDFReaderF() {
 		inner.resetRDFReaderF();
 	}
 
 	@Override
+	@Deprecated
 	public String removeReader(String s) throws IllegalArgumentException {
 		return inner.removeReader(s);
 	}
@@ -425,16 +428,19 @@ public abstract class AbstractOntModelDecorator implements OntModel {
 	}
 
 	@Override
+	@Deprecated
 	public String setWriterClassName(String lang, String className) {
 		return inner.setWriterClassName(lang, className);
 	}
 
 	@Override
+	@Deprecated
 	public void resetRDFWriterF() {
 		inner.resetRDFWriterF();
 	}
 
 	@Override
+	@Deprecated
 	public String removeWriter(String s) throws IllegalArgumentException {
 		return inner.removeWriter(s);
 	}
@@ -1054,6 +1060,7 @@ public abstract class AbstractOntModelDecorator implements OntModel {
 	}
 
 	@Override
+	@Deprecated
 	public Object executeInTransaction(Command cmd) {
 		return inner.executeInTransaction(cmd);
 	}
@@ -1798,7 +1805,7 @@ public abstract class AbstractOntModelDecorator implements OntModel {
 	}
 
 	@Override
-	public PrefixMapping clearNsPrefixMap() {
+	public Model clearNsPrefixMap() {
 		return inner.clearNsPrefixMap();
 	}
 
@@ -1806,4 +1813,10 @@ public abstract class AbstractOntModelDecorator implements OntModel {
 	public int numPrefixes() {
 		return inner.numPrefixes();
 	}
+
+	@Override
+	public RDFList getList(String s) { return inner.getList(s); }
+
+	@Override
+	public RDFList getList(Resource resource) { return inner.getList(resource); }
 }

dependencies/pom.xml

@@ -93,7 +93,7 @@
         <dependency>
             <groupId>commons-fileupload</groupId>
             <artifactId>commons-fileupload</artifactId>
-            <version>1.3.3</version>
+            <version>1.4</version>
         </dependency>
         <dependency>
             <groupId>commons-io</groupId>
@@ -176,7 +176,7 @@
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-arq</artifactId>
-            <version>3.6.0</version>
+            <version>3.11.0</version>
             <exclusions>
                 <!-- Exclude OSGi bundles from jsonld-java -->
                 <exclusion>
@@ -192,17 +192,17 @@
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-core</artifactId>
-            <version>3.6.0</version>
+            <version>3.11.0</version>
         </dependency>
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-sdb</artifactId>
-            <version>3.6.0</version>
+            <version>3.11.0</version>
         </dependency>
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-tdb</artifactId>
-            <version>3.6.0</version>
+            <version>3.11.0</version>
         </dependency>
         <dependency>
             <groupId>org.apache.solr</groupId>