Merge pull request LinkedDataFragments#56 from awoods/update-jena

Update Jena to 3.11.0

Author: mielvds

.gitignore

@@ -15,6 +15,9 @@
 log/
 target/
 
+# VI
+*~
+
 ldf-server.json
 /data/
 /nbproject/

config-example.json

@@ -18,7 +18,13 @@
       "type": "HdtDatasource",
       "description": "Semantic Web Dog Food with an HDT back-end",
       "settings": { "file": "data/swdf.hdt" }
-    }
+    },
+    "vivo": {
+      "title": "Semantic TDB",
+      "type": "JenaTDBDatasource",
+      "description": "Semantic Web with a TDB back-end",
+      "settings": { "directory": "/tmp/tdbModels",
+                    "graph": "http://vitro.mannlib.cornell.edu/default/vitro-kb-2" }
   },
 
   "prefixes": {

pom.xml

@@ -60,12 +60,12 @@
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-core</artifactId>
-            <version>3.1.0</version>
+            <version>3.11.0</version>
         </dependency>
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-arq</artifactId>
-            <version>3.1.0</version>
+            <version>3.11.0</version>
         </dependency>
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
@@ -113,7 +113,7 @@
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-tdb</artifactId>
-            <version>3.1.0</version>
+            <version>3.11.0</version>
         </dependency>
         <dependency>
             <groupId>org.rdfhdt</groupId>

src/main/java/org/linkeddatafragments/datasource/tdb/JenaTDBBasedRequestProcessorForTPFs.java

@@ -33,6 +33,7 @@ public class JenaTDBBasedRequestProcessorForTPFs
     extends AbstractRequestProcessorForTriplePatterns<RDFNode,String,String>
 {
     private final Dataset tdb;
+    private final String defaultGraph;
     private final String sparql = "CONSTRUCT WHERE { ?s ?p ?o } " +
                                     "ORDER BY ?s ?p ?o";
 
@@ -95,7 +96,13 @@ protected ILinkedDataFragment createFragment(
             //        e.g., (?x foaf:knows ?x ) or (_:bn foaf:knows _:bn)
             // see https://github.com/LinkedDataFragments/Server.Java/issues/24
 
-            Model model = tdb.getDefaultModel();
+            Model model;
+            if (defaultGraph == null) {
+                model = tdb.getDefaultModel();
+            } else {
+                model = tdb.getNamedModel(defaultGraph);
+            }
+
             QuerySolutionMap map = new QuerySolutionMap();
             if ( ! subject.isVariable() ) {
                 map.add("s", subject.asConstantTerm());
@@ -160,6 +167,11 @@ protected ILinkedDataFragment createFragment(
      * @param tdbdir directory used for TDB backing
      */
     public JenaTDBBasedRequestProcessorForTPFs(File tdbdir) {
+        this(tdbdir, null);
+    }
+
+    public JenaTDBBasedRequestProcessorForTPFs(File tdbdir, String defaultGraph) {
+        this.defaultGraph = defaultGraph;
         this.tdb = TDBFactory.createDataset(tdbdir.getAbsolutePath());
     }
 }

src/main/java/org/linkeddatafragments/datasource/tdb/JenaTDBDataSource.java

@@ -40,8 +40,8 @@ public IFragmentRequestProcessor getRequestProcessor()
      * @param description
      * @param tdbdir directory used for TDB backing
      */
-    public JenaTDBDataSource(String title, String description, File tdbdir) {
+    public JenaTDBDataSource(String title, String description, File tdbdir, String graph) {
         super(title, description);
-        requestProcessor = new JenaTDBBasedRequestProcessorForTPFs( tdbdir );
+        requestProcessor = new JenaTDBBasedRequestProcessorForTPFs( tdbdir , graph);
     }
 }

src/main/java/org/linkeddatafragments/datasource/tdb/JenaTDBDataSourceType.java

@@ -25,8 +25,14 @@ public IDataSource createDataSource( final String title,
         final String dname = settings.getAsJsonPrimitive("directory").getAsString();
         final File dir = new File( dname );
 
+        // Set the defaultGraph, if provided
+        String graph = null;
+        if (settings.has("graph")) {
+            graph = settings.getAsJsonPrimitive("graph").getAsString();
+        }
+
         try {
-            return new JenaTDBDataSource(title, description, dir);
+            return new JenaTDBDataSource(title, description, dir, graph);
         } catch (Exception ex) {
             throw new DataSourceCreationException(ex);
         }

src/main/java/org/linkeddatafragments/servlet/LinkedDataFragmentServlet.java

@@ -16,7 +16,9 @@
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.http.HttpHeaders;
+import org.apache.jena.query.ARQ;
 import org.apache.jena.riot.Lang;
+import org.apache.jena.sys.JenaSystem;
 import org.linkeddatafragments.config.ConfigReader;
 import org.linkeddatafragments.datasource.DataSourceFactory;
 import org.linkeddatafragments.datasource.DataSourceTypesRegistry;
@@ -79,6 +81,9 @@ private File getConfigFile(ServletConfig config) throws IOException {
      */
     @Override
     public void init(ServletConfig servletConfig) throws ServletException {
+        // Ensure ARQ has been initialized (needed for TDB requests)
+        ARQ.init();
+        
         try {
             // load the configuration
             File configFile = getConfigFile(servletConfig);

src/test/java/org/linkeddatafragments/test/datasource/JenaTDBDataSourceTest.java

@@ -66,7 +66,6 @@ public static void setUpClass() throws Exception {
         Model model = dataset.getDefaultModel();
         InputStream in = ClassLoader.getSystemResourceAsStream("demo.nt");
         RDFDataMgr.read(model, in, Lang.NTRIPLES);
-        model.commit();
 
         // Everything is in place, now create the LDF datasource                
         JsonObject config = createConfig("jena tdb test", "jena tdb test",