Added support for GraphDB as RDF working store

backend/conf/config.sample.properties

@@ -99,6 +99,14 @@ database.rdf.platform = localRDF
 #database.rdf.password = dba
 # }
 
+# or GraphDB {
+# database.rdf.platform = graphdb
+# database.rdf.url = http://localhost:7200
+# database.rdf.user = admin
+# database.rdf.password = admin
+# }
+
+
 # Administrator contact email for sending reports and failure notifications 
 email.enabled = false
 email.admin = admin@example.com

backend/pom.xml

@@ -69,6 +69,11 @@
             <artifactId>jetty-server</artifactId>
             <version>${jetty.server.version}</version>
         </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-core</artifactId>
+            <version>2.8.3</version>
+        </dependency>
         <dependency>
             <groupId>com.microsoft.sqlserver</groupId>
             <artifactId>sqljdbc4</artifactId>

commons-app/src/main/java/cz/cuni/mff/xrg/odcs/commons/app/rdf/RepositoryManager.java

@@ -1,22 +1,21 @@
 package cz.cuni.mff.xrg.odcs.commons.app.rdf;
 
-import java.io.File;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Map;
-
-import javax.annotation.PostConstruct;
+import cz.cuni.mff.xrg.odcs.commons.app.resource.MissingResourceException;
+import cz.cuni.mff.xrg.odcs.commons.app.resource.ResourceManager;
+import eu.unifiedviews.commons.rdf.repository.ManagableRepository;
+import eu.unifiedviews.commons.rdf.repository.RDFException;
+import eu.unifiedviews.commons.rdf.repository.RepositoryFactory;
 import org.openrdf.repository.Repository;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 
-import cz.cuni.mff.xrg.odcs.commons.app.resource.MissingResourceException;
-import cz.cuni.mff.xrg.odcs.commons.app.resource.ResourceManager;
-import eu.unifiedviews.commons.rdf.repository.ManagableRepository;
-import eu.unifiedviews.commons.rdf.repository.RDFException;
-import eu.unifiedviews.commons.rdf.repository.RepositoryFactory;
+import javax.annotation.PostConstruct;
+import java.io.File;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
 
 /**
  * Provide access to repositories.
@@ -87,6 +86,9 @@ protected void init() {
             case "remoteRDF":
                 repositoryType = ManagableRepository.Type.REMOTE_RDF;
                 break;
+            case "graphdb":
+                repositoryType = ManagableRepository.Type.GRAPHDB;
+                break;
             default:
                 throw new RuntimeException("Unknown repository type.");
         }

dataunit/pom.xml

@@ -265,6 +265,21 @@
 			<artifactId>com.openlinksw.virtuoso.virtjdbc4_1</artifactId>
 			<version>${virtuoso.jdbc.version}</version>
 		</dependency>
+
+		<!--
+		<dependency>
+			<groupId>com.complexible.stardog</groupId>
+			<artifactId>client-http</artifactId>
+			<version>4.2</version>
+			<type>pom</type>
+		</dependency>
+		<dependency>
+			<groupId>com.complexible.stardog.sesame</groupId>
+			<artifactId>stardog-sesame-core</artifactId>
+			<version>4.2</version>
+		</dependency> -->
+
+
 	</dependencies>
 
 	<build>
@@ -279,4 +294,6 @@
 			</plugin>
 		</plugins>
 	</build>
+
+
 </project>

dataunit/src/main/java/eu/unifiedviews/commons/rdf/repository/GraphDB.java

@@ -0,0 +1,79 @@
+package eu.unifiedviews.commons.rdf.repository;
+
+import eu.unifiedviews.commons.dataunit.core.ConnectionSource;
+import org.openrdf.repository.Repository;
+import org.openrdf.repository.RepositoryException;
+import org.openrdf.repository.manager.RemoteRepositoryManager;
+import org.openrdf.repository.manager.RepositoryManager;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.Collection;
+
+/**
+ * Created by tomasknap on 09/01/17.
+ */
+public class GraphDB implements ManagableRepository {
+
+    private static final Logger log = LoggerFactory.getLogger(GraphDB.class);
+
+    private Repository repository = null;
+
+
+    public GraphDB(String url, String user, String password) throws RDFException {
+
+//        String port = url.substring(url.lastIndexOf(":")+1);
+//        int portNumber = Integer.valueOf(port);
+//        log.info("Port number: {}", portNumber);
+//
+//        String host = url.substring(0,url.lastIndexOf(":"));
+//        log.info("Host: {}", host);
+
+//        Repository repository = new StardogRepository(ConnectionConfiguration.to("uv").credentials(user, password));
+
+        // Instantiate a local repository manager and initialize it
+        RepositoryManager repositoryManager = new RemoteRepositoryManager(url);
+        try {
+            repositoryManager.initialize();
+
+            Collection<Repository> allRepositories = repositoryManager.getAllRepositories();
+
+            this.repository = repositoryManager.getRepository("uv");
+
+//            Repository repository = new HTTPRepository(url, "uv");
+
+        } catch (RepositoryException ex) {
+            throw new RDFException("Could not initialize repository", ex);
+        } catch (Exception e) {
+            log.error(e.getLocalizedMessage(),e);
+        }
+
+
+
+        try {
+            repository.initialize();
+        } catch (RepositoryException ex) {
+            throw new RDFException("Could not initialize repository", ex);
+        }
+    }
+
+    @Override
+    public ConnectionSource getConnectionSource() {
+        return new ConnectionSourceImpl(repository, false);
+    }
+
+    @Override
+    public void release() throws RDFException {
+        try {
+            repository.shutDown();
+    } catch (RepositoryException ex) {
+         throw new RDFException("Can't shutDown repository.", ex);
+    }
+
+    }
+
+    @Override
+    public void delete() throws RDFException {
+        // Do nothing here.
+    }
+}

dataunit/src/main/java/eu/unifiedviews/commons/rdf/repository/ManagableRepository.java

@@ -15,7 +15,8 @@ public static enum Type {
         LOCAL_RDF,
         INMEMORY_RDF,
         REMOTE_RDF,
-        VIRTUOSO
+        VIRTUOSO,
+        GRAPHDB
     }
 
     /**

dataunit/src/main/java/eu/unifiedviews/commons/rdf/repository/RepositoryFactory.java

@@ -55,6 +55,9 @@ public ManagableRepository create(Long executionId, ManagableRepository.Type typ
             case VIRTUOSO:
                 repository = new Virtuoso(uri, user, password);
                 break;
+            case GRAPHDB:
+                repository = new GraphDB(uri, user, password);
+                break;
             default:
                 throw new RDFException("Unknown repository type: " + type.toString());
         }

frontend/src/main/webapp/WEB-INF/config.sample.properties

@@ -85,6 +85,13 @@ database.rdf.platform = localRDF
 #database.rdf.password = dba
 # }
 
+# or GraphDB {
+# database.rdf.platform = graphdb
+# database.rdf.url = http://localhost:7200
+# database.rdf.user = admin
+# database.rdf.password = admin
+# }
+
 
 # Administrator contact email for sending reports and failure notifications 
 email.enabled = false

lib/lib-core/pom.xml

@@ -50,17 +50,17 @@
 								<dependency>
 									<groupId>com.fasterxml.jackson.core</groupId>
 									<artifactId>jackson-annotations</artifactId>
-									<version>2.6.0</version>
+									<version>2.8.3</version>
 								</dependency>
 								<dependency>
 									<groupId>com.fasterxml.jackson.core</groupId>
 									<artifactId>jackson-databind</artifactId>
-									<version>2.6.0</version>
+									<version>2.8.3</version>
 								</dependency>
 								<dependency>
 									<groupId>com.fasterxml.jackson.core</groupId>
 									<artifactId>jackson-core</artifactId>
-									<version>2.6.0</version>
+									<version>2.8.3</version>
 								</dependency>
 								<dependency>
 									<groupId>org.apache.jena</groupId>

pom.xml

@@ -148,6 +148,20 @@
 			<name>SpringSource Enterprise Bundle Repository - External Bundle Releases</name>
 			<url>http://repository.springsource.com/maven/bundles/external</url>
 		</repository>
+
+		<!--
+		<repository>
+			<id>stardog-public</id>
+			<url>http://maven.stardog.com</url>
+		</repository> -->
+
+		<repository>
+			<id>ontotex-public</id>
+			<url>http://maven.ontotext.com/content/groups/all-onto</url>
+		</repository>
+
+
+
 	</repositories>
 
 	<pluginRepositories>
@@ -162,6 +176,7 @@
 					<configuration>
 						<source>${project.java.source.version}</source>
 						<target>${project.java.target.version}</target>
+						<maxmem>1024m</maxmem>
 					</configuration>
 				</plugin>
 			</plugins>
@@ -281,6 +296,7 @@
 			</plugin>
 
 		</plugins>
+
 	</build>
 
 	<profiles>