UnifiedViews · tomas-knap · Oct 21, 2016
diff --git a/backend/pom.xml b/backend/pom.xml
@@ -68,6 +68,11 @@
             <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>
     </dependencies>
 
     <build>

diff --git a/commons-app/src/main/java/cz/cuni/mff/xrg/odcs/commons/app/rdf/RepositoryManager.java b/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 "marklogic":
+                repositoryType = ManagableRepository.Type.MARKLOGIC;
+                break;
             default:
                 throw new RuntimeException("Unknown repository type.");
         }

diff --git a/dataunit/pom.xml b/dataunit/pom.xml
@@ -264,6 +264,16 @@
 			<artifactId>com.openlinksw.virtuoso.virtjdbc4_1</artifactId>
 			<version>${virtuoso.jdbc.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>com.marklogic</groupId>
+			<artifactId>marklogic-sesame</artifactId>
+			<version>1.0.2</version>
+		</dependency>
+		<dependency>
+			<groupId>com.marklogic</groupId>
+			<artifactId>java-client-api</artifactId>
+			<version>3.0.6</version>
+		</dependency>
 	</dependencies>
 
 	<build>

diff --git a/dataunit/src/main/java/eu/unifiedviews/commons/rdf/repository/ConnectionSourceImpl.java b/dataunit/src/main/java/eu/unifiedviews/commons/rdf/repository/ConnectionSourceImpl.java
@@ -36,6 +36,16 @@ public ConnectionSourceImpl(Repository repository, boolean retryOnFailure) {
         this.retryOnFailure = retryOnFailure;
     }
 
+    /**
+     * Used repository.
+     *
+     * @param repository
+     */
+    public ConnectionSourceImpl(Repository repository) {
+        this.repository = repository;
+        this.retryOnFailure = false;
+    }
+
     @Override
     public RepositoryConnection getConnection() throws RepositoryException {
         return repository.getConnection();

diff --git a/dataunit/src/main/java/eu/unifiedviews/commons/rdf/repository/InMemoryRDF.java b/dataunit/src/main/java/eu/unifiedviews/commons/rdf/repository/InMemoryRDF.java
@@ -1,6 +1,7 @@
 package eu.unifiedviews.commons.rdf.repository;
 
-import java.io.File;
+import eu.unifiedviews.commons.dataunit.core.ConnectionSource;
+import eu.unifiedviews.dataunit.DataUnitException;
 import org.openrdf.repository.Repository;
 import org.openrdf.repository.RepositoryException;
 import org.openrdf.repository.config.RepositoryConfig;
@@ -10,8 +11,7 @@
 import org.openrdf.repository.sail.config.SailRepositoryConfig;
 import org.openrdf.sail.memory.config.MemoryStoreConfig;
 
-import eu.unifiedviews.commons.dataunit.core.ConnectionSource;
-import eu.unifiedviews.dataunit.DataUnitException;
+import java.io.File;
 
 /**
  * 
@@ -53,7 +53,7 @@ public InMemoryRDF(String repositoryPath) throws RDFException {
 
     @Override
     public ConnectionSource getConnectionSource() {
-        return new ConnectionSourceImpl(repository, false);
+        return new ConnectionSourceImpl(repository);
     }
 
     @Override

diff --git a/dataunit/src/main/java/eu/unifiedviews/commons/rdf/repository/LocalRDF.java b/dataunit/src/main/java/eu/unifiedviews/commons/rdf/repository/LocalRDF.java
@@ -1,15 +1,14 @@
 package eu.unifiedviews.commons.rdf.repository;
 
-import java.io.File;
-
+import eu.unifiedviews.commons.dataunit.core.ConnectionSource;
+import eu.unifiedviews.dataunit.DataUnitException;
 import org.apache.commons.io.FileUtils;
 import org.openrdf.repository.Repository;
 import org.openrdf.repository.RepositoryException;
 import org.openrdf.repository.sail.SailRepository;
 import org.openrdf.sail.nativerdf.NativeStore;
 
-import eu.unifiedviews.commons.dataunit.core.ConnectionSource;
-import eu.unifiedviews.dataunit.DataUnitException;
+import java.io.File;
 
 /**
  *
@@ -41,7 +40,7 @@ public LocalRDF(String repositoryPath) throws RDFException {
 
     @Override
     public ConnectionSource getConnectionSource() {
-        return new ConnectionSourceImpl(repository, false);
+        return new ConnectionSourceImpl(repository);
     }
 
     @Override

diff --git a/dataunit/src/main/java/eu/unifiedviews/commons/rdf/repository/ManagableRepository.java b/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,
+        MARKLOGIC
     }
 
     /**

diff --git a/dataunit/src/main/java/eu/unifiedviews/commons/rdf/repository/MarkLogic.java b/dataunit/src/main/java/eu/unifiedviews/commons/rdf/repository/MarkLogic.java
@@ -0,0 +1,67 @@
+package eu.unifiedviews.commons.rdf.repository;
+
+import com.marklogic.client.DatabaseClient;
+import com.marklogic.client.DatabaseClientFactory;
+import com.marklogic.semantics.sesame.MarkLogicRepository;
+import eu.unifiedviews.commons.dataunit.core.ConnectionSource;
+import org.openrdf.repository.Repository;
+import org.openrdf.repository.RepositoryException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Created by tomasknap on 18/10/16.
+ */
+public class MarkLogic implements ManagableRepository {
+
+    private static final Logger log = LoggerFactory.getLogger(RepositoryFactory.class);
+
+    private final Repository repository;
+
+
+    public MarkLogic(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);
+
+        DatabaseClient adminClient =
+                DatabaseClientFactory.newClient(host, portNumber,
+                        user, password, DatabaseClientFactory.Authentication.DIGEST);
+
+        // create repo and init
+        repository = new MarkLogicRepository(adminClient);
+
+        try {
+            repository.initialize();
+        } catch (RepositoryException ex) {
+            throw new RDFException("Could not initialize repository", ex);
+        }
+    }
+
+
+        @Override
+        public ConnectionSource getConnectionSource() {
+            return new ConnectionSourceImpl(repository);
+        }
+
+
+    @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.
+    }
+
+
+}
diff --git a/dataunit/src/main/java/eu/unifiedviews/commons/rdf/repository/RemoteRDF.java b/dataunit/src/main/java/eu/unifiedviews/commons/rdf/repository/RemoteRDF.java
@@ -74,7 +74,7 @@ public RemoteRDF(String url, String user, String password, Long executionId) thr
 
     @Override
     public ConnectionSource getConnectionSource() {
-        return new ConnectionSourceImpl(repository, false);
+        return new ConnectionSourceImpl(repository);
     }
 
     @Override

diff --git a/dataunit/src/main/java/eu/unifiedviews/commons/rdf/repository/RepositoryFactory.java b/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 MARKLOGIC:
+                repository = new MarkLogic(uri, user, password);
+                break;
             default:
                 throw new RDFException("Unknown repository type: " + type.toString());
         }

diff --git a/lib/lib-core/pom.xml b/lib/lib-core/pom.xml
@@ -49,17 +49,17 @@
 								<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>