Add Store Update

LICENSE.EDL

@@ -0,0 +1,28 @@
+Eclipse Distribution License - v 1.0
+
+Copyright (c) 2007, Eclipse Foundation, Inc. and its licensors.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+* Neither the name of the Eclipse Foundation, Inc. nor the names of its
+  contributors may be used to endorse or promote products derived from this
+  software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

src/.gitignore

@@ -1 +1,3 @@
-/target/
+/.settings/
+/.project
+/.classpath

src/pom.xml

@@ -8,7 +8,7 @@
   <artifactId>store-parent</artifactId>
   <version>2.4.0-SNAPSHOT</version>
   <packaging>pom</packaging>
-  <name>Lyo Store Parent</name>
+  <name>Lyo Store :: Parent</name>
 
   <properties>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
@@ -19,25 +19,18 @@
 
   <modules>
     <module>store-core</module>
+    <module>store-sync</module>
   </modules>
 
   <dependencyManagement>
     <dependencies>
       <!-- Jena -->
+
       <dependency>
         <groupId>org.apache.jena</groupId>
-        <artifactId>jena-core</artifactId>
-        <version>3.0.1</version>
-      </dependency>
-      <dependency>
-        <groupId>org.apache.jena</groupId>
-        <artifactId>jena-arq</artifactId>
-        <version>3.0.1</version>
-      </dependency>
-      <dependency>
-        <groupId>org.apache.jena</groupId>
-        <artifactId>jena-tdb</artifactId>
-        <version>3.0.1</version>
+        <artifactId>apache-jena-libs</artifactId>
+        <version>3.6.0</version>
+        <type>pom</type>
       </dependency>
 
       <!-- Generic -->
@@ -51,12 +44,23 @@
         <artifactId>guava</artifactId>
         <version>21.0</version>
       </dependency>
+      <dependency>
+        <groupId>org.apache.httpcomponents</groupId>
+        <artifactId>httpclient</artifactId>
+        <version>4.5.5</version>
+      </dependency>
       <dependency>
         <!--TODO why is it here?-->
         <groupId>xml-apis</groupId>
         <artifactId>xml-apis</artifactId>
         <version>1.3.04</version>
       </dependency>
+      <dependency>
+        <groupId>javax.servlet</groupId>
+        <artifactId>javax.servlet-api</artifactId>
+        <version>3.1.0</version>
+        <scope>provided</scope>
+      </dependency>
 
       <!-- Test -->
       <dependency>
@@ -105,5 +109,9 @@
       <name>Eclipse Public License 1.0</name>
       <url>https://www.eclipse.org/legal/epl-v10.html</url>
     </license>
+    <license>
+      <name>Eclipse Distribution License 1.0</name>
+      <url>https://www.eclipse.org/org/documents/edl-v10.html</url>
+    </license>
   </licenses>
 </project>

src/store-core/.gitignore

@@ -13,9 +13,9 @@
 hs_err_pid*
 
 # Eclipse
-.metadata
-**/bin/
-**/tmp/
+/.project
+/.classpath
+/.metadata
 *.tmp
 *.bak
 *.swp
@@ -63,8 +63,8 @@ local.properties
 # MAVEN
 #########################
 
-**/overlays/
-**/target/
+/overlays/
+/target/
 pom.xml.tag
 pom.xml.next
 release.properties

src/store-core/pom.xml

@@ -12,7 +12,7 @@
   </parent>
 
   <artifactId>store-core</artifactId>
-  <version>2.4.0-SNAPSHOT</version>
+  <name>Lyo Store :: Core</name>
 
   <properties>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
@@ -48,37 +48,8 @@
     <!-- Jena -->
     <dependency>
       <groupId>org.apache.jena</groupId>
-      <artifactId>jena-core</artifactId>
-      <exclusions>
-        <exclusion>
-          <groupId>org.slf4j</groupId>
-          <artifactId>slf4j-log4j12</artifactId>
-        </exclusion>
-      </exclusions>
-    </dependency>
-    <dependency>
-      <groupId>org.apache.jena</groupId>
-      <artifactId>jena-arq</artifactId>
-      <exclusions>
-        <exclusion>
-          <groupId>org.slf4j</groupId>
-          <artifactId>slf4j-log4j12</artifactId>
-        </exclusion>
-        <exclusion>
-          <groupId>org.slf4j</groupId>
-          <artifactId>jcl-over-slf4j</artifactId>
-        </exclusion>
-      </exclusions>
-    </dependency>
-    <dependency>
-      <groupId>org.apache.jena</groupId>
-      <artifactId>jena-tdb</artifactId>
-      <exclusions>
-        <exclusion>
-          <groupId>org.slf4j</groupId>
-          <artifactId>slf4j-log4j12</artifactId>
-        </exclusion>
-      </exclusions>
+      <artifactId>apache-jena-libs</artifactId>
+      <type>pom</type>
     </dependency>
 
     <!-- Generic -->
@@ -272,5 +243,9 @@
       <name>Eclipse Public License 1.0</name>
       <url>https://www.eclipse.org/legal/epl-v10.html</url>
     </license>
+    <license>
+      <name>Eclipse Distribution License 1.0</name>
+      <url>https://www.eclipse.org/org/documents/edl-v10.html</url>
+    </license>
   </licenses>
 </project>

src/store-core/src/main/java/org/eclipse/lyo/store/ModelUnmarshallingException.java

@@ -24,6 +24,11 @@
  * @since 0.14.0
  */
 public class ModelUnmarshallingException extends Exception {
+    /**
+     * 
+     */
+    private static final long serialVersionUID = 7760792549346636219L;
+
     public ModelUnmarshallingException() {
         super();
     }

src/store-core/src/main/java/org/eclipse/lyo/store/StoreAccessException.java

@@ -23,6 +23,11 @@
  * @since 0.13
  */
 public class StoreAccessException extends Exception {
+    /**
+     * 
+     */
+    private static final long serialVersionUID = -7535919324037847033L;
+
     public StoreAccessException() {
         super();
     }

src/store-core/src/main/java/org/eclipse/lyo/store/internals/JenaTdbStoreImpl.java

@@ -5,7 +5,7 @@
  * Contributors:
  *     Andrew Berezovskyi - initial implementation
  * %%
- * Copyright (C) 2016 KTH Royal Institute of Technology
+ * Copyright (C) 2016 - 2018 KTH Royal Institute of Technology
  * %%
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -15,6 +15,7 @@
  */
 
 import com.google.common.collect.Sets;
+import java.util.HashSet;
 import org.apache.jena.query.Dataset;
 import org.apache.jena.query.ReadWrite;
 import org.apache.jena.rdf.model.Model;
@@ -74,6 +75,7 @@ public boolean namedGraphExists(final URI namedGraph) {
         dataset.begin(ReadWrite.READ);
         try {
             contains = dataset.containsNamedModel(namedGraph.toString());
+            dataset.commit();
         } finally {
             dataset.end();
         }
@@ -86,9 +88,9 @@ public <T extends IResource> List<T> getResources(final URI namedGraph,
         if (namedGraphExists(namedGraph)) {
             dataset.begin(ReadWrite.READ);
             final Model model = dataset.getNamedModel(namedGraph.toString());
-            dataset.end();
             try {
                 final Object[] obj = JenaModelHelper.fromJenaModel(model, clazz);
+                dataset.commit();
                 @SuppressWarnings("unchecked") final T[] castObjects = (T[]) Array.newInstance(
                         clazz, obj.length);
                 for (int i = 0; i < obj.length; i++) {
@@ -100,6 +102,8 @@ public <T extends IResource> List<T> getResources(final URI namedGraph,
                     InvocationTargetException | NoSuchMethodException | URISyntaxException e) {
                 throw new ModelUnmarshallingException(
                         "Failed to buildPersistent an " + "object from Jena model", e);
+            } finally {
+                dataset.end();
             }
         } else {
             throw new StoreAccessException(
@@ -163,7 +167,9 @@ public Set<String> keySet() {
         dataset.begin(ReadWrite.READ);
         try {
             final Iterator<String> namedGraphNames = dataset.listNames();
-            return Sets.newHashSet(namedGraphNames);
+            final HashSet<String> strings = Sets.newHashSet(namedGraphNames);
+            dataset.commit();
+            return strings;
         } finally {
             dataset.end();
         }
@@ -172,7 +178,14 @@ public Set<String> keySet() {
     @Override
     public void removeAll() {
         // TODO Andrew@2017-04-04: do we need a transaction here?
-        dataset.asDatasetGraph().clear();
+        dataset.begin(ReadWrite.WRITE);
+        try {
+            dataset.asDatasetGraph().clear();
+            dataset.commit();
+        }
+        finally {
+            dataset.end();
+        }
     }
 
     @Override
@@ -198,7 +211,7 @@ public void insertJenaModel(final URI name, final Model model) {
         } finally {
             dataset.end();
         }
-        TDB.sync(dataset);
+//        TDB.sync(dataset);
     }
 
     public void putJenaModel(final URI name, final Model model) {

src/store-core/src/main/java/org/eclipse/lyo/store/internals/query/SparqlQueryExecutorBasicAuthImpl.java

@@ -5,7 +5,7 @@
  * Contributors:
  *     Andrew Berezovskyi - initial implementation
  * %%
- * Copyright (C) 2016 KTH Royal Institute of Technology
+ * Copyright (C) 2016 - 2018 KTH Royal Institute of Technology
  * %%
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -14,12 +14,17 @@
  * #L%
  */
 
+import org.apache.http.auth.AuthScope;
+import org.apache.http.auth.UsernamePasswordCredentials;
+import org.apache.http.client.CredentialsProvider;
+import org.apache.http.impl.client.BasicCredentialsProvider;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
 import org.apache.jena.query.QueryExecution;
 import org.apache.jena.query.QueryExecutionFactory;
 import org.apache.jena.update.UpdateExecutionFactory;
 import org.apache.jena.update.UpdateFactory;
 import org.apache.jena.update.UpdateProcessor;
-import org.apache.jena.atlas.web.auth.SimpleAuthenticator;
 
 /**
  * SparqlQueryExecutorImpl is a SPARQL endpoint-based implementation of {@link JenaQueryExecutor}.
@@ -32,23 +37,30 @@ public class SparqlQueryExecutorBasicAuthImpl implements JenaQueryExecutor {
 
     private final String queryEndpoint;
     private final String updateEndpoint;
-    private final SimpleAuthenticator authenticator;
+    private final CloseableHttpClient client;
 
     public SparqlQueryExecutorBasicAuthImpl(final String sparqlEndpoint,
             final String updateEndpoint, final String login, final String password) {
         this.queryEndpoint = sparqlEndpoint;
         this.updateEndpoint = updateEndpoint;
-        authenticator = new SimpleAuthenticator(login, password.toCharArray());
+        CredentialsProvider provider = new BasicCredentialsProvider();
+        UsernamePasswordCredentials credentials = new UsernamePasswordCredentials(login, password);
+        provider.setCredentials(AuthScope.ANY, credentials);
+
+        client = HttpClientBuilder.create().setDefaultCredentialsProvider(provider).build();
     }
 
     @Override
     public QueryExecution prepareSparqlQuery(final String query) {
-        return QueryExecutionFactory.sparqlService(queryEndpoint, query, authenticator);
+        return QueryExecutionFactory.sparqlService(queryEndpoint, query, client);
     }
 
     @Override
     public UpdateProcessor prepareSparqlUpdate(final String query) {
-        return UpdateExecutionFactory.createRemote(UpdateFactory.create(query), updateEndpoint,
-                authenticator);
+        return UpdateExecutionFactory.createRemote(
+                UpdateFactory.create(query),
+                updateEndpoint,
+                client
+        );
     }
 }