MARMOTTA-659: Port Marmotta to Eclipse RDF4J

.gitignore

@@ -13,4 +13,7 @@
 target/
 .idea/
 .metadata/
-maven-eclipse.xml
+maven-eclipse.xml
+.DS_Store
+nb-configuration.xml
+nbactions.xml

.travis.yml

@@ -16,20 +16,42 @@
 #
 
 language: java
-
+dist: precise
 sudo: false
 
 branches:
   only:
+  - MARMOTTA-660 # Add just for migration testing purposes
   - master
   - develop
 
+services:
+  - mysql
+  - postgresql
+
+addons:
+  postgresql: "9.4"
+
 jdk:
 - oraclejdk7
 - oraclejdk8
 
+cache:
+  directories:
+  - .autoconf
+  - $HOME/.m2
+
 before_install:
 - echo "MAVEN_OPTS='-Xmx2g'" > ~/.mavenrc
+## Ignore for now MySQL, tests failing in most of the databases. Tried with version 5.5, 5.6, and 5.7. Travis executes version 5.5.41
+##- mysql -u root -e 'CREATE DATABASE kiwitest;'
+##- mysql -u root -e "CREATE USER 'kiwi'@'localhost' IDENTIFIED BY 'kiwi';"
+##- mysql -u root -e "GRANT ALL ON kiwitest.* TO 'kiwi'@'localhost';"
 
-script: mvn clean install
+- psql -c 'create database kiwitest;' -U postgres
+- psql -c "CREATE USER kiwi WITH PASSWORD 'kiwi';" -U postgres
+- psql -c 'GRANT ALL PRIVILEGES ON DATABASE kiwitest to kiwi;' -U postgres
+
+install: true
 
+script: mvn clean install

Dockerfile

@@ -1,3 +1,19 @@
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
 # Dockerfile for Apache Marmotta
 
 FROM debian:jessie-backports

build/archetypes/marmotta-archetype-module/pom.xml

@@ -33,7 +33,7 @@
 
     <properties>
         <marmottaVersion>${project.version}</marmottaVersion>
-        <sesameVersion>${sesame.version}</sesameVersion>
+        <rdf4jVersion>${rdf4j.version}</rdf4jVersion>
 
         <junitVersion>${junit.version}</junitVersion>
         <weldVersion>${weld.version}</weldVersion>

build/archetypes/marmotta-archetype-webapp/pom.xml

@@ -33,7 +33,7 @@
 
     <properties>
         <marmottaVersion>${project.version}</marmottaVersion>
-        <sesameVersion>${sesame.version}</sesameVersion>
+        <rdf4jVersion>${rdf4j.version}</rdf4jVersion>
 
         <junitVersion>${junit.version}</junitVersion>
         <servletApiVersion>${servlet.api.version}</servletApiVersion>

build/archetypes/marmotta-archetype-webapp/src/main/resources/archetype-resources/src/main/webapp/index.jsp

@@ -24,5 +24,5 @@
 <%@ page import="org.apache.marmotta.platform.core.util.CDIContext" %>
 <%
     ConfigurationService configurationService = CDIContext.getInstance(ConfigurationService.class);
-    response.sendRedirect(configurationService.getServerUri()+configurationService.getStringConfiguration("kiwi.pages.startup"));
+    response.sendRedirect(configurationService.getServerIri()+configurationService.getStringConfiguration("kiwi.pages.startup"));
 %>

build/plugins/pom.xml

@@ -30,6 +30,10 @@
     <name>Apache Marmotta: Maven Plugins</name>
     <description>Marmotta-specific maven plugins</description>
 
+    <properties>
+        <maven.version>3.1.1</maven.version>
+    </properties>
+
     <build>
         <plugins>
             <plugin>
@@ -125,7 +129,7 @@
             <dependency>
                 <groupId>org.apache.maven</groupId>
                 <artifactId>maven-plugin-api</artifactId>
-                <version>3.0.4</version>
+                <version>${maven.version}</version>
             </dependency>
             <dependency>
                 <groupId>org.apache.maven.plugin-tools</groupId>
@@ -136,17 +140,12 @@
             <dependency>
                 <groupId>org.apache.maven</groupId>
                 <artifactId>maven-core</artifactId>
-                <version>3.0.4</version>
+                <version>${maven.version}</version>
             </dependency>
             <dependency>
                 <groupId>org.apache.maven</groupId>
                 <artifactId>maven-model</artifactId>
-                <version>3.0.4</version>
-            </dependency>
-            <dependency>
-                <groupId>org.apache.maven</groupId>
-                <artifactId>maven-project</artifactId>
-                <version>2.2.1</version>
+                <version>${maven.version}</version>
             </dependency>
             <dependency>
                 <!-- maven is using commons-logging -->

build/plugins/refpack-maven-plugin/pom.xml

@@ -32,6 +32,10 @@
     <name>Maven Refpack Plugin</name>
     <description>This Maven Plugin allows generating IzPack Refpack descriptions out of a collection of dependencies</description>
 
+    <prerequisites>
+        <maven>${maven.version}</maven>
+    </prerequisites>
+
     <dependencies>
         <dependency>
             <groupId>org.apache.maven</groupId>
@@ -41,27 +45,6 @@
             <groupId>org.apache.maven</groupId>
             <artifactId>maven-model</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.apache.maven</groupId>
-            <artifactId>maven-project</artifactId>
-        </dependency>
-        <dependency>
-            <!-- required in all cases -->
-            <groupId>org.sonatype.aether</groupId>
-            <artifactId>aether-api</artifactId>
-            <version>1.13.1</version>
-        </dependency>
-        <dependency>
-            <!-- might be superfluous depending on your use case -->
-            <groupId>org.sonatype.aether</groupId>
-            <artifactId>aether-util</artifactId>
-            <version>1.13.1</version>
-        </dependency>
-        <dependency>
-            <groupId>com.jcabi</groupId>
-            <artifactId>jcabi-aether</artifactId>
-            <version>0.7.8</version>
-        </dependency>
         <!-- dependencies to annotations -->
         <dependency>
             <groupId>org.apache.maven.plugin-tools</groupId>

build/plugins/refpack-maven-plugin/src/main/java/org/apache/marmotta/maven/plugins/refpack/RefPackMojo.java

@@ -24,22 +24,22 @@
 import org.apache.maven.plugin.MojoExecutionException;
 import org.apache.maven.plugins.annotations.*;
 import org.apache.maven.project.*;
+import org.eclipse.aether.artifact.DefaultArtifact;
 import org.jdom2.Element;
 import org.jdom2.Text;
 import org.jdom2.output.Format;
 import org.jdom2.output.XMLOutputter;
-import org.sonatype.aether.RepositorySystem;
-import org.sonatype.aether.RepositorySystemSession;
-import org.sonatype.aether.artifact.Artifact;
-import org.sonatype.aether.collection.CollectRequest;
-import org.sonatype.aether.collection.DependencyCollectionException;
-import org.sonatype.aether.graph.Dependency;
-import org.sonatype.aether.graph.DependencyNode;
-import org.sonatype.aether.repository.RemoteRepository;
-import org.sonatype.aether.resolution.DependencyRequest;
-import org.sonatype.aether.resolution.DependencyResolutionException;
-import org.sonatype.aether.resolution.DependencyResult;
-import org.sonatype.aether.util.artifact.DefaultArtifact;
+import org.eclipse.aether.RepositorySystem;
+import org.eclipse.aether.RepositorySystemSession;
+import org.eclipse.aether.artifact.Artifact;
+import org.eclipse.aether.collection.CollectRequest;
+import org.eclipse.aether.collection.DependencyCollectionException;
+import org.eclipse.aether.graph.Dependency;
+import org.eclipse.aether.graph.DependencyNode;
+import org.eclipse.aether.repository.RemoteRepository;
+import org.eclipse.aether.resolution.DependencyRequest;
+import org.eclipse.aether.resolution.DependencyResolutionException;
+import org.eclipse.aether.resolution.DependencyResult;
 
 import java.io.File;
 import java.io.FileOutputStream;

build/plugins/repocheck-maven-plugin/pom.xml

@@ -31,7 +31,9 @@
     <name>Repository Plugin</name>
     <description>Check which repository contains which dependencies </description>
 
-
+    <prerequisites>
+        <maven>${maven.version}</maven>
+    </prerequisites>
 
 
     <dependencies>
@@ -42,7 +44,7 @@
         </dependency>
         <dependency>
             <groupId>org.apache.maven</groupId>
-            <artifactId>maven-project</artifactId>
+            <artifactId>maven-core</artifactId>
         </dependency>
         <dependency>
             <groupId>org.apache.maven.shared</groupId>

client/marmotta-client-java/pom.xml

@@ -101,25 +101,25 @@
             <artifactId>jackson-databind</artifactId>
         </dependency>
         <dependency>
-        	<groupId>org.openrdf.sesame</groupId>
-        	<artifactId>sesame-rio-api</artifactId>
+        	<groupId>org.eclipse.rdf4j</groupId>
+        	<artifactId>rdf4j-rio-api</artifactId>
         </dependency>
         <dependency>
-        	<groupId>org.openrdf.sesame</groupId>
-        	<artifactId>sesame-rio-rdfjson</artifactId>
+        	<groupId>org.eclipse.rdf4j</groupId>
+        	<artifactId>rdf4j-rio-rdfjson</artifactId>
         </dependency>
         <dependency>
-        	<groupId>org.openrdf.sesame</groupId>
-        	<artifactId>sesame-queryresultio-api</artifactId>
+        	<groupId>org.eclipse.rdf4j</groupId>
+        	<artifactId>rdf4j-queryresultio-api</artifactId>
         </dependency>
         <dependency>
-        	<groupId>org.openrdf.sesame</groupId>
-            <artifactId>sesame-queryresultio-sparqlxml</artifactId>
+        	<groupId>org.eclipse.rdf4j</groupId>
+            <artifactId>rdf4j-queryresultio-sparqlxml</artifactId>
             <scope>runtime</scope>
         </dependency>
         <dependency>
-            <groupId>org.openrdf.sesame</groupId>
-            <artifactId>sesame-queryresultio-sparqljson</artifactId>
+            <groupId>org.eclipse.rdf4j</groupId>
+            <artifactId>rdf4j-queryresultio-sparqljson</artifactId>
             <scope>runtime</scope>
         </dependency>
         <dependency>
@@ -233,8 +233,8 @@
         </dependency>
 
         <dependency>
-            <groupId>org.openrdf.sesame</groupId>
-            <artifactId>sesame-sail-memory</artifactId>
+            <groupId>org.eclipse.rdf4j</groupId>
+            <artifactId>rdf4j-sail-memory</artifactId>
             <scope>test</scope>
         </dependency>
 

client/marmotta-client-java/src/main/java/org/apache/marmotta/client/clients/SPARQLClient.java

@@ -17,6 +17,14 @@
  */
 package org.apache.marmotta.client.clients;
 
+import static com.google.common.net.HttpHeaders.ACCEPT;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URLEncoder;
+import java.util.HashMap;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
 import org.apache.http.HttpResponse;
 import org.apache.http.client.HttpClient;
 import org.apache.http.client.methods.HttpGet;
@@ -28,26 +36,25 @@
 import org.apache.marmotta.client.model.rdf.URI;
 import org.apache.marmotta.client.model.sparql.SPARQLResult;
 import org.apache.marmotta.client.util.HTTPUtil;
-import org.openrdf.model.Value;
-import org.openrdf.model.ValueFactory;
-import org.openrdf.model.impl.ValueFactoryImpl;
-import org.openrdf.query.*;
-import org.openrdf.query.resultio.*;
-import org.openrdf.query.resultio.helpers.QueryResultCollector;
+import org.eclipse.rdf4j.model.Value;
+import org.eclipse.rdf4j.model.ValueFactory;
+import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
+import org.eclipse.rdf4j.query.Binding;
+import org.eclipse.rdf4j.query.BindingSet;
+import org.eclipse.rdf4j.query.QueryResultHandler;
+import org.eclipse.rdf4j.query.QueryResultHandlerException;
+import org.eclipse.rdf4j.query.TupleQueryResultHandlerException;
+import org.eclipse.rdf4j.query.resultio.BooleanQueryResultFormat;
+import static org.eclipse.rdf4j.query.resultio.BooleanQueryResultFormat.JSON;
+import org.eclipse.rdf4j.query.resultio.QueryResultIO;
+import org.eclipse.rdf4j.query.resultio.QueryResultParseException;
+import org.eclipse.rdf4j.query.resultio.QueryResultParser;
+import org.eclipse.rdf4j.query.resultio.TupleQueryResultFormat;
+import org.eclipse.rdf4j.query.resultio.UnsupportedQueryResultFormatException;
+import org.eclipse.rdf4j.query.resultio.helpers.QueryResultCollector;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URLEncoder;
-import java.util.HashMap;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-
-import static com.google.common.net.HttpHeaders.ACCEPT;
-import static org.openrdf.query.resultio.TupleQueryResultFormat.JSON;
-
 /**
  * Add file description here!
  * <p/>
@@ -91,7 +98,7 @@ public SPARQLResult select(String query) throws IOException, MarmottaClientExcep
                     log.debug("SPARQL Query {} evaluated successfully",query);
                     QueryResultCollector results = new QueryResultCollector();
 
-                    parse(response.getEntity().getContent(), TupleQueryResultFormat.JSON, results, ValueFactoryImpl.getInstance());
+                    parse(response.getEntity().getContent(), TupleQueryResultFormat.JSON, results, SimpleValueFactory.getInstance());
 
                     if(!results.getHandledTuple() || results.getBindingSets().isEmpty()) {
                         return null;
@@ -110,14 +117,14 @@ public SPARQLResult select(String query) throws IOException, MarmottaClientExcep
                                     //Map<String,String> nodeDef = (Map<String,String>) entry.getValue();
                                     Value nodeDef = nextBinding.getValue();
                                     RDFNode node = null;
-                                    if(nodeDef instanceof org.openrdf.model.URI) {
+                                    if(nodeDef instanceof org.eclipse.rdf4j.model.IRI) {
                                         node = new URI(nodeDef.stringValue());
-                                    } else if(nodeDef instanceof org.openrdf.model.BNode) {
-                                        node = new BNode(((org.openrdf.model.BNode)nodeDef).getID());
-                                    } else if(nodeDef instanceof org.openrdf.model.Literal) {
-                                        org.openrdf.model.Literal nodeLiteral = (org.openrdf.model.Literal)nodeDef;
-                                        if(nodeLiteral.getLanguage() != null) {
-                                            node = new Literal(nodeLiteral.getLabel(), nodeLiteral.getLanguage());
+                                    } else if(nodeDef instanceof org.eclipse.rdf4j.model.BNode) {
+                                        node = new BNode(((org.eclipse.rdf4j.model.BNode)nodeDef).getID());
+                                    } else if(nodeDef instanceof org.eclipse.rdf4j.model.Literal) {
+                                        org.eclipse.rdf4j.model.Literal nodeLiteral = (org.eclipse.rdf4j.model.Literal)nodeDef;
+                                        if(nodeLiteral.getLanguage().orElse(null) != null) {
+                                            node = new Literal(nodeLiteral.getLabel(), nodeLiteral.getLanguage().orElse(null));
                                         } else if(nodeLiteral.getDatatype() != null) {
                                             node = new Literal(nodeLiteral.getLabel(), new URI(nodeLiteral.getDatatype().stringValue()));
                                         } else {
@@ -181,7 +188,7 @@ public boolean ask(String askQuery) throws IOException, MarmottaClientException
                     log.debug("SPARQL ASK Query {} evaluated successfully",askQuery);
                     QueryResultCollector results = new QueryResultCollector();
 
-                    parse(response.getEntity().getContent(), BooleanQueryResultFormat.JSON, results, ValueFactoryImpl.getInstance());
+                    parse(response.getEntity().getContent(), BooleanQueryResultFormat.JSON, results, SimpleValueFactory.getInstance());
 
                     if(!results.getHandledBoolean()) {
                         return false;
@@ -259,7 +266,7 @@ private static void parse(InputStream in, TupleQueryResultFormat format, QueryRe
         throws IOException, QueryResultParseException, QueryResultHandlerException,
         UnsupportedQueryResultFormatException
     {
-        QueryResultParser parser = QueryResultIO.createParser(format);
+        QueryResultParser parser = QueryResultIO.createTupleParser(format);
         parser.setValueFactory(valueFactory);
         parser.setQueryResultHandler(handler);
         parser.parseQueryResult(in);
@@ -282,7 +289,7 @@ private static void parse(InputStream in, BooleanQueryResultFormat format, Query
         throws IOException, QueryResultParseException, QueryResultHandlerException,
         UnsupportedQueryResultFormatException
     {
-        QueryResultParser parser = QueryResultIO.createParser(format);
+        QueryResultParser parser = QueryResultIO.createBooleanParser(format);
         parser.setValueFactory(valueFactory);
         parser.setQueryResultHandler(handler);
         parser.parseQueryResult(in);