Merge branch 'version4' of https://github.com/ontop/ontop into version4

# Conflicts:
#	test/sparql-compliance/pom.xml

.github/CONTRIBUTING.md

@@ -1,38 +1,6 @@
 # How to contribute to Ontop
 
-## General Questions and Discussion
-
-We have a Google group for anything related to support, discussion and announcements. Please join for any inquiry.
-
- ontop4obda AT googlegroups DOT com
-
-## Bug report 
-
-1. First check if you are using the latest version of Ontop
-2. If you are sure you find a bug, use GitHub Issues to submit the report; otherwise, you may want to use the mail list for the discussion.
-3. When reporting a bug, please provide a minimal use case if possible.
-
-
-## Contributing Code
-
-Do you know how to fix something or provide new features? 
-
-For trivial contribution (e.g. fixing typos in the docs), please use the Pull Request of GitHub.
-
-For non-trivial contribution, please contact us first. Contributions to the project are welcome and encouraged. The
-contributor should sign a Contribution License Agreement (CLA) that
-allows FUB and the ontop team to redistribute their work under the
-terms of the Apache 2.0 license. If the contributor works for an
-institution that owns the work being contributed by the contributor,
-then a corporate CLA must be additionally signed. The CLAs are
-available for download bellow, once signed please FAX or email a
-scanned copy of them to the ontop team.
-
-
-* [Individual Contributor License Agreement (CLA)](https://raw.github.com/ontop/ontop/master/documentation/ontop-cla-2013-11-04.txt)
-* [Corporate License Agreement](https://raw.github.com/ontop/ontop/master/documentation/ontop-cla-corporate-2013-11-04.txt)
-
-If you have any questions, please contact the ontop team.
+Please visit https://ontop-vkg.org/community/contributing/ for the guidelines.
 
 
 

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://help.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "maven" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "daily"

.mvn/wrapper/MavenWrapperDownloader.java

@@ -0,0 +1,117 @@
+/*
+ * Copyright 2007-present the original author or authors.
+ *
+ * Licensed 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.
+ */
+import java.net.*;
+import java.io.*;
+import java.nio.channels.*;
+import java.util.Properties;
+
+public class MavenWrapperDownloader {
+
+    private static final String WRAPPER_VERSION = "0.5.6";
+    /**
+     * Default URL to download the maven-wrapper.jar from, if no 'downloadUrl' is provided.
+     */
+    private static final String DEFAULT_DOWNLOAD_URL = "https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/"
+        + WRAPPER_VERSION + "/maven-wrapper-" + WRAPPER_VERSION + ".jar";
+
+    /**
+     * Path to the maven-wrapper.properties file, which might contain a downloadUrl property to
+     * use instead of the default one.
+     */
+    private static final String MAVEN_WRAPPER_PROPERTIES_PATH =
+            ".mvn/wrapper/maven-wrapper.properties";
+
+    /**
+     * Path where the maven-wrapper.jar will be saved to.
+     */
+    private static final String MAVEN_WRAPPER_JAR_PATH =
+            ".mvn/wrapper/maven-wrapper.jar";
+
+    /**
+     * Name of the property which should be used to override the default download url for the wrapper.
+     */
+    private static final String PROPERTY_NAME_WRAPPER_URL = "wrapperUrl";
+
+    public static void main(String args[]) {
+        System.out.println("- Downloader started");
+        File baseDirectory = new File(args[0]);
+        System.out.println("- Using base directory: " + baseDirectory.getAbsolutePath());
+
+        // If the maven-wrapper.properties exists, read it and check if it contains a custom
+        // wrapperUrl parameter.
+        File mavenWrapperPropertyFile = new File(baseDirectory, MAVEN_WRAPPER_PROPERTIES_PATH);
+        String url = DEFAULT_DOWNLOAD_URL;
+        if(mavenWrapperPropertyFile.exists()) {
+            FileInputStream mavenWrapperPropertyFileInputStream = null;
+            try {
+                mavenWrapperPropertyFileInputStream = new FileInputStream(mavenWrapperPropertyFile);
+                Properties mavenWrapperProperties = new Properties();
+                mavenWrapperProperties.load(mavenWrapperPropertyFileInputStream);
+                url = mavenWrapperProperties.getProperty(PROPERTY_NAME_WRAPPER_URL, url);
+            } catch (IOException e) {
+                System.out.println("- ERROR loading '" + MAVEN_WRAPPER_PROPERTIES_PATH + "'");
+            } finally {
+                try {
+                    if(mavenWrapperPropertyFileInputStream != null) {
+                        mavenWrapperPropertyFileInputStream.close();
+                    }
+                } catch (IOException e) {
+                    // Ignore ...
+                }
+            }
+        }
+        System.out.println("- Downloading from: " + url);
+
+        File outputFile = new File(baseDirectory.getAbsolutePath(), MAVEN_WRAPPER_JAR_PATH);
+        if(!outputFile.getParentFile().exists()) {
+            if(!outputFile.getParentFile().mkdirs()) {
+                System.out.println(
+                        "- ERROR creating output directory '" + outputFile.getParentFile().getAbsolutePath() + "'");
+            }
+        }
+        System.out.println("- Downloading to: " + outputFile.getAbsolutePath());
+        try {
+            downloadFileFromURL(url, outputFile);
+            System.out.println("Done");
+            System.exit(0);
+        } catch (Throwable e) {
+            System.out.println("- Error downloading");
+            e.printStackTrace();
+            System.exit(1);
+        }
+    }
+
+    private static void downloadFileFromURL(String urlString, File destination) throws Exception {
+        if (System.getenv("MVNW_USERNAME") != null && System.getenv("MVNW_PASSWORD") != null) {
+            String username = System.getenv("MVNW_USERNAME");
+            char[] password = System.getenv("MVNW_PASSWORD").toCharArray();
+            Authenticator.setDefault(new Authenticator() {
+                @Override
+                protected PasswordAuthentication getPasswordAuthentication() {
+                    return new PasswordAuthentication(username, password);
+                }
+            });
+        }
+        URL website = new URL(urlString);
+        ReadableByteChannel rbc;
+        rbc = Channels.newChannel(website.openStream());
+        FileOutputStream fos = new FileOutputStream(destination);
+        fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
+        fos.close();
+        rbc.close();
+    }
+
+}

.mvn/wrapper/maven-wrapper.properties

@@ -1 +1,2 @@
-distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.5.4/apache-maven-3.5.4-bin.zip
+distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.6.3/apache-maven-3.6.3-bin.zip
+wrapperUrl=https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/0.5.6/maven-wrapper-0.5.6.jar

.travis.yml

@@ -6,7 +6,8 @@ language: java
 
 jdk:
   - openjdk8
-
+  - openjdk11
+
 services:
   - docker
 

README.md

@@ -6,7 +6,6 @@
 | Branch    | build status  |
 |-----------|---------------|
 | [master](https://github.com/ontop/ontop/tree/master)  |[![Build Status](https://travis-ci.org/ontop/ontop.svg?branch=master)](https://travis-ci.org/ontop/ontop)|
-| [version3](https://github.com/ontop/ontop/tree/version3) |[![Build Status](https://travis-ci.org/ontop/ontop.svg?branch=version3)](https://travis-ci.org/ontop/ontop)|
 | [version4](https://github.com/ontop/ontop/tree/version4) |[![Build Status](https://travis-ci.org/ontop/ontop.svg?branch=version4)](https://travis-ci.org/ontop/ontop)|
 
 
@@ -23,7 +22,7 @@ Compiling, packing, testing, etc.
 
 The project is a [Maven](http://maven.apache.org/) project. Compiling,
 running the unit tests, building the release binaries all can be done
-using maven.  Currently we use Maven 3 and Java 8 to build the
+using maven.  Currently, we use Maven 3 and Java 8 to build the
 project.
 
 

binding/owlapi/pom.xml

@@ -42,11 +42,6 @@
 			<artifactId>owlapi-apibinding</artifactId>
 		</dependency>
 
-		<dependency>
-            <groupId>org.postgresql</groupId>
-            <artifactId>postgresql</artifactId>
-			<scope>test</scope>
-		</dependency>
 		<dependency>
 			<groupId>${project.groupId}</groupId>
 			<artifactId>ontop-system-sql-owlapi</artifactId>
@@ -58,12 +53,6 @@
 			<artifactId>h2</artifactId>
 			<scope>test</scope>
 		</dependency>
-		<dependency>
-			<groupId>mysql</groupId>
-			<artifactId>mysql-connector-java</artifactId>
-			<scope>test</scope>
-		</dependency>
-
 		<dependency>
 			<groupId>org.eclipse.rdf4j</groupId>
 			<artifactId>rdf4j-queryparser-sparql</artifactId>

binding/owlapi/src/main/java/it/unibz/inf/ontop/owlapi/connection/impl/DefaultOntopOWLStatement.java

@@ -1,25 +1,5 @@
 package it.unibz.inf.ontop.owlapi.connection.impl;
 
-/*
- * #%L
- * ontop-quest-owlapi
- * %%
- * Copyright (C) 2009 - 2014 Free University of Bozen-Bolzano
- * %%
- * Licensed 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.
- * #L%
- */
-
 import it.unibz.inf.ontop.answering.reformulation.input.*;
 import it.unibz.inf.ontop.exception.*;
 import it.unibz.inf.ontop.answering.resultset.BooleanResultSet;
@@ -36,6 +16,8 @@
 import it.unibz.inf.ontop.owlapi.resultset.impl.OntopGraphOWLResultSet;
 import it.unibz.inf.ontop.owlapi.resultset.impl.OntopBooleanOWLResultSet;
 
+import java.security.SecureRandom;
+
 /***
  * A Statement to execute queries over a QuestOWLConnection. The logic of this
  * statement is equivalent to that of JDBC's Statements.
@@ -84,13 +66,22 @@ public TupleOWLResultSet executeSelectQuery(String inputQuery) throws OntopOWLEx
 			SelectQuery query = inputQueryFactory.createSelectQuery(inputQuery);
 			TupleResultSet resultSet = st.execute(query);
 
-			return new OntopTupleOWLResultSet(resultSet);
+
+
+			return new OntopTupleOWLResultSet(resultSet, generateSalt());
 
 		} catch (OntopQueryEngineException e) {
 			throw new OntopOWLException(e);
 		}
 	}
 
+	private byte[] generateSalt() {
+		SecureRandom random = new SecureRandom();
+		byte[] salt = new byte[20];
+		random.nextBytes(salt);
+		return salt;
+	}
+
 	@Override
 	public BooleanOWLResultSet executeAskQuery(String inputQuery) throws OntopOWLException {
 		try {
@@ -139,7 +130,7 @@ private GraphOWLResultSet executeGraph(GraphSPARQLQuery query)
 			OntopResultConversionException {
 
 		SimpleGraphResultSet resultSet = st.execute(query);
-		return new OntopGraphOWLResultSet(resultSet);
+		return new OntopGraphOWLResultSet(resultSet, generateSalt());
 	}
 
 	public int getMaxRows() throws OntopOWLException {

binding/owlapi/src/main/java/it/unibz/inf/ontop/owlapi/impl/DefaultOntopOWLAPIMaterializer.java

@@ -1,25 +1,5 @@
 package it.unibz.inf.ontop.owlapi.impl;
 
-/*
- * #%L
- * ontop-quest-owlapi
- * %%
- * Copyright (C) 2009 - 2014 Free University of Bozen-Bolzano
- * %%
- * Licensed 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.
- * #L%
- */
-
 import com.google.common.collect.ImmutableSet;
 import it.unibz.inf.ontop.answering.resultset.MaterializedGraphResultSet;
 import it.unibz.inf.ontop.exception.OBDASpecificationException;
@@ -37,6 +17,7 @@
 import org.semanticweb.owlapi.model.OWLException;
 
 import javax.annotation.Nonnull;
+import java.security.SecureRandom;
 
 public class DefaultOntopOWLAPIMaterializer implements OntopOWLAPIMaterializer {
 
@@ -95,6 +76,9 @@ public ImmutableSet<IRI> getProperties() {
 	}
 
 	private MaterializedGraphOWLResultSet wrap(MaterializedGraphResultSet graphResultSet) {
-		return new OntopMaterializedGraphOWLResultSet(graphResultSet);
+		SecureRandom random = new SecureRandom();
+		byte[] salt = new byte[20];
+		random.nextBytes(salt);
+		return new OntopMaterializedGraphOWLResultSet(graphResultSet, salt);
 	}
 }

binding/owlapi/src/main/java/it/unibz/inf/ontop/owlapi/resultset/OWLBindingSet.java

@@ -9,14 +9,14 @@
 import org.semanticweb.owlapi.model.OWLPropertyAssertionObject;
 
 import java.util.Iterator;
-import java.util.List;
+import java.util.Set;
 
 public interface OWLBindingSet extends Iterable<OWLBinding> {
 
     @Override
     Iterator<OWLBinding> iterator();
 
-    List<String> getBindingNames() throws OWLException;
+    Set<String> getBindingNames() throws OWLException;
 
     OWLBinding getBinding(String bindingName) throws OWLException;