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

binding/owlapi/pom.xml

@@ -1,13 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 
     <modelVersion>4.0.0</modelVersion>
 
     <parent>
         <groupId>it.unibz.inf.ontop</groupId>
         <artifactId>ontop-binding</artifactId>
-        <version>4.1.0-beta-1-SNAPSHOT</version>
+        <version>4.1.1-SNAPSHOT</version>
     </parent>
 
     <artifactId>ontop-owlapi</artifactId>

binding/pom.xml

@@ -1,13 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 
     <modelVersion>4.0.0</modelVersion>
 
     <parent>
         <groupId>it.unibz.inf.ontop</groupId>
         <artifactId>ontop</artifactId>
-        <version>4.1.0-beta-1-SNAPSHOT</version>
+        <version>4.1.1-SNAPSHOT</version>
     </parent>
 
     <artifactId>ontop-binding</artifactId>

binding/rdf4j/pom.xml

@@ -1,13 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 
     <modelVersion>4.0.0</modelVersion>
 
     <parent>
         <groupId>it.unibz.inf.ontop</groupId>
         <artifactId>ontop-binding</artifactId>
-        <version>4.1.0-beta-1-SNAPSHOT</version>
+        <version>4.1.1-SNAPSHOT</version>
     </parent>
 
     <artifactId>ontop-rdf4j</artifactId>

build/distribution/README.md

@@ -1,30 +1,30 @@
-# Ontop  
+# Ontop
 
-The [Ontop](http://ontop-vkg.org) framework is an open source project available under the terms of the 
-[Apache 2.0 License](http://www.apache.org/licenses/LICENSE-2.0.txt). 
-By downloading these packages you are agreeing with them.
+The [Ontop](http://ontop-vkg.org) framework is an open source project available under the terms of the
+[Apache 2.0 License](http://www.apache.org/licenses/LICENSE-2.0.txt).
 
-* Current version: 4.0.3
-* Release date: 16/10/2020
+* Current version: 4.1.0
+* Release date: 28/02/2021
 * [Changelog](https://ontop-vkg.org/guide/releases.html)
 
+## Downloads
 
-## Main downloads
+### Command line interface of Ontop
 
-- `ontop-cli-[version].zip`: Command line interface of Ontop.
+- `ontop-cli-[version].zip`
 
-- `it.unibz.inf.ontop.protege-[version].jar`: plugin for Protege 5.x installation files (drop it in Protege’s plugins folder).
+### Platform-specific Ontop Protégé bundles with JRE 8 embedded
 
-- `ontop-protege-bundle-[version].zip` : Protege bundled with Ontop. This is a ready-to-run package. Unzip and use the run.sh or run.bat start scripts.
+- `ontop-protege-bundle-linux-[version].tar.gz`:  Linux bundle (start with `run.sh`)
+- `ontop-protege-bundle-macos-[version].zip`: macOS bundle (first run: right click `Protégé.app` and select `Open` in
+  the warning dialog)
+- `ontop-protege-bundle-windows-[version].zip`: Windows bundle (start with `run.bat` and `Protege.exe`)
 
+### Platform-independent Ontop Protégé plugin and bundle (JRE 8 needs to be installed manually)
 
-## RDF4J Workbench/Server-based SPARQL Endpoint (DEPRECATED)
-
-- `ontop-webapps-[version].zip`: (DEPRECATED) WAR files required to create an Ontop SPARQL end-point webapp. Drop this into the webapps folder of your Servlet server .
-
-- `ontop-tomcat-bundle-[version].zip` : (DEPRECATED) Tomcat + RDF4J workbench + Ontop ready to run a SPARQL endpoint.
-
-- `ontop-jetty-bundle-[version].zip` : (DEPRECATED) Jetty + RDF4J workbench + Ontop ready to run a SPARQL endpoint.
+- `it.unibz.inf.ontop.protege-[version].jar`: platform-independent plugin (drop it into Protege’s `plugins` folder).
+- `ontop-protege-bundle-platform-independent-[version].zip`: platform-independent plugin (start with `run.sh`, `run.command`
+  or `run.bat`)
 
 ## Links
 

build/distribution/pom.xml

@@ -1,13 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 
     <modelVersion>4.0.0</modelVersion>
 
     <parent>
         <groupId>it.unibz.inf.ontop</groupId>
         <artifactId>ontop-build</artifactId>
-        <version>4.1.0-beta-1-SNAPSHOT</version>
+        <version>4.1.1-SNAPSHOT</version>
     </parent>
 
     <artifactId>ontop-distribution</artifactId>

build/pom.xml

@@ -1,13 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 
     <modelVersion>4.0.0</modelVersion>
 
     <parent>
         <groupId>it.unibz.inf.ontop</groupId>
         <artifactId>ontop</artifactId>
-        <version>4.1.0-beta-1-SNAPSHOT</version>
+        <version>4.1.1-SNAPSHOT</version>
     </parent>
 
     <artifactId>ontop-build</artifactId>

client/cli/pom.xml

@@ -1,13 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 
     <modelVersion>4.0.0</modelVersion>
 
     <parent>
         <groupId>it.unibz.inf.ontop</groupId>
         <artifactId>ontop-client</artifactId>
-        <version>4.1.0-beta-1-SNAPSHOT</version>
+        <version>4.1.1-SNAPSHOT</version>
     </parent>
 
     <artifactId>ontop-cli</artifactId>

client/docker/build-image.sh

@@ -12,5 +12,5 @@ unzip -o ontop-cli*.zip -d ontop
 cd ontop
 rm -r ontop.bat ontop ontop-completion.sh jdbc
 cp ${ONTOP_HOME}/client/docker/entrypoint.sh .
-docker build -t ontop/ontop-endpoint:4.1-snapshot-jre -f ${ONTOP_HOME}/client/docker/Dockerfile .
+docker build -t ontop/ontop-endpoint:4.1 -f ${ONTOP_HOME}/client/docker/Dockerfile .
 cd ${CURRENT_DIR}

client/endpoint/pom.xml

@@ -1,13 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 
     <modelVersion>4.0.0</modelVersion>
 
     <parent>
         <groupId>it.unibz.inf.ontop</groupId>
         <artifactId>ontop-client</artifactId>
-        <version>4.1.0-beta-1-SNAPSHOT</version>
+        <version>4.1.1-SNAPSHOT</version>
     </parent>
 
     <artifactId>ontop-endpoint</artifactId>

client/pom.xml

@@ -1,13 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 
     <modelVersion>4.0.0</modelVersion>
 
     <parent>
         <groupId>it.unibz.inf.ontop</groupId>
         <artifactId>ontop</artifactId>
-        <version>4.1.0-beta-1-SNAPSHOT</version>
+        <version>4.1.1-SNAPSHOT</version>
     </parent>
 
     <artifactId>ontop-client</artifactId>

client/protege/README.html

@@ -6,8 +6,8 @@ <h1>Ontop</h1>
     virtual RDF graphs defined through declarative mappings to relational databases.</p>
 
 <ul>
-    <li>Current version: 4.0.3</li>
-    <li>Release date: 16/10/2020</li>
+    <li>Current version: 4.1.0</li>
+    <li>Release date: 28/02/2021</li>
     <li><a href="https://ontop-vkg.org/guide/releases.html">Changelog</a></li>
 </ul>
 

client/protege/pom.xml

@@ -1,13 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 
     <modelVersion>4.0.0</modelVersion>
 
     <parent>
         <groupId>it.unibz.inf.ontop</groupId>
         <artifactId>ontop-client</artifactId>
-        <version>4.1.0-beta-1-SNAPSHOT</version>
+        <version>4.1.1-SNAPSHOT</version>
     </parent>
 
     <artifactId>ontop-protege</artifactId>

client/protege/src/main/java/it/unibz/inf/ontop/protege/connection/DataSource.java

@@ -114,16 +114,25 @@ public Properties asProperties() {
 		return p;
 	}
 
+	public void clear() {
+		properties.clear();
+		driver = "";
+		url = "";
+		username = "";
+		password = "";
+	}
+
 	/**
-	 * No need to remove listeners - this is handled by OBDAModelManager
+	 * Should not be called twice in a row without clear() in between.
+	 *
+	 * No need to remove listeners - this is handled by OBDAModelManager.
 	 * @param listener
 	 */
 	public void addListener(DataSourceListener listener) {
 		listeners.add(listener);
 	}
 
 	public void load(File propertyFile) throws IOException {
-		properties.clear();
 		if (propertyFile.exists())
 			try (FileReader reader = new FileReader(propertyFile)) {
 				properties.load(reader);

client/protege/src/main/java/it/unibz/inf/ontop/protege/core/OBDAModel.java

@@ -106,6 +106,17 @@ public QueryManager getQueryManager() {
 
     public OntopConfigurationManager getConfigurationManager() { return configurationManager; }
 
+    public void clear() {
+        configurationManager.clear();
+        datasource.clear();
+        triplesMapCollection.clear();
+        queryManager.clear();
+    }
+
+    /**
+        should not be called twice in a row without clear() in between
+     */
+
     public void load() throws Exception {
         String owlFilename = getOwlFilename();
         if (owlFilename == null)

client/protege/src/main/java/it/unibz/inf/ontop/protege/core/OBDAModelManager.java

@@ -208,7 +208,8 @@ public void handleChange(OWLModelManagerChangeEvent event) {
 					break;
 
 				case ONTOLOGY_LOADED: // fired after ACTIVE_ONTOLOGY_CHANGED
-					ontologyLoaded();
+				case ONTOLOGY_RELOADED:
+					ontologyLoadedReloaded();
 					break;
 
 				case ONTOLOGY_SAVED:
@@ -217,7 +218,6 @@ public void handleChange(OWLModelManagerChangeEvent event) {
 
 				case ABOUT_TO_CLASSIFY:
 				case ONTOLOGY_CLASSIFIED:
-				case ONTOLOGY_RELOADED:
 				case ENTITY_RENDERER_CHANGED:
 				case REASONER_CHANGED:
 				case ONTOLOGY_VISIBILITY_CHANGED:
@@ -277,8 +277,9 @@ private void activeOntologyChanged() {
 		listeners.fire(l -> l.activeOntologyChanged(getCurrentOBDAModel()));
 	}
 
-	private void ontologyLoaded() {
+	private void ontologyLoadedReloaded() {
 		try {
+			getCurrentOBDAModel().clear();
 			getCurrentOBDAModel().load();
 		}
 		catch (Exception e) {

client/protege/src/main/java/it/unibz/inf/ontop/protege/core/OntopConfigurationManager.java

@@ -23,6 +23,7 @@ public class OntopConfigurationManager {
     public static final String DBMETADATA_EXT = ".json"; // The default db-metadata file extension.
 
     private final OBDAModelManager obdaModelManager;
+    // settings are loaded once in the constructor and not modified afterwards
     private final Properties settings = new Properties();
 
     @Nullable
@@ -38,14 +39,25 @@ public class OntopConfigurationManager {
         this.dbMetadataFile = null;
     }
 
+    public void clear() {
+        this.implicitDBConstraintFile = null;
+        this.dbMetadataFile = null;
+    }
+
+    /**
+        Can be called twice in a row without clear(), at least for now.
+     */
+
     public void load(String owlName) {
         File implicitDBConstraintFile = new File(URI.create(owlName + DBPREFS_EXT));
-        if (implicitDBConstraintFile.exists())
-            this.implicitDBConstraintFile = implicitDBConstraintFile;
+        this.implicitDBConstraintFile = implicitDBConstraintFile.exists()
+                ? implicitDBConstraintFile
+                : null;
 
         File dbMetadataFile = new File(URI.create(owlName + DBMETADATA_EXT));
-        if (dbMetadataFile.exists())
-            this.dbMetadataFile = dbMetadataFile;
+        this.dbMetadataFile = dbMetadataFile.exists()
+                ? dbMetadataFile
+                : null;
     }
 
     private static Properties union(Properties settings, DataSource datasource) {