Merge pull request #590 from dgarijo/develop

Develop

Author: dgarijo

.github/workflows/ci.yml

@@ -54,7 +54,7 @@ jobs:
       # https://github.com/docker/metadata-action (lower cases image name, etc.)
       - name: Extract Docker metadata
         id: meta
-        uses: docker/metadata-action@v4.3.0
+        uses: docker/metadata-action@v4.4.0
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
       - name: Build and push

README.md

@@ -7,7 +7,7 @@ WIDOCO helps you to publish and create an enriched and customized documentation
 
 **Author**: Daniel Garijo Verdejo (@dgarijo)
 
-**Contributors**: María Poveda, Idafen Santana, Almudena Ruiz, Miguel Angel García, Oscar Corcho, Daniel Vila, Sergio Barrio, Martin Scharm, Maxime Lefrancois, Alfredo Serafini, @kartgk, Pat Mc Bennett, Christophe Camel, Jacobus Geluk, Martin Scharm, @rpietzsch, Jonathan Leitschuh, Jodi Schneider, Giacomo Lanza, Alejandra Gonzalez-Beltran, Mario Scrocca, Miguel Angel García, Flores Bakker, @JohnnyMoonlight and René Fritze.
+**Contributors**: María Poveda, Idafen Santana, Almudena Ruiz, Miguel Angel García, Oscar Corcho, Daniel Vila, Sergio Barrio, Martin Scharm, Maxime Lefrancois, Alfredo Serafini, @kartgk, Pat Mc Bennett, Christophe Camel, Jacobus Geluk, Martin Scharm, @rpietzsch, Jonathan Leitschuh, Jodi Schneider, Giacomo Lanza, Alejandra Gonzalez-Beltran, Mario Scrocca, Miguel Angel García, Flores Bakker, @JohnnyMoonlight,  René Fritze, @telecsur, Jan Vlug, Han Kruiger, Johannes Theissen-Lipp and Roberto Polli.
 
 **Citing WIDOCO**: If you used WIDOCO in your work, please cite the ISWC 2017 paper: https://iswc2017.semanticweb.org/paper-138
 
@@ -75,7 +75,7 @@ Examples of the features of WIDOCO can be seen on [the gallery](https://dgarijo.
 A tutorial explaining the main features of the GUI can be found [here](https://dgarijo.github.io/Widoco/doc/tutorial/)  
 
 ## Metadata usage
-To see how WIDOCO recognizes metadata annotations in your ontology to create the documentation files, see [the Widoco metadata documentation](doc/metadataGuide/guide.md). To learn which metadata properties we recommend adding to your ontology for producing a nice-looking documentation, have a look at our [best practices guide](https://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html).
+To see how WIDOCO recognizes metadata annotations in your ontology to create the documentation files, see [the Widoco metadata documentation](doc/metadataGuide/guide.md). To learn which metadata properties we recommend adding to your ontology for producing a nice-looking documentation, have a look at our [best practices guide](doc/bestPractices/index-en.html).
 
 ## How to use WIDOCO
 
@@ -164,6 +164,8 @@ docker run -ti --rm \
 
 `--help`: Shows a help message and exits.
 
+`--version`: Shows the version of WIDOCO.
+
 
 ## How can I make WIDOCO automatically recognize my vocabulary annotations?
 There are two alternative ways for making WIDOCO get your vocabulary metadata annotations and use them automatically to document the ontology.

pom.xml

@@ -4,7 +4,7 @@
 	<groupId>es.oeg</groupId>
 	<artifactId>widoco</artifactId>
 	<packaging>jar</packaging>
-	<version>1.4.17</version>
+	<version>1.4.19</version>
 	<name>Widoco</name>
 
 	<properties>
@@ -16,6 +16,13 @@
 
 	<dependencies>
 
+		<dependency>
+			<groupId>org.apache.maven</groupId>
+			<artifactId>maven-model</artifactId>
+			<version>3.9.0</version>
+		</dependency>
+
+
 		<dependency>
 			<groupId>com.github.VisualDataWeb</groupId>
 			<artifactId>OWL2VOWL</artifactId>
@@ -131,35 +138,6 @@
 					<target>11</target>
 				</configuration>
 			</plugin>
-                        <plugin>
-                                <groupId>org.owasp</groupId>
-                                <artifactId>dependency-check-maven</artifactId>
-                                <version>6.0.1</version>
-                                <executions>
-                                        <execution>
-                                                <goals>
-                                                        <goal>check</goal>
-                                                </goals>
-                                        </execution>
-                                </executions>
-                        </plugin>
-                        <plugin>
-                                <groupId>org.apache.maven.plugins</groupId>
-                                <artifactId>maven-dependency-plugin</artifactId>
-                                <version>3.2.0</version>
-                                <executions>
-                                        <execution>
-                                                <phase>validate</phase>
-                                                <goals>
-                                                        <goal>list</goal>
-                                                </goals>
-                                        </execution>
-                                </executions>
-                                <configuration>
-                                        <outputFile>pom.lock</outputFile>
-                                </configuration>
-                        </plugin>
-
 
 		</plugins>
 

src/main/java/oops/OOPSevaluation.java

@@ -15,9 +15,7 @@
  */
 package oops;
 
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStreamWriter;
+import java.io.*;
 import java.net.HttpURLConnection;
 import java.net.URL;
 import java.util.ArrayList;
@@ -57,21 +55,26 @@ public class OOPSevaluation {
 	public boolean error = false;
 	private OWLOntology model = null;
         private int pitfallNumber;
-        
-        
-	public OOPSevaluation(String content) throws IOException {
+
+
+    /**
+     * Main constructor: given an ontology file, a request will be issue to the OOPS! server
+     * @param ontologyContent
+     * @throws IOException
+     */
+	public OOPSevaluation(String ontologyContent) throws IOException {
             //always query by content
             pitfallNumber = 0;
             String request = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" + "<OOPSRequest><OntologyUrl>";
             request += "</OntologyUrl><OntologyContent>";
-            if (content != null && !"".equals(content)) {
-                    request += "<![CDATA[ " + content + " ]]>";
+            if (ontologyContent != null && !"".equals(ontologyContent)) {
+                    request += "<![CDATA[ " + ontologyContent + " ]]>";
             }
             request += "</OntologyContent>" + "<Pitfalls></Pitfalls>" + "<OutputFormat>RDF/XML</OutputFormat>"
                             + "</OOPSRequest>";
             String uri = Constants.OOPS_SERVICE_URL;
             URL url = new URL(uri);
-            System.out.println(request);
+            //System.out.println(request);
             HttpURLConnection connection = (HttpURLConnection) url.openConnection();
             connection.setConnectTimeout(Constants.OOPS_TIME_OUT);
             connection.setRequestMethod("POST");
@@ -82,19 +85,34 @@ public OOPSevaluation(String content) throws IOException {
             wr.write(request);
             wr.flush();
             InputStream in = (InputStream) connection.getInputStream();
-            try{
-                OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
-                model = manager.loadOntologyFromOntologyDocument(in);
-                OWLClass pitfall = model.getOWLOntologyManager().getOWLDataFactory().getOWLClass(Constants.OOPS_NS + "pitfall");
-                this.pitfallNumber = EntitySearcher.getIndividuals(pitfall, model).collect(Collectors.toSet()).size();
-            }catch(OWLOntologyCreationException e){
-                logger.warn("Could not extract the number of pitfalls from response");
-            }
+            initializeEvaluation(in);
             in.close();
             wr.close();
             connection.disconnect();
 
 	}
+
+    /**
+     * Auxiliary constructor in case the response from OOPS! is downloaded elsewhere
+     * @param OOPSResponse
+     * @throws IOException
+     */
+    public OOPSevaluation(InputStream OOPSResponse){
+        initializeEvaluation(OOPSResponse);
+    }
+
+
+    private void initializeEvaluation(InputStream OOPSResponse){
+        try{
+            OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+            model = manager.loadOntologyFromOntologyDocument(OOPSResponse);
+            OWLClass pitfall = model.getOWLOntologyManager().getOWLDataFactory().getOWLClass(Constants.OOPS_NS + "pitfall");
+            this.pitfallNumber = EntitySearcher.getIndividuals(pitfall, model).collect(Collectors.toSet()).size();
+        }catch(OWLOntologyCreationException e){
+            logger.warn("Could not extract the number of pitfalls from response");
+        }
+
+    }
 
 
         /**

src/main/java/widoco/Configuration.java

@@ -210,7 +210,7 @@ private void initializeOntology() {
 		mainOntologyMetadata.setLicense(l);
 		mainOntologyMetadata.setSerializations(new HashMap<>());
 		// add default serializations: rdf/xml, n3, turtle and json-ld
-		mainOntologyMetadata.addSerialization("RDF/XML", "ontology.rdf");
+		mainOntologyMetadata.addSerialization("RDF/XML", "ontology.owl");
 		mainOntologyMetadata.addSerialization("TTL", "ontology.ttl");
 		mainOntologyMetadata.addSerialization("N-Triples", "ontology.nt");
 		mainOntologyMetadata.addSerialization("JSON-LD", "ontology.jsonld");
@@ -226,7 +226,6 @@ private void initializeOntology() {
 	}
 
 	private void loadPropertyFile(String path) throws IOException {
-		// try {
 		try {
 			initializeOntology();
 			// this forces the property file to be in UTF 8 instead of the ISO
@@ -438,21 +437,21 @@ public void loadPropertiesFromOntology(OWLOntology o) {
 		}
 		// default citation if none is given
 		if (mainOntologyMetadata.getCiteAs() == null || mainOntologyMetadata.getCiteAs().isEmpty()) {
-			String cite = "";
+			StringBuilder cite = new StringBuilder();
 			for (Agent a : mainOntologyMetadata.getCreators()) {
-				cite += a.getName() + ", ";
+				cite.append(a.getName()).append(", ");
 			}
 			if (cite.length() > 1) {
 				// remove the last ","
-				cite = cite.substring(0, cite.length() - 2);
-				cite += ".";
+				cite = new StringBuilder(cite.substring(0, cite.length() - 2));
+				cite.append(".");
 			}
 
-			cite += appendDetails(mainOntologyMetadata.getTitle(), " ", true);
-			cite += appendDetails(mainOntologyMetadata.getRevision(), " Revision: ", true);
-			cite += appendDetails(mainOntologyMetadata.getThisVersion(), " Retrieved from: ", false);
+			cite.append(appendDetails(mainOntologyMetadata.getTitle(), " ", true));
+			cite.append(appendDetails(mainOntologyMetadata.getRevision(), " Revision: ", true));
+			cite.append(appendDetails(mainOntologyMetadata.getThisVersion(), " Retrieved from: ", false));
 
-			mainOntologyMetadata.setCiteAs(cite);
+			mainOntologyMetadata.setCiteAs(cite.toString());
 		}
 		//load all namespaces in the ontology document.
 		this.namespaceDeclarations = new HashMap<>();

src/main/java/widoco/Constants.java

@@ -156,8 +156,8 @@ public class Constants {
 	public static final String PROP_VCARD_EMAIL_OLD = NS_VCARD_OLD + "EMAIL";
 
 	public static final String PROP_FOAF_NAME = NS_FOAF + "name";
-	public static final String PROP_FOAF_GIVEN_NAME = NS_FOAF + "givenName";
-	public static final String PROP_FOAF_FAMILY_NAME = NS_FOAF + "familyName";
+	public static final String PROP_FOAF_GIVEN_NAME = NS_FOAF + "givenname";
+	public static final String PROP_FOAF_FAMILY_NAME = NS_FOAF + "family_name";
 	public static final String PROP_FOAF_MBOX = NS_FOAF + "mbox";
 	public static final String PROP_FOAF_HOME_PAGE = NS_FOAF + "homepage";
 	public static final String PROP_FOAF_IMAGE = NS_FOAF + "img";
@@ -651,15 +651,18 @@ public static String getIndexDocument(String resourcesFolderName, Configuration
 		/* Style selection */
 		if (c.isUseW3CStyle()) {
 			document += " <link rel=\"stylesheet\" href=\"" + resourcesFolderName
-					+ "/primer.css\" media=\"screen\" />   " + " <link rel=\"stylesheet\" href=\"" + resourcesFolderName
-					+ "/rec.css\" media=\"screen\" />   " + " <link rel=\"stylesheet\" href=\"" + resourcesFolderName
-					+ "/extra.css\" media=\"screen\" />   " + " <link rel=\"stylesheet\" href=\"" + resourcesFolderName
-					+ "/owl.css\" media=\"screen\" />   ";
+					+ "/primer.css\" media=\"screen\" />   \n" +
+					" <link rel=\"stylesheet\" href=\"" + resourcesFolderName
+					+ "/rec.css\" media=\"screen\" />   \n" + " <link rel=\"stylesheet\" href=\"" + resourcesFolderName
+					+ "/extra.css\" media=\"screen\" />   \n" + " <link rel=\"stylesheet\" href=\"" + resourcesFolderName
+					+ "/owl.css\" media=\"screen\" />   \n";
 
 		} else {
-			document += " <link rel=\"stylesheet\" href=\"" + resourcesFolderName + "/yeti.css\" media=\"screen\" />   "
-					+ " <link rel=\"stylesheet\" href=\"" + resourcesFolderName + "/site.css\" media=\"screen\" />";
+			document += " <link rel=\"stylesheet\" href=\"" + resourcesFolderName + "/yeti.css\" media=\"screen\" />   \n"
+					+ " <link rel=\"stylesheet\" href=\"" + resourcesFolderName + "/site.css\" media=\"screen\" />\n";
 		}
+		// add a favicon (rdf logo)
+		document += "<link rel=\"icon\" type=\"image/png\" href=\"" + resourcesFolderName + "/rdf.icon\"/>";
 
 		// add a title to the document
 		if (c.getMainOntology().getTitle() != null && !"".equals(c.getMainOntology().getTitle()))

src/main/java/widoco/CreateOOPSEvalInThread.java

@@ -65,7 +65,7 @@ public void run() {
 			if (!c.getMainOntology().isHashOntology()) {
 				ontologyXMLPath += File.separator + "doc";
 			}
-			ontologyXMLPath += File.separator + "ontology.rdf";
+			ontologyXMLPath += File.separator + "ontology.owl";
 
 			// read file
 			String content = null;

src/main/java/widoco/CreateResources.java

@@ -125,7 +125,7 @@ public static void generateDocumentation(String outFolder, Configuration c, File
 		// serialize the model in different serializations.
 		OWLOntologyManager om = c.getMainOntology().getOWLAPIOntologyManager();
 		OWLOntology o = c.getMainOntology().getOWLAPIModel();
-		WidocoUtils.writeModel(om, o, new RDFXMLDocumentFormat(), folderOut + File.separator + "ontology.rdf");
+		WidocoUtils.writeModel(om, o, new RDFXMLDocumentFormat(), folderOut + File.separator + "ontology.owl");
 		WidocoUtils.writeModel(om, o, new TurtleDocumentFormat(), folderOut + File.separator + "ontology.ttl");
 		WidocoUtils.writeModel(om, o, new NTriplesDocumentFormat(), folderOut + File.separator + "ontology.nt");
 		WidocoUtils.writeModel(om, o, new RDFJsonLDDocumentFormat(), folderOut + File.separator + "ontology.jsonld");
@@ -442,6 +442,9 @@ private static void createFolderStructure(String s, Configuration c, Properties
 				new File(resources.getAbsolutePath() + File.separator + "jquery.js"));
 		WidocoUtils.copyLocalResource("/lode/marked.min.js",
 				new File(resources.getAbsolutePath() + File.separator + "marked.min.js"));
+		// icon
+		WidocoUtils.copyLocalResource("/widoco/images/rdf.icon",
+				new File(resources.getAbsolutePath() + File.separator + "rdf.icon"));
 		// copy css
 		if (c.isUseW3CStyle()) {
 			WidocoUtils.copyLocalResource("/lode/lodeprimer.css",

src/main/java/widoco/gui/GuiController.java

@@ -17,7 +17,9 @@
 package widoco.gui;
 
 import java.awt.Desktop;
+import java.io.FileReader;
 import java.io.IOException;
+import java.io.InputStream;
 import java.net.URI;
 import java.util.Date;
 import java.util.Properties;
@@ -35,6 +37,9 @@
 import widoco.LoadOntologyInThread;
 import widoco.WidocoUtils;
 
+import org.apache.maven.model.Model;
+import org.apache.maven.model.io.xpp3.MavenXpp3Reader;
+
 /**
  *
  * @author Daniel Garijo
@@ -77,6 +82,23 @@ public GuiController() {
 	public GuiController(String[] args) {
 
 		logger.info("\n\n--WIzard for DOCumenting Ontologies (WIDOCO).\n https://w3id.org/widoco/\n");
+		String version = "";
+		try {
+			MavenXpp3Reader reader = new MavenXpp3Reader();
+			Model model = reader.read(new FileReader("pom.xml"));
+			version = model.getVersion();
+		} catch (Exception e) {
+			try{
+				InputStream inputStream = GuiController.class.getResourceAsStream("/META-INF/maven/es.oeg/widoco/pom.xml");
+				MavenXpp3Reader reader = new MavenXpp3Reader();
+				Model model = reader.read(inputStream);
+				version = model.getVersion();
+			}catch (Exception e2) {
+				logger.error("Could not read the project version from pom");
+			}
+
+		}
+
 		// get the arguments
 		String outFolder = "myDocumentation" + (new Date().getTime()), ontology = "", rb = null, configOutFile = null;
 		boolean isFromFile = false, oops = false, rewriteAll = false, getOntoMetadata = true, useW3Cstyle = true,
@@ -176,6 +198,11 @@ public GuiController(String[] args) {
 			case "--help":
 				System.out.println(Constants.HELP_TEXT);
 				return;
+			case "--version":
+				if (!version.isEmpty()) {
+					System.out.println("Version: "+version);
+				}
+				return;
 			default:
 				System.out.println("Command" + s + " not recognized.");
 				System.out.println(Constants.HELP_TEXT);