Merge pull request #462 from dgarijo/develop

Prepare for new release

README.md

@@ -105,14 +105,16 @@ java -jar widoco-VERSION-jar-with-dependencies.jar [OPTIONS]
 `-lang LANG1-LANG2`: Generate documentation in multiple languages (separated by "-"). Note that if the language is not supported, the system will load the labels in english. For example: en-pt-es
 
 `-includeImportedOntologies`: Indicates whether the terms of the imported ontologies of the current ontology should be documented as well or not.
--htaccess: Create a bundle for publication ready to be deployed on your Apache server.
+
+`-htaccess`: Create a bundle for publication ready to be deployed on your Apache server.
 
 `-webVowl`: Create a visualization based on WebVowl (http://vowl.visualdataweb.org/webvowl/index.html#) in the documentation.
 
 `-licensius`: Use the Licensius web services (http://licensius.com/apidoc/index.html) to retrieve license metadata. Only works if the -getOntologyMetadata  flag is enabled.
 
 `-ignoreIndividuals`: Individuals will not be included in the documentation.
--includeAnnotationProperties: Include annotation properties defined in your ontology in the documentation (by default they are not included)
+
+`-includeAnnotationProperties`: Include annotation properties defined in your ontology in the documentation (by default they are not included)
 
 `-analytics CODE`: Add a code snippet for Google analytics to track your HTML documentation. You need to add your CODE next to the flag. For example: UA-1234
 
@@ -130,10 +132,10 @@ java -jar widoco-VERSION-jar-with-dependencies.jar [OPTIONS]
 
 
 ## How can I make WIDOCO automatically recognize my vocabulary annotations?
-There are two ways for making WIDOCO get your vocabulary metadata annotations and use them automatically to document the ontology. 
+There are two alternative ways for making WIDOCO get your vocabulary metadata annotations and use them automatically to document the ontology. 
 
-* Add them in your OWL file. For guidelines on which ones to include, follow our [best practices document](https://w3id.org/widoco/bestPractices), which indicates which ones we recommend.
-* Edit the project properties of /config/config.properties. This is a key-value pair file with metadata properties. Some people consider it easier than adding the property annotations to the OWL file, although I recommend doing the former option. Note that the character ";" is used for lists (for instance first author; second author; third author).
+* The recommended way: add them in your OWL file. For guidelines on which ones to include, follow our [best practices document](https://w3id.org/widoco/bestPractices), which indicates which ones we recommend.
+* Alternatively, edit the project properties of /config/config.properties. This is a key-value pair file with metadata properties. Some people consider it easier than adding the property annotations to the OWL file, although I recommend doing the former option. Note that the character ";" is used for lists (for instance first author; second author; third author).
 
 ## Browser issues (Why can't I see the generated documentation / visualization?)
 WIDOCO separates the contents of different sections in HTML files, which are then loaded in the `index.html` file. WIDOCO was designed this way because it's easier to edit your introduction or description sections independently without being all aggregated together in a huge HTML document.  **When all the contents generated by WIDOCO are stored in a server, you will be able to see the documentation of your ontology using any browser**. However, if you open the `index.html` file **on your local browser**, you may see a document missing most of the sections in your documentation. This happens because browsers don't allow loading separate content when opening a file locally for security reasons. If you want to explore how your ontology would look locally, you have two options:

src/main/java/widoco/Configuration.java

@@ -211,10 +211,10 @@ 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.xml");
+		mainOntologyMetadata.addSerialization("RDF/XML", "ontology.rdf");
 		mainOntologyMetadata.addSerialization("TTL", "ontology.ttl");
 		mainOntologyMetadata.addSerialization("N-Triples", "ontology.nt");
-		mainOntologyMetadata.addSerialization("JSON-LD", "ontology.json");
+		mainOntologyMetadata.addSerialization("JSON-LD", "ontology.jsonld");
 		mainOntologyMetadata.setCreators(new ArrayList<>());
 		mainOntologyMetadata.setContributors(new ArrayList<>());
 		mainOntologyMetadata.setCiteAs("");

src/main/java/widoco/Constants.java

@@ -119,7 +119,7 @@ public class Constants {
 																						// authors
 
 	public static final String PROP_VANN_PREFIX = NS_VANN + "preferredNamespacePrefix";
-	public static final String PROP_VANN_URI = NS_VANN + "preferredNamespaceURI";
+	public static final String PROP_VANN_URI = NS_VANN + "preferredNamespaceUri";
 
 	public static final String PROP_SKOS_NOTE = NS_SKOS + "note";
 
@@ -861,7 +861,7 @@ public static String getHeadSection(Configuration c, Properties l) {
 					+ "</dd>\n";
 		}
                 //add commented a reference in case the evaluation is to be included
-                head+="<!-- <dt>Evaluation:</dt><dd><a href=\"OOPSEvaluation/OOPSeval.html#\" target=\"_blank\"><img src=\"https://img.shields.io/badge/Evaluate_with-OOPS! (OntOlogy Pitfall Scanner!)-blue.svg\" alt=\"Evaluate with OOPS!\" /></a></dd> -->";
+                head+="<!-- <dt>Evaluation:</dt><dd><a href=\"OOPSEvaluation/oopsEval.html#\" target=\"_blank\"><img src=\"https://img.shields.io/badge/Evaluate_with-OOPS! (OntOlogy Pitfall Scanner!)-blue.svg\" alt=\"Evaluate with OOPS!\" /></a></dd> -->";
 		if (!"".equals(c.getMainOntology().getCiteAs()) && c.getMainOntology().getCiteAs() != null) {
 			head += "<dt>" + l.getProperty(LANG_CITE_AS) + "</dt>\n<dd>" + c.getMainOntology().getCiteAs() + "</dd>\n";
 		}
@@ -1150,7 +1150,7 @@ public static final String getHTACCESS(Configuration c) {
 				+ "# Directive to ensure *.rdf files served as appropriate content type,\n"
 				+ "# if not present in main apache config\n" + "AddType application/rdf+xml .rdf\n"
 				+ "AddType application/rdf+xml .owl\n" + "AddType text/turtle .ttl\n"
-				+ "AddType application/n-triples .n3\n" + "AddType application/ld+json .json\n"
+				+ "AddType application/n-triples .n3\n" + "AddType application/ld+json .jsonld\n"
 				+ "# Rewrite engine setup\n" + "RewriteEngine On\n" + "#Change the path to the folder here\n"
 				+ "RewriteBase " + c.getRewriteBase() + projectFolder + " \n\n";
 

src/main/java/widoco/CreateOOPSEvalInThread.java

@@ -103,20 +103,20 @@ public void run() {
                                     this.pointerToMain.switchState("savingResponse");
                             }
                             logger.info("Saving response...");
-                            CreateResources.saveDocument(evalFolder.getAbsolutePath() + File.separator + "OOPSeval.html",
+                            CreateResources.saveDocument(evalFolder.getAbsolutePath() + File.separator + "oopsEval.html",
                                             Constants.getEvaluationText(evaluation, c), c);
                             //edit html file with the right pointer to the evaluation. For all languages
                             for (String lang: c.getLanguagesToGenerateDoc()){    
                                 Path path = Paths.get(pathOut+File.separator+"index-"+lang+".html");
                                 Charset charset = StandardCharsets.UTF_8;
                                 String htmlContent = new String(Files.readAllBytes(path), charset);
-                                content = htmlContent.replace("<!-- <dt>Evaluation:</dt><dd><a href=\"OOPSevaluation/OOPSeval.html#\" target=\"_blank\"><img src=\"https://img.shields.io/badge/Evaluate_with-OOPS! (OntOlogy Pitfall Scanner!)-blue.svg\" alt=\"Evaluate with OOPS!\" /></a></dd> -->",
+                                content = htmlContent.replace("<!-- <dt>Evaluation:</dt><dd><a href=\"OOPSEvaluation/OOPSeval.html#\" target=\"_blank\"><img src=\"https://img.shields.io/badge/Evaluate_with-OOPS! (OntOlogy Pitfall Scanner!)-blue.svg\" alt=\"Evaluate with OOPS!\" /></a></dd> -->",
                                         "<dt>Evaluation:</dt><dd><a href=\"OOPSEvaluation/OOPSeval.html#\" target=\"_blank\"><img src=\"https://img.shields.io/badge/Evaluate_with-OOPS! (OntOlogy Pitfall Scanner!)-blue.svg\" alt=\"Evaluate with OOPS!\" /></a></dd>");
                                 Files.write(path, content.getBytes(charset));
                             }
                             if (showGui) {
                                     pointerToMain.openBrowser(
-                                                    new File(evalFolder.getAbsolutePath() + File.separator + "OOPSeval.html").toURI());
+                                                    new File(evalFolder.getAbsolutePath() + File.separator + "oopsEval.html").toURI());
                             }
 			} else {
 				throw new Exception("OOPS server did not return an evaluation report");

src/main/java/widoco/CreateResources.java

@@ -125,10 +125,10 @@ 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.xml");
+		WidocoUtils.writeModel(om, o, new RDFXMLDocumentFormat(), folderOut + File.separator + "ontology.rdf");
 		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.json");
+		WidocoUtils.writeModel(om, o, new RDFJsonLDDocumentFormat(), folderOut + File.separator + "ontology.jsonld");
 		if (c.isIncludeIndex()) {
                     if(c.isIncludeAllSectionsInOneDocument()){
                         createUnifiedIndexDocument(abs,intro,overview,description,crossref,ref,changeLog, folderOut, c, lode, languageFile);

src/test/java/oops/OOPSevaluationTest.java

@@ -23,7 +23,7 @@ public OOPSevaluationTest() {
     /**
      * Test of printEvaluation method, of class OOPSevaluation.
      */
-   // @Test (Commented out because OOPS! WS seems to be down
+    @Test //(Commented out because OOPS! WS seems to be down
     public void testPrintEvaluation()  {
         try{
         System.out.println("printEvaluation with alo");
@@ -51,7 +51,7 @@ public void testPrintEvaluation()  {
         }
     }
 
-    //@Test
+    @Test
     public void testPrintEvaluation2()  {
         try{
         System.out.println("printEvaluation with p-plan");