Fix dgarijo#150

And also i fixed a small typo when creating the ids of the terms.

README.md

@@ -49,7 +49,7 @@ The character ";" is used for lists (for instance first author; second author; t
 
 Now you can execute Widoco through the console. Usage:
 
-	java -jar widoco.jar [-ontFile file] or [-ontURI uri] [-outFolder folderName] [-confFile propertiesFile] or [-getOntologyMetadata] [-oops] [-rewriteAll] [-saveConfig configOutFile] [-useCustomStyle] [-lang lang1;lang2]
+	java -jar widoco.jar [-ontFile file] or [-ontURI uri] [-outFolder folderName] [-confFile propertiesFile] or [-getOntologyMetadata] [-oops] [-rewriteAll] [-saveConfig configOutFile] [-useCustomStyle] [-lang lang1;lang2] [-includeImportedOntologies]
 
 The ontFile and ontURI options allow you to choose the ontology file or ontology URI of your ontology.
 
@@ -67,6 +67,8 @@ The -useCustomStyle option allows exporting the documentation using alternate cs
 
 The -lang option allows showing the languages in which the documentation will be published (separated by ";"). Note that if the language is not supported, the system will load the labels in english. For example: en;pt;es
 
+The -includeImportedOntologies flag indicates whether the terms of the imported ontologies of the current ontology should be documented as well or not.
+
 Browser problems
 ==========
 The result of executing Widoco is an html file. We have tested it in Mozilla, IE and Chrome, and when the page is stored in a server all the browsers work correctly. If you view the file locally, we recommend you to use Mozilla Firefox (or Internet Explorer, if you must). Google Chrome will not show the contents correctly, as it doesn't allow  XMLHttpRequest without HTTP. If you want to view the page locally with Google Chrome you have two possibilities:

src/main/java/lode/LODEGeneration.java

@@ -29,6 +29,8 @@
 import java.io.StringReader;
 import java.io.UnsupportedEncodingException;
 import java.net.URISyntaxException;
+import java.util.HashSet;
+import java.util.Set;
 import javax.xml.transform.Transformer;
 import javax.xml.transform.TransformerException;
 import javax.xml.transform.TransformerFactory;
@@ -60,7 +62,7 @@ public static String getLODEhtml(Configuration c, File lodeResources) throws Exc
                     lang = "en";
             }
             //load with jena in rdf xml
-            content = parseWithOWLAPI(c.getOntologyPath(), c.isFromFile());
+            content = parseWithOWLAPI(c.getOntologyPath(), c.isFromFile(), c.isUseImported());
             content = applyXSLTTransformation(content, c.getOntologyURI(), lang, lodeResources);
             return(content);
         }
@@ -73,7 +75,8 @@ public static String getLODEhtml(Configuration c, File lodeResources) throws Exc
 
 	private static String parseWithOWLAPI(
 			String ontologyURL,
-                        boolean loadFromFile) 
+                        boolean loadFromFile, 
+                        boolean considerImportedOntologies) 
 	throws OWLOntologyCreationException, OWLOntologyStorageException, URISyntaxException {
             String result = "";
             OWLOntologyManager manager = OWLManager.createOWLOntologyManager();			
@@ -84,18 +87,17 @@ private static String parseWithOWLAPI(
             else{
                 ontology = manager.loadOntology(IRI.create(ontologyURL));
             }
-            //this adds extra complexity that I don't want to include yet in the tool
-//                    if (considerImportedClosure || considerImportedOntologies) {
-//                            Set<OWLOntology> setOfImportedOntologies = new HashSet<OWLOntology>();
-//                            if (considerImportedOntologies) {
-//                                    setOfImportedOntologies.addAll(ontology.getDirectImports());
-//                            } else {
-//                                    setOfImportedOntologies.addAll(ontology.getImportsClosure());
-//                            }
-//                            for (OWLOntology importedOntology : setOfImportedOntologies) {
-//                                    manager.addAxioms(ontology, importedOntology.getAxioms());
-//                            }
-//                    }
+            if (considerImportedOntologies) {
+                //considerImportedClosure || //<- removed for the moment
+                Set<OWLOntology> setOfImportedOntologies = new HashSet<OWLOntology>();
+                setOfImportedOntologies.addAll(ontology.getDirectImports());
+//                else {
+//                        setOfImportedOntologies.addAll(ontology.getImportsClosure());
+//                }
+                for (OWLOntology importedOntology : setOfImportedOntologies) {
+                        manager.addAxioms(ontology, importedOntology.getAxioms());
+                }
+            }
 
             OWLOntologyDocumentTarget parsedOntology = new StringDocumentTarget();
             manager.saveOntology(ontology, new RDFXMLOntologyFormat(), parsedOntology);

src/main/java/widoco/Configuration.java

@@ -107,6 +107,9 @@ public class Configuration {
 
     private String error;//Latest error to show to user via interface.
 
+    //add imported ontologies in the doc as well
+    private boolean addImportedOntologies;
+
     //model everything as a singleton object. No need: only the controller accesses this file.
     public Configuration() {
         propertyFile = new Properties();
@@ -159,6 +162,7 @@ private void cleanConfig(){
         }
         useW3CStyle = true;//by default
         error = "";
+        addImportedOntologies = false;
     }
 
     private void loadConfigPropertyFile(String path){
@@ -815,6 +819,15 @@ public void setError(String error) {
     public String getError() {
         return error;
     }
+
+    public boolean isAddImportedOntologies() {
+        return addImportedOntologies;
+    }
+
+    public void setAddImportedOntologies(boolean addImportedOntologies) {
+        this.addImportedOntologies = addImportedOntologies;
+    }
+
 
 
 }

src/main/java/widoco/LODEParser.java

@@ -18,6 +18,7 @@
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.StringWriter;
+import java.net.URLDecoder;
 import java.util.HashMap;
 import java.util.logging.Level;
 import java.util.logging.Logger;
@@ -253,6 +254,13 @@ private  Node fixAnchor(Node nodeToFix) {
                     Node secondAnchor = firstAnchor.getNextSibling();
                     String newID = firstAnchor.getAttributes().getNamedItem("name").getNodeValue();
                     newID = newID.replace(c.getMainOntology().getNamespaceURI(), "");
+
+                    try{
+                        //if the URI contains special characters, we must decode them for referencing them properly.
+                        newID = URLDecoder.decode(newID, "UTF-8");
+                    }catch(Exception e){
+                        System.err.println("Error when encoding node.");
+                    }                        
                     if (newID.startsWith("#")){
                         newID = newID.replace("#", "");
                     }//fix in case the author insert the NS URI without "#"
@@ -261,9 +269,10 @@ private  Node fixAnchor(Node nodeToFix) {
                     }
                     //we save the the id for derreferencing properly the resource. Note that
                     //if a property has the same name as a Class this could lead to problems                
-                    replacements.put(currentNode.getAttributes().getNamedItem("id").getNodeValue(), newID);
+                    replacements.put(currentNode.getAttributes().getNamedItem("id").getNodeValue()+"\"", newID+"\"");
+                    //I include the comma at the end so smaller ids don't replace larger ids. (quick fix)
 
-                    //we remove the anchor, which make an error in the visualization
+                    //we remove the anchor, which makes an error in the visualization
                     currentNode.removeChild(firstAnchor);
                 }
             }

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

@@ -79,7 +79,8 @@ public GuiController(String[] args){
         config = new Configuration();
         //get the arguments
         String outFolder="myDocumentation"+(new Date().getTime()), ontology="", configOutFile=null;
-        boolean  isFromFile=false, oops = false, rewriteAll=false, getOntoMetadata = false, useW3Cstyle = true;
+        boolean  isFromFile=false, oops = false, rewriteAll=false, getOntoMetadata = false, useW3Cstyle = true,
+                includeImportedOntologies = false;
         String[] languages = null;
         int i=0;
         while(i< args.length){
@@ -123,13 +124,16 @@ else if(s.equals("-saveConfig")){
             else if(s.equals("-useCustomStyle")){
                 useW3Cstyle = false;
             }
+            else if(s.equals("-includeImportedOntologies")){
+                includeImportedOntologies = true;
+            }
             else if(s.equals("-lang")){
                 languages = args[i+1].replace(" ","").split(";");
                 i++;
             }
             else{
                 System.out.println("Command"+s+" not recognized.");
-                System.out.println("Usage: java -jar widoco.jar [-ontFile file] or [-ontURI uri] [-outFolder folderName] [-confFile propertiesFile] [-getOntologyMetadata] [-oops] [-rewriteAll] [-saveConfig configOutFile]\n");
+                System.out.println("Usage: java -jar widoco.jar [-ontFile file] or [-ontURI uri] [-outFolder folderName] [-confFile propertiesFile] [-getOntologyMetadata] [-oops] [-rewriteAll] [-saveConfig configOutFile] [-lang lang1;lang2] [-includeImportedOntologies]\n");
                 return;
             }
             i++;
@@ -148,6 +152,7 @@ else if(s.equals("-lang")){
         this.config.setOntologyPath(ontology);
         this.config.setOverwriteAll(rewriteAll);
         this.config.setUseW3CStyle(useW3Cstyle);
+        this.config.setUseImported(includeImportedOntologies);
         if(languages!=null){
             config.removeLanguageToGenerate("en");//default
             for (String language : languages) {