Merge pull request #341 from dgarijo/develop

Preparing for WIDOCO v1.4.10

src/main/java/diagram/DiagramGeneration.java

@@ -1,8 +1,3 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package diagram;
 
 import de.uni_stuttgart.vis.vowl.owl2vowl.Owl2Vowl;
@@ -19,10 +14,6 @@ public static void generateOntologyDiagram(String outFolder, Configuration c){
             //extract resource to target folder
             Owl2Vowl o = new Owl2Vowl(c.getMainOntology().getOWLAPIModel()); //TO DO: Use this function instead of reading the ontology again
             o.writeToFile(new File(outFolder+File.separator+"webvowl"+File.separator+"data"+File.separator+"ontology.json"));
-//            IRI ontologyIRI = IRI.create(new File(c.getOntologyPath()));
-//            Converter converter = new IRIConverter(ontologyIRI);
-//            converter.convert();
-//            converter.export(new FileExporter(new File(outFolder+File.separator+"webvowl"+File.separator+"data"+File.separator+"ontology.json")));    
         } catch (Exception e) {
             System.err.println("FAILED TO LOAD " + e.getMessage());
         }

src/main/java/diff/OntologyDifferencesRenderer.java

@@ -267,65 +267,65 @@ public static String differencesToHTML(CompareOntologies c, String ontologyNamep
         if(changesInClasses>0){
             changelog+="<h3 id=\"changeClass\" class=\"list\">"+language.getProperty(Constants.LANG_CLASSES)+"</h3>\n";//this will be on the lang file later
             if(!c.getModifiedClasses().isEmpty()){
-                changelog+="<p><u>"+language.getProperty(Constants.LANG_MODIFIED_CLASS)+"</u></p>\n";
+                changelog+="<details><summary><u>"+language.getProperty(Constants.LANG_MODIFIED_CLASS)+"</u></summary>\n";
                 changelog+="<ul>";
                 changelog += axiomInfoSetToHTML(c.getModifiedClasses(), ontologyNamepsace, true, true, language);
-                changelog+="</ul>";
+                changelog+="</ul></details>";
             }
             if(!c.getNewClasses().isEmpty()){
-                changelog+="<p><u>"+language.getProperty(Constants.LANG_ADDED_CLASS)+"</u></p>\n";
+                changelog+="<details><summary><u>"+language.getProperty(Constants.LANG_ADDED_CLASS)+"</u></summary>\n";
                 changelog+="<ul>";
                 changelog += axiomInfoSetToHTML(c.getNewClasses(), ontologyNamepsace, true, false, language);
-                changelog+="</ul>";
+                changelog+="</ul></details>";
             }
             if(!c.getDeletedClasses().isEmpty()){
-                changelog+="<p><u>"+language.getProperty(Constants.LANG_DELETED_CLASS)+"</u></p>\n";
+                changelog+="<details><summary><u>"+language.getProperty(Constants.LANG_DELETED_CLASS)+"</u></summary>\n";
                 changelog+="<ul>";
                 changelog += axiomInfoSetToHTML(c.getDeletedClasses(), ontologyNamepsace, false, false, language);
-                changelog+="</ul>";
+                changelog+="</ul></details>";
             }
 
         }
         if(changesInProps>0){
             changelog+="<h3 id=\"changeProp\" class=\"list\">"+language.getProperty(Constants.LANG_OBJ_PROP)+"</h3>\n";
             if(!c.getModifiedProperties().isEmpty()){
-                changelog+="<p><u>"+language.getProperty(Constants.LANG_MODIFIED_PROP)+"</u></p>\n";
+                changelog+="<details><summary><u>"+language.getProperty(Constants.LANG_MODIFIED_PROP)+"</u></summary>\n";
                 changelog+="<ul>";
                 changelog += axiomInfoSetToHTML(c.getModifiedProperties(), ontologyNamepsace, true, true, language);
-                changelog+="</ul>";
+                changelog+="</ul></details>";
             }
             if(!c.getNewProperties().isEmpty()){
-                changelog+="<p><u>"+language.getProperty(Constants.LANG_ADDED_PROP)+"</u></p>\n";
+                changelog+="<details><summary><u>"+language.getProperty(Constants.LANG_ADDED_PROP)+"</u></summary>\n";
                 changelog+="<ul>";
                 changelog += axiomInfoSetToHTML(c.getNewProperties(), ontologyNamepsace, true, false, language);
-                changelog+="</ul>";
+                changelog+="</ul></details>";
             }
             if(!c.getDeletedProperties().isEmpty()){
-                changelog+="<p><u>"+language.getProperty(Constants.LANG_DELETED_PROP)+"</u></p>\n";
+                changelog+="<details><summary><u>"+language.getProperty(Constants.LANG_DELETED_PROP)+"</u></summary>\n";
                 changelog+="<ul>";
                 changelog += axiomInfoSetToHTML(c.getDeletedProperties(), ontologyNamepsace, false, false, language);
-                changelog+="</ul>";
+                changelog+="</ul></details>";
             }
         }
         if(changesInDataProps>0){
             changelog+="<h3 id=\"changeDataProp\" class=\"list\">"+language.getProperty(Constants.LANG_DATA_PROP)+"</h3>\n";
             if(!c.getModifiedDataProperties().isEmpty()){
-                changelog+="<p><u>"+language.getProperty(Constants.LANG_MODIFIED_DATA_PROP)+"</u></p>\n";
+                changelog+="<details><summary><u>"+language.getProperty(Constants.LANG_MODIFIED_DATA_PROP)+"</u></summary>\n";
                 changelog+="<ul>";
                 changelog += axiomInfoSetToHTML(c.getModifiedDataProperties(), ontologyNamepsace, true, true, language);
-                changelog+="</ul>";
+                changelog+="</ul></details>";
             }
             if(!c.getNewDataProperties().isEmpty()){
-                changelog+="<p><u>"+language.getProperty(Constants.LANG_ADDED_DATA_PROP)+"</u></p>\n";
+                changelog+="<details><summary><u>"+language.getProperty(Constants.LANG_ADDED_DATA_PROP)+"</u></summary>\n";
                 changelog+="<ul>";
                 changelog += axiomInfoSetToHTML(c.getNewDataProperties(), ontologyNamepsace, true, false, language);
-                changelog+="</ul>";
+                changelog+="</ul></details>";
             }
             if(!c.getDeletedDataProperties().isEmpty()){
-                changelog+="<p><u>"+language.getProperty(Constants.LANG_DELETED_DATA_PROP)+"</u></p>\n";
+                changelog+="<details><summary><u>"+language.getProperty(Constants.LANG_DELETED_DATA_PROP)+"</u></summary>\n";
                 changelog+="<ul>";
                 changelog += axiomInfoSetToHTML(c.getDeletedDataProperties(), ontologyNamepsace, false, false, language);
-                changelog+="</ul>";
+                changelog+="</ul></details>";
             }
         }
         return changelog;

src/main/java/licensius/GetLicense.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2012-2013 Ontology Engineering Group, Universidad Polit�cnica de Madrid, Spain
+ * Copyright 2012-2013 Ontology Engineering Group, Universidad Politecnica de Madrid, Spain
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
  *  you may not use this file except in compliance with the License.

src/main/java/lode/LODEGeneration.java

@@ -7,7 +7,7 @@
  * Permission to use, copy, modify, and/or distribute this software for any
  * purpose with or without fee is hereby granted, provided that the above
  * copyright notice and this permission notice appear in all copies.
- * Copyright 2012-2013 Ontology Engineering Group, Universidad Politécnica de Madrid, Spain
+ * Copyright 2012-2013 Ontology Engineering Group, Universidad Politecnica de Madrid, Spain
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
  *  you may not use this file except in compliance with the License.

src/main/java/oops/OOPSevaluation.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2012-2013 Ontology Engineering Group, Universidad Politécnica de Madrid, Spain
+ * Copyright 2012-2013 Ontology Engineering Group, Universidad Politecnica de Madrid, Spain
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
  *  you may not use this file except in compliance with the License.
@@ -199,7 +199,7 @@ public String printEvaluation (){
             //    				title = ind.getPropertyValue(hasTitleDTP).asLiteral().getString();
             //    			}
 
-                                    // c—digo y titulo
+                                    // codigo y titulo
                                     evaluationOutput = evaluationOutput + "<div class=\"panel panel-default\">\n";
                                     evaluationOutput = evaluationOutput + "<div class=\"panel-heading\">\n";
                                     evaluationOutput = evaluationOutput + "<h4 class=\"panel-title\">\n";
@@ -246,7 +246,7 @@ else if (importanceLevel.equalsIgnoreCase("minor")){
                                     evaluationOutput = evaluationOutput + "</div>\n";
                                     evaluationOutput = evaluationOutput + "<div id=\"collapse"+i+"\" class=\"panel-collapse collapse\">\n";
                                     evaluationOutput = evaluationOutput + "<div class=\"panel-body\">\n";
-                                    //descripci—n
+                                    //descripcion
                                     evaluationOutput = evaluationOutput + "<p>" +  description + "</p>";
 
                                     // affected elements

src/main/java/widoco/Configuration.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2012-2013 Ontology Engineering Group, Universidad Politécnica de Madrid, Spain
+ * Copyright 2012-2013 Ontology Engineering Group, Universidad Politecnica de Madrid, Spain
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
  *  you may not use this file except in compliance with the License.
@@ -79,6 +79,7 @@ public class Configuration {
     private String descriptionPath;
     private String referencesPath;
     private String googleAnalyticsCode = null;
+    private String contextURI; //not added with an ontology because it's independent
 
     /**
      * Property for including an ontology diagram (future work)
@@ -178,6 +179,7 @@ public final void initializeConfig(){
         displaySerializations = true;
         displayDirectImportsOnly = false;
         rewriteBase = "/";
+        contextURI ="";
         initializeOntology();
     }
 
@@ -221,6 +223,7 @@ private void loadPropertyFile(String path){
             propertyFile.load(new InputStreamReader(new FileInputStream(path), "UTF-8"));
             //We try to load from the configuration file. If it fails, then we should try to load from the ontology. Then, if it fails, we should ask the user.
             abstractSection = propertyFile.getProperty(Constants.ABSTRACT_SECTION_CONTENT);
+            contextURI = propertyFile.getProperty(Constants.CONTEXT_URI, "");
             mainOntologyMetadata.setTitle (propertyFile.getProperty(Constants.ONT_TITLE,"Title goes here"));
             mainOntologyMetadata.setReleaseDate(propertyFile.getProperty(Constants.DATE_OF_RELEASE, "Date of release"));
             mainOntologyMetadata.setPreviousVersion(propertyFile.getProperty(Constants.PREVIOUS_VERSION));
@@ -1037,6 +1040,12 @@ public void setRewriteBase(String rewriteBase) {
         }
         this.rewriteBase = rewriteBase;
     }
+
+    public String getContextURI() {
+        return contextURI;
+    }
+
+
 
 
 

src/main/java/widoco/Constants.java

@@ -132,6 +132,7 @@ public class Constants {
      */
 
     public static final String ABSTRACT_SECTION_CONTENT="abstract";
+    public static final String CONTEXT_URI="contextURI";
     public static final String ONT_TITLE="ontologyTitle";
     public static final String ONT_NAME="ontologyName";
     public static final String ONT_PREFIX="ontologyPrefix";
@@ -680,6 +681,10 @@ public static String getHeadSection(Configuration c, Properties l){
             }
             head+="</dd>";
         }
+        String context= c.getContextURI();
+        if(context!=null && !context.equals("")){
+            head+="<dt>JSON-LD Context</dt><dd><a href=\""+context+"\">"+context+"</a></dd>";
+        }
 
         if(c.getMainOntology().getLicense()!=null){
             String lname = c.getMainOntology().getLicense().getName();//"license name goes here";
@@ -851,7 +856,7 @@ public static String getProvenanceRDF(Configuration c){
 
     public static final String LODE_RESOURCES= "/lode.zip";
     public static final String OOPS_RESOURCES = "/oops.zip";
-    public static final String WEBVOWL_RESOURCES = "/webvowl.zip";
+    public static final String WEBVOWL_RESOURCES = "/webvowl_1.1.4_patched.zip";
 
     public static final String CONFIG_PATH = "config"+File.separator+"config.properties";
 

src/main/java/widoco/CreateDocInThread.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2012-2013 Ontology Engineering Group, Universidad Politécnica de Madrid, Spain
+ * Copyright 2012-2013 Ontology Engineering Group, Universidad Politecnica de Madrid, Spain
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
  *  you may not use this file except in compliance with the License.

src/main/java/widoco/CreateOOPSEvalInThread.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2012-2013 Ontology Engineering Group, Universidad Politécnica de Madrid, Spain
+ * Copyright 2012-2013 Ontology Engineering Group, Universidad Politecnica de Madrid, Spain
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
  *  you may not use this file except in compliance with the License.

src/main/java/widoco/CreateResources.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2012-2013 Ontology Engineering Group, Universidad Politécnica de Madrid, Spain
+ * Copyright 2012-2013 Ontology Engineering Group, Universidad Politecnica de Madrid, Spain
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
  *  you may not use this file except in compliance with the License.
@@ -72,15 +72,15 @@ public static void generateDocumentation(String outFolder, Configuration c, File
         lodeContent = LODEGeneration.getLODEhtml(c, lodeResources);
         LODEParser lode = new LODEParser(lodeContent,c,languageFile);
         if(c.isCreateHTACCESS()){
-            File f = new File (folderOut);
-            if(!f.exists()){
-                f.mkdir();
+            File fOut = new File(folderOut);
+            if(!fOut.exists()){
+                fOut.mkdirs();
             }
             createHTACCESSFile(folderOut+File.separator+".htaccess",c);
-            //slash ontologies require a special type of redirection
-            if(!c.getMainOntology().isHashOntology()){
-                folderOut+=File.separator+"doc";
-            }
+        }
+        //slash ontologies require a special type of redirection
+        if(!c.getMainOntology().isHashOntology()){
+            folderOut+=File.separator+"doc";
         }
         createFolderStructure(folderOut,c,languageFile);
         if(c.isIncludeAbstract()){

src/main/java/widoco/LODEParser.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2012-2013 Ontology Engineering Group, Universidad Politécnica de Madrid, Spain
+ * Copyright 2012-2013 Ontology Engineering Group, Universidad Politecnica de Madrid, Spain
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
  *  you may not use this file except in compliance with the License.

src/main/java/widoco/LoadOntologyInThread.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2012-2013 Ontology Engineering Group, Universidad Politécnica de Madrid, Spain
+ * Copyright 2012-2013 Ontology Engineering Group, Universidad Politecnica de Madrid, Spain
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
  *  you may not use this file except in compliance with the License.

src/main/java/widoco/WidocoUtils.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2012-2013 Ontology Engineering Group, Universidad Politécnica de Madrid, Spain
+ * Copyright 2012-2013 Ontology Engineering Group, Universidad Politecnica de Madrid, Spain
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
  *  you may not use this file except in compliance with the License.
@@ -66,7 +66,7 @@ public static void loadModelToDocument(Configuration c) throws Exception{
         manager.getIRIMappers().add(jenaCatalogMapper);
         ((JenaCatalogIRIMapper) jenaCatalogMapper).printMap();
         OWLOntologyLoaderConfiguration loadingConfig = new OWLOntologyLoaderConfiguration();
-        loadingConfig = loadingConfig.setMissingImportHandlingStrategy(MissingImportHandlingStrategy.THROW_EXCEPTION);
+        loadingConfig = loadingConfig.setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT);
         OWLOntology ontology= manager.loadOntologyFromOntologyDocument(new FileDocumentSource(new File(c.getOntologyPath())),loadingConfig);
         c.getMainOntology().setMainOntology(ontology);
         c.getMainOntology().setMainOntologyManager(manager);

src/main/java/widoco/entities/Agent.java

@@ -1,10 +1,5 @@
 /*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-/*
- * Copyright 2012-2013 Ontology Engineering Group, Universidad Politécnica de Madrid, Spain
+ * Copyright 2012-2013 Ontology Engineering Group, Universidad Politecnica de Madrid, Spain
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
  *  you may not use this file except in compliance with the License.

src/main/java/widoco/entities/License.java

@@ -1,10 +1,5 @@
 /*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-/*
- * Copyright 2012-2013 Ontology Engineering Group, Universidad Politécnica de Madrid, Spain
+ * Copyright 2012-2013 Ontology Engineering Group, Universidad Politecnica de Madrid, Spain
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
  *  you may not use this file except in compliance with the License.

src/main/java/widoco/entities/Ontology.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2012-2013 Ontology Engineering Group, Universidad Politécnica de Madrid, Spain
+ * Copyright 2012-2013 Ontology Engineering Group, Universidad Politecnica de Madrid, Spain
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
  *  you may not use this file except in compliance with the License.

src/main/java/widoco/gui/AddProperty.java

@@ -1,9 +1,3 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-
 package widoco.gui;
 
 import java.awt.Dimension;

src/main/java/widoco/gui/BiggerTextArea.java

@@ -1,8 +1,3 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package widoco.gui;
 
 import java.awt.Dimension;

src/main/java/widoco/gui/EditProperty.java

@@ -1,9 +1,3 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
-
 package widoco.gui;
 
 import java.awt.Dimension;

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

@@ -1,5 +1,5 @@
 /*
- * Copyright 2012-2013 Ontology Engineering Group, Universidad Politécnica de Madrid, Spain
+ * Copyright 2012-2013 Ontology Engineering Group, Universidad Politecnica de Madrid, Spain
  *
  *  Licensed under the Apache License, Version 2.0 (the "License");
  *  you may not use this file except in compliance with the License.
@@ -239,7 +239,7 @@ public GuiController(String[] args){
                 config.vocabularySuccessfullyGenerated();
             }
         }catch(Exception e){
-            System.err.println("Error while generating the documentation " +e.getMessage());
+            logger.error("Error while generating the documentation: " +e.getMessage(), e);
             errors = true;
         }
 

src/main/java/widoco/gui/SelectLanguage.java

@@ -1,8 +1,3 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package widoco.gui;
 
 import java.awt.Dimension;

src/main/java/widoco/gui/TestInterface.java

@@ -1,8 +1,3 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package widoco.gui;
 
 import java.awt.Color;

src/main/java/widoco/gui/TestStep0.java

@@ -1,12 +1,6 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package widoco.gui;
 
 import java.awt.Color;
-import java.awt.Cursor;
 import java.awt.Dimension;
 import java.awt.Image;
 import java.awt.image.BufferedImage;