Several fixes and additional metadata

Fix #164, Fix #211, Fix #198, Fix #203, Fix #34, Fix #147, Fix #118, Fix
#210

README.md

@@ -61,7 +61,7 @@ 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] [-crossRef] [-saveConfig configOutFile] [-useCustomStyle] [-lang lang1-lang2] [-includeImportedOntologies] [-htaccess] [-webVowl] [-licensius]
+	java -jar widoco.jar [-ontFile file] or [-ontURI uri] [-outFolder folderName] [-confFile propertiesFile] or [-getOntologyMetadata] [-oops] [-rewriteAll] [-crossRef] [-saveConfig configOutFile] [-useCustomStyle] [-lang lang1-lang2] [-includeImportedOntologies] [-htaccess] [-webVowl] [-licensius] [-ignoreIndividuals]
 
 The ontFile and ontURI options allow you to choose the ontology file or ontology URI of your ontology.
 
@@ -89,6 +89,8 @@ The -webVowl flag provides a link to a visualization based on WebVowl (http://vo
 
 The -licensius flag uses the Licensius web services (http://licensius.com/apidoc/index.html) to retrieve license metadata. Only works if the -getOntologyMetadata flag is enabled.
 
+The -ignoreIndividuals allows you to ignore the named individuals in the ontology.
+
 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 Safari (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

@@ -37,11 +37,18 @@
 import javax.xml.transform.stream.StreamResult;
 import javax.xml.transform.stream.StreamSource;
 import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.FileDocumentSource;
+import org.semanticweb.owlapi.io.OWLOntologyDocumentSource;
 import org.semanticweb.owlapi.io.OWLOntologyDocumentTarget;
 import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
+import org.semanticweb.owlapi.io.StringDocumentSource;
 import org.semanticweb.owlapi.io.StringDocumentTarget;
+import org.semanticweb.owlapi.model.MissingImportEvent;
+import org.semanticweb.owlapi.model.MissingImportHandlingStrategy;
+import org.semanticweb.owlapi.model.MissingImportListener;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.OWLOntologyLoaderConfiguration;
 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
 import widoco.Configuration;
@@ -76,13 +83,12 @@ private static String parseWithOWLAPI(
                         boolean considerImportedOntologies) 
 	throws OWLOntologyCreationException, OWLOntologyStorageException, URISyntaxException {
             String result = "";
-            OWLOntologyManager manager = OWLManager.createOWLOntologyManager();			
+            OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+            OWLOntologyLoaderConfiguration loadingConfig = new OWLOntologyLoaderConfiguration();
+            loadingConfig = loadingConfig.setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT);
             OWLOntology ontology;
-            ontology= manager.loadOntologyFromOntologyDocument(new File(ontologyURL));
-//            
-//            else{
-//                ontology = manager.loadOntology(IRI.create(ontologyURL));
-//            }
+//            ontology = manager.loadOntologyFromOntologyDocument(new OWLOntologyDocumentSource, config)
+            ontology= manager.loadOntologyFromOntologyDocument(new FileDocumentSource(new File(ontologyURL)),loadingConfig);
             if (considerImportedOntologies) {
                 //considerImportedClosure || //<- removed for the moment
                 Set<OWLOntology> setOfImportedOntologies = new HashSet<OWLOntology>();

src/main/java/oops/OOPSevaluation.java

@@ -139,7 +139,7 @@ public String printEvaluation (){
 
             ExtendedIterator<Individual> p = model.listIndividuals(pitfallClass);	
             List<Individual> plist = p.toList();
-            System.out.println("Numero de pitfalls: " + plist.size() );
+            System.out.println("Pitfall number: " + plist.size() );
 
             if (plist.size() > 0){
 
@@ -460,6 +460,8 @@ else if (nextNode.isURIResource()){
                             }
                     }
                     evaluationOutput = evaluationOutput + "</div>\n"; //close div accordion
+            }else{
+                evaluationOutput = "<h2>Congratulations! OOPS did not find a single pitfall</h2>";
             }
 
 

src/main/java/widoco/Configuration.java

@@ -115,6 +115,12 @@ public class Configuration {
     private boolean createWebVowlVisualization;
     private boolean useLicensius;//optional usage of Licensius service.
 
+    /**
+     * Variable to keep track of possible errors in the changelog. If there are errors, the 
+     * section will not be produced. True by default.
+     */
+    private boolean changeLogSuccessfullyCreated = true;
+
     public Configuration() {
         initializeConfig();
         try {
@@ -198,6 +204,7 @@ private void initializeOntology(){
         mainOntologyMetadata.setCiteAs("");
         mainOntologyMetadata.setDoi("");
         mainOntologyMetadata.setStatus("");
+        mainOntologyMetadata.setBackwardsCompatibleWith("");
     }
 
     private void loadPropertyFile(String path){
@@ -321,6 +328,7 @@ private void loadPropertyFile(String path){
             mainOntologyMetadata.setStatus(propertyFile.getProperty(Constants.STATUS,"Specification Draft"));
             mainOntologyMetadata.setCiteAs(propertyFile.getProperty(Constants.CITE_AS, ""));
             mainOntologyMetadata.setDoi(propertyFile.getProperty(Constants.DOI, ""));
+            mainOntologyMetadata.setBackwardsCompatibleWith(propertyFile.getProperty(Constants.COMPATIBLE, ""));
             //vocabLoadedSerialization = propertyFile.getProperty(TextConstants.deafultSerialization, "RDF/XML");
             String serializationRDFXML = propertyFile.getProperty(Constants.RDF,"");
             if(!"".equals(serializationRDFXML)){
@@ -431,6 +439,18 @@ public void loadPropertiesFromOntology(OntModel m){
                 if(propertyName.equals("modified")){
                     mainOntologyMetadata.setReleaseDate(value);
                 }else
+                if(propertyName.equals("bibliographicCitation")){
+                    mainOntologyMetadata.setCiteAs(value);
+                }else
+                if(propertyName.equals("doi")||propertyName.equals("hasDOI")){
+                    mainOntologyMetadata.setDoi(value);
+                }else
+                if(propertyName.equals("backwardsCompatibleWith")){
+                    mainOntologyMetadata.setBackwardsCompatibleWith(value);
+                }else
+                if(propertyName.equals("status")){
+                    mainOntologyMetadata.setStatus(value);
+                }else
                 if(propertyName.equals("imports")){
                     Ontology o = new Ontology();
                     if(isURL(value)){
@@ -518,6 +538,16 @@ public String getOntologyURI() {
     public boolean isPublishProvenance() {
         return publishProvenance;
     }
+
+    public boolean isChangeLogSuccessfullyCreated() {
+        return changeLogSuccessfullyCreated;
+    }
+
+    public void setChangeLogSuccessfullyCreated(boolean changeLogSuccessfullyCreated) {
+        this.changeLogSuccessfullyCreated = changeLogSuccessfullyCreated;
+    }
+
+
 
 
     public void setDocumentationURI(String documentationURI) {

src/main/java/widoco/Constants.java

@@ -85,6 +85,7 @@ public class Constants {
 
     /*Property that will retrieve the status of the document from the property file*/
     public static final String STATUS="status";
+    public static final String COMPATIBLE="backwardsCompatibleWith";
 
 
     //Constants for language tags. These are the names used in the property file
@@ -136,6 +137,10 @@ public class Constants {
     public static final String LANG_DATA_PROP = "dataProp";
     public static final String LANG_ANN_PROP = "annProp";
     public static final String LANG_NAMED_INDIV = "namedIndiv";
+    public static final String LANG_TABLE_OF_CONTENTS = "tableOfContents";
+    public static final String LANG_COMPATIBLE = "compatible";
+    public static final String LANG_LEGEND = "legend";
+
     //labels for the changelog
     public static final String LANG_CHANGELOG_HEAD = "changelogHead";
     public static final String LANG_ADDED_CLASS = "addedClass";
@@ -445,7 +450,7 @@ public static String getIndexDocument(String resourcesFolderName,Configuration c
                      "}\n"
                      + "function loadTOC(){\n" +
                     "	//process toc dynamically\n" +
-                    "	  var t='<h2>Table of contents</h2><ul>';i = 1;j=0;\n" +
+                    "	  var t='<h2>"+lang.getProperty(LANG_TABLE_OF_CONTENTS)+"</h2><ul>';i = 1;j=0;\n" +
                     "	  jQuery(\".list\").each(function(){\n" +
                     "		if(jQuery(this).is('h2')){\n" +
                     "			if(j>0){\n" +
@@ -475,7 +480,7 @@ public static String getIndexDocument(String resourcesFolderName,Configuration c
         if(c.isIncludeDescription()) document += "      $(\"#description\").load(\"sections/description-"+c.getCurrentLanguage()+".html\"); \n";
         if(c.isIncludeReferences()) document += "      $(\"#references\").load(\"sections/references-"+c.getCurrentLanguage()+".html\"); \n";
         if(c.isIncludeChangeLog()){
-            if(c.getMainOntology().getPreviousVersion()!=null &&!"".equals(c.getMainOntology().getPreviousVersion())){
+            if(c.getMainOntology().getPreviousVersion()!=null &&!"".equals(c.getMainOntology().getPreviousVersion()) && c.isChangeLogSuccessfullyCreated()){
                 document += "      $(\"#changelog\").load(\"sections/changelog-"+c.getCurrentLanguage()+".html\"); \n";
             }
         }
@@ -584,6 +589,10 @@ public static String getHeadSection(Configuration c, Properties l){
             //doi is common for all languages
             head+="<dl><dt>DOI:</dt>\n<dd><a href=\"http://dx.doi.org/"+c.getMainOntology().getDoi()+"\"><img src =\"https://img.shields.io/badge/DOI-"+c.getMainOntology().getDoi()+"-blue.svg\" alt=\""+c.getMainOntology().getDoi()+"\"></img></a></dd>\n</dl>\n";
         }
+        if(!"".equals(c.getMainOntology().getBackwardsCompatibleWith()) && c.getMainOntology().getBackwardsCompatibleWith()!=null){
+            //doi is common for all languages
+            head+="<dl><dt>"+l.getProperty(LANG_COMPATIBLE)+":</dt>\n<dd>"+c.getMainOntology().getBackwardsCompatibleWith()+"</dd>\n</dl>\n";
+        }
         if(c.isPublishProvenance()){
             head+="<dl><a href=\"provenance/provenance-"+c.getCurrentLanguage()+".html\" target=\"_blank\">"+l.getProperty(LANG_PRPOV_HEAD)+"</a></dl>";
         }
@@ -946,4 +955,16 @@ public static String get406(Configuration c, Properties lang) {
         return page406;
     }
 
+    public static String getLegend(Properties lang){
+        return "<div id=\"legend\">\n" +
+        "<h2>"+lang.getProperty(Constants.LANG_LEGEND)+" <span class=\"backlink\"> "+lang.getProperty(Constants.LANG_BACK)+" <a href=\"#toc\">ToC</a></span></h2>\n" +
+        "<div   class=\"entity\">\n" +
+        "<sup class=\"type-c\" title=\""+lang.getProperty(Constants.LANG_CLASSES)+"\">c</sup>: "+lang.getProperty(Constants.LANG_CLASSES)+" <br/>\n" +
+        "<sup class=\"type-op\" title=\""+lang.getProperty(Constants.LANG_OBJ_PROP)+"\">op</sup>: "+lang.getProperty(Constants.LANG_OBJ_PROP)+" <br/>\n" +
+        "<sup class=\"type-dp\" title=\""+lang.getProperty(Constants.LANG_DATA_PROP)+"\">dp</sup>: "+lang.getProperty(Constants.LANG_DATA_PROP)+" <br/>\n" +
+        "<sup class=\"type-ni\" title=\""+lang.getProperty(Constants.LANG_NAMED_INDIV)+"\">ni</sup>: "+lang.getProperty(Constants.LANG_NAMED_INDIV)+"\n" +
+        "</div>\n" +
+        "</div>";
+    }
+
 }

src/main/java/widoco/CreateOOPSEvalInThread.java

@@ -43,19 +43,13 @@ public void run() {
             this.pointerToMain.switchState("sendingRequest");
         }
         System.out.println("Sending request to OOPS server...");
-        File evalFolder = new File(c.getDocumentationURI()+File.separator+"OOPSevaluation");
-        File evalResourcesFolder = new File(evalFolder.getAbsolutePath()+File.separator+"evaluation");//for the css etc.
         try{
-            if(!evalFolder.exists())evalFolder.mkdir();
-            evalResourcesFolder.mkdir();
-            //CreateResources.copyResourceFolder(TextConstants.oopsResources, evalResourcesFolder.getAbsolutePath());
-            WidocoUtils.unZipIt(Constants.oopsResources, evalResourcesFolder.getAbsolutePath());
             //do POST petition with evaluation.
             String evaluation;
             OOPSevaluation eval;
 
             //read file
-            String content;
+            String content=null;
             BufferedReader br = new BufferedReader(new FileReader(c.getOntologyPath()));
             try {
                 StringBuilder sb = new StringBuilder();
@@ -70,18 +64,27 @@ public void run() {
             } finally {
                 br.close();
             }
-            eval = new OOPSevaluation("",content);
-            //eval = new OOPSevaluation(c.getMainOntology().getNamespaceURI(),"");
-
-            evaluation = eval.printEvaluation();
-            //SAVE File
-            if(showGui){
-                this.pointerToMain.switchState("savingResponse");
-            }
-            System.out.println("Saving response...");
-            CreateResources.saveDocument(evalFolder.getAbsolutePath()+File.separator+"oopsEval.html", Constants.getEvaluationText(evaluation, c),c);
-            if(showGui){
-                pointerToMain.openBrowser(new File(evalFolder.getAbsolutePath()+File.separator+"oopsEval.html").toURI());
+            if(content!=null && !content.equals("")){
+                File evalFolder = new File(c.getDocumentationURI()+File.separator+"OOPSevaluation");
+                File evalResourcesFolder = new File(evalFolder.getAbsolutePath()+File.separator+"evaluation");//for the css etc.
+                if(!evalFolder.exists())evalFolder.mkdir();
+                evalResourcesFolder.mkdir();
+                //CreateResources.copyResourceFolder(TextConstants.oopsResources, evalResourcesFolder.getAbsolutePath());
+                WidocoUtils.unZipIt(Constants.oopsResources, evalResourcesFolder.getAbsolutePath());
+                eval = new OOPSevaluation("",content);
+                //eval = new OOPSevaluation(c.getMainOntology().getNamespaceURI(),"");
+                evaluation = eval.printEvaluation();
+                //SAVE File
+                if(showGui){
+                    this.pointerToMain.switchState("savingResponse");
+                }
+                System.out.println("Saving response...");
+                CreateResources.saveDocument(evalFolder.getAbsolutePath()+File.separator+"oopsEval.html", Constants.getEvaluationText(evaluation, c),c);
+                if(showGui){
+                    pointerToMain.openBrowser(new File(evalFolder.getAbsolutePath()+File.separator+"oopsEval.html").toURI());
+                }
+            }else{
+                throw new Exception("OOPS server did not return an evaluation report");
             }
         }catch(Exception e){
             System.err.println("Error while saving OOPS evaluation: "+e.getMessage());

src/main/java/widoco/CreateResources.java

@@ -176,9 +176,9 @@ private static void createChangeLog(String path, Configuration c, Properties lan
             saveDocument(path+File.separator+"changelog-"+c.getCurrentLanguage()+".html", Constants.getChangeLogSection(c, comparison, lang),c);
             System.out.println("Changelog successfully created");
         }catch(Exception e){
+            c.setChangeLogSuccessfullyCreated(false);
             System.out.println("Could not generate changelog: "+e.getMessage());
         }
-
     }
 
     /**
@@ -267,6 +267,8 @@ private static void createCrossReferenceSection(String path,LODEParser lodeParse
         if(c.isIncludeNamedIndividuals() && namedIndividualList!=null && !"".equals(namedIndividualList)){
             crossRef += lodeParser.getNamedIndividuals();
         }
+        //add legend
+        crossRef+=Constants.getLegend(lang);
         saveDocument(path+File.separator+"crossref-"+c.getCurrentLanguage()+".html", crossRef,c);
     }
 
@@ -375,6 +377,7 @@ public static void saveConfigFile(String path, Configuration conf)throws IOExcep
             textProperties+=Constants.CITE_AS+"="+conf.getMainOntology().getCiteAs()+"\n";
             textProperties+=Constants.DOI+"="+conf.getMainOntology().getDoi()+"\n";
             textProperties+=Constants.STATUS+"="+conf.getMainOntology().getStatus()+"\n";
+            textProperties+=Constants.COMPATIBLE+"="+conf.getMainOntology().getBackwardsCompatibleWith()+"\n";
             if(conf.getMainOntology().getPublisher()!=null){
                 textProperties+=Constants.PUBLISHER+"="+conf.getMainOntology().getPublisher().getName()+"\n";
                 textProperties+=Constants.PUBLISHER_URI+"="+conf.getMainOntology().getPublisher().getURL()+"\n";

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

@@ -106,6 +106,11 @@ public class Ontology {
      * DOI of the ontology, if available
      */
     private String doi;
+
+    /**
+     * Compatible with
+     */
+    private String backwardsCompatibleWith;
 
     public Ontology() {
     }
@@ -291,4 +296,14 @@ public Agent getPublisher() {
     public void setPublisher(Agent publisher) {
         this.publisher = publisher;
     }
+
+    public String getBackwardsCompatibleWith() {
+        return backwardsCompatibleWith;
+    }
+
+    public void setBackwardsCompatibleWith(String backwardsCompatibleWith) {
+        this.backwardsCompatibleWith = backwardsCompatibleWith;
+    }
+
+
 }

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

@@ -72,7 +72,7 @@ public GuiController(String[] args){
         String outFolder="myDocumentation"+(new Date().getTime()), ontology="", configOutFile=null;
         boolean  isFromFile=false, oops = false, rewriteAll=false, getOntoMetadata = false, useW3Cstyle = true,
                 includeImportedOntologies = false, htAccess = false, webVowl=false, errors = false, licensius = false,
-                generateOnlyCrossRef = false;
+                generateOnlyCrossRef = false, includeNamedIndividuals=true;
         String[] languages = null;
         int i=0;
         while(i< args.length){
@@ -135,9 +135,13 @@ else if(s.equals("-webVowl")){
             else if (s.equals("-licensius")){
                 licensius = true;
             }
+            else if(s.equals("-ignoreIndividuals")){
+                includeNamedIndividuals=false;
+                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] [-crossRef] [-saveConfig configOutFile] [-lang lang1-lang2] [-includeImportedOntologies] [-htaccess] [-licensius]\n");
+                System.out.println("Usage: java -jar widoco.jar [-ontFile file] or [-ontURI uri] [-outFolder folderName] [-confFile propertiesFile] [-getOntologyMetadata] [-oops] [-rewriteAll] [-crossRef] [-saveConfig configOutFile] [-lang lang1-lang2] [-includeImportedOntologies] [-htaccess] [-licensius] [-ignoreIndividuals]\n");
                 return;
             }
             i++;
@@ -169,6 +173,7 @@ else if (s.equals("-licensius")){
         this.config.setCreateHTACCESS(htAccess);
         this.config.setCreateWebVowlVisualization(webVowl);
         this.config.setUseLicensius(licensius);
+        this.config.setIncludeNamedIndividuals(includeNamedIndividuals);
         if(languages!=null){
             config.removeLanguageToGenerate("en");//default
             for (String language : languages) {