Merge pull request #626 from dgarijo/develop

Fix #609, Fix #588 Fix #530

src/main/java/widoco/Configuration.java

@@ -450,7 +450,31 @@ public void loadPropertiesFromOntology(OWLOntology o) {
 			});
 		}
 		this.mainOntologyMetadata.setThisVersion(versionUri);
+		// process ontology annotations
 		o.annotations().forEach(a -> completeOntologyMetadata(a,o));
+		// in some cases, properties and data properties extend annotation properties, so we need to process them
+		// separately. In this case we go through all axioms and look for any props that have the own ontology as subject
+		for (OWLAxiom axiom : o.getAxioms()) {
+			String subject = "", predicate ="", object ="";
+			if (axiom instanceof OWLDataPropertyAssertionAxiom) {
+				OWLDataPropertyAssertionAxiom dataPropertyAssertionAxiom = (OWLDataPropertyAssertionAxiom) axiom;
+				subject = dataPropertyAssertionAxiom.getSubject().toStringID();
+				predicate = dataPropertyAssertionAxiom.getProperty().asOWLDataProperty().toStringID();
+				object = dataPropertyAssertionAxiom.getObject().getLiteral();
+			} else if (axiom instanceof OWLObjectPropertyAssertionAxiom) {
+				OWLObjectPropertyAssertionAxiom objectPropertyAssertionAxiom = (OWLObjectPropertyAssertionAxiom) axiom;
+				subject = objectPropertyAssertionAxiom.getSubject().toStringID();
+				predicate = objectPropertyAssertionAxiom.getProperty().asOWLObjectProperty().toStringID();
+				object = objectPropertyAssertionAxiom.getObject().toStringID();
+			}
+			if (subject.equals(uri)){
+				OWLDataFactory dataFactory = this.mainOntologyMetadata.getOWLAPIOntologyManager().getOWLDataFactory();
+				OWLAnnotationProperty pAux = dataFactory.getOWLAnnotationProperty(IRI.create(predicate));
+				OWLAnnotationValue oAux = dataFactory.getOWLLiteral(object);
+				completeOntologyMetadata(dataFactory.getOWLAnnotation(pAux,oAux),o);
+			}
+		}
+
 		if (isUseLicensius()) {
 			String licName;
 			String lic = GetLicense.getFirstLicenseFound(mainOntologyMetadata.getNamespaceURI());
@@ -513,7 +537,7 @@ private void completeOntologyMetadata(OWLAnnotation a, OWLOntology o) {
 		String propertyName = a.getProperty().getIRI().getIRIString();
 		String value;
 		String valueLanguage;
-//		 System.out.println(propertyName);
+		//System.out.println(propertyName);
 		switch (propertyName) {
 		case Constants.PROP_RDFS_LABEL:
 		case Constants.PROP_SKOS_PREF_LABEL:

src/main/java/widoco/Constants.java

@@ -791,6 +791,9 @@ public static String getIndexDocument(String resourcesFolderName, Configuration
 				document += "      $(\"#introduction\").load(\"sections/introduction-" + c.getCurrentLanguage()
 						+ ".html\"); \n";
 			}
+			//namespace table is always a separated document
+			document += "      $(\"#nstable\").load(\"sections/ns-" + c.getCurrentLanguage()
+					+ ".html\"); \n";
 		}
 		if (c.isIncludeOverview()){
 			if(c.getOverviewPath()!=null && !c.getOverviewPath().isEmpty()){
@@ -835,9 +838,10 @@ public static String getIndexDocument(String resourcesFolderName, Configuration
 		if (c.isIncludeAbstract())
 			document += "     <div id=\"abstract\"></div>\n";
 		document += "<div id=\"toc\"></div>";
-		if (c.isIncludeIntroduction())
+		if (c.isIncludeIntroduction()) {
 			document += "     <div id=\"introduction\"></div>\n";
-		// else document += "<div id=\"namespacedeclaration\"></div>\n";
+			document += "	  <div id=\"nstable\"></div>\n"; //ns declaration is part of the intro
+		}
 		if (c.isIncludeOverview())
 			document += "     <div id=\"overview\"></div>\n";
 		if (c.isIncludeDescription())

src/main/java/widoco/CreateResources.java

@@ -232,21 +232,23 @@ private static String createAbstractSection(String path, Configuration c, Proper
 	}
 
 	private static String createIntroductionSection(String path, Configuration c,Properties lang) {
-            String textToWrite;
+            String introText;
+			String nsText="";
             HashMap<String,String> nsDecl = c.getNamespaceDeclarations();
             if ((c.getIntroductionPath() != null) && (!"".equals(c.getIntroductionPath()))) {
-                textToWrite = WidocoUtils.readExternalResource(c.getIntroductionPath());
+				introText = WidocoUtils.readExternalResource(c.getIntroductionPath());
             } else {
-                textToWrite = Constants.getIntroductionSectionTitleAndPlaceHolder(c, lang);
+				introText = Constants.getIntroductionSectionTitleAndPlaceHolder(c, lang);
                 if (nsDecl != null && !nsDecl.isEmpty()) {
-                    textToWrite += Constants.getNameSpaceDeclaration(nsDecl, c, lang);
+					nsText = Constants.getNameSpaceDeclaration(nsDecl, c, lang);
                 }
                 //only save if separating sections
                 if(!c.isIncludeAllSectionsInOneDocument()){
-                    saveDocument(path + File.separator + "introduction-" + c.getCurrentLanguage() + ".html", textToWrite,c);
+                    saveDocument(path + File.separator + "introduction-" + c.getCurrentLanguage() + ".html", introText,c);
+					saveDocument(path + File.separator + "ns-" + c.getCurrentLanguage() + ".html", nsText,c);
                 }
             }
-            return textToWrite;
+            return introText + nsText;
 	}
 
 	// the lists passed onto this method are the fixed lists

src/main/resources/lode/extraction.xsl

@@ -1045,7 +1045,8 @@ http://www.oxygenxml.com/ns/doc/xsl ">
                     <dd>
                         <xsl:choose>
                             <xsl:when test="normalize-space(@*:resource) = ''">
-                                <xsl:value-of select="$ontology-url"/>
+                                <!--<xsl:value-of select="$ontology-url"/>-->
+                                <xsl:value-of select="text()"/>
                             </xsl:when>
                             <xsl:otherwise>
                                 <a href="{@*:resource}">

src/test/java/widoco/CreateDocInThreadTest.java

@@ -263,6 +263,31 @@ public void testAdvancedAnnotationsInOntology() {
             fail("Error while running the test: " +e.getMessage());
         }
     }
+
+    /**
+     * Test to see if annotation properties that document the ontology and also are extended in the ontology itself
+     * are being recognized.
+     * Issue 530 (https://github.com/dgarijo/Widoco/issues/530)
+     */
+    @org.junit.Test
+    public void testIssue530() {
+        try {
+            String pathToOnto = "test" + File.separator + "medatatestont.ttl";
+            c.setFromFile(true);
+            this.c.setOntologyPath(pathToOnto);
+            //read the model from file
+            WidocoUtils.loadModelToDocument(c);
+            c.loadPropertiesFromOntology(c.getMainOntology().getOWLAPIModel());
+            //title is the property being extended
+            if(c.getMainOntology().getTitle().isEmpty()){
+                fail("Could not extract title!");
+            }
+            //not needed, but added for consistency with the other tests.
+            CreateResources.generateDocumentation(c.getDocumentationURI(), c, c.getTmpFile());
+        }catch(Exception e){
+            fail("Error while running the test: " +e.getMessage());
+        }
+    }
 //    
     /**
      * This is a test to see if a big ontology works (several MB)

test/example_test.owl

@@ -126,6 +126,14 @@ xsd:date rdf:type rdfs:Datatype .
         rdfs:comment "This property links instances from Researcher to Organization"@en ;
         rdfs:label "part of"@en .
 
+###  http://www.w3.org/2006/time#hasBeginning
+<http://www.w3.org/2006/time#hasBeginning> rdf:type owl:ObjectProperty ;
+                                           rdfs:domain <http://www.w3.org/2006/time#TemporalEntity> ;
+                                           rdfs:range <http://www.w3.org/2006/time#Instant> ;
+                                           rdfs:comment "Beginning of a temporal entity."^^xsd:anyURI ;
+                                           rdfs:isDefinedBy "http://www.w3.org/2006/time"^^xsd:anyURI ;
+                                           rdfs:label "has beginning"^^xsd:anyURI .
+
 
 #################################################################
 #    Data properties
@@ -146,6 +154,7 @@ xsd:date rdf:type rdfs:Datatype .
 
 ###  http://xmlns.com/foaf/0.1/Organization
 <http://xmlns.com/foaf/0.1/Organization> rdf:type owl:Class ;
+                                         rdfs:isDefinedBy <http://xmlns.com/foaf/0.1/> ;
                                          owl:equivalentClass :Organization .
 
 
@@ -156,6 +165,7 @@ xsd:date rdf:type rdfs:Datatype .
               skos:editorialNote "SKOS note"@en ;
               owl:equivalentClass <http://xmlns.com/foaf/0.1/Organization>;
               skos:prefLabel "organization";
+              rdfs:isDefinedBy <https://w3id.org/example> ;
               rdfs:label "Organization"@en, "org"@fr .
 
 

test/medatatestont.ttl

@@ -0,0 +1,13 @@
+@prefix myont: <https://identifier.my.ont/ont/> .
+@prefix dcterms: <http://purl.org/dc/terms/> .
+
+<https://identifier.my.ont/ont/>
+  a owl:Ontology ;
+  rdfs:label "ontology";
+  dcterms:title "Example title" ;
+.
+
+<myont:citationtitle>
+  a owl:DatatypeProperty ;
+  rdfs:subPropertyOf dcterms:title ;
+.