Merge pull request #684 from dgarijo/develop

Develop

.github/workflows/ci.yml

@@ -54,11 +54,11 @@ jobs:
       # https://github.com/docker/metadata-action (lower cases image name, etc.)
       - name: Extract Docker metadata
         id: meta
-        uses: docker/metadata-action@v5.4.0
+        uses: docker/metadata-action@v5.5.1
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
       - name: Build and push
-        uses: docker/build-push-action@v5.1.0
+        uses: docker/build-push-action@v5.3.0
         with:
           push: ${{ github.event_name != 'pull_request' && github.actor != 'dependabot[bot]' }}
           tags: ${{ steps.meta.outputs.tags }}

README.md

@@ -132,58 +132,61 @@ docker run -ti --rm \
 
 ### Options
 
-`-ontFile PATH`  [required (unless -ontURI is used)]: Load a local ontology file (from PATH) to document. This option is incompatible with -ontURI
+`-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
 
-`-ontURI  URI`   [required (unless -ontFile is used)]: Load an ontology to document from its URI. This option is incompatible with -ontFile
+`-confFile PATH`: Load your own configuration file for the ontology metadata. Incompatible with -getOntologyMetadata. See [the configuration documentation](doc/configuration/configuration_doc.md) for more information about the accepted fields.
 
-`-outFolder folderName`: Specifies the name of the folder where to save the documentation. By default is 'myDocumentation'
+`-crossRef`: ONLY generate the overview and cross reference sections. The index document will NOT be generated. The htaccess, provenance page, etc., will not be generated unless requested by other flags. This flag is intended to be used only after a first version of the documentation exists.
 
-`-confFile PATH`: Load your own configuration file for the ontology metadata. Incompatible with -getOntologyMetadata. See [the configuration documentation](doc/configuration/configuration_doc.md) for more information about the accepted fields.
+`-displayDirectImportsOnly`: Only those imported ontologies that are directly imported in the ontology being documented.
 
-`-getOntologyMetadata`: Extract ontology metadata from the given ontology
+`-doNotDisplaySerializations`: The serializations of the ontology will not be displayed.
 
-`-oops`: Create an html page with the evaluation from the OOPS service (http://oops.linkeddata.es/)
+`-excludeIntroduction`: Skip the introduction section in the documentation.
 
-`-rewriteAll`: Replace any existing files when documenting an ontology (e.g., from a previous execution)
+`-getOntologyMetadata`: Extract ontology metadata from the given ontology
 
-`-crossRef`: ONLY generate the overview and cross reference sections. The index document will NOT be generated. The htaccess, provenance page, etc., will not be generated unless requested by other flags. This flag is intended to be used only after a first version of the documentation exists.
+`--help`: Shows a help message and exits.
 
-`-saveConfig PATH`: Save a configuration file on PATH with the properties of a given ontology
+`-htaccess`: Create a bundle for publication ready to be deployed on your Apache server.
 
-`-useCustomStyle`: Export the documentation using alternate css files (by Daniel Vila).
 
-`-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
+`-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)
 
 `-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.
+`-import`: imports a local ontology (e.g., if you don't want to load an online ontology, you may load its local version)
 
-`-webVowl`: Create a visualization based on WebVowl (http://vowl.visualdataweb.org/webvowl/index.html#) in the documentation.
+`-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
 
 `-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.
+`-noPlaceHolderText`: Do not add any placeholder text (this will remove intro, abstract (if empty) and description sections).
 
-`-includeAnnotationProperties`: Include annotation properties defined in your ontology in the documentation (by default they are not included)
+`-ontFile PATH`  [required (unless -ontURI is used)]: Load a local ontology file (from PATH) to document. This option is incompatible with -ontURI
 
-`-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
+`-outFolder folderName`: Specifies the name of the folder where to save the documentation. By default is 'myDocumentation'
 
-`-doNotDisplaySerializations`: The serializations of the ontology will not be displayed.
+`-ontURI  URI`   [required (unless -ontFile is used)]: Load an ontology to document from its URI. This option is incompatible with -ontFile
 
-`-displayDirectImportsOnly`: Only those imported ontologies that are directly imported in the ontology being documented.
+`-oops`: Create an html page with the evaluation from the OOPS service (http://oops.linkeddata.es/)
+
+`-rewriteAll`: Replace any existing files when documenting an ontology (e.g., from a previous execution)
 
 `-rewriteBase PATH`: Change the default rewrite base path. The default value is "/". This flag can only be used with the htaccess option.
 
-`-excludeIntroduction`: Skip the introduction section in the documentation.
+`-saveConfig PATH`: Save a configuration file on PATH with the properties of a given ontology
 
 `-uniteSections`: Write all HTML sections into a single HTML document.
 
-`-noPlaceHolderText`: Do not add any placeholder text (this will remove intro, abstract (if empty) and description sections).
-
-`--help`: Shows a help message and exits.
+`-useCustomStyle`: Export the documentation using alternate css files (by Daniel Vila).
 
 `--version`: Shows the version of WIDOCO.
 
+`-webVowl`: Create a visualization based on WebVowl (http://vowl.visualdataweb.org/webvowl/index.html#) in the documentation.
+
 
 ## How can I make WIDOCO automatically recognize my vocabulary annotations?
 There are two alternative ways for making WIDOCO get your vocabulary metadata annotations and use them automatically to document the ontology.

pom.xml

@@ -22,7 +22,11 @@
 			<version>3.9.0</version>
 		</dependency>
 
-
+		<dependency>
+			<groupId>org.jsoup</groupId>
+			<artifactId>jsoup</artifactId>
+			<version>1.17.2</version>
+		</dependency>
 		<dependency>
 			<groupId>com.github.VisualDataWeb</groupId>
 			<artifactId>OWL2VOWL</artifactId>

src/main/java/oops/OOPSevaluation.java

@@ -280,11 +280,13 @@ else if (code.contentEquals("P36")) {
                                                                             collect(Collectors.toList())).iterator();
                                                 if(elementos.hasNext()){
                                                     String first = ((OWLAnnotationAssertionAxiom)elementos.next()).getValue().asLiteral().get().getLiteral();
-                                                    String second = ((OWLAnnotationAssertionAxiom)elementos.next()).getValue().asLiteral().get().getLiteral();
-                                                    evaluationOutput = evaluationOutput + "<li>" + "<a href=\"" + first
-                                                            + "\" target=\"_blank\">" + first + "</a>" + " may not be inverse of "
-                                                            + "<a href=\"" + second + "\" target=\"_blank\">" + second + "</a>" + "</li>";
-                                                    evaluationOutput = evaluationOutput + "</ul>";
+                                                    if (elementos.hasNext()) {
+                                                        String second = ((OWLAnnotationAssertionAxiom) elementos.next()).getValue().asLiteral().get().getLiteral();
+                                                        evaluationOutput = evaluationOutput + "<li>" + "<a href=\"" + first
+                                                                + "\" target=\"_blank\">" + first + "</a>" + " may not be inverse of "
+                                                                + "<a href=\"" + second + "\" target=\"_blank\">" + second + "</a>" + "</li>";
+                                                        evaluationOutput = evaluationOutput + "</ul>";
+                                                    }
                                                 }
                                             }
                                             break;
@@ -324,10 +326,12 @@ else if (code.contentEquals("P36")) {
                                                                             collect(Collectors.toList())).iterator();
                                                 while(elementos.hasNext()) {
                                                     String first = ((OWLAnnotationAssertionAxiom) elementos.next()).getValue().asLiteral().get().toString();
-                                                    String second = ((OWLAnnotationAssertionAxiom) elementos.next()).getValue().asLiteral().get().toString();
-                                                    evaluationOutput = evaluationOutput + "<li>" + "<a href=\"" + first
-                                                            + "\" target=\"_blank\">" + first + "</a>" + " , " + "<a href=\"" + second
-                                                            + "\" target=\"_blank\">" + second + "</a>" + "</li>";
+                                                    if(elementos.hasNext()) {
+                                                        String second = ((OWLAnnotationAssertionAxiom) elementos.next()).getValue().asLiteral().get().toString();
+                                                        evaluationOutput = evaluationOutput + "<li>" + "<a href=\"" + first
+                                                                + "\" target=\"_blank\">" + first + "</a>" + " , " + "<a href=\"" + second
+                                                                + "\" target=\"_blank\">" + second + "</a>" + "</li>";
+                                                    }
                                                 }       
                                                 evaluationOutput = evaluationOutput + "</ul>";
                                             }
@@ -347,10 +351,12 @@ else if (code.contentEquals("P36")) {
                                                                             collect(Collectors.toList())).iterator();
                                                 while(elementos.hasNext()) {
                                                     String first = ((OWLAnnotationAssertionAxiom) elementos.next()).getValue().asLiteral().get().toString();
-                                                    String second = ((OWLAnnotationAssertionAxiom) elementos.next()).getValue().asLiteral().get().toString();
-                                                    evaluationOutput = evaluationOutput + "<li>" + "<a href=\"" + first
-                                                            + "\" target=\"_blank\">" + first + "</a>" + " , " + "<a href=\"" + second
-                                                            + "\" target=\"_blank\">" + second + "</a>" + "</li>";
+                                                    if(elementos.hasNext()) {
+                                                        String second = ((OWLAnnotationAssertionAxiom) elementos.next()).getValue().asLiteral().get().toString();
+                                                        evaluationOutput = evaluationOutput + "<li>" + "<a href=\"" + first
+                                                                + "\" target=\"_blank\">" + first + "</a>" + " , " + "<a href=\"" + second
+                                                                + "\" target=\"_blank\">" + second + "</a>" + "</li>";
+                                                    }
                                                 }       
                                                 evaluationOutput = evaluationOutput + "</ul>";
                                             }

src/main/java/widoco/Configuration.java

@@ -121,6 +121,7 @@ public class Configuration {
     private boolean includeAllSectionsInOneDocument; //boolean to indicate all sections should be included in a single big HTML
 	private HashMap<String, String> namespaceDeclarations; //Namespace declarations to be included in the documentation.
 	private String introText;// in case there is an explicit annotation in the ontology
+	private List<File> imports = new ArrayList<>();
 
 	/**
 	 * Variable to keep track of possible errors in the changelog. If there are
@@ -1050,6 +1051,12 @@ public void setOntologyURI(String ontologyURI) {
 		this.mainOntologyMetadata.setNamespaceURI(ontologyURI);
 	}
 
+	public void setImports(List<String> imports) {
+		for (String importStr:imports) {
+			this.imports.add(new File(importStr));
+		}
+	}
+
 	public void setPublishProvenance(boolean publishProvenance) {
 		this.publishProvenance = publishProvenance;
 	}
@@ -1074,6 +1081,10 @@ public String getReferencesPath() {
 		return referencesPath;
 	}
 
+	public List<File> getImports() {
+		return this.imports;
+	}
+
 	public boolean isIncludeAbstract() {
 		return includeAbstract;
 	}

src/main/java/widoco/Constants.java

@@ -25,6 +25,7 @@
 
 import widoco.entities.Agent;
 import widoco.entities.Ontology;
+import widoco.ExternalPropertyParser;
 
 /**
  *
@@ -337,6 +338,7 @@ public class Constants {
 	public static final String LANG_CLASSES = "classes";
 	public static final String LANG_OBJ_PROP = "objProp";
 	public static final String LANG_DATA_PROP = "dataProp";
+	public static final String LANG_EXT_PROP = "extProp";
 	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";
@@ -732,16 +734,11 @@ public static String getIndexDocument(String resourcesFolderName, Configuration
 		String document = OPENING;
 		/* Style selection */
 		if (c.isUseW3CStyle()) {
-			document += " <link rel=\"stylesheet\" href=\"" + resourcesFolderName
-					+ "/primer.css\" media=\"screen\" />   \n" +
-					" <link rel=\"stylesheet\" href=\"" + resourcesFolderName
-					+ "/rec.css\" media=\"screen\" />   \n" + " <link rel=\"stylesheet\" href=\"" + resourcesFolderName
-					+ "/extra.css\" media=\"screen\" />   \n" + " <link rel=\"stylesheet\" href=\"" + resourcesFolderName
-					+ "/owl.css\" media=\"screen\" />   \n";
+			document += getW3CStyleDoc(resourcesFolderName);
 
 		} else {
-			document += " <link rel=\"stylesheet\" href=\"" + resourcesFolderName + "/yeti.css\" media=\"screen\" />   \n"
-					+ " <link rel=\"stylesheet\" href=\"" + resourcesFolderName + "/site.css\" media=\"screen\" />\n";
+			document += htmlStyleSheet(resourcesFolderName+"/yeti.css","screen")
+						+htmlStyleSheet(resourcesFolderName+"/site.css","screen");
 		}
 		// add a favicon (rdf logo)
 		document += "<link rel=\"icon\" type=\"image/png\" href=\"" + resourcesFolderName + "/rdf.icon\"/>";
@@ -862,7 +859,25 @@ public static String getIndexDocument(String resourcesFolderName, Configuration
 
 		return document;
 	}
-
+
+	private static String htmlStyleSheet(String resource,String media) {
+		return "<link rel=\"stylesheet\" href=\""+ resource+"\" media=\""+media+"\"/>\n";
+	}
+
+	private static String getW3CStyleDoc(String rsrcFolder){
+		return htmlStyleSheet(rsrcFolder+"/primer.css","screen")
+		+ htmlStyleSheet(rsrcFolder+"/rec.css","screen")
+		+ htmlStyleSheet(rsrcFolder+"/extra.css","screen")
+		+ htmlStyleSheet(rsrcFolder+"/owl.css","screen")
+		+ htmlStyleSheet(rsrcFolder+"/dark.css","(prefers-color-scheme: dark)")
+		+ htmlStyleSheet(rsrcFolder+"/light.css","(prefers-color-scheme: light)")
+		+ htmlStyleSheet(rsrcFolder+"/slider.css","screen")
+		+ "<meta name=\"color-scheme\" content=\"dark light\">\n"
+		+ "<script type=\"module\" src=\"resources/dark-mode-toggle.mjs\"></script>"
+		+"<div class=\"darkmode\">\n"
+		+"\t<dark-mode-toggle class=\"slider\"></dark-mode-toggle>\n"
+		+"</div>\n";
+	}
         /**
          * Function that includes all the sections as part of the index document.
          * This makes the documentation more difficult to edit, but simpler for production
@@ -884,14 +899,11 @@ public static String getUnifiedIndexDocument(String resourcesFolderName, Configu
 		String document = OPENING;
 		/* Style selection */
 		if (c.isUseW3CStyle()) {
-			document += " <link rel=\"stylesheet\" href=\"" + resourcesFolderName
-					+ "/primer.css\" media=\"screen\" />   " + " <link rel=\"stylesheet\" href=\"" + resourcesFolderName
-					+ "/rec.css\" media=\"screen\" />   " + " <link rel=\"stylesheet\" href=\"" + resourcesFolderName
-					+ "/extra.css\" media=\"screen\" />   " + " <link rel=\"stylesheet\" href=\"" + resourcesFolderName
-					+ "/owl.css\" media=\"screen\" />   ";
+			document += getW3CStyleDoc(resourcesFolderName);
+
 		} else {
-			document += " <link rel=\"stylesheet\" href=\"" + resourcesFolderName + "/yeti.css\" media=\"screen\" />   "
-					+ " <link rel=\"stylesheet\" href=\"" + resourcesFolderName + "/site.css\" media=\"screen\" />";
+			document += htmlStyleSheet(resourcesFolderName+"/yeti.css","screen")
+						+htmlStyleSheet(resourcesFolderName+"/site.css","screen");
 		}
 		// add a title to the document
 		if (c.getMainOntology().getTitle() != null && !"".equals(c.getMainOntology().getTitle()))
@@ -1500,25 +1512,30 @@ public static String getLegend(
 				+ " <span class=\"backlink\"> " + lang.getProperty(Constants.LANG_BACK)
 				+ " <a href=\"#toc\">ToC</a></span></h2>\n"
 				+ "<div   class=\"entity\">\n"
-				+ (includesClass ?
+				+ (includesClass || ExternalPropertyParser.hasClasses()?
 				  "<sup class=\"type-c\" title=\""
 				  + lang.getProperty(Constants.LANG_CLASSES)
 				  + "\">c</sup>: " + lang.getProperty(Constants.LANG_CLASSES) + " <br/>\n"
 				  : "")
-				+ (includesProperty ?
+				+ (includesProperty || ExternalPropertyParser.hasObjProps()?
 				  "<sup class=\"type-op\" title=\""
 				  + lang.getProperty(Constants.LANG_OBJ_PROP) + "\">op</sup>: "
 				  + lang.getProperty(Constants.LANG_OBJ_PROP) + " <br/>\n"
 				  : "")
-				+ (includesDatatypeProperty ?
+				+ (includesDatatypeProperty  || ExternalPropertyParser.hasDataProps()?
 				  "<sup class=\"type-dp\" title=\""
 				  + lang.getProperty(Constants.LANG_DATA_PROP) + "\">dp</sup>: "
 				  + lang.getProperty(Constants.LANG_DATA_PROP) + " <br/>\n"
 				  : "")
-				+ (includesNamedIndividual ?
+				+ (includesNamedIndividual || ExternalPropertyParser.hasNamedIndiv() ?
 				  "<sup class=\"type-ni\" title=\""
 				  + lang.getProperty(Constants.LANG_NAMED_INDIV) + "\">ni</sup>: "
-				  + lang.getProperty(Constants.LANG_NAMED_INDIV) + "\n"
+				  + lang.getProperty(Constants.LANG_NAMED_INDIV) + " <br/>\n"
+				: "")
+				+ (ExternalPropertyParser.hasExternalProps() ?
+				"<sup class=\"type-ep\" title=\""
+						+ lang.getProperty(Constants.LANG_EXT_PROP) + "\">ep</sup>: "
+						+ lang.getProperty(Constants.LANG_EXT_PROP) + "\n"
 				: "")
 				+ "</div>\n" + "</div>"
 				+ "\n";