From 4b96b33ad6d3e0d89262991e4d586cb12e8566cb Mon Sep 17 00:00:00 2001
From: Daniel Garijo <dgarijov@gmail.com>
Date: Wed, 3 Apr 2024 00:35:57 +0200
Subject: [PATCH] Fix #648

---
 doc/bestPractices/sections/checklist-en.html  |  4 +-
 doc/configuration/config.properties           |  9 +++--
 doc/configuration/configuration_doc.md        | 37 +++++++++++--------
 doc/configurationSamples/README.md            |  1 -
 .../config/config.properties                  |  2 +-
 doc/metadataGuide/guide.md                    | 33 ++++++++++-------
 src/main/java/lode/LODEGeneration.java        |  5 ++-
 src/main/java/widoco/Configuration.java       | 34 +++++++++--------
 src/main/java/widoco/Constants.java           |  7 +++-
 src/main/java/widoco/gui/GuiStep3.java        |  5 +++
 10 files changed, 83 insertions(+), 54 deletions(-)
 delete mode 100644 doc/configurationSamples/README.md

diff --git a/doc/bestPractices/sections/checklist-en.html b/doc/bestPractices/sections/checklist-en.html
index faab43e3..2bed613b 100644
--- a/doc/bestPractices/sections/checklist-en.html
+++ b/doc/bestPractices/sections/checklist-en.html
@@ -23,7 +23,7 @@ <h5>Example:</h5>
 @prefix rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt; .
 @prefix vann: &lt;http://purl.org/vocab/vann/&gt; .
 &lt;https://w3id.org/example&gt; rdf:type owl:Ontology ;
-	vann:preferredNamespaceUri "https://w3id.org/example" .
+	vann:preferredNamespaceUri &lt;https://w3id.org/example#&gt; .
 </pre>
 
 <h4 class="list" id="prefix">Prefix [<em class="rfc2119" title="RECOMMENDED">RECOMMENDED</em>]</h4>
@@ -698,7 +698,7 @@ <h5>Example:</h5>
 
 <h4 class="list" id="status1">Status [<em class="rfc2119" title="OPTIONAL">OPTIONAL</em>]</h4>
 <p>
-Property indicating the usage status of the term. For example, whether the term is mature enough, whether it has been deprecated, curated, etc. Note that some of the properties proposed below, such as obo:IAO_0000114, have as range a set of fixed values. The <a href="/UKGovLD/registry-core/wiki/Principles-and-concepts#status-and-life-cycle">registry vocabulary</a> proposes a hierarchy of status that may be used to represent terms as well (reg:statusAccepted, reg:statusValid, reg:statusDeprecated, etc.).
+Property indicating the usage status of the term. For example, whether the term is mature enough, whether it has been deprecated, curated, etc. Note that some of the properties proposed below, such as obo:IAO_0000114, have as range a set of fixed values. The <a href="/UKGovLD/registry-core/wiki/Principles-and-concepts#status-and-life-cycle">registry vocabulary</a> proposes a hierarchy of status that may be used to represent terms as well (reg:statusAccepted, reg:statusValid, reg:statusDeprecated, etc.). 
 </p>
 
 <ul class="hlist"><strong>Properties you may use</strong>:
diff --git a/doc/configuration/config.properties b/doc/configuration/config.properties
index 5a7e4103..e22cb3ec 100644
--- a/doc/configuration/config.properties
+++ b/doc/configuration/config.properties
@@ -1,7 +1,7 @@
 
 abstract=An example ontology
 backwardCompatibleWith=https://w3id.org/example/1.0.0
-citeAs="add some citattion text here."
+citeAs="add some citation text here."
 dateCreated="13 Nov, 2022"
 dateModified="15 Nov, 2022"
 authors=First Author;Second Author
@@ -16,10 +16,11 @@ description="A description of what the ontology does goes here"
 diagram="https://example.org/diagram.svg"
 DOI=
 funders=
-fundingGrants=
+funding=
 incompatibleWith=
-issued=
 images=image1.png;image2.png
+introduction="This is some introduction text"
+issued=
 licenseURI=http://creativecommons.org/licenses/by/2.0/
 licenseName=CC-BY
 licenseIconURL=https://i.creativecommons.org/l/by/2.0/88x31.png
@@ -45,3 +46,5 @@ extendedOntologyURIs=http://example.org/test1; http://example.org/test2
 RDFXMLSerialization=ontology.xml
 TurtleSerialization=ontology.ttl
 NTSerialization=ontology.nt
+pathToOverview=overview.html
+pathToReferences=references.html
diff --git a/doc/configuration/configuration_doc.md b/doc/configuration/configuration_doc.md
index 9935407f..4d7ae370 100644
--- a/doc/configuration/configuration_doc.md
+++ b/doc/configuration/configuration_doc.md
@@ -6,33 +6,35 @@ In order to have Widoco accept a configuration file, you need to create a `confi
 
 ```
 abstract=An example ontology
-backwardCompatibleWith=https://w3id.org/example/1.0.0
-citeAs="add some citattion text here."
-dateCreated="13 Nov, 2022"
-dateIssued=
-dateModified="15 Nov, 2022"
 authors=First Author;Second Author
 authorsURI=http://example.org/author1;http://example.org/author2
 authorsInstitution=First author institution;Second author institution
 authorsInstitutionURI=https://www.isi.edu/;https://www.isi.edu/
+backwardCompatibleWith=https://w3id.org/example/1.0.0
+citeAs="add some citattion text here."
 contributors=First contributor;Second contributor
 contributorsURI=http://example.org/contributor1;http://example.org/contributor2
 contributorsInstitution=First contributor institution;Second contributor institution
 contributorsInstitutionURI=https://isi.edu/;https://isi.edu/
+dateCreated="13 Nov, 2022"
+dateIssued=
+dateModified="15 Nov, 2022"
 description="A description of what the ontology does goes here"
-diagram="https://example.org/diagram.svg"
 DOI=
 funder=
-fundingGrant=
+funding=
 incompatibleWith=
+introduction=A brief text for the introduction section may be written here.
 images=image1.png;image2.png
 licenseURI=http://creativecommons.org/licenses/by/2.0/
 licenseName=CC-BY
 licenseIconURL=https://i.creativecommons.org/l/by/2.0/88x31.png
 logo="https://example.org/logo.svg"
 ontologyName=Example
-ontologyPrefix=exo
 ontologyNamespaceURI=https://w3id.org/example
+ontologyRevisionNumber=1.0.0
+ontologyTitle=The Example Ontology
+ontologyPrefix=exo
 previousVersionURI=https://w3id.org/example/1.0.0
 publisher=Ontology Engineering Group
 publisherURI=https://oeg-upm.es
@@ -40,24 +42,27 @@ publisherInstitution=UPM
 publisherInstitutionURI=https://www.upm.es
 source=http://source1;http://source2
 seeAlso=http://firstResource
-ontologyTitle=The Example Ontology
 thisVersionURI=https://w3id.org/example/1.0.1
-ontologyRevisionNumber=v1.0.0
 status=Ontology Specification Draft
 ```
 
 Additional configuration options include the following
 ```
-importedOntologyNames=Imported Ontology 1; Imported Ontology 2
-importedOntologyURIs=http://example.org/test11; http://example.org/test22
+contextURI=JSON-LD context URI.
 extendedOntologyNames=test1; test2
 extendedOntologyURIs=http://example.org/test1; http://example.org/test2
+importedOntologyNames=Imported Ontology 1; Imported Ontology 2
+importedOntologyURIs=http://example.org/test11; http://example.org/test22
+pathToAbstract=abstract.html (superseedes abstract)
+pathToDescription=description.html (superseedes description)
+pathToIntro=intro.html (supersedes introduction)
+pathToOverview=overview.html
+pathToReferences=references.html 
+GoogleAnalyticsCode=UA-TestCodeGoesHere
+JSONLDSerialization=URL of the file with JSON-LD serialization. E.g., http://my-onto/onto.jsonld
+NTSerialization=URL of the file with N3 serialization. E.g., http://my-onto/onto.n3
 RDFXMLSerialization=URL of the file with RDF-XML serialization. E.g., http://my-onto/onto.owl
 TurtleSerialization=URL of the file with Turtle serialization. E.g., http://my-onto/onto..ttl;
-NTSerialization=URL of the file with N3 serialization. E.g., http://my-onto/onto.n3
-JSONLDSerialization=URL of the file with JSON-LD serialization. E.g., http://my-onto/onto.jsonld
-GoogleAnalyticsCode=UA-TestCodeGoesHere
-contextURI=JSON-LD context URI. 
 ```
 
 For more information, see the [Widoco readme options](https://github.com/dgarijo/Widoco/#options).
diff --git a/doc/configurationSamples/README.md b/doc/configurationSamples/README.md
deleted file mode 100644
index 1a2df36c..00000000
--- a/doc/configurationSamples/README.md
+++ /dev/null
@@ -1 +0,0 @@
-You can find Widoco's latest JAR on the Release tab in Github: https://github.com/dgarijo/Widoco/releases
diff --git a/doc/configurationSamples/config/config.properties b/doc/configurationSamples/config/config.properties
index 70b73b0e..91839f3b 100644
--- a/doc/configurationSamples/config/config.properties
+++ b/doc/configurationSamples/config/config.properties
@@ -1,7 +1,7 @@
 
 abstract=An example ontology
 backwardCompatibleWith=https://w3id.org/example/1.0.0
-citeAs="add some citattion text here."
+citeAs="add some citation text here."
 creationDate="13 Nov, 2022"
 authors=First Author;Second Author
 authorsURI=http://example.org/author1;http://example.org/author2
diff --git a/doc/metadataGuide/guide.md b/doc/metadataGuide/guide.md
index 94817556..f1faeb08 100644
--- a/doc/metadataGuide/guide.md
+++ b/doc/metadataGuide/guide.md
@@ -212,27 +212,27 @@ Create a `config.properties` file and use the `-confFile` option to invoke Widoc
 
 ```
 abstract=An example ontology
-backwardCompatibleWith=https://w3id.org/example/1.0.0
-citeAs="add some citattion text here."
 authors=First Author;Second Author
 authorsURI=http://example.org/author1;http://example.org/author2
 authorsInstitution=First author institution;Second author institution
 authorsInstitutionURI=https://www.isi.edu/;https://www.isi.edu/
+backwardCompatibleWith=https://w3id.org/example/1.0.0
+citeAs="add some citattion text here."
 contributors=First contributor;Second contributor
 contributorsURI=http://example.org/contributor1;http://example.org/contributor2
 contributorsInstitution=First contributor institution;Second contributor institution
 contributorsInstitutionURI=https://isi.edu/;https://isi.edu/
-description=A description of what the ontology does goes here
 dateCreated="13 Nov, 2022"
 dateIssued="14 Nov, 2022"
 dateModified="15 April, 2023"
-diagram="https://example.org/diagram.svg"
+description=A description of what the ontology does goes here
 extendedOntologyNames=test1; test2
 extendedOntologyURIs=http://example.org/test1; http://example.org/test2
 DOI=https://dx.doi.org/SOME/DOI
 funder=https://example.org/institution
 funding=https://example.org/fundingGrant
 incompatibleWith=https://w3id.org/example/0.0.1
+images=image1.png;image2.png
 importedOntologyNames=Imported Ontology 1; Imported Ontology 2
 importedOntologyURIs=http://example.org/test11; http://example.org/test22
 introduction=A brief text for the introduction section may be written here.
@@ -241,21 +241,28 @@ licenseName=CC-BY
 licenseIconURL=https://i.creativecommons.org/l/by/2.0/88x31.png
 logo="https://example.org/logo.svg"
 ontologyName=The Cohort Ontology
-ontologyPrefix=exo
 ontologyNamespaceURI=https://w3id.org/example
-previousVersionURI=https://w3id.org/example/1.0.0
-publisher=
-publisherURI=
-publisherInstitution=
-publisherInstitutionURI=
 ontologyTitle=The Example Ontology
+ontologyPrefix=exo
+ontologyRevisionNumber=1.0.0
+pathToAbstract=abstract.html (superseedes abstract)
+pathToDescription=description.html (superseedes description)
+pathToIntro=intro.html (supersedes introduction)
+pathToOverview=overview.html
+pathToReferences=references.html
+previousVersionURI=https://w3id.org/example/1.0.0
+publisher=Ontology Engineering Group
+publisherURI=https://oeg-upm.es
+publisherInstitution=UPM
+publisherInstitutionURI=https://www.upm.es
 thisVersionURI=https://w3id.org/example/1.0.1
-ontologyRevisionNumber=v1.0.0
+source=http://source1;http://source2
+seeAlso=http://firstResource
 status=Ontology Specification Draft
+JSONLDSerialization=ontology.nt
+NTSerialization=ontology.nt
 RDFXMLSerialization=ontology.xml
 TurtleSerialization=ontology.ttl
-NTSerialization=ontology.nt
-JSONLDSerialization=ontology.nt
 ```
 
 ## Glossary (<a href="#table">Back to table</a>)
diff --git a/src/main/java/lode/LODEGeneration.java b/src/main/java/lode/LODEGeneration.java
index 82ee47cc..c8f5eaf0 100644
--- a/src/main/java/lode/LODEGeneration.java
+++ b/src/main/java/lode/LODEGeneration.java
@@ -29,6 +29,7 @@
 import java.io.StringReader;
 import java.io.UnsupportedEncodingException;
 import java.net.URISyntaxException;
+import java.nio.charset.StandardCharsets;
 import java.util.HashSet;
 import java.util.Set;
 import javax.xml.transform.Transformer;
@@ -61,7 +62,7 @@ public static String getLODEhtml(Configuration c, File lodeResources) throws Exc
 
 			String content = "";
 			String lang = c.getCurrentLanguage();
-			if (lang == null || "".equals(lang)) {
+			if (lang == null || lang.isEmpty()) {
 				lang = "en";
 			}
 			// we have stored the ontology locally
@@ -318,7 +319,7 @@ private static String applyXSLTTransformation(String source, String ontologyUrl,
 
 		transformer.transform(inputSource, new StreamResult(output));
 
-		return output.toString("UTF-8").replace("any u r i", "anyURI");
+		return output.toString(StandardCharsets.UTF_8).replace("any u r i", "anyURI");
 	}
 
 }
diff --git a/src/main/java/widoco/Configuration.java b/src/main/java/widoco/Configuration.java
index 5829962d..cce21507 100644
--- a/src/main/java/widoco/Configuration.java
+++ b/src/main/java/widoco/Configuration.java
@@ -259,7 +259,7 @@ private void loadPropertyFile(String path) throws IOException {
 			mainOntologyMetadata.setPublisher(publisher);
 			String aux = propertyFile.getProperty(Constants.PF_AUTHORS, "");
 			String[] names, urls, authorInst, authorInstURI;
-			if (!aux.equals("")) {
+			if (!aux.isEmpty()) {
 				names = aux.split(";");
 				aux = propertyFile.getProperty(Constants.PF_AUTHORS_URI, "");
 				urls = aux.split(";");
@@ -289,7 +289,7 @@ private void loadPropertyFile(String path) throws IOException {
 				}
 			}
 			aux = propertyFile.getProperty(Constants.PF_CONTRIBUTORS, "");
-			if (!aux.equals("")) {
+			if (!aux.isEmpty()) {
 				names = aux.split(";");
 				aux = propertyFile.getProperty(Constants.PF_CONTRIBUTORS_URI, "");
 				urls = aux.split(";");
@@ -406,7 +406,11 @@ private void loadPropertyFile(String path) throws IOException {
 			if (!"".equals(funding)){
 				mainOntologyMetadata.setFundingGrants(new ArrayList<String>(Arrays.asList(funding.split(";"))));
 			}
-
+			this.setAbstractPath(propertyFile.getProperty(Constants.PF_ABSTRACT_PATH, null));
+			this.setDescriptionPath(propertyFile.getProperty(Constants.PF_DESCRIPTION_PATH, null));
+			this.setIntroductionPath(propertyFile.getProperty(Constants.PF_INTRO_PATH, null));
+			this.setOverviewPath(propertyFile.getProperty(Constants.PF_OVERVIEW_PATH, null));
+			this.setReferencesPath(propertyFile.getProperty(Constants.PF_REFERENCES_PATH, null));
 		} catch (IOException ex) {
 			// Only a warning, as we can continue safely without a property file.
 			logger.warn("Error while reading configuration properties from [" + path + "]: " + ex.getMessage());
@@ -486,14 +490,14 @@ public void loadPropertiesFromOntology(OWLOntology o) {
 				mainOntologyMetadata.getLicense().setName(licName);
 			}
 		}
-		if (this.mainOntologyMetadata.getName() == null || this.mainOntologyMetadata.getName().equals("")) {
+		if (this.mainOntologyMetadata.getName() == null || this.mainOntologyMetadata.getName().isEmpty()) {
 			this.mainOntologyMetadata.setName(mainOntologyMetadata.getTitle());
 		}
-		if (mainOntologyMetadata.getStatus() == null || mainOntologyMetadata.getStatus().equals("")) {
+		if (mainOntologyMetadata.getStatus() == null || mainOntologyMetadata.getStatus().isEmpty()) {
 			mainOntologyMetadata.setStatus("Ontology Specification Draft");
 		}
 		// default name if no annotations are found
-		if (mainOntologyMetadata.getName() == null || mainOntologyMetadata.getName().equals("")) {
+		if (mainOntologyMetadata.getName() == null || mainOntologyMetadata.getName().isEmpty()) {
 			this.mainOntologyMetadata.setName("[Ontology Name]");
 		}
 		// default citation if none is given
@@ -522,7 +526,7 @@ public void loadNamespaceDeclarations(OWLOntology o){
 		OWLOntologyXMLNamespaceManager nsManager = new OWLOntologyXMLNamespaceManager(o, o.getFormat());
 		for (String prefix : nsManager.getPrefixes()) {
 			String namespaceURI = nsManager.getNamespaceForPrefix(prefix);
-			if ("".equals(prefix) || namespaceURI.equals(mainOntologyMetadata.getNamespaceURI())){
+			if (prefix.isEmpty() || namespaceURI.equals(mainOntologyMetadata.getNamespaceURI())){
 				namespaceDeclarations.put(mainOntologyMetadata.getNamespacePrefix(),namespaceURI);
 			}else{
 				namespaceDeclarations.put(prefix,nsManager.getNamespaceForPrefix(prefix));
@@ -531,7 +535,7 @@ public void loadNamespaceDeclarations(OWLOntology o){
 	}
 
 	private String appendDetails(final String detail, final String prefix, final boolean useFullStop) {
-		if (detail == null || detail.equals("")) {
+		if (detail == null || detail.isEmpty()) {
 			return "";
 		}
 
@@ -581,7 +585,7 @@ private void completeOntologyMetadata(OWLAnnotation a, OWLOntology o) {
 				valueLanguage = a.getValue().asLiteral().get().getLang();
 				value = a.getValue().asLiteral().get().getLiteral();
 				if (this.currentLanguage.equals(valueLanguage)
-						|| (abstractSection == null || "".equals(abstractSection))) {
+						|| (abstractSection == null || abstractSection.isEmpty())) {
 					abstractSection = value;
 					this.setIncludeAbstract(true); // in case users set no place holder text but added their own
 				}
@@ -689,11 +693,11 @@ private void completeOntologyMetadata(OWLAnnotation a, OWLOntology o) {
 						o.getAnnotationAssertionAxioms(valueURI).stream().forEach(i -> {
 							completeAgentMetadata(i, ag, o);
 						});
-						if(ag.getName()==null || ag.getName().equals("")){
+						if(ag.getName()==null || ag.getName().isEmpty()){
 							//the value does not have annotations, so we keep it as it is.
 							ag.setName(valueURI.getIRIString());
 						}
-						if(ag.getURL()==null || ag.getURL().equals("")){
+						if(ag.getURL()==null || ag.getURL().isEmpty()){
 							ag.setURL(valueURI.getIRIString());
 						}
 					}
@@ -826,7 +830,7 @@ private void completeOntologyMetadata(OWLAnnotation a, OWLOntology o) {
 				valueLanguage = a.getValue().asLiteral().get().getLang();
 				value = a.getValue().asLiteral().get().getLiteral();
 				if (this.currentLanguage.equals(valueLanguage)
-						|| (introText == null || "".equals(introText))) {
+						|| (introText == null || introText.isEmpty())) {
 					introText = value;
 					this.setIncludeIntroduction(true);
 				}
@@ -937,11 +941,11 @@ private void completeAgentMetadata(OWLAnnotationAssertionAxiom ann, Agent ag, OW
 						o.getAnnotationAssertionAxioms(valueURI).stream().forEach(i -> {
 							completeAgentMetadata(i,aux,o);
 						});
-						if(aux.getName()==null || aux.getName().equals("")){
+						if(aux.getName()==null || aux.getName().isEmpty()){
 							//the value does not have annotations, so we keep it as it is.
 							aux.setName(valueURI.getIRIString());
 						}
-						if(aux.getURL()==null || aux.getURL().equals("")){
+						if(aux.getURL()==null || aux.getURL().isEmpty()){
 							aux.setURL(valueURI.getIRIString());
 						}
 					}
@@ -1267,7 +1271,7 @@ public void setIncludeNamedIndividuals(boolean includeNamedIndividuals) {
 	public void addLanguageToGenerate(String lang) {
 		if (!this.languages.containsKey(lang)) {
 			this.languages.put(lang, false);
-			if (currentLanguage.equals("")) {
+			if (currentLanguage.isEmpty()) {
 				currentLanguage = lang;
 			}
 		}
diff --git a/src/main/java/widoco/Constants.java b/src/main/java/widoco/Constants.java
index 9f9088ad..58654641 100644
--- a/src/main/java/widoco/Constants.java
+++ b/src/main/java/widoco/Constants.java
@@ -273,6 +273,11 @@ public class Constants {
 	public static final String PF_SERIALIZATION_JSON = "JSONLDSerialization";
 	public static final String PF_SERIALIZATION_RDF = "RDFXMLSerialization";
 	public static final String PF_SERIALIZATION_TTL = "TurtleSerialization";
+	public static final String PF_ABSTRACT_PATH = "pathToAbstract";
+	public static final String PF_INTRO_PATH = "pathToIntro";
+	public static final String PF_DESCRIPTION_PATH = "pathToDescription";
+	public static final String PF_OVERVIEW_PATH = "pathToOverview";
+	public static final String PF_REFERENCES_PATH = "pathToReferences";
 
 	/*OWL_API RDF Serializations*/
 	public static final String RDF_XML = "RDF/XML";
@@ -568,7 +573,7 @@ private static String getOntologies(ArrayList<Ontology> ontos) {
 		while (it.hasNext()) {
 			Ontology currentOnto = it.next();
 			String currentOntoName = currentOnto.getName();
-			if (currentOntoName == null || "".equals(currentOntoName)) {
+			if (currentOntoName == null || currentOntoName.isEmpty()) {
 				currentOntoName = "Onto" + i;
 				i++;
 			}
diff --git a/src/main/java/widoco/gui/GuiStep3.java b/src/main/java/widoco/gui/GuiStep3.java
index 8c7ea117..865a9388 100644
--- a/src/main/java/widoco/gui/GuiStep3.java
+++ b/src/main/java/widoco/gui/GuiStep3.java
@@ -82,6 +82,11 @@ private void initializeGUI(){
         checkBoxWebVowl.setSelected(true);
         checkBoxAutomatedChangeLog.setSelected(true);
         if(g.getConfig().getGoogleAnalyticsCode()!=null)analyticsField.setText(g.getConfig().getGoogleAnalyticsCode());
+        abstractPath = g.getConfig().getAbstractPath();
+        introductionPath = g.getConfig().getIntroductionPath();
+        descriptionPath = g.getConfig().getDescriptionPath();
+        overviewPath = g.getConfig().getOverviewPath();
+        referencesPath = g.getConfig().getReferencesPath();
     }
 
     /** This method is called from within the constructor to