Fix #314, #317, #316, #309, #311, #305

Several issue fixes (See issues for more details)
dgarijo · Nov 12, 2018 · ef8c2b7 · ef8c2b7
1 parent 79e8b03
commit ef8c2b7
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Showing 11 changed files with 129 additions and 114 deletions.
diff --git a/pom.xml b/pom.xml
@@ -3,7 +3,7 @@
   <groupId>es.oeg</groupId>
   <artifactId>widoco</artifactId>
   <packaging>jar</packaging>
-  <version>1.4.6</version>
+  <version>1.4.7</version>
   <name>Widoco</name>
 
 
@@ -30,13 +30,6 @@
 	    <artifactId>OWL2VOWL</artifactId>
 	    <version>0.3.4</version>
 	</dependency>
-
-
-        <dependency>
-                <groupId>org.restlet.jse</groupId>
-                <artifactId>org.restlet</artifactId>
-                <version>2.2.0</version>
-        </dependency>
 
 
         <dependency>
@@ -171,17 +164,9 @@
     <dependency>
             <groupId>net.sourceforge.owlapi</groupId>
             <artifactId>owlapi-distribution</artifactId>
-            <!--<artifactId>owlapi-osgidistribution</artifactId>
-            5.1.0 was the previous one. Test to align to webVowl-->
             <version>5.1.7</version>
     </dependency>
 
-    <!--<dependency>
-        <groupId>org.openrdf.sesame</groupId>
-        <artifactId>sesame-rio-ntriples</artifactId>
-        <version>2.7.12</version>
-    </dependency>-->
-
     <dependency>
         <groupId>com.googlecode.json-simple </groupId>
         <artifactId>json-simple</artifactId>
@@ -205,11 +190,6 @@
         <artifactId>jackson-mapper-asl</artifactId>
         <version>1.9.13</version>
     </dependency>
-   <dependency>
-    <groupId>unknown.binary</groupId>
-    <artifactId>AbsoluteLayout</artifactId>
-    <version>SNAPSHOT</version>
-   </dependency>
   </dependencies>
 
   <dependencyManagement> 	
@@ -218,31 +198,6 @@
   <build>
 
     <plugins>
-       <!--     <plugin>
-        <artifactId>maven-assembly-plugin</artifactId>
-        <version>2.4.1</version>
-        <configuration>
-          <outputDirectory>jar/</outputDirectory>
-          <descriptorRefs>
-            <descriptorRef>jar-with-dependencies</descriptorRef>
-          </descriptorRefs>
-          <archive>
-            <manifest>
-              <mainClass>widoco.gui.GuiController</mainClass>
-            </manifest>
-          </archive>
-        </configuration>
-        <executions>
-          <execution>
-            <id>make-assembly</id> 
-            <phase>package</phase> 
-            <goals>
-              <goal>simple</goal>
-            </goals>
-          </execution>
-        </executions>
-        </plugin>-->
-     <!-- Previous plugin was replaced becaude it didin't pack sesame jars correctly-->   
     <plugin>
     <groupId>org.apache.maven.plugins</groupId>
     <artifactId>maven-shade-plugin</artifactId>

diff --git a/src/main/java/widoco/Constants.java b/src/main/java/widoco/Constants.java
@@ -255,14 +255,14 @@ public class Constants {
 
 
     public static String  getAbstractSection(String abstractContent, Configuration c, Properties langFile){
-        String abstractSection = "<h2>"+langFile.getProperty(LANG_ABSTRACT)+"</h2><span class=\"markdown\">\n";
+        String abstractSection = "<html>\n<h2>"+langFile.getProperty(LANG_ABSTRACT)+"</h2><span class=\"markdown\">\n";
         if(abstractContent!=null && !"".equals(abstractContent)){
             abstractSection+=abstractContent;
         }
         else{
             abstractSection+=langFile.getProperty(LANG_ABSTRACT_PLACEHOLDER);
         }
-        abstractSection+="</span>\n";
+        abstractSection+="</span>\n</html>\n";
         return abstractSection;
     }
 
@@ -287,19 +287,21 @@ public static String getIntroductionSectionTitleAndPlaceHolder(Configuration c,
     }
 
     public static String getReferencesSection(Configuration c, Properties lang){
-        String s ="<h2 id=\"ref\" class=\"list\">"+lang.getProperty(LANG_REFERENCES_PLACEHOLDER);
+        String s ="<html>\n<h2 id=\"ref\" class=\"list\">"+lang.getProperty(LANG_REFERENCES_PLACEHOLDER)+"\n</html>\n";
         return s;
     }
+
     public static String getAcknowledgementsSection(Configuration c, Properties lang){
-        String s = "<div id=\"acknowledgements\">\n"+
-                    "<h2 id=\"ack\" class=\"list\">"+lang.getProperty(LANG_AC_TEXT);
+        String s = "<html>\n<div id=\"acknowledgements\">\n"+
+                    "<h2 id=\"ack\" class=\"list\">"+lang.getProperty(LANG_AC_TEXT)+"\n</html>\n";
         return s;
     }
+
     public static String getChangeLogSection(Configuration c, CompareOntologies comp, Properties lang){
-        String s = "<div id=\"changelog\">\n"+
+        String s = "<html>\n<div id=\"changelog\">\n"+
                     "<h2 id=\"changes\" class=\"list\">"+lang.getProperty(LANG_CHANGELOG_HEAD)+"</h2>\n";
         s+=OntologyDifferencesRenderer.differencesToHTML(comp, c.getMainOntology().getNamespaceURI(), lang);
-        s+="</div>";
+        s+="</div>\n<html>\n";
         //return lang.getProperty("changeLog");
         return s;
     }
@@ -568,21 +570,23 @@ public static String getIndexDocument(String resourcesFolderName,Configuration c
                     "				t+='</ul>';\n" +
                     "				j=0;\n" +
                     "			}\n" +
-                    "			t+= '<li>'+i+'. <a href=#'+ jQuery(this).attr('id')+'>'+ jQuery(this).text()+'</a></li>';\n" +
+                    "			t+= '<li>'+i+'. <a href=#'+ jQuery(this).attr('id')+'>'+ jQuery(this).ignore(\"span\").text()+'</a></li>';\n" +
                     "			i++;\n" +
                     "		}\n" +
                     "		if(jQuery(this).is('h3')){\n" +
                     "			if(j==0){\n" +
                     "				t+='<ul>';\n" +
                     "			}\n" +
                     "			j++;\n" +
-                    "			t+= '<li>'+(i-1)+'.'+j+'. '+'<a href=#'+ jQuery(this).attr('id')+'>'+ jQuery(this).text()+'</a></li>';\n" +
+                    "			t+= '<li>'+(i-1)+'.'+j+'. '+'<a href=#'+ jQuery(this).attr('id')+'>'+ jQuery(this).ignore(\"span\").text()+'</a></li>';\n" +
                     "		}\n" +
-                    "		t = t.replace(' "+lang.getProperty(LANG_BACK3).replace("&iacute;", "í")+"','');\n" +//back to ToC
                     "	  });\n" +
                     "	  t+='</ul>';\n" +
                     "	  $(\"#toc\").html(t); \n" +
                     "}\n"+
+                    " $.fn.ignore = function(sel){\n" +
+                    "        return this.clone().find(sel||\">*\").remove().end();\n" +
+                    " };"+
                      "    $(function(){\n";
         //the script for loading the table is called after loading everything else, after the loadHash function
         if(c.isIncludeAbstract()) document += "      $(\"#abstract\").load(\"sections/abstract-"+c.getCurrentLanguage()+".html\"); \n";
@@ -726,11 +730,11 @@ public static String getOverviewSectionTitleAndPlaceHolder(Configuration c, Prop
     }
 
     public static String getDescriptionSectionTitleAndPlaceHolder(Configuration c, Properties lang){
-        return "<h2 id=\"desc\" class=\"list\">"+c.getMainOntology().getName()+": "+lang.getProperty(LANG_DESCRIPTION_PLACEHOLDER);
+        return "<html>\n<h2 id=\"desc\" class=\"list\">"+c.getMainOntology().getName()+": "+lang.getProperty(LANG_DESCRIPTION_PLACEHOLDER)+"\n</html>\n";
     }
 
     public static String getCrossReferenceSectionTitleAndPlaceHolder(Configuration c, Properties lang){
-        return "<h2  id=\"crossreference\" class=\"list\">"+lang.getProperty(LANG_CROSS_REF_TITLE)+" "+c.getMainOntology().getName()+" "+lang.getProperty(LANG_CROSS_REF_TITLE2)+"</h2>"+"\n" +
+        return "<h2 id=\"crossreference\" class=\"list\">"+lang.getProperty(LANG_CROSS_REF_TITLE)+" "+c.getMainOntology().getName()+" "+lang.getProperty(LANG_CROSS_REF_TITLE2)+"</h2>"+"\n" +
                lang.getProperty(LANG_CROSS_REF_PLACEHOLDER)+c.getMainOntology().getName()+".\n";
     }
 

diff --git a/src/main/java/widoco/CreateResources.java b/src/main/java/widoco/CreateResources.java
@@ -198,10 +198,11 @@ private static void createIntroductionSection(String path, HashMap<String,String
         if((c.getIntroductionPath()!=null) && (!"".equals(c.getIntroductionPath()))){
             WidocoUtils.copyExternalResource(c.getIntroductionPath(),new File(path+File.separator+"introduction-"+c.getCurrentLanguage()+".html"));
         }else{
-            String introSectionText = Constants.getIntroductionSectionTitleAndPlaceHolder(c, lang);
+            String introSectionText = "<html>"+Constants.getIntroductionSectionTitleAndPlaceHolder(c, lang);
             if(nsDecl!=null && !nsDecl.isEmpty()){
                 introSectionText += Constants.getNameSpaceDeclaration(nsDecl,c, lang);
             }
+            introSectionText+="</html>";
             saveDocument(path+File.separator+"introduction-"+c.getCurrentLanguage()+".html", introSectionText,c);
         }
     }
@@ -211,7 +212,7 @@ private static void createOverviewSection(String path, Configuration c, String c
         if((c.getOverviewPath()!=null) && (!"".equals(c.getOverviewPath()))){
             WidocoUtils.copyExternalResource(c.getOverviewPath(), new File(path+File.separator+"overview-"+c.getCurrentLanguage()+".html"));
         }else{
-            String overViewSection = Constants.getOverviewSectionTitleAndPlaceHolder(c, lang);
+            String overViewSection = "<html>"+Constants.getOverviewSectionTitleAndPlaceHolder(c, lang);
             if(!"".equals(classesList) && classesList!=null){
                 overViewSection+=("<h4>"+lang.getProperty(Constants.LANG_CLASSES)+"</h4>\n");
                 overViewSection+=(classesList);
@@ -236,6 +237,7 @@ private static void createOverviewSection(String path, Configuration c, String c
             if(c.isCreateWebVowlVisualization()){
                 overViewSection +="<iframe align=\"center\" width=\"100%\" height =\"500px\" src=\"webvowl/index.html#\"></iframe> ";
             }
+            overViewSection+="</html>\n";
             saveDocument(path+File.separator+"overview-"+c.getCurrentLanguage()+".html", overViewSection,c);
         }
     }
@@ -250,7 +252,7 @@ private static void createDescriptionSection(String path, Configuration c, Prope
 
     private static void createCrossReferenceSection(String path,LODEParser lodeParser, Configuration c, Properties lang){
         //cross reference section has to be included always.
-        String crossRef = Constants.getCrossReferenceSectionTitleAndPlaceHolder(c, lang);
+        String crossRef = "<html>"+Constants.getCrossReferenceSectionTitleAndPlaceHolder(c, lang);
         String classesList = lodeParser.getClassList(),propList = lodeParser.getPropertyList(), dataPropList = lodeParser.getDataPropList(),
                 annotationPropList = lodeParser.getAnnotationPropList(), namedIndividualList = lodeParser.getNamedIndividualList();
         if(classesList!=null && !"".equals(classesList)){
@@ -269,7 +271,7 @@ private static void createCrossReferenceSection(String path,LODEParser lodeParse
             crossRef += lodeParser.getNamedIndividuals();
         }
         //add legend
-        crossRef+=Constants.getLegend(lang);
+        crossRef+=Constants.getLegend(lang)+"\n</html>\n";
         saveDocument(path+File.separator+"crossref-"+c.getCurrentLanguage()+".html", crossRef,c);
     }
 

diff --git a/src/main/java/widoco/gui/EditProperty.java b/src/main/java/widoco/gui/EditProperty.java
@@ -82,7 +82,7 @@ public EditProperty(GuiStep2 g, Configuration c, PropertyType p) {
                 this.setTitle("Editing Imported Ontologies");
                 this.addRowButton.setText("Add ontology...");
                 this.deleteRowButton.setText("Delete ontology...");
-                createTable(new String[]{"Extended Ontology Name","Extended Ontology URI"});
+                createTable(new String[]{"Imported Ontology Name","Imported Ontology URI"});
                 loadOntologies(c.getMainOntology().getImportedOntologies());
                 break;
             case license:

diff --git a/src/main/java/widoco/gui/GuiController.java b/src/main/java/widoco/gui/GuiController.java
@@ -52,12 +52,20 @@ public enum State{initial, metadata, loadingConfig, sections, loading, generated
     public GuiController() {
         this.state = State.initial;  
         config = new Configuration();
+        System.out.println("\n\n--WIzard for DOCumenting Ontologies (WIDOCO).\n https://w3id.org/widoco/\n");
+        System.out.println("\nYou are launching WIDOCO GUI\n");
+        System.out.println("\nTo use WIDOCO through the command line please do:\n");
+        System.out.println("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] [-webVowl] "
+                            + "[-ignoreIndividuals] [-includeAnnotationProperties] [-analytics analyticsCode] [-doNotDisplaySerializations] [-displayDirectImportsOnly]"
+                            + "[-rewriteBase rewriteBasePath]. \nSee more information in https://github.com/dgarijo/Widoco/#how-to-use-widoco\n");
         //read logo
-        gui = new GuiStep1(this);
-        gui.setVisible(true);
         try { 
+            gui = new GuiStep1(this);
+            gui.setVisible(true);
             UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
         } catch (Exception e) {
+            System.out.println("Error while launching the GUI"+e.getMessage());
         }
     }
 

diff --git a/src/main/java/widoco/gui/GuiStep2.java b/src/main/java/widoco/gui/GuiStep2.java
@@ -159,7 +159,7 @@ public void stopLoadingAnimation(){
     }
 
     private void refreshTable(){
-        String authors="", contributors="", imported="", extended="";
+        String authors="", contributors="", imported="", extended="", publisher="";
         for(Agent a: conf.getMainOntology().getCreators()){
             if(a.getName()==null || a.getName().equals("")){
                 authors+="creator; ";
@@ -192,6 +192,13 @@ private void refreshTable(){
                 extended+=a.getName()+"; ";
             }
         }
+        Agent p = conf.getMainOntology().getPublisher();
+        if(p.getName()==null || p.getName().equals("")){
+                publisher+="publisherName ";
+            }
+        else{
+            publisher+=p.getName();
+        }
         tableProperties.setModel(new javax.swing.table.DefaultTableModel(
             new Object [][] {
                 {"abstract", conf.getAbstractSection()},
@@ -206,7 +213,7 @@ private void refreshTable(){
                 {"ontology revision", conf.getMainOntology().getRevision()},
                 {"authors", authors},
                 {"contributors", contributors},
-                {"publisher", conf.getMainOntology().getPublisher().getURL()},
+                {"publisher", publisher},
                 {"imported ontologies", imported},
                 {"extended ontologies", extended},
                 {"license", conf.getMainOntology().getLicense().getUrl()},

diff --git a/src/main/java/widoco/gui/TestInterface.form b/src/main/java/widoco/gui/TestInterface.form
@@ -45,8 +45,25 @@
         </Property>
       </Properties>
 
-      <Layout class="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout">
-        <Property name="useNullLayout" type="boolean" value="false"/>
+      <Layout>
+        <DimensionLayout dim="0">
+          <Group type="103" groupAlignment="0" attributes="0">
+              <Group type="102" attributes="0">
+                  <Component id="sidePanel" min="-2" pref="200" max="-2" attributes="0"/>
+                  <EmptySpace min="340" pref="340" max="-2" attributes="0"/>
+                  <Component id="labelChangeAtTheEnd" min="-2" max="-2" attributes="0"/>
+              </Group>
+          </Group>
+        </DimensionLayout>
+        <DimensionLayout dim="1">
+          <Group type="103" groupAlignment="0" attributes="0">
+              <Component id="sidePanel" min="-2" max="-2" attributes="0"/>
+              <Group type="102" attributes="0">
+                  <EmptySpace min="450" pref="450" max="-2" attributes="0"/>
+                  <Component id="labelChangeAtTheEnd" min="-2" max="-2" attributes="0"/>
+              </Group>
+          </Group>
+        </DimensionLayout>
       </Layout>
       <SubComponents>
         <Container class="javax.swing.JPanel" name="sidePanel">
@@ -55,11 +72,6 @@
               <Color blue="ff" green="ff" red="ff" type="rgb"/>
             </Property>
           </Properties>
-          <Constraints>
-            <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
-              <AbsoluteConstraints x="0" y="0" width="200" height="500"/>
-            </Constraint>
-          </Constraints>
 
           <Layout>
             <DimensionLayout dim="0">
@@ -320,11 +332,6 @@
           <Properties>
             <Property name="text" type="java.lang.String" value="Change to white at the end"/>
           </Properties>
-          <Constraints>
-            <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
-              <AbsoluteConstraints x="540" y="450" width="-1" height="-1"/>
-            </Constraint>
-          </Constraints>
         </Component>
       </SubComponents>
     </Container>

diff --git a/src/main/java/widoco/gui/TestInterface.java b/src/main/java/widoco/gui/TestInterface.java
@@ -85,7 +85,6 @@ private void initComponents() {
 
         backgroundPanel.setBackground(new java.awt.Color(204, 204, 204));
         backgroundPanel.setPreferredSize(new java.awt.Dimension(1000, 500));
-        backgroundPanel.setLayout(new org.netbeans.lib.awtextra.AbsoluteLayout());
 
         sidePanel.setBackground(new java.awt.Color(255, 255, 255));
 
@@ -263,10 +262,24 @@ public void mouseEntered(java.awt.event.MouseEvent evt) {
                 .addGap(102, 102, 102))
         );
 
-        backgroundPanel.add(sidePanel, new org.netbeans.lib.awtextra.AbsoluteConstraints(0, 0, 200, 500));
-
         labelChangeAtTheEnd.setText("Change to white at the end");
-        backgroundPanel.add(labelChangeAtTheEnd, new org.netbeans.lib.awtextra.AbsoluteConstraints(540, 450, -1, -1));
+
+        javax.swing.GroupLayout backgroundPanelLayout = new javax.swing.GroupLayout(backgroundPanel);
+        backgroundPanel.setLayout(backgroundPanelLayout);
+        backgroundPanelLayout.setHorizontalGroup(
+            backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addGroup(backgroundPanelLayout.createSequentialGroup()
+                .addComponent(sidePanel, javax.swing.GroupLayout.PREFERRED_SIZE, 200, javax.swing.GroupLayout.PREFERRED_SIZE)
+                .addGap(340, 340, 340)
+                .addComponent(labelChangeAtTheEnd))
+        );
+        backgroundPanelLayout.setVerticalGroup(
+            backgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
+            .addComponent(sidePanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+            .addGroup(backgroundPanelLayout.createSequentialGroup()
+                .addGap(450, 450, 450)
+                .addComponent(labelChangeAtTheEnd))
+        );
 
         javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
         getContentPane().setLayout(layout);