New Version with Linkkeys : parsing and rendering with RDF

examples/omwg/total.xml

@@ -752,5 +752,31 @@
 	</edoal:transformation>
       </Cell>
     </map>
+    <!-- test on linkkeys -->
+    <map>
+      <Cell rdf:about="LinkkeyTest">
+	<entity1>
+          <edoal:Class rdf:about="&wine;VintageYear" />
+	</entity1>
+	<entity2>
+          <edoal:Class rdf:about="&vin;Millesime" />
+	</entity2>
+        <measure rdf:datatype='&xsd;float'>1.</measure>        
+        <edoal:linkkey> 
+          <Linkkey edoal:type="weak">
+            <binding>
+              <Corresp edoal:type="eq">
+                <property1>
+                  <edoal:Property rdf:about="&wine;yearValue" />
+                </property1>
+                <property2>
+                  <edoal:Property rdf:about="&vin;annee_millesime" />
+                </property2>
+              </Corresp>
+            </binding>
+          </Linkkey>
+        </edoal:linkkey>
+      </Cell>
+    </map>
   </Alignment>
 </rdf:RDF>

lib/align.pom

@@ -17,13 +17,13 @@
   <groupId>org.semanticweb.owl</groupId>
   <artifactId>align</artifactId>
   <version>4.6</version>
-  <!-- Rev 1874M 22/01/2014 -->
+  <!-- Rev 1954M 10/07/2014 -->
   <name>The Alignment API</name>
   <description>The Alignment API is an API for manipulating ontology alignments.</description>
   <url>http://alignapi.gforge.inria.fr</url>
   <organization>
     <name>INRIA Exmo team</name>
-    <url>http://exmo.inrialpes.fr</url>
+    <url>http://exmo.inria.fr</url>
   </organization>
   <!-- (C) INRIA, 2003-2014 -->
   <licenses>

lib/alignsvc.pom

@@ -17,13 +17,13 @@
   <groupId>fr.inrialpes.exmo.align</groupId>
   <artifactId>alignsvc</artifactId>
   <version>4.6</version>
-  <!-- Rev 1874M 22/01/2014 -->
+  <!-- Rev 1954M 10/07/2014 -->
   <name>Alignment server</name>
   <description>A server for storing and sharing ontology alignments.</description>
   <url>http://alignapi.gforge.inria.fr</url>
   <organization>
     <name>INRIA Exmo team</name>
-    <url>http://exmo.inrialpes.fr</url>
+    <url>http://exmo.inria.fr</url>
   </organization>
   <!-- (C) INRIA, 2003-2014 -->
   <licenses>

lib/ontowrap.pom

@@ -17,13 +17,13 @@
   <groupId>fr.inrialpes.exmo</groupId>
   <artifactId>ontowrap</artifactId>
   <version>4.6</version>
-  <!-- Rev 1874M 22/01/2014 -->
+  <!-- Rev 1954M 10/07/2014 -->
   <name>Ontology wrapping API</name>
   <description>An ontology wrapping API and library.</description>
   <url>http://alignapi.gforge.inria.fr</url>
   <organization>
     <name>INRIA Exmo team</name>
-    <url>http://exmo.inrialpes.fr</url>
+    <url>http://exmo.inria.fr</url>
   </organization>
   <!-- (C) INRIA, 2003-2014 -->
   <licenses>

lib/procalign.pom

@@ -17,13 +17,13 @@
   <groupId>fr.inrialpes.exmo.align</groupId>
   <artifactId>procalign</artifactId>
   <version>4.6</version>
-  <!-- Rev 1874M 22/01/2014 -->
+  <!-- Rev 1954M 10/07/2014 -->
   <name>Reference implementation of the Alignment API</name>
   <description>Implementation of the Alignment API for manipulating ontology alignments.</description>
   <url>http://alignapi.gforge.inria.fr</url>
   <organization>
     <name>INRIA Exmo team</name>
-    <url>http://exmo.inrialpes.fr</url>
+    <url>http://exmo.inria.fr</url>
   </organization>
   <!-- (C) INRIA, 2003-2014 -->
   <licenses>

src/fr/inrialpes/exmo/align/impl/edoal/ClassRestriction.java

@@ -22,9 +22,6 @@
 
 package fr.inrialpes.exmo.align.impl.edoal;
 
-import org.semanticweb.owl.align.AlignmentException;
-import org.semanticweb.owl.align.AlignmentVisitor;
-
 /**
  * <p>
  * Superclass for all ClassRestrictions.

src/fr/inrialpes/exmo/align/impl/edoal/EDOALCell.java

@@ -22,15 +22,8 @@
 
 package fr.inrialpes.exmo.align.impl.edoal;
 
-import java.io.PrintStream;
-import java.io.IOException;
-import java.util.Comparator;
 import java.util.Set;
 import java.util.HashSet;
-import java.lang.ClassNotFoundException;
-import java.lang.Float;
-import java.lang.Double;
-import java.net.URISyntaxException;
 import java.net.URI;
 
 import org.semanticweb.owl.align.Alignment;
@@ -40,7 +33,6 @@ import org.semanticweb.owl.align.Cell;
 import org.semanticweb.owl.align.Relation;
 
 import fr.inrialpes.exmo.align.impl.BasicCell;
-import fr.inrialpes.exmo.align.impl.rel.*;
 
 import fr.inrialpes.exmo.align.parser.TypeCheckingVisitor;
 
@@ -72,6 +64,7 @@ public class EDOALCell extends BasicCell {
     private URI id; // This is the id
 
     private Set<Transformation> transformations;
+    private Set<Linkkey> linkkeys;
 
     public void accept( AlignmentVisitor visitor) throws AlignmentException {
         visitor.visit( this );
@@ -110,6 +103,16 @@ public class EDOALCell extends BasicCell {
     public Set<Transformation> transformations() {
 	return transformations;
     }
+    
+    public void addLinkkey( Linkkey linkkey ){
+	if ( linkkeys == null ) {
+	    linkkeys = new HashSet<Linkkey>();
+	}
+	linkkeys.add( linkkey );
+    }
+    public Set<Linkkey> linkkeys() {
+	return linkkeys;
+    }
 
     public Cell inverse() throws AlignmentException {
 	EDOALCell invcell = new EDOALCell( (String)null, (Expression)object2, (Expression)object1, relation.inverse(), strength );

src/fr/inrialpes/exmo/align/impl/edoal/EDOALVisitor.java

@@ -45,6 +45,8 @@ public interface EDOALVisitor {
     public void visit( Value o ) throws AlignmentException;
     public void visit( Apply o ) throws AlignmentException;
     public void visit( Datatype o ) throws AlignmentException;
+    public void visit( Linkkey o ) throws AlignmentException;
+    public void visit( LinkkeyBinding o ) throws AlignmentException;
     //public void visit( Comparator o ) throws AlignmentException;
     //public void visit( EDOALCell o ) throws AlignmentException;
 }

src/fr/inrialpes/exmo/align/impl/edoal/Linkkey.java

+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package fr.inrialpes.exmo.align.impl.edoal;
+
+import fr.inrialpes.exmo.align.parser.TypeCheckingVisitor;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import org.semanticweb.owl.align.AlignmentException;
+
+/**
+ *
+ * @author Nicolas Guillouet <nicolas@meaningengines.com>
+ */
+public class Linkkey {
+    public static final String PLAIN = "plain";
+    public static final String WEAK = "weak";
+    public static final String STRONG = "strong";
+    private static List<String> ALLOWED_TYPES = Arrays.asList(PLAIN, WEAK, STRONG);
+    
+    private String type;
+    private Set<LinkkeyBinding> bindings;
+    
+    public void accept(EDOALVisitor visitor) throws AlignmentException {
+        visitor.visit(this);
+    }
+    
+    public TypeCheckingVisitor.TYPE accept( TypeCheckingVisitor visitor ) throws AlignmentException {
+	return visitor.visit(this);
+    }
+
+    public Linkkey() throws AlignmentException {
+        this(PLAIN);
+    }
+
+    public Linkkey(String type) throws AlignmentException {
+        if(!ALLOWED_TYPES.contains(type)){
+            throw new AlignmentException("The  type " + type + " is not allowed !");
+        }
+        this.type = type;
+        bindings = new HashSet<>();
+    }
+
+    public void addBinding(LinkkeyBinding binding){
+        bindings.add(binding);
+    }
+    
+    public Set<LinkkeyBinding> bindings(){
+        return bindings;
+    }
+    
+    public String getType() {
+        return type;
+    }
+}

src/fr/inrialpes/exmo/align/impl/edoal/LinkkeyBinding.java

+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+
+package fr.inrialpes.exmo.align.impl.edoal;
+
+import fr.inrialpes.exmo.align.parser.TypeCheckingVisitor;
+import java.util.Arrays;
+import java.util.List;
+import org.semanticweb.owl.align.AlignmentException;
+import org.semanticweb.owl.align.AlignmentVisitor;
+import org.semanticweb.owl.align.Visitable;
+
+/**
+ *
+ * @author Nicolas Guillouet <nicolas@meaningengines.com>
+ */
+public class LinkkeyBinding {
+    public static final String IN = "in";
+    public static final String EQ = "eq";
+    private static List<String> ALLOWED_TYPES = Arrays.asList(IN, EQ);
+    
+    private PathExpression expression1;
+    private PathExpression expression2;
+    private String type;
+    
+    public LinkkeyBinding(PathExpression expression1, PathExpression expression2, String type) throws AlignmentException {
+        if(!ALLOWED_TYPES.contains(type)){
+            throw new AlignmentException("The  type " + type + " is not allowed !");
+        }
+        this.type = type;
+        this.expression1 = expression1;
+        this.expression2 = expression2;
+    }
+    
+    public void accept(EDOALVisitor visitor) throws AlignmentException {
+        visitor.visit(this);
+    }
+    
+    public TypeCheckingVisitor.TYPE accept( TypeCheckingVisitor visitor ) throws AlignmentException {
+	return visitor.visit(this);
+    }
+    
+    public String getType(){
+        return type;
+    }
+    
+    public PathExpression getExpression1(){
+        return expression1;
+    }
+    public PathExpression getExpression2(){
+        return expression2;
+    }
+}

src/fr/inrialpes/exmo/align/impl/edoal/PropertyExpression.java

@@ -22,9 +22,6 @@
 
 package fr.inrialpes.exmo.align.impl.edoal;
 
-import java.util.Collection;
-import java.util.Set;
-
 /**
  * <p>
  * Represents a PropertyExpression.

src/fr/inrialpes/exmo/align/impl/renderer/JSONRendererVisitor.java

@@ -78,6 +78,8 @@ import fr.inrialpes.exmo.align.impl.edoal.Datatype;
 import fr.inrialpes.exmo.align.impl.edoal.Comparator;
 import fr.inrialpes.exmo.align.impl.edoal.EDOALCell;
 import fr.inrialpes.exmo.align.impl.edoal.EDOALVisitor;
+import fr.inrialpes.exmo.align.impl.edoal.Linkkey;
+import fr.inrialpes.exmo.align.impl.edoal.LinkkeyBinding;
 
 /**
  * Renders an alignment in JSON (and in fact in JSON-LD)
@@ -646,5 +648,13 @@ public class JSONRendererVisitor extends IndentedRendererVisitor implements Alig
 	decreaseIndent();
 	decreaseIndent();
     }
+    
+    public void visit(final Linkkey linkkey) throws AlignmentException {
+        throw new AlignmentException("NOT IMPLEMENTED !");
+    }
+    
+    public void visit(final LinkkeyBinding linkkeyBinding) throws AlignmentException {
+        throw new AlignmentException("NOT IMPLEMENTED !");
+    }
 	
 }

src/fr/inrialpes/exmo/align/impl/renderer/OWLAxiomsRendererVisitor.java

@@ -81,6 +81,8 @@ import fr.inrialpes.exmo.align.impl.edoal.Comparator;
 import fr.inrialpes.exmo.align.impl.edoal.EDOALCell;
 import fr.inrialpes.exmo.align.impl.edoal.EDOALAlignment;
 import fr.inrialpes.exmo.align.impl.edoal.EDOALVisitor;
+import fr.inrialpes.exmo.align.impl.edoal.Linkkey;
+import fr.inrialpes.exmo.align.impl.edoal.LinkkeyBinding;
 
 /**
  * Renders an alignment as a new ontology merging these.
@@ -846,4 +848,11 @@ public class OWLAxiomsRendererVisitor extends IndentedRendererVisitor implements
 	indentedOutput("<owl:Datatype><owl:onDataType rdf:resource=\""+e.getType()+"\"/></owl:Datatype>");
     }
 
+    public void visit(final Linkkey linkkey) throws AlignmentException {
+        throw new AlignmentException("NOT IMPLEMENTED !");
+    }
+    
+    public void visit(final LinkkeyBinding linkkeyBinding) throws AlignmentException {
+        throw new AlignmentException("NOT IMPLEMENTED !");
+    }
 }

src/fr/inrialpes/exmo/align/impl/renderer/SILKRendererVisitor.java

@@ -33,6 +33,8 @@ import fr.inrialpes.exmo.ontowrap.Ontology;
 import fr.inrialpes.exmo.align.impl.Namespace;
 import fr.inrialpes.exmo.align.impl.BasicAlignment;
 import fr.inrialpes.exmo.align.impl.edoal.Expression;
+import fr.inrialpes.exmo.align.impl.edoal.Linkkey;
+import fr.inrialpes.exmo.align.impl.edoal.LinkkeyBinding;
 
 import java.net.URI;
 import java.util.Enumeration;
@@ -252,5 +254,12 @@ public class SILKRendererVisitor extends GraphPatternRendererVisitor implements
 	// default behaviour
 	// rel.write( writer );
     }
+    public void visit(final Linkkey linkkey) throws AlignmentException {
+        throw new AlignmentException("NOT IMPLEMENTED !");
+    }
+    
+    public void visit(final LinkkeyBinding linkkeyBinding) throws AlignmentException {
+        throw new AlignmentException("NOT IMPLEMENTED !");
+    }
 	
 }

src/fr/inrialpes/exmo/align/impl/renderer/SPARQLConstructRendererVisitor.java

@@ -28,6 +28,8 @@ import org.semanticweb.owl.align.Relation;
 import fr.inrialpes.exmo.align.impl.BasicAlignment;
 import fr.inrialpes.exmo.align.impl.edoal.EDOALAlignment;
 import fr.inrialpes.exmo.align.impl.edoal.Expression;
+import fr.inrialpes.exmo.align.impl.edoal.Linkkey;
+import fr.inrialpes.exmo.align.impl.edoal.LinkkeyBinding;
 
 import java.io.PrintWriter;
 import java.net.URI;
@@ -142,6 +144,13 @@ public class SPARQLConstructRendererVisitor extends GraphPatternRendererVisitor
         // default behaviour
         // rel.write( writer );
     }
+    public void visit(final Linkkey linkkey) throws AlignmentException {
+        throw new AlignmentException("NOT IMPLEMENTED !");
+    }
+    
+    public void visit(final LinkkeyBinding linkkeyBinding) throws AlignmentException {
+        throw new AlignmentException("NOT IMPLEMENTED !");
+    }
 
     protected void generateConstruct(Cell cell, Expression expr1, Expression expr2) throws AlignmentException {
         // Here the generation is dependent on global variables