diff --git a/src/fr/inrialpes/exmo/align/gen/alt/BasicAlterator.java b/src/fr/inrialpes/exmo/align/gen/alt/BasicAlterator.java
index 4b2180d7c067b23f4547661dccf1a2979a1506f6..4db3f5ffd228e837b13526e6254e5c989ac3b60e 100644
--- a/src/fr/inrialpes/exmo/align/gen/alt/BasicAlterator.java
+++ b/src/fr/inrialpes/exmo/align/gen/alt/BasicAlterator.java
@@ -1,7 +1,7 @@
/**
* $Id$
*
- * Copyright (C) 2011, INRIA
+ * Copyright (C) 2011-2012, INRIA
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -43,6 +43,13 @@ import java.util.Properties;
import java.util.Random;
import java.util.Enumeration;
+import java.lang.StringBuffer;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.OutputStream;
+import java.io.StringWriter;
+import com.hp.hpl.jena.rdf.model.RDFWriter;
+
//Alignment API classes
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentException;
@@ -135,43 +142,25 @@ public abstract class BasicAlterator implements Alterator {
// -------------------------
// Accessors
- public void setDebug( boolean d ) {
- debug = d;
- }
+ public void setDebug( boolean d ) { debug = d; }
//returns the modified ontology after changing the namespace
- public OntModel getModifiedOntology () {
- return modifiedModel;
- }
+ public OntModel getModifiedOntology () { return modifiedModel; }
- public void setModifiedModel(OntModel model) {
- modifiedModel = model;
- }
+ public void setModifiedModel( OntModel model ) { modifiedModel = model; }
- public OntModel getModifiedModel() {
- return modifiedModel;
- }
+ public OntModel getModifiedModel() { return modifiedModel; }
- public ClassHierarchy getHierarchy() {
- return classHierarchy;
- }
+ public ClassHierarchy getHierarchy() { return classHierarchy; }
//get properties
- public Properties getProtoAlignment() {
- return alignment;
- }
+ public Properties getProtoAlignment() { return alignment; }
- public OntModel getProtoOntology() {
- return modifiedModel;
- }
+ public OntModel getProtoOntology() { return modifiedModel; }
- public String getNamespace() {
- return modifiedOntologyNS;
- }
+ public String getNamespace() { return modifiedOntologyNS; }
- public String getBase() {
- return initOntologyNS;
- }
+ public String getBase() { return initOntologyNS; }
// -------------------------
// Utility (string) functions
@@ -226,6 +215,8 @@ public abstract class BasicAlterator implements Alterator {
//classHierarchy.printClassHierarchy();
}
+ // JE: this is usually not efficient, since these lists will likely be used for iterating
+
//gets the Ontology classes
@SuppressWarnings("unchecked")
public List<OntClass> getOntologyClasses () {
@@ -265,64 +256,28 @@ public abstract class BasicAlterator implements Alterator {
//changes the unionOf, intersectionOf
public OntModel changeDomainRange ( HashMap<String, String> uris ) {
OntModel newModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);//create new Model
- boolean isSubj, isObj, isPred;
- String subjectNameSpace, subjectLocalName;
- String objectNameSpace, objectLocalName;
- String predicateNameSpace, predicateLocalName;
//iterate and modify the identifiers
for ( Statement stm : modifiedModel.listStatements().toList() ) {
Resource subject = stm.getSubject(); //the subject
Property predicate = stm.getPredicate(); //the predicate
RDFNode object = stm.getObject(); //the object
- Resource subj = null;
- Property pred = null;
- Resource obj = null;
- isSubj = isObj = isPred = false;
//if the class appears as the subject of a proposition
- if ( subject.getURI() != null )
- if ( uris.containsKey( subject.getURI() ) ) {
- isSubj = true;
- subj = newModel.createResource( uris.get( subject.getURI() ) );
+ if ( ( subject.getURI() != null ) && ( uris.containsKey( subject.getURI() ) ) ) {
+ subject = newModel.createResource( uris.get( subject.getURI() ) );
}
//if appears as the predicate - never
- if ( predicate.getURI() != null )
- if ( uris.containsKey( predicate.getURI() ) ) {
- isPred = true;
- pred = newModel.createProperty( uris.get( predicate.getURI() ) );
+ if ( ( predicate.getURI() != null ) && ( uris.containsKey( predicate.getURI() ) ) ) {
+ predicate = newModel.createProperty( uris.get( predicate.getURI() ) );
}
-
//if appears as the object of the statement
- if ( object.canAs( Resource.class ) )
- if ( object.isURIResource() ) {
- if ( object.asResource().getURI() != null )
- if ( uris.containsKey( object.asResource().getURI() ) ) {
- isObj = true;
- obj = newModel.createResource( uris.get( object.asResource().getURI() ) );
- }
- }
-
- if ( isSubj ) {
- if ( isPred ) {
- if ( isObj ) newModel.add( subj, pred, obj );
- else newModel.add( subj, pred, object );
- }
- else {
- if ( isObj ) newModel.add( subj, predicate, obj );
- else newModel.add( subj, predicate, object );
- }
- } else {
- if ( isPred ) {
- if ( isObj ) newModel.add( subject, pred, obj );
- else newModel.add( subject, pred, object );
- }
- else {
- if ( isObj ) newModel.add( subject, predicate, obj );
- else newModel.add( subject, predicate, object );
- }
- }
+ if ( ( object.canAs( Resource.class ) ) && ( object.isURIResource() )
+ && ( object.asResource().getURI() != null ) && ( uris.containsKey( object.asResource().getURI() ) ) ) {
+ object = newModel.createResource( uris.get( object.asResource().getURI() ) );
+ }
+ newModel.add( subject, predicate, object );
}
return newModel;
}
@@ -330,26 +285,21 @@ public abstract class BasicAlterator implements Alterator {
//check if the removed class appears as AllValueFrom or SomeValueFrom in a restriction
@SuppressWarnings("unchecked")
public void checkClassesRestrictions ( OntClass childClass, OntClass parentClass ) {
- Restriction restr = null;
+ String uri = childClass.getURI();
for ( Iterator it = modifiedModel.listRestrictions(); it.hasNext(); ) {
- restr = (Restriction)it.next(); //get the restriction
+ Restriction restr = (Restriction)it.next(); //get the restriction
/* isAllValuesFromRestriction */
if ( restr.isAllValuesFromRestriction() ) {
AllValuesFromRestriction av = restr.asAllValuesFromRestriction();
- if ( av.getAllValuesFrom().getURI() != null ) //if points to the childClass
- //if ( av.getNameSpace().equals( this.modifiedOntologyNS ) )
- if ( av.getAllValuesFrom().getURI().equals( childClass.getURI() ) )
- av.setAllValuesFrom( parentClass ); //change to point to the parentClass
- }
- /* isHasValueRestriction */
+ if ( uri.equals( av.getAllValuesFrom().getURI() ) ) //if points to the childClass
+ av.setAllValuesFrom( parentClass ); //change to point to the parentClass
+ }
+ /* SomeValueFromRestriction */
if ( restr.isSomeValuesFromRestriction() ) {
SomeValuesFromRestriction sv = restr.asSomeValuesFromRestriction();
- if ( sv.getSomeValuesFrom().getURI() != null ) //if points to the childClass
- //if ( sv.getNameSpace().equals( this.modifiedOntologyNS ) )
- if ( sv.getSomeValuesFrom().getURI().equals( childClass.getURI() ) )
- sv.setSomeValuesFrom( parentClass ); //change to point to the parentClass
+ if ( uri.equals( sv.getSomeValuesFrom().getURI() ) ) //if points to the childClass
+ sv.setSomeValuesFrom( parentClass ); //change to point to the parentClass
}
-
}
}
@@ -363,8 +313,8 @@ public abstract class BasicAlterator implements Alterator {
parentClass = this.classHierarchy.removeClass( modifiedModel, cls );//get the parent of the class
for (Iterator it1 = cls.listSubClasses(); it1.hasNext(); ) { //build the list of subclasses
- OntClass subCls = (OntClass)it1.next(); //because we can't change the
- subClasses.add( subCls ); //model while we are iterating
+ //because we can't change the
+ subClasses.add( (OntClass)it1.next() ); //model while we are iterating
}
if ( parentClass != thing ) //now we change the superclass of classes
@@ -395,8 +345,9 @@ public abstract class BasicAlterator implements Alterator {
}
public void relocateTest( String base1, String base2 ) {
- extractedAlignment = extractAlignment( base1, base2 );
- modifiedModel = changeNamespace( base2 );
+ extractedAlignment = extractAlignment( base1, base2 );
+ modifiedModel = changeNamespace2( base2 );
+ modifiedOntologyNS = base2;
}
@SuppressWarnings("unchecked")
@@ -444,65 +395,110 @@ public abstract class BasicAlterator implements Alterator {
/**
* Modifies the namespace of the generated ontology
+ * This is the initial implementation.
+ * However... it has some problem with Jena treating fragments (containing numbers and / in them).
*/
- // It may be in fact faster to output in a String and to modify namespaces on the fly
- // To be tested.
public OntModel changeNamespace ( String ns ) {
- boolean isSubj, isPred, isObj;
-
- OntModel newModel = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM );//create new Model
+ OntModel newModel = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM ); //create new Model
//iterate through all the statements and change the namespace
for ( Statement stm : modifiedModel.listStatements().toList() ) {
Resource subject = stm.getSubject(); //the subject
Property predicate = stm.getPredicate(); //the predicate
RDFNode object = stm.getObject(); //the object
-
- Resource subj = null;
- Property pred = null;
- Resource obj = null;
-
- isPred = isSubj = isObj = false;
if ( ( subject.getLocalName() != null ) && ( !subject.isLiteral() )
&& ( subject.getNameSpace().equals( modifiedOntologyNS ) ) ) {
- subj = newModel.createResource( ns + subject.getLocalName() );
- isSubj = true;
+ subject = newModel.createResource( ns + subject.getLocalName() );
}
if ( !object.isLiteral() && ( object.canAs( Resource.class ) ) && ( object.isURIResource() )
&& ( object.asResource().getNameSpace().equals( modifiedOntologyNS ) ) ) {
- obj = newModel.createResource( ns + object.asResource().getLocalName() );
- isObj = true;
+ object = newModel.createResource( ns + object.asResource().getLocalName() );
}
if ( !predicate.isLiteral() && ( predicate.getNameSpace().equals( modifiedOntologyNS ) ) ) {
- pred = newModel.createProperty( ns + predicate.getLocalName() );
- isPred = true;
+ predicate = newModel.createProperty( ns + predicate.getLocalName() );
}
- if ( isSubj ) {
- if ( isPred ) {
- if ( isObj )
- newModel.add( subj, pred, obj );
- else
- newModel.add(subj, pred, object);
- } else if ( isObj )
- newModel.add( subj, predicate, obj );
- else
- newModel.add( subj, predicate, object );
- } else if ( isPred ) {
- if ( isObj ) newModel.add( subject, pred, obj );
- else newModel.add( subject, pred, object );
- } else if ( isObj ) newModel.add( subject, predicate, obj );
- else newModel.add( subject, predicate, object );
+ newModel.add( subject, predicate, object );
}
- //rename the namespace of owl:Ontology
- List<Ontology> ontos = newModel.listOntologies().toList();
- for ( Ontology o : ontos ) {
- ResourceUtils.renameResource( o, ns );
- }
-
+ /*
+ Ontology onto = newModel.getOntology( modifiedOntologyNS );
+ if ( onto == null ) { // Ugly but efficient
+ for ( Ontology o : newModel.listOntologies().toList() ) {
+ onto = o;
+ }
+ }
+ ResourceUtils.renameResource( onto, ns );
+ */
+ renameOntology( newModel, modifiedOntologyNS, ns );
return newModel;
}
+ /**
+ * JE: starting an attempt to do the relocation through String reading and writing:
+ * The ideal case is that in the generated files, the namespace appears exactly twice:
+ * in xmlns and in xml:base.
+ * But it depends on the actual seed.
+ * Two versions would be possible:
+ * OntModel.write( OutputStream out ) / OntModel.write( Writer writer )
+ * new Model().read( InputStream in, String base ) / new Model().read(Reader reader, String base)
+ * So far this is less efficient (and less correct) than the modifications above
+ * However, it solves a problem that has been observed in Jena:
+ * Jena does not like to have fragment identividers containing numbers! (and other combinations)
+ */
+
+ // At the moment, this is slower... and likely to be wrong...
+ // Why would it be wrong? It is however strange...
+ public OntModel changeNamespace2( String base2 ) {
+ OntModel model = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM );
+ try {
+ //Charset defaultCharset = Charset.forName("UTF8");
+ ByteArrayOutputStream out = new ByteArrayOutputStream();
+ //StringWriter sout = new StringWriter();
+ RDFWriter writer = modifiedModel.getWriter("RDF/XML-ABBREV");
+ writer.setProperty( "showXmlDeclaration","true" );
+ writer.setProperty( "relativeURIs", "" );//faster 26.6 -> 26.03 (?)
+ // -------- critical section
+ // I am curious: isn't it possible to set new ns here? Apparently NO
+ writer.setProperty( "xmlbase", modifiedOntologyNS );
+ modifiedModel.setNsPrefix( "", modifiedOntologyNS );
+ renameOntology( modifiedModel, modifiedOntologyNS, modifiedOntologyNS );
+ // --------
+ writer.write( modifiedModel.getBaseModel(), out, "");
+ //writer.write( modifiedModel.getBaseModel(), sout, "");
+ String serial = out.toString( "UTF8" );
+ //StringBuffer serial = sout.getBuffer();
+ // Can be printed right away
+ String sout = serial.replace( modifiedOntologyNS, base2 ); // Does not work well with StringBuffer
+ // JE: This part below is unnecessary if we just want to print the result and close the story
+ // But suppressing it makes problems even in random...
+ // Using the read allocate as much as before
+ //InputStream in = null; from the string
+ ByteArrayInputStream in = new ByteArrayInputStream( sout.getBytes("UTF8") );
+ model.read( in, null );
+ } catch ( Exception ex ) { //UnsupportedEncodingException;
+ ex.printStackTrace();
+ }
+ return model;
+ }
+
+ /**
+ * Rename the ontology, just in case it does not have the same URI as its content...
+ * This happens
+ * oldURI should be useless
+ */
+ public void renameOntology( OntModel model, String oldURI, String newURI ) {
+ Ontology onto = model.getOntology( oldURI );
+ if ( onto == null ) { // Ugly but efficient
+ for ( Ontology o : model.listOntologies().toList() ) {
+ onto = o; break;
+ }
+ }
+ if ( onto == null ) {
+ model.createOntology( newURI );
+ } else {
+ ResourceUtils.renameResource( onto, newURI );
+ }
+ }
}