diff --git a/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/OfflineAlign.java b/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/OfflineAlign.java
index 1a1370a7ebd92cf8ceb3f2234efd29e981261d42..660743bf1e0fc759005c8d9adb13613a770f5f59 100755
--- a/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/OfflineAlign.java
+++ b/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/OfflineAlign.java
@@ -50,12 +50,12 @@ public class OfflineAlign {
File alignFolder = null;
File ontoFolder = null;
- public OfflineAlign(File al, File on) {
+ public OfflineAlign( File al, File on ) {
ontoFolder = on;
alignFolder = al;
}
- String matchAndExportAlign (String method, String proj1, String selectedNeOnOnto1, String proj2, String selectedNeOnOnto2) {
+ String matchAndExportAlign (String method, String proj1, String selectedNeOnOnto1, String proj2, String selectedNeOnOnto2) throws Exception {
//export ontologies
//ImportExportControl ieControl = new ImportExportControl();
//Integer name1 = new Integer(AlignView.alignId++);
@@ -68,11 +68,11 @@ public class OfflineAlign {
//Vector corrList = new Vector();
Integer name = new Integer(AlignView.getNewAlignId());
- Vector<URI> uris = new Vector<URI>();
+ //Vector<URI> uris = new Vector<URI>();
- try {
- uris.add( new URI(selectedNeOnOnto1) );
- uris.add( new URI(selectedNeOnOnto2 ) );
+ //try {
+ //uris.add( new URI(selectedNeOnOnto1) );
+ //uris.add( new URI(selectedNeOnOnto2 ) );
Object[] mparams = {};
Class<?> alignmentClass = Class.forName(method);
Class[] cparams = {};
@@ -81,8 +81,8 @@ public class OfflineAlign {
OntologyFactory factory = null;
// This should also be a static getInstance!
factory = OntologyFactory.getFactory();
- fr.inrialpes.exmo.ontowrap.LoadedOntology onto1 = loadOntology( factory, uris.get(0) );
- fr.inrialpes.exmo.ontowrap.LoadedOntology onto2 = loadOntology( factory, uris.get(1) );
+ fr.inrialpes.exmo.ontowrap.LoadedOntology onto1 = loadOntology( factory, proj1, selectedNeOnOnto1 );
+ fr.inrialpes.exmo.ontowrap.LoadedOntology onto2 = loadOntology( factory, proj2, selectedNeOnOnto2 );
A1.init( onto1, onto2 );
// A1.init( (URI)uris.get(0), (URI)uris.get(1) );
A1.align( (Alignment)null, p );
@@ -105,139 +105,131 @@ public class OfflineAlign {
A1.render(V);
owlF.flush();
owlF.close();
- } catch ( Exception ex ) {
- };
+ //} catch ( Exception ex ) {};
//System.out.println("match=" +name.toString());
return alignFolder.getAbsolutePath() + File.separator + name.toString();
}
- public LoadedOntology loadOntology( OntologyFactory factory, URI uri ) {
+ public LoadedOntology loadOntology( OntologyFactory factory, String project, String ontoURI ) throws org.semanticweb.owlapi.model.OWLOntologyCreationException {
fr.inrialpes.exmo.ontowrap.owlapi30.OWLAPI3Ontology onto = null;
org.semanticweb.owlapi.model.OWLOntology ontology = null;
- try {
- ontology = ((fr.inrialpes.exmo.ontowrap.owlapi30.OWLAPI3OntologyFactory)factory).getManager().loadOntology( org.semanticweb.owlapi.model.IRI.create( uri ) );
- } catch ( org.semanticweb.owlapi.model.OWLOntologyCreationException e ) {
+
+ try { // Try to get the local ontology object
+ com.ontoprise.ontostudio.owl.model.OWLModel model = com.ontoprise.ontostudio.owl.model.OWLModelFactory.getOWLModel( ontoURI, project );
+ ontology = model.getOntology();
+ } catch ( org.neontoolkit.core.exception.NeOnCoreException e ) {
e.printStackTrace();
//throw new org.semanticweb.owl.align.AlignmentException("Cannot load " + uri, e);
+ // Let's try to load it from the web...
+ }
+ if ( ontology == null ) { // try to upload
+ ontology = ((fr.inrialpes.exmo.ontowrap.owlapi30.OWLAPI3OntologyFactory)factory).getManager().loadOntology( org.semanticweb.owlapi.model.IRI.create( ontoURI ) );
}
onto = new fr.inrialpes.exmo.ontowrap.owlapi30.OWLAPI3Ontology();
onto.setFormalism( "OWL 2.0" );
try {
onto.setFormURI( new URI("http://www.w3.org/2002/07/owl#") );
+ onto.setFile( new URI( ontoURI ) );
} catch ( Exception ex ) {}; // never happens
onto.setOntology( ontology );
- onto.setFile( uri );
//onto.setURI( ontology.getURI() );
onto.setURI( ontology.getOntologyID().getOntologyIRI().toURI() );
return onto;
}
- String trimAndExportAlign (Double thres, String id) {
-
- Integer name = new Integer(AlignView.getNewAlignId());
-
- Alignment A1 = AlignView.alignmentTable.get( id );
- //BasicAlignment clonedA1 = (BasicAlignment)((BasicAlignment)A1).clone();
- BasicAlignment clonedA1 = null;
+ String trimAndExportAlign (Double thres, String id) {
+ Integer name = new Integer(AlignView.getNewAlignId());
+ Alignment A1 = AlignView.alignmentTable.get( id );
+ //BasicAlignment clonedA1 = (BasicAlignment)((BasicAlignment)A1).clone();
+ BasicAlignment clonedA1 = null;
- try {
-
- File exFile = new File(id + ".rdf");
-
- AlignmentParser ap = new AlignmentParser(0);
- ap.setEmbedded(true);
- clonedA1 = (BasicAlignment) ap.parse(exFile.toURI().toString());
+ try {
+ File exFile = new File(id + ".rdf");
+ AlignmentParser ap = new AlignmentParser(0);
+ ap.setEmbedded(true);
+ clonedA1 = (BasicAlignment) ap.parse(exFile.toURI().toString());
- File fnRdf = new File( alignFolder.getAbsolutePath() + File.separator + name.toString()+ ".rdf" );
- if (fnRdf.exists()) fnRdf.delete();
+ File fnRdf = new File( alignFolder.getAbsolutePath() + File.separator + name.toString()+ ".rdf" );
+ if (fnRdf.exists()) fnRdf.delete();
- FileWriter rdfF = new FileWriter( fnRdf );
- AlignmentVisitor rdfV = new RDFRendererVisitor( new PrintWriter ( rdfF ) );
+ FileWriter rdfF = new FileWriter( fnRdf );
+ AlignmentVisitor rdfV = new RDFRendererVisitor( new PrintWriter ( rdfF ) );
- clonedA1.render(rdfV);
- rdfF.flush();
- rdfF.close();
+ clonedA1.render(rdfV);
+ rdfF.flush();
+ rdfF.close();
- clonedA1.cut(thres);
- AlignView.alignmentTable.put( alignFolder.getAbsolutePath() + File.separator + name.toString(), clonedA1 );
+ clonedA1.cut(thres);
+ AlignView.alignmentTable.put( alignFolder.getAbsolutePath() + File.separator + name.toString(), clonedA1 );
- File owlFile = new File( ontoFolder.getAbsolutePath() + File.separator + name.toString()+ ".owl");
- if (owlFile.exists()) owlFile.delete();
+ File owlFile = new File( ontoFolder.getAbsolutePath() + File.separator + name.toString()+ ".owl");
+ if (owlFile.exists()) owlFile.delete();
- FileWriter owlF = new FileWriter( owlFile );
+ FileWriter owlF = new FileWriter( owlFile );
- AlignmentVisitor owlV = new OWLAxiomsRendererVisitor( new PrintWriter ( owlF ) );
- ObjectAlignment al = ObjectAlignment.toObjectAlignment( (URIAlignment)clonedA1 );
- al.render( owlV );
- //clonedA1.render(owlV);
- owlF.flush();
- owlF.close();
- }
- catch ( Exception ex ) { ex.printStackTrace();};
- //System.out.println("trim=" +name.toString());
- return alignFolder.getAbsolutePath() + File.separator + name.toString();
- }
+ AlignmentVisitor owlV = new OWLAxiomsRendererVisitor( new PrintWriter ( owlF ) );
+ ObjectAlignment al = ObjectAlignment.toObjectAlignment( (URIAlignment)clonedA1 );
+ al.render( owlV );
+ //clonedA1.render(owlV);
+ owlF.flush();
+ owlF.close();
+ } catch ( Exception ex ) { ex.printStackTrace();};
+ //System.out.println("trim=" +name.toString());
+ return alignFolder.getAbsolutePath() + File.separator + name.toString();
+ }
public String[] getAllAlign() {
-
- if (AlignView.alignmentTable.keys() == null) return null;
- Vector<String> v = new Vector<String>();
+ if (AlignView.alignmentTable.keys() == null) return null;
+ Vector<String> v = new Vector<String>();
- for (Enumeration e = AlignView.alignmentTable.keys() ; e.hasMoreElements() ;) {
- v.add((String)e.nextElement());
- }
+ for (Enumeration e = AlignView.alignmentTable.keys() ; e.hasMoreElements() ;) {
+ v.add((String)e.nextElement());
+ }
- String[] ls = new String[v.size()];
- for(int i=0; i< v.size(); i++) ls[i] = v.get(i);
+ String[] ls = new String[v.size()];
+ for(int i=0; i< v.size(); i++) ls[i] = v.get(i);
- return ls;
+ return ls;
}
public void getAllAlignFromFiles() {
-
- String[] nameL = alignFolder.list();
+ String[] nameL = alignFolder.list();
Vector<String> v = new Vector<String>();
for(int i=0; i< nameL.length; i++)
if(nameL[i].contains(".rdf")) v.add(nameL[i]);
try {
-
- AlignmentParser parser = new AlignmentParser( 0 );
- parser.setEmbedded( true );
+ AlignmentParser parser = new AlignmentParser( 0 );
+ parser.setEmbedded( true );
- for(int i=0; i< v.size(); i++) {
+ for(int i=0; i< v.size(); i++) {
- String key = v.get(i).replace(".rdf", "");
- //System.out.println("Path ="+ alignFolder.getAbsolutePath() + File.separator + v.get(i) );
- AlignView.alignmentTable.put( alignFolder.getAbsolutePath() + File.separator + key ,
- parser.parse( alignFolder.getAbsolutePath() + File.separator + v.get(i)) );
- }
-
+ String key = v.get(i).replace(".rdf", "");
+ //System.out.println("Path ="+ alignFolder.getAbsolutePath() + File.separator + v.get(i) );
+ AlignView.alignmentTable.put( alignFolder.getAbsolutePath() + File.separator + key ,
+ parser.parse( alignFolder.getAbsolutePath() + File.separator + v.get(i)) );
+ }
} catch ( Exception ex ) { ex.printStackTrace();};
-
}
public static String fileToString(File f){
- String texto = "";
- int i=0;
- try{
-
+ String texto = "";
+ int i=0;
+ try{
FileReader rd = new FileReader(f);
i = rd.read();
-
- while(i!=-1){
- texto = texto+(char)i;
- i = rd.read();
- }
-
- }catch(IOException e){
- System.err.println(e.getMessage());
- }
- return texto;
- }
+ while(i!=-1){
+ texto = texto+(char)i;
+ i = rd.read();
+ }
+ } catch(IOException e){
+ System.err.println(e.getMessage());
+ }
+ return texto;
+ }
}