--Improved portability of plugin

plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/AlignView.java

@@ -402,21 +402,21 @@ public class AlignView extends ViewPart
 
 		//fill "alignmentTable"
 		public String fetchAlignFromServer(String id) {
-			   URIAlignment align = null;
+			   Alignment align = null;
 			   String alignKey = null;
 			   
 			   if( idMap.containsKey(id) ) {
 				   alignKey = idMap.get(id);
-				   align = (URIAlignment)AlignView.alignmentTable.get( alignKey );
+				   align =  AlignView.alignmentTable.get( alignKey );
 			   } else {
-				   onlineAlign.getRDFAlignmentMonoThread( id );
-			   	    
+				     
 			   	   FileWriter out = null;
 						
-			   	   String rdfalignStr = onlineAlign.getRDFAlignmentParsed( );// selectedAlign , alignImportButton, alignStoreButton, 
-						                                            //serverAlignTrimButton, allAlignButton, alignFindButton, mapButton );
+			   	   String rdfalignStr = onlineAlign.getRDFAlignment( id );
 				 	
 			   	   alignKey =  alignFolder.getAbsolutePath() + File.separator + getNewAlignId();
+			   	   
+			   	   //System.out.println("alignKey="+alignKey);
 			   	   String rdfPath =  alignKey + ".rdf";
 				
 			   	   try {
@@ -431,12 +431,18 @@ public class AlignView extends ViewPart
 					
 					AlignmentParser ap = new AlignmentParser(0);
 					ap.setEmbedded( true );
-					align = (URIAlignment)ap.parse(file.toURI().toString());	
+					
+					//System.out.println(" parsing string ... ");
+					//align = ap.parseString( rdfalignStr  );
+					align = ap.parse( file.toURI().toString() );
+ 				
+					//if(align==null) System.out.println("align null" ); else System.out.println("align non null" );
+					
 					AlignView.alignmentTable.put( alignKey , (Alignment)align );
 					idMap.put(id, alignKey);
 					localAlignBox.setEnabled(true);
        			   	localAlignBox.add(alignKey, 0);
-       			   	selectedLocalAlign = alignKey; 	
+       			   	selectedLocalAlign = alignKey;
        			   	localAlignBox.select(0);
        			   	localAlignBox.redraw();
 					

plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/OfflineAlign.java

@@ -29,7 +29,7 @@ import java.net.URI;
 import java.util.Vector;
 import java.util.Enumeration;
 
-import org.semanticweb.kaon2.api.formatting.OntologyFileFormat;
+//import org.semanticweb.kaon2.api.formatting.OntologyFileFormat;
 import org.semanticweb.owl.align.Alignment;
 import fr.inrialpes.exmo.align.impl.BasicAlignment;
 import fr.inrialpes.exmo.align.impl.ObjectAlignment;
@@ -68,14 +68,9 @@ public class OfflineAlign {
       ImportExportControl ieControl = new ImportExportControl();
       //Integer name1 = new Integer(AlignView.alignId++);  
 	  //Integer name2 = new Integer(AlignView.alignId++);
-	  File f1 = new File( selectedNeOnOnto1.replace("file:","") );
-	  File f2 = new File( selectedNeOnOnto2.replace("file:","") );
+	  //File f1 = new File( selectedNeOnOnto1.replace("file:","") );
+	  //File f2 = new File( selectedNeOnOnto2.replace("file:","") );
 	  
-	  //String fname1 =  f1.getName();
-	  //String fname2 =  f2.getName();
-	  
-	  //System.out.println("Filename 1="+ selectedNeOnOnto1);
-	  //System.out.println("Filename 2="+ selectedNeOnOnto2);
 	  
       Parameters p = new BasicParameters();
       AlignmentProcess A1 = null;
@@ -100,6 +95,7 @@ public class OfflineAlign {
 	  	A1.align((Alignment)null,p);
 	  	
 	  	//AlignView.alignObjects.clear();
+	  	//System.out.println(" alignKey From Offline"+ alignFolder.getAbsolutePath() + File.separator + name.toString());
 	  	AlignView.alignmentTable.put( alignFolder.getAbsolutePath() + File.separator + name.toString(), (Alignment)A1 );
 	  
 	  	
@@ -207,7 +203,7 @@ public class OfflineAlign {
     	   		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)) );
+    	   				parser.parse( alignFolder.getAbsolutePath() + File.separator  + v.get(i)) );
     	   	}
 			   
        } catch ( Exception ex ) { ex.printStackTrace();};

plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/OnlineAlign.java

@@ -525,7 +525,7 @@ public class OnlineAlign {
  			return result[0];
 	    }
 	    
-	    public void getRDFAlignment(String alignId ) {
+	    public String getRDFAlignment(String alignId ) {
 			
 			//retrieve alignment for storing in OWL file
 			 
@@ -538,7 +538,7 @@ public class OnlineAlign {
 	    	params.setParameter( "arg1", alignId);
 	    	params.setParameter( "arg2", "fr.inrialpes.exmo.align.impl.renderer.RDFRendererVisitor");
 			
-			//String answer = null;
+			String answer = null;
 		     
 			try {
 				// Read parameters
@@ -546,18 +546,26 @@ public class OnlineAlign {
 				
 				// Create the SOAP message
 				String message = createMessage( params );
-				//globalMess = createMessage( globalParam );
-				//System.out.println("URL SOAP :"+ SOAPUrl + ",  Action:"+  SOAPAction);
-				//System.out.println("Message :" + message);
-				
-				// Send message
-				//answer = sendMessage( message, params );
-				
-				//the result is put in "globalAnswer"
-				sendMessageMonoThread( message, params );
+				 
+				answer = sendMessageMonoThread( message, params );
  				//if(! connected ) return null; 
 				
 			} catch ( Exception ex ) { ex.printStackTrace();  };
+			
+			Document domMessage = null;
+			try {
+			    domMessage = BUILDER.parse( new ByteArrayInputStream( answer.getBytes()) );
+			    
+			} catch  ( IOException ioex ) {
+			    ioex.printStackTrace();
+			} catch  ( SAXException saxex ) {
+			    saxex.printStackTrace();
+			}
+			
+ 			String result[] = getTagFromSOAP( domMessage,  "retrieveResponse/result/RDF" );
+ 			
+			return result[0];
+			
  		}
 	    
 	    public void getRDFAlignmentMonoThread(String alignId) {
@@ -907,8 +915,8 @@ public class OnlineAlign {
 	        
 	        		StringBuffer lineBuff =  new StringBuffer();
 	        		String line;
-	        		while ((line = in.readLine()) != null) {
-	        			lineBuff.append(line + "\n");
+	        		while ( (line = in.readLine()) != null) {
+	        			lineBuff.append( line + "\n");
 	        		}
 	        		if (in != null) 
 	        			in.close();