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 4181edb497b44da3b14afc5e970c81df8379e79a..44661bc5b50659a2d44ab8250d59dbbef48e4663 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
@@ -27,9 +27,16 @@ import java.io.IOException;
import java.io.PrintWriter;
import java.net.URI;
import java.util.Vector;
+import java.util.Enumeration;
+
+import org.omwg.mediation.parser.rdf.RDFParser;
+import org.omwg.mediation.parser.rdf.RDFParserException;
+//import javax.xml.parsers.SAXParser;
+//import javax.xml.parsers.SAXParserFactory;
import org.semanticweb.kaon2.api.formatting.OntologyFileFormat;
import org.semanticweb.owl.align.Alignment;
+import fr.inrialpes.exmo.align.impl.BasicAlignment;
import org.semanticweb.owl.align.AlignmentProcess;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.Parameters;
@@ -38,19 +45,29 @@ import com.ontoprise.ontostudio.io.ImportExportControl;
import fr.inrialpes.exmo.align.impl.BasicParameters;
import fr.inrialpes.exmo.align.impl.OntologyCache;
+import fr.inrialpes.exmo.align.parser.AlignmentParser;
import fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor;
import fr.inrialpes.exmo.align.impl.renderer.OWLAxiomsRendererVisitor;
+import fr.inrialpes.exmo.align.impl.renderer.RDFRendererVisitor;
public class OfflineAlign {
+ File alignFolder = null;
+ File ontoFolder = null;
+
+ public OfflineAlign(File on, File al) {
+ ontoFolder = on;
+ alignFolder = al;
+ }
+
String matchAndExportAlign (String method, String selectedNeOnOnto1, String selectedNeOnOnto2) {
//export ontologies
ImportExportControl ieControl = new ImportExportControl();
Integer name1 = new Integer(SWTInterface.alignId++);
Integer name2 = new Integer(SWTInterface.alignId++);
- File f1 = new File("onto-" + name1.toString() + ".owl");
- File f2 = new File("onto-" + name2.toString() + ".owl");
+ File f1 = new File( ontoFolder.getAbsolutePath() + ontoFolder.separator + name1.toString() + ".owl");
+ File f2 = new File( ontoFolder.getAbsolutePath() + ontoFolder.separator + name2.toString() + ".owl");
String fname1 = "file:" + f1.getAbsolutePath();
String fname2 = "file:" + f2.getAbsolutePath();
@@ -85,27 +102,32 @@ public class OfflineAlign {
A1 = (AlignmentProcess)alignmentConstructor.newInstance(mparams);
A1.init( (URI)uris.get(0), (URI)uris.get(1), (OntologyCache)null );
-
A1.align((Alignment)null,p);
- SWTInterface.alignObjects.clear();
- SWTInterface.alignObjects.add(A1);
+ //SWTInterface.alignObjects.clear();
+ SWTInterface.alignmentTable.put( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString(), (Alignment)A1 );
- //for exporting to NeonToolkit
-
- FileWriter owlF = new FileWriter(new File( "align-" + name.toString()+ ".owl" ));
+ // for saving locally
+ FileWriter rdfF = new FileWriter(new File( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString()+ ".rdf" ));
+ AlignmentVisitor rdfV = new RDFRendererVisitor( new PrintWriter ( rdfF ) );
+ A1.render(rdfV);
+ rdfF.close();
+
+ // for exporting to NeonToolkit
+ FileWriter owlF = new FileWriter(new File( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString()+ ".owl" ));
+
AlignmentVisitor V = new OWLAxiomsRendererVisitor( new PrintWriter ( owlF ) );
-
+
+
A1.render(V);
owlF.close();
-
- String str1 = fileToString(new File("align-" + name.toString()+ ".owl") );
+ String str1 = fileToString(new File(alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString()+ ".owl") );
//Add URI to OWL file : rethink !!!
- File f0 = new File( "align-" + name.toString()+ ".owl" );
+ File f0 = new File( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString()+ ".owl" );
String s1 = str1.substring(0, str1.indexOf('>') + 1 );
String s2 = str1.substring(str1.indexOf('>') + 2, str1.length());
@@ -122,19 +144,14 @@ public class OfflineAlign {
}
- File owlFile = new File( "align-" + name.toString()+ ".owl" );
+ File owlFile = new File( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString()+ ".owl" );
FileWriter out = new FileWriter( owlFile );
out.write( s3 + s2 );
//out.write( answer );
out.close();
-
-
-
- //String[] importedModules = ieControl.importFileSystem(proj, "align-" + name.toString()+ ".owl", null, null);
- //ieControl.addOntologies2Project(importedModules, proj);
//for displaying
- FileWriter htmlF = new FileWriter( "align.html" );
+ FileWriter htmlF = new FileWriter( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString() + ".html" );
AlignmentVisitor V1 = new HTMLRendererVisitor(
new PrintWriter ( htmlF ) );
@@ -143,39 +160,44 @@ public class OfflineAlign {
} catch ( Exception ex ) { ex.printStackTrace(); };
- return "align-" + name.toString()+ ".owl";
+ return alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString();
}
- String trimAndExportAlign (Double thres) {
+ String trimAndExportAlign (Double thres, String id) {
-
//String htmlString = null;
//Vector corrList = new Vector();
Integer name = new Integer(SWTInterface.alignId++);
- AlignmentProcess A1 = SWTInterface.alignObjects.get(0);
+ Alignment A1 = SWTInterface.alignmentTable.get( id );
+ Alignment clonedA1 = (BasicAlignment)((BasicAlignment)A1).clone();
try {
- A1.cut(thres);
- SWTInterface.alignObjects.clear();
- SWTInterface.alignObjects.add(A1);
+ clonedA1.cut(thres);
+ SWTInterface.alignmentTable.put( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString(), clonedA1 );
+ //SWTInterface.alignObjects.clear();
+ //SWTInterface.alignmentTable.put(A1);
+ FileWriter rdfF = new FileWriter(new File( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString()+ ".rdf" ));
+ AlignmentVisitor rdfV = new RDFRendererVisitor( new PrintWriter ( rdfF ) );
+ clonedA1.render(rdfV);
+ rdfF.close();
- FileWriter owlF = new FileWriter(new File( "align-" + name.toString()+ ".owl" ));
+ FileWriter owlF = new FileWriter(new File( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString()+ ".owl" ));
AlignmentVisitor V = new OWLAxiomsRendererVisitor( new PrintWriter ( owlF ) );
- A1.render(V);
+ clonedA1.render(V);
owlF.close();
- String str1 = fileToString(new File("align-" + name.toString()+ ".owl") );
+ String str1 = fileToString(new File( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString()+ ".owl") );
//Add URI to OWL file : rethink !!!
- File f0 = new File( "align-" + name.toString()+ ".owl" );
+ File f0 = new File( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString()+ ".owl" );
String s1 = str1.substring(0, str1.indexOf('>') + 1 );
String s2 = str1.substring(str1.indexOf('>') + 2, str1.length());
@@ -192,27 +214,69 @@ public class OfflineAlign {
}
- File owlFile = new File( "align-" + name.toString()+ ".owl" );
+ File owlFile = new File( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString()+ ".owl" );
FileWriter out = new FileWriter( owlFile );
out.write( s3 + s2 );
//out.write( answer );
out.close();
-
-
//for displaying
- FileWriter htmlF = new FileWriter( "align.html" );
+ FileWriter htmlF = new FileWriter( alignFolder.getAbsolutePath()+ ontoFolder.separator + name.toString()+ ".html" );
AlignmentVisitor V1 = new HTMLRendererVisitor(
new PrintWriter ( htmlF ) );
- A1.render(V1);
+ clonedA1.render(V1);
htmlF.close();
}
catch ( Exception ex ) { ex.printStackTrace();};
- return "align-" + name.toString()+ ".owl";
+ return alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString();
+ }
+
+ public String[] getAllAlign() {
+ //Enumeration ls = SWTInterface.alignmentTable.keys();
+ //getAllAlignFromFiles();
+ if (SWTInterface.alignmentTable.keys()==null) return null;
+ Vector<String> v = new Vector<String>();
+
+ for (Enumeration e = SWTInterface.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);
+
+ return ls;
+
+ }
+
+ public void getAllAlignFromFiles() {
+ //Enumeration ls = SWTInterface.alignmentTable.keys();
+ //if (SWTInterface.alignmentTable.keys()==null) return null;
+ 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 );
+
+ for(int i=0; i< v.size(); i++) {
+
+ String key = v.get(i).replace(".rdf", "");
+ System.out.println("Path ="+ alignFolder.getAbsolutePath() + alignFolder.separator + v.get(i) );
+ SWTInterface.alignmentTable.put( alignFolder.getAbsolutePath() + alignFolder.separator + key ,
+ parser.parse(alignFolder.getAbsolutePath() + alignFolder.separator + v.get(i)) );
+ }
+
+ } catch ( Exception ex ) { ex.printStackTrace();};
+
+ }
+
+
public static String fileToString(File f){
String texto = "";
diff --git a/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/OnlineAlign.java b/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/OnlineAlign.java
index b957bc4ba3249e880dfe25f2b911baf9c53a220d..905cb919d9d078bdc3b47d19ccb8c9f8bb296478 100755
--- a/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/OnlineAlign.java
+++ b/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/OnlineAlign.java
@@ -21,7 +21,7 @@
package fr.inrialpes.exmo.align.plugin.neontk;
import java.io.BufferedReader;
-
+import java.io.File;
import java.io.InputStreamReader;
import java.io.OutputStream;
import java.net.HttpURLConnection;
@@ -36,7 +36,6 @@ import org.semanticweb.owl.align.Parameters;
import fr.inrialpes.exmo.align.impl.BasicParameters;
-
public class OnlineAlign {
//public AlignmentClient ws = null;
@@ -46,6 +45,7 @@ public class OnlineAlign {
public boolean connected = false;
URL SOAPUrl = null;
String SOAPAction = null;
+ String uploadFile = null;
public OnlineAlign( String htmlPort, String host) {
@@ -75,6 +75,37 @@ public class OnlineAlign {
return conn;
}
*/
+
+ public String uploadAlign(String alignId) {
+
+ String answer = null;
+ try {
+ Parameters params = new BasicParameters();
+ params.setParameter( "host", HOST );
+ //params.setParameter( "http", PORT );
+ //params.setParameter( "wsdl", WSDL );
+ params.setParameter( "command","load");
+ //params.setParameter( "arg1", alignId);
+
+ uploadFile = alignId;
+
+
+ // Create the SOAP message
+ String message = createMessage( params );
+
+ System.out.println("HOST= :"+ HOST + ", PORT= " + PORT + ", Action = "+ SOAPAction);
+ System.out.println("Message :"+ message);
+
+ // Send message
+ answer = sendMessage( message, params );
+
+ System.out.println("Loaded Align="+ answer);
+
+ } catch ( Exception ex ) { ex.printStackTrace(); };
+ if(! connected ) return null;
+ return answer;
+ }
+
public String trimAlign(String alignId, String thres) {
String answer = null;
@@ -483,14 +514,19 @@ public class OnlineAlign {
SOAPAction = "loadRequest";
//usage();
//System.exit(-1);
+ /*
BufferedReader in = new BufferedReader(new InputStreamReader(System.in));
- String line;
- String content = "";
+ //String line;
+ //String content = "";
while ((line = in.readLine()) != null) {
content += line + "\n";
}
if (in != null) in.close();
System.err.println(content);
+ */
+
+ String content = OfflineAlign.fileToString(new File(uploadFile));
+
messageBody = "<content>"+content+"</content>";
} else {
SOAPAction = "loadfileRequest";
diff --git a/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/SWTInterface.java b/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/SWTInterface.java
index 6926e06666a7a560812559fffb60ef2306ece640..5b3caa8525f740132c1d550514e6fbbbb1b45839 100644
--- a/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/SWTInterface.java
+++ b/plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/SWTInterface.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA Rh�ne-Alpes, 2007-2008
+ * Copyright (C) INRIA Rh�ne-Alpes, 2007-2008
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -39,6 +39,7 @@ import java.awt.event.ItemEvent;
import java.awt.event.ActionEvent;
import java.util.Vector;
+import java.util.Hashtable;
//import java.io.PrintWriter;
//import javax.swing.*;
@@ -56,7 +57,8 @@ import javax.swing.JOptionPane;
import javax.swing.JScrollPane;
import javax.swing.BorderFactory;
-import org.semanticweb.owl.align.AlignmentProcess;
+//import org.semanticweb.owl.align.AlignmentProcess;
+import org.semanticweb.owl.align.Alignment;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
@@ -80,45 +82,46 @@ public class SWTInterface extends JPanel {
//private URL SOAPUrl = null;
//private String SOAPAction = null;
- JLabel hostName, portName, thresLabel, alignProjLabel;
+ JLabel hostName, portName;//, thresLabel;//, alignProjLabel;
//JComboBox hostList, portList;
String selectedHost = null;
String selectedPort = null;
-
String selectedOnto1 = null;
String selectedOnto2 = null;
String selectedAlign = null;
+ String selectedLocalAlign = null;
String selectedNeOnOnto1 = null;
String selectedNeOnOnto2 = null;
//String[] hostNames = new String[2];
//String[] ports = new String[2];
-
//int hostInd, portInd;
public static int alignId = 0;
- public static Vector<AlignmentProcess> alignObjects = new Vector<AlignmentProcess>();
+ public static Hashtable<String,Alignment> alignmentTable = new Hashtable<String,Alignment>();
+
+ //public static Vector<String> alignProjects = new Vector<String>();
//Procalign procalign = null;
//Parameters p = new BasicParameters();
public JComponent phrases, phrases1, Res=null;
- public JTextField fileName1, fileName2, threshold, hostField, portField, alignProj;
+ public JTextField fileName1, fileName2, hostField, portField; // threshold// alignProj;
public SWTInterface frame;
//public JFileChooser open;
//public JLabel explain;
public JPanel pane;
public JButton openbutton1, openbutton2, mapButton, resButton, ontoRefresh, allAlignButton,
- alignImportButton, alignTrimButton, alignFindButton, alignStoreButton,
- connButton, offlineButton, onlineButton, disconnButton ;
+ alignImportButton, localAlignImportButton, alignUploadButton, alignTrimButton, alignFindButton,
+ alignStoreButton, connButton, offlineButton, onlineButton, disconnButton ;
public JPanel pane2;
public Component result=null;
public JTextArea jan=null;
- JComboBox strategy, renderer, alignBox, ontoBox1, ontoBox2;
- JLabel strat, render, alignLabel, ontoLabel1, ontoLabel2;
+ JComboBox strategy, renderer, alignBox, localAlignBox, ontoBox1, ontoBox2;
+ JLabel strat, render, ontoLabel1, ontoLabel2, alignLabel, localAlignLabel;
//boolean autointerations=false, efficients=true;
//String aux_tres;
public String [] aux = new String[5];
@@ -131,9 +134,8 @@ public class SWTInterface extends JPanel {
public String [] ontoList = new String[0];
public String [] NeOnOntoList = new String[0];
public String [] alignIdList = new String[0];
- //public String [] alignList = null;
+ public String [] localAlignIdList = new String[0];
- //
public Vector corrList = new Vector();
public String [] aservArgs = null;
public String [] aservArgRetrieve = null;
@@ -153,103 +155,123 @@ public class SWTInterface extends JPanel {
public OnlineAlign onAlign = null;
public OfflineAlign offAlign = null;
-
+ public File ontoFolder = null;
+ public File alignFolder = null;
+
+ public void offlineInit(boolean init){
+ online = false;
+ offAlign = new OfflineAlign(ontoFolder, alignFolder);
+
+ ontoBox1.setEnabled(true);
+ ontoBox2.setEnabled(true);
+ ontoRefresh.setEnabled(true);
+ strategy.setEnabled(true);
+
+ mapButton.setEnabled(true);
+
+ localAlignBox.setEnabled(true);
+
+ onlineButton.setEnabled(true);
+
+ localAlignImportButton.setEnabled(true);
+ allAlignButton.setEnabled(true);
+
+ //threshold.setEnabled(true);
+ alignTrimButton.setEnabled(true);
+
+ //alignProject = alignProj.getText();
+ //alignProj.setEnabled(false);
+
+ alignFindButton.setEnabled(false);
+
+ alignImportButton.setEnabled(false);
+ alignUploadButton.setEnabled(false);
+
+ alignBox.setEnabled(false);
+ //alignRetrieveButton.setEnabled(false);
+ alignStoreButton.setEnabled(false);
+
+ offlineButton.setEnabled(false);
+ disconnButton.setEnabled(false);
+ hostField.setEnabled(false);
+ portField.setEnabled(false);
+ connButton.setEnabled(false);
+
+ strategy.removeAllItems();
+ alignBox.removeAllItems();
+ localAlignBox.removeAllItems();
+ ontoBox1.removeAllItems();
+ ontoBox2.removeAllItems();
+
+ ontoList = new String[0];
+ NeOnOntoList = new String[0];
+ alignIdList = new String[0];
+ //localAlignIdList = new String[0];
+
+ selectedOnto1 = null;
+ selectedOnto2 = null;
+ selectedAlign = null;
+ selectedNeOnOnto1 = null;
+ selectedNeOnOnto2 = null;
+
+ methodList = new String[9];
+ methodList[0] = "fr.inrialpes.exmo.align.impl.method.NameEqAlignment";
+ strategy.addItem(methodList[0]);
+ methodList[1] = "fr.inrialpes.exmo.align.impl.method.StringDistAlignment";
+ strategy.addItem(methodList[1]);
+ methodList[2] = "fr.inrialpes.exmo.align.impl.method.SMOANameAlignment";
+ strategy.addItem(methodList[2]);
+ methodList[3] = "fr.inrialpes.exmo.align.impl.method.SubsDistNameAlignment";
+ strategy.addItem(methodList[3]);
+ methodList[4] = "fr.inrialpes.exmo.align.impl.method.StrucSubsDistAlignment";
+ strategy.addItem(methodList[4]);
+ methodList[5] = "fr.inrialpes.exmo.align.impl.method.NameAndPropertyAlignment";
+ strategy.addItem(methodList[5]);
+ methodList[6] = "fr.inrialpes.exmo.align.impl.method.ClassStructAlignment";
+ strategy.addItem(methodList[6]);
+ methodList[7] = "fr.inrialpes.exmo.align.impl.method.EditDistNameAlignment";
+ strategy.addItem(methodList[7]);
+ methodList[8] = "fr.inrialpes.exmo.align.ling.JWNLAlignment";
+ strategy.addItem(methodList[8]);
+
+ if(init) offAlign.getAllAlignFromFiles();
+
+ String[] list = offAlign.getAllAlign();
+ if(list!=null) {
+ localAlignIdList = new String[list.length];
+ localAlignBox.removeAllItems();
+
+ for(int i=0; i< list.length; i++){
+ localAlignIdList[i]= list[i];
+ localAlignBox.addItem(list[i]);
+ }
+
+ if(localAlignIdList.length > 0) {
+ selectedLocalAlign = localAlignIdList[0];
+ }
+ }
+ //if ( localAlignIdList!= null )
+ //for(int i=0; i < localAlignIdList.length; i++) localAlignBox.addItem(i);
+ }
+
+
public void initialize() {
//selectedHost = "aserv.inrialpes.fr";
//selectedPort = "8089";
-
+ ontoFolder = new File("onto");
+ if (!ontoFolder.exists()) ontoFolder.mkdir();
+ alignFolder = new File("align");
+ if (!alignFolder.exists()) alignFolder.mkdir();
+
+ //System.out.println("alignFolder=" + alignFolder.getAbsolutePath());
+
offlineButton = new JButton("Offline",null);
offlineButton.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent e) {
if (e.getSource() == offlineButton) {
- online = false;
- offAlign = new OfflineAlign();
-
-
- ontoBox1.setEnabled(true);
- ontoBox2.setEnabled(true);
- ontoRefresh.setEnabled(true);
- strategy.setEnabled(true);
-
- mapButton.setEnabled(true);
- alignBox.setEnabled(true);
- onlineButton.setEnabled(true);
- alignImportButton.setEnabled(true);
-
- threshold.setEnabled(true);
- alignTrimButton.setEnabled(true);
-
- alignProject = alignProj.getText();
- alignProj.setEnabled(false);
-
- alignFindButton.setEnabled(false);
- allAlignButton.setEnabled(false);
-
- //alignRetrieveButton.setEnabled(false);
- alignStoreButton.setEnabled(false);
-
- offlineButton.setEnabled(false);
- disconnButton.setEnabled(false);
- hostField.setEnabled(false);
- portField.setEnabled(false);
- connButton.setEnabled(false);
-
- strategy.removeAllItems();
- alignBox.removeAllItems();
- ontoBox1.removeAllItems();
- ontoBox2.removeAllItems();
- ontoList = new String[0];
- NeOnOntoList = new String[0];
- alignIdList = new String[0];
-
-
- selectedOnto1 = null;
- selectedOnto2 = null;
- selectedAlign = null;
- selectedNeOnOnto1 = null;
- selectedNeOnOnto2 = null;
-
- methodList = new String[9];
- methodList[0] = "fr.inrialpes.exmo.align.impl.method.NameEqAlignment";
- strategy.addItem(methodList[0]);
- methodList[1] = "fr.inrialpes.exmo.align.impl.method.StringDistAlignment";
- strategy.addItem(methodList[1]);
- methodList[2] = "fr.inrialpes.exmo.align.impl.method.SMOANameAlignment";
- strategy.addItem(methodList[2]);
- methodList[3] = "fr.inrialpes.exmo.align.impl.method.SubsDistNameAlignment";
- strategy.addItem(methodList[3]);
- methodList[4] = "fr.inrialpes.exmo.align.impl.method.StrucSubsDistAlignment";
- strategy.addItem(methodList[4]);
- methodList[5] = "fr.inrialpes.exmo.align.impl.method.NameAndPropertyAlignment";
- strategy.addItem(methodList[5]);
- methodList[6] = "fr.inrialpes.exmo.align.impl.method.ClassStructAlignment";
- strategy.addItem(methodList[6]);
- methodList[7] = "fr.inrialpes.exmo.align.impl.method.EditDistNameAlignment";
- strategy.addItem(methodList[7]);
- methodList[8] = "fr.inrialpes.exmo.align.ling.JWNLAlignment";
- strategy.addItem(methodList[8]);
-
- alignObjects = new Vector<AlignmentProcess>();
-
- try {
-
- String[] projects = DatamodelPlugin.getDefault().getOntologyProjects();
- if(projects!=null) {
- boolean found = false;
-
- for(int i=0; i < projects.length; i++) {
- if(projects[i].equals(alignProject)) {
- found = true;break;
- }
- }
-
- if(!found)
- ProjectControl.getDefault().createNewOntologyProject(alignProject, new String[0]);
- }
- }
- catch ( Exception ex ) { ex.printStackTrace(); };
+ offlineInit(false);
}
@@ -262,11 +284,8 @@ public class SWTInterface extends JPanel {
if (e.getSource() == onlineButton) {
online = true;
-
- alignProject = alignProj.getText();
- alignProj.setEnabled(false);
-
-
+ //alignProject = alignProj.getText();
+ //alignProj.setEnabled(false);
offlineButton.setEnabled(true);
hostField.setEnabled(true);
@@ -278,10 +297,13 @@ public class SWTInterface extends JPanel {
ontoBox1.setEnabled(false);
ontoBox2.setEnabled(false);
alignBox.setEnabled(false);
+ localAlignBox.setEnabled(false);
alignImportButton.setEnabled(false);
+ localAlignImportButton.setEnabled(false);
+ alignUploadButton.setEnabled(false);
allAlignButton.setEnabled(false);
alignFindButton.setEnabled(false);
- threshold.setEnabled(false);
+ //threshold.setEnabled(false);
alignTrimButton.setEnabled(false);
//alignRetrieveButton.setEnabled(false);
@@ -307,7 +329,8 @@ public class SWTInterface extends JPanel {
selectedNeOnOnto1 = null;
selectedNeOnOnto2 = null;
- alignObjects.clear();
+ //alignObjects.clear();
+ //alignProjects = new Vector<String>();
}
@@ -329,6 +352,10 @@ public class SWTInterface extends JPanel {
ontoRefresh.setEnabled(false);
alignBox.setEnabled(false);
alignImportButton.setEnabled(false);
+
+ localAlignImportButton.setEnabled(false);
+ alignUploadButton.setEnabled(false);
+
alignFindButton.setEnabled(false);
alignTrimButton.setEnabled(false);
@@ -344,16 +371,18 @@ public class SWTInterface extends JPanel {
hostField.setEnabled(false);
portField.setEnabled(false);
connButton.setEnabled(false);
- threshold.setEnabled(false);
+ //threshold.setEnabled(false);
strategy.removeAllItems();
alignBox.removeAllItems();
+ localAlignBox.removeAllItems();
ontoBox1.removeAllItems();
ontoBox2.removeAllItems();
ontoList = new String[0];
NeOnOntoList = new String[0];
alignIdList = new String[0];
+ localAlignIdList = new String[0];
methodList = new String[0];
@@ -408,15 +437,15 @@ public class SWTInterface extends JPanel {
});
*/
- thresLabel = new JLabel("Threshold");
- threshold = new JTextField("1.0", 4);
- threshold.setEnabled(false);
- threshold.setEditable( true );
+ //thresLabel = new JLabel("Threshold");
+ //threshold = new JTextField("1.0", 4);
+ //threshold.setEnabled(false);
+ //threshold.setEditable( true );
- alignProjLabel = new JLabel("Alignment project name ");
- alignProj = new JTextField(alignProject, 10);
- alignProj.setEnabled(true);
- alignProj.setEditable( true );
+ //alignProjLabel = new JLabel("Alignment project name ");
+ //alignProj = new JTextField(alignProject, 10);
+ //alignProj.setEnabled(true);
+ //alignProj.setEditable( true );
connButton = new JButton("Connect",null);
connButton.setEnabled(false);
@@ -459,12 +488,15 @@ public class SWTInterface extends JPanel {
mapButton.setEnabled(true);
disconnButton.setEnabled(true);
alignBox.setEnabled(true);
+ localAlignBox.setEnabled(true);
alignImportButton.setEnabled(true);
+ localAlignImportButton.setEnabled(true);
+ alignUploadButton.setEnabled(true);
alignFindButton.setEnabled(true);
allAlignButton.setEnabled(true);
alignTrimButton.setEnabled(true);
- threshold.setEnabled(true);
+ //threshold.setEnabled(true);
//alignRetrieveButton.setEnabled(true);
alignStoreButton.setEnabled(true);
@@ -472,33 +504,14 @@ public class SWTInterface extends JPanel {
portField.setEnabled(false);
connButton.setEnabled(false);
-
- try {
-
- String[] projects = DatamodelPlugin.getDefault().getOntologyProjects();
- if(projects!=null) {
- boolean found = false;
-
- for(int i=0; i < projects.length; i++) {
- if(projects[i].equals(alignProject)) {
- found = true;break;
- }
- }
-
- if(!found)
- ProjectControl.getDefault().createNewOntologyProject(alignProject, new String[0]);
- }
-
-
- } catch ( Exception ex ) { ex.printStackTrace(); };
-
+
}//connect
}
};
});
- alignLabel = new JLabel("Alignments found : ");
+ alignLabel = new JLabel("Alignments from server");
alignBox = new JComboBox(alignIdList);
alignBox.setEnabled(false);
alignBox = new JComboBox(alignIdList);
@@ -518,14 +531,105 @@ public class SWTInterface extends JPanel {
}
});
- alignImportButton = new JButton("Export To Ontology Navigator",null);
+ localAlignLabel = new JLabel("Local alignments");
+ localAlignBox = new JComboBox(localAlignIdList);
+ localAlignBox.setEnabled(false);
+ localAlignBox = new JComboBox(localAlignIdList);
+ localAlignBox.setEnabled(false);
+
+ localAlignBox.setMaximumRowCount(20);
+ localAlignBox.addItemListener(new ItemListener() {
+ public void itemStateChanged(ItemEvent event)
+ {
+ int id = 0;
+ if (event.getStateChange()==ItemEvent.SELECTED)
+ id = localAlignBox.getSelectedIndex();
+
+ selectedLocalAlign = localAlignIdList[id];
+
+ System.out.println("Local align selected =" + selectedLocalAlign);
+ }
+ });
+
+ localAlignImportButton = new JButton("Export",null);
+ localAlignImportButton.setEnabled(false);
+ localAlignImportButton.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource() == localAlignImportButton) {
+ if(selectedLocalAlign == null)
+ JOptionPane.showMessageDialog(null, "Choose an alignment ID from list!","Warning",2);
+
+ File fn = new File(selectedLocalAlign + ".owl");
+ //System.out.println("file name off to export :"+ fn.getName());
+ String inputName=null;
+
+ try {
+
+ do {
+ inputName = JOptionPane.showInputDialog(null, "Enter a project name", "AlignmentProject");
+ }
+ while (inputName==null || inputName.equals(""));
+
+ String[] projects = DatamodelPlugin.getDefault().getOntologyProjects();
+ if(projects!=null) {
+ boolean found = false;
+
+ for(int i=0; i < projects.length; i++) {
+
+ if(projects[i].equals(inputName)) {
+ found = true;break;
+ }
+ }
+
+ if(!found)
+ ProjectControl.getDefault().createNewOntologyProject(inputName, new String[0]);
+ }
+
+ ImportExportControl ieControl = new ImportExportControl();
+
+ String[] importedModules = ieControl.importFileSystem(inputName, fn.getAbsolutePath(), null, null);
+ ieControl.addOntologies2Project(importedModules, inputName);
+ }
+ catch ( Exception ex ) { ex.printStackTrace();};
+
+
+ }//choose an align
+
+
+ }
+ });
+
+ alignUploadButton = new JButton("Upload",null);
+ alignUploadButton.setEnabled(false);
+ alignUploadButton.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource() == alignUploadButton) {
+ if(selectedLocalAlign == null)
+ JOptionPane.showMessageDialog(null, "Choose an alignment ID from list!","Warning",2);
+ else {
+
+ //File fn = new File( selectedLocalAlign + ".rdf" );
+ //System.out.println("file name off to export :"+ fn.getName());
+
+ try {
+ onAlign.uploadAlign(selectedLocalAlign + ".rdf");
+
+ localAlignIdList = new String[1];
+ localAlignIdList[0] = selectedLocalAlign;
+ localAlignBox.removeAllItems();
+ localAlignBox.addItem(selectedLocalAlign);
+
+ } catch ( Exception ex ) { ex.printStackTrace();}
+ }
+ }
+ }
+ });
+
+ alignImportButton = new JButton("Export",null);
alignImportButton.setEnabled(false);
alignImportButton.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent e) {
if (e.getSource() == alignImportButton) {
- if(selectedAlign == null)
- JOptionPane.showMessageDialog(null, "Choose an alignment ID from list!","Warning",2);
- else {
//the name is originated from the server with slash
String [] sali = selectedAlign.split("/");
@@ -533,46 +637,58 @@ public class SWTInterface extends JPanel {
if(online) {
+ if(selectedAlign == null)
+ JOptionPane.showMessageDialog(null, "Choose an alignment ID from list!","Warning",2);
+ else {
+
String owlalignStr = onAlign.getOWLAlignment( selectedAlign );
if(owlalignStr==null) JOptionPane.showMessageDialog(null, "Alignment can not be exported.","Warning",2);
else {
- //extract id from "alid"
-
- //Store it
+ String inputName = null;
+ //Store it
FileWriter out = null;
-
try {
- File owlFile = new File( uniqueId + ".owl");
- out = new FileWriter( owlFile );
- out.write( owlalignStr );
+ do {
+ inputName = JOptionPane.showInputDialog(null, "Enter a project name", "AlignmentProject");
+ }
+ while (inputName==null || inputName.equals(""));
+
+ String[] projects = DatamodelPlugin.getDefault().getOntologyProjects();
+ if(projects!=null) {
+ boolean found = false;
+
+ for(int i=0; i < projects.length; i++) {
+
+ if(projects[i].equals(inputName)) {
+ found = true;break;
+ }
+
+ }
+
+ if(!found)
+ ProjectControl.getDefault().createNewOntologyProject(inputName, new String[0]);
+ }
+
+ File owlFile = new File( uniqueId + ".owl");
+ out = new FileWriter( owlFile );
+ out.write( owlalignStr );
//out.write( answer );
- out.close();
+ out.close();
//Redo : Have to create a list of imported alig. ontos
//System.out.println("file name on to export :"+ uniqueId + ".owl");
- ImportExportControl ieControl = new ImportExportControl();
- String[] importedModules = ieControl.importFileSystem(alignProject, uniqueId + ".owl", null, null);
- ieControl.addOntologies2Project(importedModules, alignProject);
+ ImportExportControl ieControl = new ImportExportControl();
+ String[] importedModules = ieControl.importFileSystem(inputName, uniqueId + ".owl", null, null);
+ ieControl.addOntologies2Project(importedModules, inputName);
}
catch ( Exception ex ) { ex.printStackTrace();};
}
}
- else { //offline
-
- File fn = new File(selectedAlign);
- //System.out.println("file name off to export :"+ fn.getName());
- try{
- ImportExportControl ieControl = new ImportExportControl();
- String[] importedModules = ieControl.importFileSystem(alignProject, fn.getName(), null, null);
- ieControl.addOntologies2Project(importedModules, alignProject);
- }
- catch ( Exception ex ) { ex.printStackTrace();};
-
}
- }//choose an align
+
}
};
});
@@ -585,26 +701,44 @@ public class SWTInterface extends JPanel {
// for connecting to server
//onAlign = new OnlineAlign(selectedPort, selectedHost);
- String aa = onAlign.getAllAlign();
- if(aa == null)
- JOptionPane.showMessageDialog(null, "Impossible connection!","Warning",2);
- else {
- String[] list = getResultsFromAnswer( aa , "alid", null );
+ if(online) {
+ String aa = onAlign.getAllAlign();
+ if(aa == null)
+ JOptionPane.showMessageDialog(null, "Impossible connection!","Warning",2);
+ else {
+ String[] list = getResultsFromAnswer( aa , "alid", null );
- alignIdList = new String[list.length];
- alignBox.removeAllItems();
+ alignIdList = new String[list.length];
+ alignBox.removeAllItems();
- for(int i=0; i< list.length; i++){
- alignIdList[i]= list[i];
- alignBox.addItem(list[i]);
- }
+ for(int i=0; i< list.length; i++){
+ alignIdList[i]= list[i];
+ alignBox.addItem(list[i]);
+ }
- if(alignIdList.length > 0) {
- selectedAlign = alignIdList[0];
- }
+ if(alignIdList.length > 0) {
+ selectedAlign = alignIdList[0];
+ }
- }
- }
+ }
+ }
+ else { //offline
+ String[] list = offAlign.getAllAlign( );
+ if(list!=null) {
+ localAlignIdList = new String[list.length];
+ localAlignBox.removeAllItems();
+
+ for(int i=0; i< list.length; i++){
+ localAlignIdList[i]= list[i];
+ localAlignBox.addItem(list[i]);
+ }
+
+ if(localAlignIdList.length > 0) {
+ selectedLocalAlign = localAlignIdList[0];
+ }
+ }
+ }
+ }
};
});
@@ -651,13 +785,19 @@ public class SWTInterface extends JPanel {
public void actionPerformed(ActionEvent e) {
if (e.getSource() == alignTrimButton) {
- if(selectedAlign == null )
- JOptionPane.showMessageDialog(null, "Choose an alignment ID from list!","Warning",2);
- else {
- if(online) {
+ if(online) {
//onAlign = new OnlineAlign(selectedPort, selectedHost);
-
- String at = onAlign.trimAlign(selectedAlign, threshold.getText());
+ if(selectedAlign == null )
+ JOptionPane.showMessageDialog(null, "Choose an alignment ID from list!","Warning",2);
+ else {
+ String thres = null;
+ do {
+ thres = JOptionPane.showInputDialog(null, "Enter a threshold ", "0.5");
+ }
+ while (thres==null || thres.equals(""));
+
+ String at = onAlign.trimAlign(selectedAlign, thres);
+
if(at == null)
JOptionPane.showMessageDialog(null, "Impossible connection!","Warning",2);
else {
@@ -676,34 +816,41 @@ public class SWTInterface extends JPanel {
}
}
}
- else { //offline
- String resId = offAlign.trimAndExportAlign( new Double(threshold.getText()) );
+ }
+ else { //offline
+ if(selectedLocalAlign == null )
+ JOptionPane.showMessageDialog(null, "Choose an alignment ID from list!","Warning",2);
+ else {
+ String thres = null;
+ do {
+ thres = JOptionPane.showInputDialog(null, "Enter a threshold ", "0.5");
+ }
+ while (thres==null || thres.equals(""));
+
+ String resId = offAlign.trimAndExportAlign( new Double(thres), selectedLocalAlign );
+ localAlignBox.removeAllItems();
+ localAlignIdList = new String[1];
- alignBox.removeAllItems();
- alignIdList = new String[1];
+ localAlignIdList[0] = resId;
- File f1 = new File(resId);
- alignIdList[0] = "file:" + f1.getAbsolutePath();
-
- alignBox.addItem(alignIdList[0]);
+ localAlignBox.addItem( resId );
- selectedAlign = alignIdList[0];
+ selectedLocalAlign = localAlignIdList[0];
}
}
}
};
});
-
-
+ //store an alignment on server or locally
alignStoreButton = new JButton("Store an alignment in the server", null);
alignStoreButton.setEnabled(false);
alignStoreButton.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent e) {
if (e.getSource() == alignStoreButton) {
- // for connecting to server
+ //for connecting to server
//onAlign = new OnlineAlign(selectedPort, selectedHost);
if(selectedAlign == null )
JOptionPane.showMessageDialog(null, "Choose an alignment ID from list!","Warning",2);
@@ -713,8 +860,6 @@ public class SWTInterface extends JPanel {
if(sto == null)
JOptionPane.showMessageDialog(null, "Impossible connection!","Warning",2);
-
-
}
}
@@ -740,10 +885,10 @@ public class SWTInterface extends JPanel {
public void actionPerformed(ActionEvent e) {
if (e.getSource() == mapButton) {
if (selectedNeOnOnto1 == null || selectedNeOnOnto2 == null )
- {JOptionPane.showMessageDialog(null, "Choose two ontologies from lists ","Warning",2);}
+ {JOptionPane.showMessageDialog(null, "Choose two ontologies from lists ","Warning",2);
+ }
else {
-
if(online) {
String answer = onAlign.getAlignId( matchMethod, selectedOnto1, selectedOnto2 );
@@ -797,18 +942,17 @@ public class SWTInterface extends JPanel {
String resId = offAlign.matchAndExportAlign( matchMethod, selectedNeOnOnto1, selectedNeOnOnto2);
+ localAlignBox.removeAllItems();
+ localAlignIdList = new String[1];
- alignBox.removeAllItems();
- alignIdList = new String[1];
-
- File f1 = new File(resId);
- alignIdList[0] = "file:" + f1.getAbsolutePath();
+ //File f1 = new File(resId);
+ localAlignIdList[0] = resId;//"file:" + f1.getAbsolutePath();
- alignBox.addItem(alignIdList[0]);
+ localAlignBox.addItem(localAlignIdList[0]);
- selectedAlign = alignIdList[0];
+ selectedLocalAlign = localAlignIdList[0];
- String htmlString = OfflineAlign.fileToString(new File ("align.html"));
+ String htmlString = OfflineAlign.fileToString(new File ( resId + ".html"));
System.out.println("htmlString =" + htmlString);
@@ -818,7 +962,7 @@ public class SWTInterface extends JPanel {
pane2.removeAll();
- for(int i=0;i< corrList.size();i++) {
+ for(int i=0;i< corrList.size();i++) {
String[] li= (String [])corrList.get(i);
String n = "";
for(int j=0;j<li.length;j++)
@@ -837,7 +981,7 @@ public class SWTInterface extends JPanel {
}
- } // else for ""offline"
+ } //else for ""offline"
}
}
};
@@ -901,7 +1045,6 @@ public class SWTInterface extends JPanel {
}
});
-
setLayout (new BorderLayout());
add (new JLabel ("Computing and managing ontology alignments"), BorderLayout.NORTH);
createFirstPane();//
@@ -922,6 +1065,9 @@ public class SWTInterface extends JPanel {
add(_mainSplitter,BorderLayout.CENTER); //Main Window of the Plugin
+ //offline is default mode
+ offlineInit(true);
+
}
public void createFirstPane () {
@@ -941,6 +1087,7 @@ private JPanel createPhraseList () {
JPanel twoLabel = new JPanel (new FlowLayout(10));
JPanel threeLabel = new JPanel (new FlowLayout(10));
JPanel fourLabel = new JPanel (new FlowLayout(10));
+ JPanel four2Label = new JPanel (new FlowLayout(10));
JPanel fiveLabel = new JPanel (new FlowLayout(10));
JPanel sixLabel = new JPanel (new FlowLayout(10));
//JPanel sevenLabel = new JPanel (new FlowLayout(10));
@@ -949,8 +1096,8 @@ private JPanel createPhraseList () {
minusLabel.add(onlineButton);
minusLabel.add(offlineButton);
- minusLabel.add(alignProjLabel);
- minusLabel.add(alignProj);
+ //minusLabel.add(alignProjLabel);
+ //minusLabel.add(alignProj);
zeroLabel.add(hostName);
@@ -981,8 +1128,13 @@ private JPanel createPhraseList () {
fourLabel.add(alignBox);
fourLabel.add(alignImportButton);
- sixLabel.add(thresLabel);
- sixLabel.add(threshold);
+ four2Label.add(localAlignLabel);
+ four2Label.add(localAlignBox);
+ four2Label.add(localAlignImportButton);
+ four2Label.add(alignUploadButton);
+
+ //sixLabel.add(thresLabel);
+ //sixLabel.add(threshold);
sixLabel.add(alignTrimButton);
fiveLabel.add(alignFindButton);
@@ -999,12 +1151,15 @@ private JPanel createPhraseList () {
phrasePane.add(twoLabel);
phrasePane.add(threeLabel);
phrasePane.add(fourLabel);
+ phrasePane.add(four2Label);
+ phrasePane.add(nineLabel);
+
phrasePane.add(sixLabel);
phrasePane.add(fiveLabel);
//phrasePane.add(sevenLabel);
phrasePane.add(eightLabel);
- phrasePane.add(nineLabel);
+
return phrasePane;
@@ -1023,7 +1178,6 @@ return pane2;
}
-
private void refreshOntoList() {
Vector<String> vec = new Vector<String>();
@@ -1032,13 +1186,15 @@ private void refreshOntoList() {
String[] projects = DatamodelPlugin.getDefault().getOntologyProjects();
for(int i=0; i < projects.length; i++) {
- if( ! projects[i].equals(alignProject)) {
- NeOnOntoList = DatamodelPlugin.getDefault().getProjectOntologies(projects[i]);
- for(int j=0; j < NeOnOntoList.length; j++) {
- //System.out.printf("Project Onto = " + NeOnOntoList[j] );
- vec.add(NeOnOntoList[j]);
- }
- }
+ //for(int j=0; j < alignProjects.size(); j++) {
+ // if( ! projects[i].equals( alignProjects.get(j)) ) {
+ NeOnOntoList = DatamodelPlugin.getDefault().getProjectOntologies(projects[i]);
+ for(int k=0; k < NeOnOntoList.length; k++) {
+ //System.out.printf("Project Onto = " + NeOnOntoList[j] );
+ vec.add(NeOnOntoList[k]);
+ }
+ //}
+ //}
}
} catch ( Exception ex ) { ex.printStackTrace();};