From 2a1c871b63299dfc79fc3505a3b72d8eccaa75dd Mon Sep 17 00:00:00 2001
From: Chan Le Duc <chan.leduc@univ-paris13.fr>
Date: Tue, 5 May 2009 08:27:33 +0000
Subject: [PATCH] --Improved data transfer from server
---
.../exmo/align/plugin/neontk/OnlineAlign.java | 280 ++++++++++++++++--
.../align/plugin/neontk/SWTInterface.java | 91 ++++--
2 files changed, 319 insertions(+), 52 deletions(-)
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 3f59907f..6eee68d6 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
@@ -28,8 +28,13 @@ import java.io.FileInputStream;
//import java.io.FileWriter;
import java.io.IOException;
//import java.io.InputStream;
+import java.io.FileReader;
+import java.io.FileWriter;
import java.io.InputStreamReader;
+import java.io.BufferedOutputStream;
import java.io.ByteArrayInputStream;
+import java.io.PrintWriter;
+import java.io.StringWriter;
//mport javax.swing.JOptionPane;
import javax.swing.ProgressMonitorInputStream;
@@ -46,6 +51,7 @@ import java.net.HttpURLConnection;
import java.net.URL;
import java.net.URLConnection;
+import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.Parameters;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
@@ -65,7 +71,11 @@ import javax.xml.transform.OutputKeys;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
+import fr.inrialpes.exmo.align.impl.BasicAlignment;
import fr.inrialpes.exmo.align.impl.BasicParameters;
+import fr.inrialpes.exmo.align.impl.renderer.RDFRendererVisitor;
+import fr.inrialpes.exmo.align.parser.AlignmentParser;
+import org.semanticweb.owl.align.AlignmentException;
public class OnlineAlign {
@@ -127,7 +137,7 @@ public class OnlineAlign {
//System.out.println("SOAP loaded align=" + answer );
} catch ( Exception ex ) { ex.printStackTrace(); };
- if(! connected ) return null;
+ //if(! connected ) return null;
Document domMessage = null;
try {
@@ -168,12 +178,13 @@ public class OnlineAlign {
//System.out.println("Message :"+ message);
// Send message
+ System.out.println("Trim Message="+ message);
answer = sendMessage( message, params );
-
+ System.out.println("Trim Align="+ answer);
}
catch ( Exception ex ) { ex.printStackTrace(); };
- if(! connected ) return null;
+ //if(! connected ) return null;
Document domMessage = null;
try {
@@ -216,7 +227,7 @@ public class OnlineAlign {
answer = sendMessage( message, params );
}
catch ( Exception ex ) { ex.printStackTrace(); };
- if(! connected ) return null;
+ //if(! connected ) return null;
Document domMessage = null;
try {
@@ -259,7 +270,7 @@ public class OnlineAlign {
//System.out.println("answer find=" + answer);
}
catch ( Exception ex ) { ex.printStackTrace(); };
- if(!connected ) return null;
+ //if(!connected ) return null;
Document domMessage = null;
try {
@@ -304,7 +315,7 @@ public class OnlineAlign {
}
catch ( Exception ex ) { ex.printStackTrace(); };
- if(! connected ) return null;
+ //if(! connected ) return null;
// Cut SOAP header
//answer = "<?xml version='1.0' encoding='utf-8' standalone='no'?>" + answer ;
@@ -324,6 +335,57 @@ public class OnlineAlign {
}
+ //Used without ProgressBar
+ public String getAlignIdMonoThread(String method, String wserver, String wsmethod, String onto1, String onto2) {
+
+ String answer = null ;
+
+ Parameters params = new BasicParameters();
+ params.setParameter( "host", HOST );
+ params.setParameter( "command","match");
+ params.setParameter( "arg1", method);
+ params.setParameter( "arg2", onto1);
+ params.setParameter( "arg3", onto2);
+ params.setParameter( "arg4", wserver);
+ if(wsmethod != null )
+ params.setParameter( "arg5", wsmethod);
+
+ try {
+ // Read parameters
+ // Create the SOAP message
+ String message = createMessage( params );
+
+ // Send message
+ answer = sendMessageMonoThread( message, params );
+
+ //System.out.println("SOAP Match align=" + answer );
+
+ }
+
+ catch ( Exception ex ) { ex.printStackTrace(); };
+ //if(! connected ) return null;
+
+ // Cut SOAP header
+ //answer = "<?xml version='1.0' encoding='utf-8' standalone='no'?>" + answer ;
+ 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, "matchResponse" );
+
+ //System.out.println("Match align Id=" + result[0]);
+
+ return result[0];
+
+ }
+
public void getAlignId(String method, String wserver, String wsmethod, String onto1, String onto2 ) {
@@ -420,7 +482,7 @@ public class OnlineAlign {
// Send message
answer = sendMessage( message, params );
- if(! connected ) return null;
+ //if(! connected ) return null;
} catch ( Exception ex ) { ex.printStackTrace(); };
@@ -497,7 +559,57 @@ public class OnlineAlign {
} catch ( Exception ex ) { ex.printStackTrace(); };
}
-
+ public void getRDFAlignmentMonoThread(String alignId) {
+
+ //retrieve alignment for storing in OWL file
+
+
+ Parameters params = new BasicParameters();
+ params.setParameter( "host", HOST );
+ //params.setParameter( "http", PORT );
+ //params.setParameter( "wsdl", WSDL );
+ params.setParameter( "command","retrieve");
+ params.setParameter( "arg1", alignId);
+ params.setParameter( "arg2", "fr.inrialpes.exmo.align.impl.renderer.RDFRendererVisitor" );
+
+ String answer=null;
+
+ try {
+ // Read parameters
+ //Parameters params = ws.readParameters( aservArgRetrieve );
+
+ // Create the SOAP message
+ String message = createMessage( params );
+
+ //System.out.println("URL SOAP :"+ SOAPUrl + ", Action:"+ SOAPAction);
+ //System.out.println("Message :" + message);
+
+ // Send message
+ answer = sendMessageMonoThread( message, params );
+
+
+ } 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" );
+
+ globalAnswer = result[0];
+ */
+ globalAnswer = answer;
+
+ //return result[0];
+ }
public String storeAlign(String alignId) {
@@ -530,7 +642,7 @@ public class OnlineAlign {
}
catch ( Exception ex ) { ex.printStackTrace() ;};
- if(! connected ) return null;
+ //if(! connected ) return null;
Document domMessage = null;
try {
@@ -759,6 +871,96 @@ public class OnlineAlign {
return message;
}
+ public String sendMessageMonoThread( String message, Parameters param ) {
+ // Create the connection
+
+ byte[] b = message.getBytes();
+
+ String answer = "";
+ // Create HTTP Request
+ try {
+
+ URLConnection connection = SOAPUrl.openConnection();
+ HttpURLConnection httpConn = (HttpURLConnection) connection;
+
+ httpConn.setRequestProperty( "Content-Length",
+ String.valueOf( b.length ) );
+ httpConn.setRequestProperty("Content-Type","text/xml; charset=utf-8");
+
+
+ httpConn.setRequestProperty("SOAPAction",SOAPAction);
+ httpConn.setRequestMethod( "POST" );
+ httpConn.setDoOutput(true);
+ httpConn.setDoInput(true);
+
+ // Send the request through the connection
+ OutputStream out = httpConn.getOutputStream();
+
+ out.write( b );
+ out.close( );
+
+ if( param.getParameter("command").equals("retrieve") ) {
+ /*
+ try {
+
+ AlignmentParser parser = new AlignmentParser( 0 );
+ parser.initAlignment( null );
+ parser.setEmbedded( true );
+ BasicAlignment clonedA1 = (BasicAlignment) parser.parse( httpConn.getInputStream() );
+
+ StringWriter sw = new StringWriter();
+ AlignmentVisitor rdfV = new RDFRendererVisitor( new PrintWriter ( sw ) );
+ clonedA1.render( rdfV );
+ answer = sw.toString();
+
+
+ } catch (SAXException saxex) {
+ throw new AlignmentException( "Malformed XML/SOAP result ("+saxex.getMessage()+")", saxex );
+ } catch (IOException ioex) {
+ throw new AlignmentException( "XML/SOAP parsing error", ioex );
+ } catch (javax.xml.parsers.ParserConfigurationException pcex) {
+ throw new AlignmentException( "XML/SOAP parsing error", pcex );
+ }
+
+ System.out.println("RDF=" + answer );
+ */
+ InputStreamReader isr = new InputStreamReader(httpConn.getInputStream());
+ BufferedReader in = new BufferedReader(isr);
+
+ StringBuffer lineBuff = new StringBuffer();
+ String line;
+ while ((line = in.readLine()) != null) {
+ lineBuff.append(line + "\n");
+ }
+ if (in != null)
+ in.close();
+ answer = lineBuff.toString();
+
+ //System.out.println("RDF=" + answer );
+ }
+ else {
+ // Read the response and write it to standard output
+ InputStreamReader isr = new InputStreamReader(httpConn.getInputStream());
+ BufferedReader in = new BufferedReader(isr);
+
+ String line;
+ while ((line = in.readLine()) != null) {
+ answer += line + "\n";
+ }
+ if (in != null)
+ in.close();
+
+ if(httpConn.HTTP_REQ_TOO_LONG == httpConn.getResponseCode()) System.err.println("Request too long");
+ }
+
+
+ } catch (Exception ex) {
+ connected= false; ex.printStackTrace() ; return null;
+ }
+
+ return answer;
+ }
+
public String sendMessage( String message, Parameters param ) {
// Create the connection
@@ -790,6 +992,8 @@ public class OnlineAlign {
if( param.getParameter("command").equals("match") ) {
globalAnswer = "";
+
+
Thread th = new Thread() {
public void run() {
@@ -803,14 +1007,15 @@ public class OnlineAlign {
BufferedReader in = new BufferedReader(isr);
String line;
- String alignRes = "";
-
+ //String alignRes = "";
+ StringBuffer strBuff = new StringBuffer();
while ((line = in.readLine()) != null) {
- alignRes += line + "\n";
+ //alignRes += line + "\n";
+ strBuff.append(line + "\n");
}
- String alignId = getAlignIdParsed( alignRes );
-
+ //String alignId = getAlignIdParsed( alignRes );
+ String alignId = getAlignIdParsed( strBuff.toString() );
if(alignId == null || alignId.equals("")) {
JOptionPane.showMessageDialog(null, "Alignment is not produced.","Warning",2);
SWTInterface.set3Buttons();
@@ -863,9 +1068,10 @@ public class OnlineAlign {
//String line;
int co = 0;
-
+ StringBuffer strBuff2 = new StringBuffer();
while ((line = in2.readLine()) != null) {
- globalAnswer += line + "\n";
+ strBuff2.append( line + "\n");
+ //globalAnswer += line + "\n";
co += line.length();
pm.setNote(co + " bytes read.");
if( co >= maxSize -10000 ) {
@@ -874,6 +1080,7 @@ public class OnlineAlign {
pm.setProgress( co );
}
}
+ globalAnswer = strBuff2.toString();
SWTInterface.resetActionButtons( true );
@@ -885,8 +1092,7 @@ public class OnlineAlign {
SWTInterface.set3Buttons();
}
e.printStackTrace();
- }
-
+ }
}
};
@@ -916,9 +1122,11 @@ public class OnlineAlign {
String line;
int co = 0;
- //int coL = 0;
+ StringBuffer strBuff3 = new StringBuffer();
+
while ((line = in.readLine()) != null) {
- globalAnswer += line + "\n";
+ //globalAnswer += line + "\n";
+ strBuff3.append( line + "\n" );
co += line.length();
pm.setNote(co + " bytes read.");
if( co >= maxSize -10000 ) {
@@ -927,7 +1135,7 @@ public class OnlineAlign {
pm.setProgress( co );
}
}
-
+ globalAnswer = strBuff3.toString();
SWTInterface.resetActionButtons( true );
pm.setProgress( maxSize - 1 );
@@ -949,10 +1157,12 @@ public class OnlineAlign {
InputStreamReader isr = new InputStreamReader( httpConn.getInputStream() );
BufferedReader in = new BufferedReader( isr );
String line;
+ StringBuffer strBuff4 = new StringBuffer();
while ((line = in.readLine()) != null) {
- answer += line + "\n";
+ strBuff4.append( line + "\n" );
+ //answer += line + "\n";
}
-
+ answer = strBuff4.toString();
in.close();
}
//System.out.println("answer= " + answer);
@@ -1047,4 +1257,28 @@ public class OnlineAlign {
return answer;
}
+ public static String fileToString(File f){
+ String texto = "";
+ StringBuffer toto = new StringBuffer();
+ int i=0;
+ try{
+
+ FileReader rd = new FileReader(f);
+ i = rd.read();
+
+ while(i!=-1){
+ //texto = texto+(char)i;
+ toto.append((char)i);
+ i = rd.read();
+ }
+
+ } catch(IOException e){
+ System.err.println(e.getMessage());
+ }
+
+ return toto.toString();
+ }
+
+
+
}
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 0118924c..455f1a0b 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
@@ -155,7 +155,7 @@ public class SWTInterface extends JPanel {
public static Hashtable<String,Alignment> alignmentTable = new Hashtable<String,Alignment>();
static String [] forUniqueness = new String[0];
static int alignId = 0;
-
+
JComponent phrases;
JTextField fileName1, fileName2, hostField, portField, serverField, methodField;
@@ -163,11 +163,11 @@ public class SWTInterface extends JPanel {
JEditorPane htmlView;
- JButton cancelButton, discardButton, fetchButton, resButton, ontoRefresh,
+ JButton cancelButton, discardButton, resButton, ontoRefresh,
localAlignImportButton, alignUploadButton,
localAlignTrimButton, connButton, goButton, offlineButton, onlineButton;
- static JButton alignStoreButton, alignImportButton, serverAlignTrimButton, mapButton, alignFindButton, allAlignButton;
+ static JButton alignStoreButton, alignImportButton, serverAlignTrimButton, mapButton, alignFindButton, allAlignButton, fetchButton;
JDialog connDialog, matchDialog;
//JPanel pane2;
@@ -212,11 +212,8 @@ public class SWTInterface extends JPanel {
public File ontoFolder = null;
public File alignFolder = null;
public static File basicFolder = null;
- public Frame rootFrame;
- //public SWTInterface(Frame f) {
- //It is needed
- // rootFrame = f;
- //}
+
+
public void offlineInit(boolean init){
//OntologyFactory.setDefaultFactory("fr.inrialpes.exmo.align.onto.owlapi2.OWLAPI2OntologyFactory");
online = false;
@@ -349,9 +346,9 @@ public class SWTInterface extends JPanel {
alignImportButton.setEnabled( flag );
alignStoreButton.setEnabled( flag );
serverAlignTrimButton.setEnabled( flag );
- mapButton.setEnabled( flag );
- alignFindButton.setEnabled( flag );
- allAlignButton.setEnabled( flag );
+ //mapButton.setEnabled( flag );
+ //alignFindButton.setEnabled( flag );
+ //allAlignButton.setEnabled( flag );
}
@@ -361,6 +358,17 @@ public class SWTInterface extends JPanel {
allAlignButton.setEnabled( true );
}
+ public static void setFetchButton( boolean flag) {
+ fetchButton.setEnabled( flag );
+ //alignFindButton.setEnabled( flag );
+ //allAlignButton.setEnabled( flag );
+ alignImportButton.setEnabled( !flag );
+ alignStoreButton.setEnabled( !flag );
+ serverAlignTrimButton.setEnabled( !flag );
+ }
+
+
+
public void initialize() {
//selectedHost = "aserv.inrialpes.fr";
@@ -688,12 +696,22 @@ public class SWTInterface extends JPanel {
JOptionPane.showMessageDialog(null, "Choose an alignment ID from list!","Warning",2);
return;
}
-
+ /*
alignIdList = new String[1];
alignIdList[0] = selectedAlign;
alignBox.removeAllItems();
alignBox.addItem(selectedAlign);
onAlign.getRDFAlignment( selectedAlign );
+ */
+
+ JOptionPane.showMessageDialog(null, "This operation may take a while.","Warning",2);
+ alignIdList = new String[1];
+ alignIdList[0] = selectedAlign;
+ alignBox.removeAllItems();
+ alignBox.addItem(selectedAlign);
+ onAlign.getRDFAlignmentMonoThread( selectedAlign );
+ setFetchButton( false );
+
}
};
});
@@ -726,7 +744,7 @@ public class SWTInterface extends JPanel {
alignIdList = new String[1];
alignIdList[0] = selectedAlign;
alignBox.removeAllItems();
- alignBox.addItem(alignIdList[0]);
+ alignBox.addItem( alignIdList[0] );
String rdfPath = alignKey + ".rdf";
@@ -736,8 +754,7 @@ public class SWTInterface extends JPanel {
try {
File rdfFile = new File( rdfPath );
- //if (rdfFile.exists()) rdfFile.delete();
-
+
out = new FileWriter( rdfFile );
out.write( rdfalignStr );
out.flush();
@@ -753,7 +770,7 @@ public class SWTInterface extends JPanel {
String[] list = offAlign.getAllAlign( );
- if(list!=null) {
+ if(list != null) {
localAlignIdList = new String[1];
localAlignBox.removeAllItems();
@@ -882,9 +899,7 @@ public class SWTInterface extends JPanel {
if(alignIdList.length > 0) {
selectedAlign = alignIdList[0];
}
-
-
-
+
String[] list1 = offAlign.getAllAlign( );
if(list1!=null) {
localAlignIdList = new String[list1.length];
@@ -940,7 +955,7 @@ public class SWTInterface extends JPanel {
String[] list = onAlign.findAlignForOntos(selectedOnto1, selectedOnto2);
if(list == null || list.length==0)
- JOptionPane.showMessageDialog(null, "Impossible connection!","Warning",2);
+ JOptionPane.showMessageDialog(null, "No alignment is found!","Warning",2);
else {
//String[] list = getResultsFromAnswer(ao, "alid", null );
@@ -985,7 +1000,7 @@ public class SWTInterface extends JPanel {
String at = onAlign.trimAlign(selectedAlign, thres);
if(at == null || at.equals(""))
- JOptionPane.showMessageDialog(null, "Impossible connection!","Warning",2);
+ JOptionPane.showMessageDialog(null, "No alignment is obtained!","Warning",2);
else {
alignIdList = new String[1];
@@ -1084,17 +1099,27 @@ public class SWTInterface extends JPanel {
public void actionPerformed(ActionEvent e) {
if (e.getSource() == goButton) {
wserver = serverField.getText();
- if(wserver.equals("")) wserver = null;
+ if(wserver.equals(""))
+ wserver = null;
wsmethod = methodField.getText();
- if(wsmethod.equals("")) wsmethod = null;
+ if(wsmethod.equals(""))
+ wsmethod = null;
matchDialog.dispose();
resetActionButtons( false );
- onAlign.getAlignId( matchMethod, wserver, wsmethod, selectedOnto1, selectedOnto2 );
-
+ //onAlign.getAlignId( matchMethod, wserver, wsmethod, selectedOnto1, selectedOnto2 );
+
+ String alignId = onAlign.getAlignIdMonoThread( matchMethod, wserver, wsmethod, selectedOnto1, selectedOnto2 );
+ //System.out.println("match from sji finished ");
+ alignIdList = new String[1];
+ alignIdList[0] = alignId;
+ selectedAlign = alignIdList[0];
+ alignBox.removeAllItems();
+ alignBox.addItem(selectedAlign);
+ setFetchButton( true );
+
} // getsource
-
};
});
@@ -1137,8 +1162,16 @@ public class SWTInterface extends JPanel {
matchDialog.setVisible(true);
} else {
resetActionButtons( false );
- onAlign.getAlignId( matchMethod, wserver, wsmethod, selectedOnto1, selectedOnto2 );
+ String alignId = onAlign.getAlignIdMonoThread( matchMethod, wserver, wsmethod, selectedOnto1, selectedOnto2 );
+ //onAlign.getAlignId( matchMethod, wserver, wsmethod, selectedOnto1, selectedOnto2 );
+ alignIdList = new String[1];
+ alignIdList[0] = alignId;
+ selectedAlign = alignIdList[0];
+ alignBox.removeAllItems();
+ alignBox.addItem(selectedAlign);
+ setFetchButton( true );
}
+
//String answer = onAlign.getAlignId( matchMethod, selectedOnto1, selectedOnto2 );
//if(answer==null || answer.equals("")) {
// JOptionPane.showMessageDialog(null, "Alignment is not produced.","Warning",2);
@@ -1222,7 +1255,7 @@ public class SWTInterface extends JPanel {
this.setLayout (new BorderLayout());
this.add (new JLabel ("Computing and managing ontology alignments"), BorderLayout.NORTH);
- phrases = createPhraseList(rootFrame);
+ phrases = createPhraseList( );
phrases.setBorder(BorderFactory.createEmptyBorder (10, 5, 10, 5) );
JScrollPane top = new JScrollPane( phrases );
@@ -1242,7 +1275,7 @@ public class SWTInterface extends JPanel {
}
-private JPanel createPhraseList (Frame root) {
+private JPanel createPhraseList ( ) {
JPanel phrasePane = new JPanel (new GridLayout (0, 1, 0, 10));
--
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