diff --git a/plugins/neon/lib/datamodel.jar b/plugins/neon/lib/datamodel.jar
new file mode 100644
index 0000000000000000000000000000000000000000..68cf809328c951b1a20cf8dd9c63a9e86e44980c
Binary files /dev/null and b/plugins/neon/lib/datamodel.jar differ
diff --git a/plugins/neon/lib/datamodelBase.jar b/plugins/neon/lib/datamodelBase.jar
index fa47137b6f3cf240a6c156e7ea167e54c590baa7..fc87a655225e8dbc7079438e94c2f275fe3bfc8f 100644
Binary files a/plugins/neon/lib/datamodelBase.jar and b/plugins/neon/lib/datamodelBase.jar differ
diff --git a/plugins/neon/lib/ontostudio-datamodel.jar b/plugins/neon/lib/ontostudio-datamodel.jar
index 8310c2216ebc64fd94c10535ac8d215a217d9e37..3091f17eb01f6f1fc76d630ab1bf3eaf8b1e4baa 100644
Binary files a/plugins/neon/lib/ontostudio-datamodel.jar and b/plugins/neon/lib/ontostudio-datamodel.jar differ
diff --git a/plugins/neon/lib/ontostudio-gui.jar b/plugins/neon/lib/ontostudio-gui.jar
index 97223dd33ab0784e03b27e01fccd363e24d88a5d..69e6f6969b7d7c0399b61af4c2da3caa6102023a 100644
Binary files a/plugins/neon/lib/ontostudio-gui.jar and b/plugins/neon/lib/ontostudio-gui.jar differ
diff --git a/plugins/neon/lib/ontostudio-io.jar b/plugins/neon/lib/ontostudio-io.jar
index fd4a596e79fec900529f0a7c0a303fb8853a2ec8..a335abab6f6e4067dcd2127c5bd2f0a7a211c613 100644
Binary files a/plugins/neon/lib/ontostudio-io.jar and b/plugins/neon/lib/ontostudio-io.jar differ
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 f301b2ab2788fe6ef793211777f0c08edce6f9c9..c1f26ea68ad48a3cf89a087d9a9379f67ce3ad69 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
@@ -29,8 +29,10 @@ 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 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;
@@ -39,58 +41,58 @@ import org.semanticweb.owl.align.AlignmentProcess;
import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.Parameters;
+//import com.ontoprise.api.formatting.OntoBrokerOntologyFileFormat;
+//import com.ontoprise.config.IConfig;
+//import com.ontoprise.config.IConfig.OntologyLanguage;
import com.ontoprise.ontostudio.io.ImportExportControl;
import fr.inrialpes.exmo.align.impl.BasicParameters;
+import fr.inrialpes.exmo.align.onto.OntologyCache;
import fr.inrialpes.exmo.align.parser.AlignmentParser;
-import fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor;
+//import fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor;
import fr.inrialpes.exmo.align.impl.renderer.OWLAxiomsRendererVisitor;
import fr.inrialpes.exmo.align.impl.renderer.RDFRendererVisitor;
-import fr.inrialpes.exmo.align.onto.OntologyCache;
+import fr.inrialpes.exmo.align.impl.OWLAPIAlignment;
public class OfflineAlign {
File alignFolder = null;
File ontoFolder = null;
- public OfflineAlign(File on, File al) {
+ public OfflineAlign(File al, File on) {
ontoFolder = on;
alignFolder = al;
}
- String matchAndExportAlign (String method, String selectedNeOnOnto1, String selectedNeOnOnto2) {
+ String matchAndExportAlign (String method, String proj1, String selectedNeOnOnto1, String proj2, String selectedNeOnOnto2) {
//export ontologies
ImportExportControl ieControl = new ImportExportControl();
- Integer name1 = new Integer(SWTInterface.alignId++);
- Integer name2 = new Integer(SWTInterface.alignId++);
- 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();
+ //Integer name1 = new Integer(SWTInterface.alignId++);
+ //Integer name2 = new Integer(SWTInterface.alignId++);
+ File f1 = new File( selectedNeOnOnto1.replace("file:","") );
+ File f2 = new File( selectedNeOnOnto2.replace("file:","") );
- System.out.println("Filename 1="+ fname1);
- System.out.println("Filename 2="+ fname2);
-
- try {
- //String format1 = DatamodelPlugin.getDefault().getKaon2Connection( <project> ).getParameter(IConfig.ONTOLOGY_LANGUAGE)
- ieControl.exportFileSystem( OntologyFileFormat.OWLEASY, selectedNeOnOnto1, fname1 );
- ieControl.exportFileSystem( OntologyFileFormat.OWLEASY, selectedNeOnOnto2, fname2 );
-
- } catch ( Exception ex ) { ex.printStackTrace(); };
+ //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;
//String htmlString = null;
//Vector corrList = new Vector();
- Integer name = new Integer(SWTInterface.alignId++);
+ Integer name = new Integer(SWTInterface.getNewAlignId());
try {
Vector<URI> uris = new Vector<URI>();
- uris.add( new URI("file:"+ f1.getAbsolutePath()) );
- uris.add( new URI("file:"+ f2.getAbsolutePath()) );
+ uris.add( new URI(selectedNeOnOnto1) );
+ uris.add( new URI(selectedNeOnOnto2 ) );
// Create alignment object
Object[] mparams = {};
@@ -103,29 +105,30 @@ public class OfflineAlign {
A1.align((Alignment)null,p);
//SWTInterface.alignObjects.clear();
- SWTInterface.alignmentTable.put( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString(), (Alignment)A1 );
+ SWTInterface.alignmentTable.put( alignFolder.getAbsolutePath() + File.separator + name.toString(), (Alignment)A1 );
// for saving locally
- FileWriter rdfF = new FileWriter(new File( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString()+ ".rdf" ));
+ FileWriter rdfF = new FileWriter(new File( alignFolder.getAbsolutePath() + File.separator + name.toString()+ ".rdf" ));
AlignmentVisitor rdfV = new RDFRendererVisitor( new PrintWriter ( rdfF ) );
A1.render(rdfV);
+ rdfF.flush();
rdfF.close();
// for exporting to NeonToolkit
- FileWriter owlF = new FileWriter(new File( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString()+ ".owl" ));
+ FileWriter owlF = new FileWriter(new File( ontoFolder.getAbsolutePath() + File.separator + name.toString()+ ".owl" ));
AlignmentVisitor V = new OWLAxiomsRendererVisitor( new PrintWriter ( owlF ) );
A1.render(V);
+ owlF.flush();
owlF.close();
- String str1 = fileToString(new File(alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString()+ ".owl") );
+ String str1 = fileToString(new File(ontoFolder.getAbsolutePath() + File.separator + name.toString()+ ".owl") );
-
//Add URI to OWL file : rethink !!!
- File f0 = new File( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString()+ ".owl" );
+ File f0 = new File( ontoFolder.getAbsolutePath() + File.separator + name.toString()+ ".owl" );
String s1 = str1.substring(0, str1.indexOf('>') + 1 );
String s2 = str1.substring(str1.indexOf('>') + 2, str1.length());
@@ -142,23 +145,26 @@ public class OfflineAlign {
}
- File owlFile = new File( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString()+ ".owl" );
+ File owlFile = new File( ontoFolder.getAbsolutePath() + File.separator + name.toString()+ ".owl" );
FileWriter out = new FileWriter( owlFile );
out.write( s3 + s2 );
- //out.write( answer );
+ out.flush();
out.close();
//for displaying
- FileWriter htmlF = new FileWriter( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString() + ".html" );
+ /*
+ FileWriter htmlF = new FileWriter( alignFolder.getAbsolutePath() + File.separator + name.toString() + ".html" );
AlignmentVisitor V1 = new HTMLRendererVisitor(
new PrintWriter ( htmlF ) );
A1.render(V1);
+ htmlF.flush();
htmlF.close();
+ */
} catch ( Exception ex ) { ex.printStackTrace(); };
- return alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString();
+ return alignFolder.getAbsolutePath() + File.separator + name.toString();
}
@@ -166,7 +172,7 @@ public class OfflineAlign {
//String htmlString = null;
//Vector corrList = new Vector();
- Integer name = new Integer(SWTInterface.alignId++);
+ Integer name = new Integer(SWTInterface.getNewAlignId());
Alignment A1 = SWTInterface.alignmentTable.get( id );
Alignment clonedA1 = (BasicAlignment)((BasicAlignment)A1).clone();
@@ -174,28 +180,37 @@ public class OfflineAlign {
try {
clonedA1.cut(thres);
- SWTInterface.alignmentTable.put( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString(), clonedA1 );
- //SWTInterface.alignObjects.clear();
- //SWTInterface.alignmentTable.put(A1);
+ SWTInterface.alignmentTable.put( alignFolder.getAbsolutePath() + File.separator + name.toString(), clonedA1 );
-
- FileWriter rdfF = new FileWriter(new File( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString()+ ".rdf" ));
+ 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 ) );
+
clonedA1.render(rdfV);
+ rdfF.flush();
rdfF.close();
- FileWriter owlF = new FileWriter(new File( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString()+ ".owl" ));
- AlignmentVisitor V = new OWLAxiomsRendererVisitor( new PrintWriter ( owlF ) );
+ File owlFile = new File( ontoFolder.getAbsolutePath() + File.separator + name.toString()+ ".owl");
+ if (owlFile.exists()) owlFile.delete();
+
+ FileWriter owlF = new FileWriter( owlFile );
+
+ AlignmentVisitor owlV = new OWLAxiomsRendererVisitor( new PrintWriter ( owlF ) );
- clonedA1.render(V);
+ //OWLAPIAlignment owla = OWLAPIAlignment.toOWLAPIAlignment(fnRdf.toURI(), clonedA1);
+
+ clonedA1.render(owlV);
+ owlF.flush();
owlF.close();
- String str1 = fileToString(new File( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString()+ ".owl") );
+ String str1 = fileToString(new File( ontoFolder.getAbsolutePath() + File.separator + name.toString()+ ".owl") );
//Add URI to OWL file : rethink !!!
- File f0 = new File( alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString()+ ".owl" );
+ File f0 = new File( ontoFolder.getAbsolutePath() + File.separator + name.toString()+ ".owl" );
String s1 = str1.substring(0, str1.indexOf('>') + 1 );
String s2 = str1.substring(str1.indexOf('>') + 2, str1.length());
@@ -209,27 +224,34 @@ public class OfflineAlign {
for(int i=2; i<ss2.length;i++) {
s3 = s3 + ss2[i];
if(i != ss2.length-1 ) s3 = s3 + "xmlns";
- }
+ }
- 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();
+ File owlFile2 = new File( ontoFolder.getAbsolutePath() + File.separator + name.toString()+ ".owl" );
+ if (owlFile2.exists()) owlFile2.delete();
+ FileWriter out = new FileWriter( owlFile2 );
+ out.write( s3 + s2 );
+ out.flush();
+ out.close();
- //for displaying
- FileWriter htmlF = new FileWriter( alignFolder.getAbsolutePath()+ ontoFolder.separator + name.toString()+ ".html" );
+ //for displaying
+ /*
+ File htmlFile = new File( ontoFolder.getAbsolutePath()+ File.separator + name.toString()+ ".html" );
+ if (htmlFile.exists()) htmlFile.delete();
+ FileWriter htmlF = new FileWriter( htmlFile );
+
AlignmentVisitor V1 = new HTMLRendererVisitor(
new PrintWriter ( htmlF ) );
clonedA1.render(V1);
+ htmlF.flush();
htmlF.close();
+ */
}
catch ( Exception ex ) { ex.printStackTrace();};
- return alignFolder.getAbsolutePath() + ontoFolder.separator + name.toString();
+ return alignFolder.getAbsolutePath() + File.separator + name.toString();
}
public String[] getAllAlign() {
@@ -265,9 +287,9 @@ public class OfflineAlign {
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)) );
+ System.out.println("Path ="+ alignFolder.getAbsolutePath() + File.separator + v.get(i) );
+ SWTInterface.alignmentTable.put( alignFolder.getAbsolutePath() + File.separator + key ,
+ parser.parse(alignFolder.getAbsolutePath() + File.separator + v.get(i)) );
}
} catch ( Exception ex ) { ex.printStackTrace();};
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 905cb919d9d078bdc3b47d19ccb8c9f8bb296478..afe284fc4db088c646d1792ee194984cfcdab370 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
@@ -22,13 +22,21 @@ package fr.inrialpes.exmo.align.plugin.neontk;
import java.io.BufferedReader;
import java.io.File;
+import java.io.FileReader;
+import java.io.InputStream;
+
+import java.io.FileInputStream;
+import java.io.DataOutputStream;
+import java.io.IOException;
import java.io.InputStreamReader;
+
import java.io.OutputStream;
import java.net.HttpURLConnection;
import java.net.URL;
import java.net.URLConnection;
import java.util.Vector;
+import java.util.zip.ZipInputStream;
import javax.swing.JOptionPane;
@@ -58,23 +66,6 @@ public class OnlineAlign {
} catch ( Exception ex ) { ex.printStackTrace(); };
}
- /*
- public boolean isConnected() {
- boolean conn = true;
- try {
- connection = SOAPUrl.openConnection();
- httpConn = (HttpURLConnection) connection;
- httpConn.setDoOutput(true);
- httpConn.setDoInput(true);
-
-
- OutputStream out = httpConn.getOutputStream();
-
- } catch ( Exception ex ) { conn = false; ex.printStackTrace(); };
-
- return conn;
- }
- */
public String uploadAlign(String alignId) {
@@ -88,16 +79,17 @@ public class OnlineAlign {
//params.setParameter( "arg1", alignId);
uploadFile = alignId;
-
+ System.out.println("Load file= "+ uploadFile);
// Create the SOAP message
String message = createMessage( params );
- System.out.println("HOST= :"+ HOST + ", PORT= " + PORT + ", Action = "+ SOAPAction);
+ System.out.println("HOST= "+ HOST + ", PORT= " + PORT + ", Action = "+ SOAPAction);
System.out.println("Message :"+ message);
// Send message
- answer = sendMessage( message, params );
+ //answer = sendMessage( message, params );
+ answer = sendFile( message, params );
System.out.println("Loaded Align="+ answer);
@@ -345,6 +337,68 @@ public class OnlineAlign {
return s3 + s2;
}
+ public String getRDFAlignment(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 = sendMessage( message, params );
+ if(! connected ) return null;
+
+ System.out.println("RDFAlign="+ answer);
+
+ } catch ( Exception ex ) { ex.printStackTrace(); };
+
+
+ // Cut SOAP header
+ String [] cutResult = answer.split("result");
+
+ if(cutResult==null) return null;
+
+ String str = "";
+
+ for(int i= 0; i< cutResult.length; i++){
+
+ if(i >= 1 && i <= cutResult.length -2)
+ str = str + cutResult[i];
+ }
+
+ //System.out.println("OwlAlign STR ="+ str);
+
+ if(str.equals("")) return null;
+
+ String str1 = str.substring(1, str.length() - 3);
+
+ //Add URI to RDF file : rethink !!!
+ String s1 = str1.substring(0, str1.indexOf('>') + 1 );
+ String s2 = str1.substring(str1.indexOf('>') + 2, str1.length());
+
+
+
+ return s2;
+ }
+
public String getHTMLAlignment(String alignId) {
//retrieve alignment for displaying
@@ -412,7 +466,7 @@ public class OnlineAlign {
// Send message
answer = sendMessage( message, params );
- System.out.println("Store Align="+ answer);
+ System.out.println("Stored Align="+ answer);
//corrList = getCorresFromAnswer( answer, "tr", "#" );
}
@@ -503,7 +557,7 @@ public class OnlineAlign {
} else if ( cmd.equals("store" ) ) {
SOAPAction = "storeRequest";
String uri = (String)params.getParameter( "arg1" );
- if ( uri == null ){
+ if ( uri == null ) {
//usage();
//System.exit(-1);
}
@@ -512,22 +566,20 @@ public class OnlineAlign {
String url = (String)params.getParameter( "arg1" );
if ( url == null ){
SOAPAction = "loadRequest";
- //usage();
- //System.exit(-1);
- /*
- BufferedReader in = new BufferedReader(new InputStreamReader(System.in));
- //String line;
- //String content = "";
+ /*
+ BufferedReader in = new BufferedReader(new FileReader( new File(uploadFile) ));
+ 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>";
+ return content;
+
+ //messageBody = "<content>"+content+"</content>";
} else {
SOAPAction = "loadfileRequest";
messageBody = "<url>"+url+"</url>";
@@ -574,19 +626,20 @@ public class OnlineAlign {
public String sendMessage( String message, Parameters param ) {
// Create the connection
-
-
byte[] b = message.getBytes();
String answer = "";
- // Create HTTP Request
+ // 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);
@@ -594,10 +647,14 @@ public class OnlineAlign {
// Send the request through the connection
OutputStream out = httpConn.getOutputStream();
-
- out.write( b );
+
+ //System.out.println("ResponseMessage= "+httpConn.getResponseMessage());
+
+ out.write( b );
out.close();
-
+
+ System.out.println("Message Length= "+String.valueOf( b.length ));
+
// Read the response and write it to standard output
InputStreamReader isr = new InputStreamReader(httpConn.getInputStream());
BufferedReader in = new BufferedReader(isr);
@@ -607,10 +664,94 @@ public class OnlineAlign {
answer += line + "\n";
}
if (in != null) in.close();
- } catch (Exception ex) { connected= false; ex.printStackTrace() ; return null;}
+
+ if(httpConn.HTTP_REQ_TOO_LONG == httpConn.getResponseCode()) System.out.println("Request too long");
+
+ if(httpConn.HTTP_OK == httpConn.getResponseCode()) System.out.println("Request OK");
+
+ } catch (Exception ex) {
+ connected= false; ex.printStackTrace() ; return null;
+ }
connected = true;
return answer;
}
+ public String sendFile( 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("SOAPAction",SOAPAction);
+ httpConn.setRequestMethod( "POST" );
+ httpConn.setDoOutput( true );
+ httpConn.setDoInput( true );
+
+ // Don't use a cached version of URL connection.
+ httpConn.setUseCaches ( false );
+ httpConn.setDefaultUseCaches (false);
+
+ File f = new File(uploadFile);
+ FileInputStream fi = new FileInputStream(f);
+ // set headers and their values.
+ httpConn.setRequestProperty("Content-Type",
+ "application/octet-stream");
+ httpConn.setRequestProperty("Content-Length",
+ Long.toString(f.length()));
+
+ // create file stream and write stream to write file data.
+
+ OutputStream os = httpConn.getOutputStream();
+ String str ="";
+ try
+ {
+ // transfer the file in 4K chunks.
+ byte[] buffer = new byte[4096];
+ //long byteCnt = 0;
+ int bytes=0;
+ while (true)
+ {
+ bytes = fi.read(buffer);
+
+ if (bytes < 0) break;
+
+ os.write(buffer, 0, bytes );
+ //String st = new String( buffer );
+ //str = str + st.substring(0, bytes);
+ //System.out.println("st="+st.substring(0, bytes));
+ }
+
+
+ os.flush();
+ } catch (Exception ex) {}
+
+ os.close();
+ fi.close();
+ System.out.println("Upload Read done.");
+
+ // Read the response
+ 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();
+
+
+ } catch (Exception ex) {
+ connected= false; ex.printStackTrace() ; return null;
+ }
+
+ connected = true;
+ return answer;
+ }
}
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 5b3caa8525f740132c1d550514e6fbbbb1b45839..606cc7ab1f0ba55df79f7329fab7dedac37a5147 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
@@ -23,6 +23,7 @@ package fr.inrialpes.exmo.align.plugin.neontk;
import java.io.File;
import java.io.FileWriter;
import java.net.MalformedURLException;
+import java.net.URI;
//import java.io.FileReader;
//import java.io.IOException;
@@ -37,9 +38,16 @@ import java.awt.event.ActionListener;
import java.awt.event.ItemListener;
import java.awt.event.ItemEvent;
import java.awt.event.ActionEvent;
+import java.awt.Container;
+import java.awt.Dimension;
+
+import java.util.Properties;
+import java.util.Set;
import java.util.Vector;
+import java.util.ArrayList;
import java.util.Hashtable;
+import java.util.HashMap;
//import java.io.PrintWriter;
//import javax.swing.*;
@@ -56,6 +64,8 @@ import javax.swing.JOptionPane;
//import javax.swing.SwingConstants;
import javax.swing.JScrollPane;
import javax.swing.BorderFactory;
+import javax.swing.JDialog;
+
//import org.semanticweb.owl.align.AlignmentProcess;
import org.semanticweb.owl.align.Alignment;
@@ -63,15 +73,35 @@ import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
+
+//import org.eclipse.core.resources.ResourcesPlugin;
+//import org.eclipse.core.resources.IWorkspace;
+import org.eclipse.core.resources.IWorkspaceRoot;
+import org.eclipse.core.runtime.IPath;
//import org.eclipse.core.resources.IProject;
+//import org.semanticweb.kaon2.api.Ontology;
+import org.semanticweb.kaon2.api.KAON2Connection;
+import org.semanticweb.kaon2.api.KAON2Exception;
+//import org.semanticweb.kaon2.api.formatting.OntologyFileFormat;
+import com.ontoprise.config.IConfig;
import com.ontoprise.ontostudio.datamodel.DatamodelPlugin;
+import com.ontoprise.ontostudio.datamodel.DatamodelTypes;
//import com.ontoprise.ontostudio.gui.navigator.module.ModuleTreeElement;
import com.ontoprise.ontostudio.io.ImportExportControl;
//import com.ontoprise.ontostudio.gui.commands.CreateProject;
-import com.ontoprise.ontostudio.gui.navigator.project.ProjectControl;
+import com.ontoprise.ontostudio.gui.commands.project.CreateProject;
+import com.ontoprise.ontostudio.datamodel.exception.ControlException;
+//import com.ontoprise.ontostudio.gui.navigator.project.ProjectControl;
//import org.semanticweb.kaon2.api.formatting.OntologyFileFormat;
//import org.eclipse.core.runtime.IProgressMonitor;
+//import com.ontoprise.ontostudio.owl.datamodel.*;
+import fr.inrialpes.exmo.align.parser.AlignmentParser;
+
+import org.semanticweb.owl.align.Cell;
+//import org.semanticweb.owl.align.Relation;
+
+import fr.inrialpes.exmo.align.impl.BasicAlignment;
public class SWTInterface extends JPanel {
@@ -92,49 +122,50 @@ public class SWTInterface extends JPanel {
String selectedOnto2 = null;
String selectedAlign = null;
String selectedLocalAlign = null;
- String selectedNeOnOnto1 = null;
- String selectedNeOnOnto2 = 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 Hashtable<String,Alignment> alignmentTable = new Hashtable<String,Alignment>();
-
+ public static String [] forUniqueness = new String[0];
+ public static int alignId = 0;
//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, 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, localAlignImportButton, alignUploadButton, alignTrimButton, alignFindButton,
- alignStoreButton, connButton, offlineButton, onlineButton, disconnButton ;
-
+ public JButton cancelButton, mapButton, resButton, ontoRefresh, allAlignButton,
+ alignImportButton, localAlignImportButton, alignUploadButton,
+ localAlignTrimButton, serverAlignTrimButton, alignFindButton,
+ alignStoreButton, connButton, offlineButton, onlineButton;// disconnButton ;
+ public JDialog dialog;
public JPanel pane2;
public Component result=null;
public JTextArea jan=null;
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];
//lists obtained from from server
public String [] methodList = new String[0];
- public String [] rendererList = null;
+
//lists obtained from Neontk
public String [] ontoList = new String[0];
- public String [] NeOnOntoList = new String[0];
+ public HashMap<String,String> onto_proj = new HashMap<String,String>(0);
+ //public String [] NeOnOntoList = new String[0];
public String [] alignIdList = new String[0];
public String [] localAlignIdList = new String[0];
+
public Vector corrList = new Vector();
public String [] aservArgs = null;
@@ -157,10 +188,11 @@ public class SWTInterface extends JPanel {
public OfflineAlign offAlign = null;
public File ontoFolder = null;
public File alignFolder = null;
+ public static File basicFolder = null;
public void offlineInit(boolean init){
online = false;
- offAlign = new OfflineAlign(ontoFolder, alignFolder);
+ offAlign = new OfflineAlign( alignFolder, ontoFolder );
ontoBox1.setEnabled(true);
ontoBox2.setEnabled(true);
@@ -177,10 +209,8 @@ public class SWTInterface extends JPanel {
allAlignButton.setEnabled(true);
//threshold.setEnabled(true);
- alignTrimButton.setEnabled(true);
-
- //alignProject = alignProj.getText();
- //alignProj.setEnabled(false);
+ localAlignTrimButton.setEnabled(true);
+ serverAlignTrimButton.setEnabled(false);
alignFindButton.setEnabled(false);
@@ -188,14 +218,11 @@ public class SWTInterface extends JPanel {
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();
@@ -204,17 +231,19 @@ public class SWTInterface extends JPanel {
ontoBox2.removeAllItems();
ontoList = new String[0];
- NeOnOntoList = new String[0];
+ onto_proj = new HashMap<String,String>(0);
+ //NeOnOntoList = new String[0];
alignIdList = new String[0];
//localAlignIdList = new String[0];
selectedOnto1 = null;
selectedOnto2 = null;
selectedAlign = null;
- selectedNeOnOnto1 = null;
- selectedNeOnOnto2 = null;
+ //selectedNeOnOnto1 = null;
+ //selectedNeOnOnto2 = null;
- methodList = new String[9];
+ //methodList = new String[9];
+ methodList = new String[8];
methodList[0] = "fr.inrialpes.exmo.align.impl.method.NameEqAlignment";
strategy.addItem(methodList[0]);
methodList[1] = "fr.inrialpes.exmo.align.impl.method.StringDistAlignment";
@@ -231,8 +260,8 @@ public class SWTInterface extends JPanel {
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]);
+ //methodList[8] = "fr.inrialpes.exmo.align.ling.JWNLAlignment";
+ //strategy.addItem(methodList[8]);
if(init) offAlign.getAllAlignFromFiles();
@@ -240,10 +269,14 @@ public class SWTInterface extends JPanel {
if(list!=null) {
localAlignIdList = new String[list.length];
localAlignBox.removeAllItems();
-
+
+ forUniqueness = new String[list.length];
+
for(int i=0; i< list.length; i++){
localAlignIdList[i]= list[i];
localAlignBox.addItem(list[i]);
+ File f = new File(list[i]);
+ forUniqueness[i] = f.getName();
}
if(localAlignIdList.length > 0) {
@@ -254,14 +287,41 @@ public class SWTInterface extends JPanel {
//for(int i=0; i < localAlignIdList.length; i++) localAlignBox.addItem(i);
}
+ public static int getNewAlignId() {
+
+ boolean found = false;
+ alignId++;
+ while(!found) {
+
+ boolean sw = false;
+ for(int i=0;i< forUniqueness.length; i++)
+ if(forUniqueness[i].equals((new Integer(alignId)).toString())) {
+ alignId++;
+ sw = true;
+ break;
+ }
+
+ if(!sw) found = true;
+
+ }
+
+ return alignId;
+ }
public void initialize() {
//selectedHost = "aserv.inrialpes.fr";
//selectedPort = "8089";
- ontoFolder = new File("onto");
+
+ IWorkspaceRoot root = org.eclipse.core.resources.ResourcesPlugin.getWorkspace().getRoot();
+ IPath location = root.getLocation();
+ String path = location.toOSString();
+
+ ontoFolder = new File(path + location.SEPARATOR + "onto");
+
if (!ontoFolder.exists()) ontoFolder.mkdir();
- alignFolder = new File("align");
+ basicFolder = new File(path + location.SEPARATOR );
+ alignFolder = new File(path + location.SEPARATOR + "align");
if (!alignFolder.exists()) alignFolder.mkdir();
//System.out.println("alignFolder=" + alignFolder.getAbsolutePath());
@@ -270,11 +330,8 @@ public class SWTInterface extends JPanel {
offlineButton.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent e) {
if (e.getSource() == offlineButton) {
-
- offlineInit(false);
-
+ offlineInit(false);
}
-
};
});
@@ -284,190 +341,68 @@ public class SWTInterface extends JPanel {
if (e.getSource() == onlineButton) {
online = true;
- //alignProject = alignProj.getText();
- //alignProj.setEnabled(false);
-
- offlineButton.setEnabled(true);
- hostField.setEnabled(true);
- portField.setEnabled(true);
- connButton.setEnabled(true);
-
- onlineButton.setEnabled(false);
- disconnButton.setEnabled(false);
- 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);
-
- alignTrimButton.setEnabled(false);
- //alignRetrieveButton.setEnabled(false);
- alignStoreButton.setEnabled(false);
-
- ontoRefresh.setEnabled(false);
- //openbutton1.setEnabled(false);
- //openbutton2.setEnabled(false);
-
- mapButton.setEnabled(false);
- strategy.removeAllItems();
- alignBox.removeAllItems();
- ontoBox1.removeAllItems();
- ontoBox2.removeAllItems();
- ontoList = new String[0];
- NeOnOntoList = new String[0];
- alignIdList = new String[0];
- methodList = new String[0];
-
- selectedOnto1 = null;
- selectedOnto2 = null;
- selectedAlign = null;
- selectedNeOnOnto1 = null;
- selectedNeOnOnto2 = null;
-
- //alignObjects.clear();
- //alignProjects = new Vector<String>();
-
- }
-
- };
- });
-
- disconnButton = new JButton("Disconnect",null);
- disconnButton.setEnabled(false);
- disconnButton.addActionListener(new ActionListener(){
- public void actionPerformed(ActionEvent e) {
- if (e.getSource() == disconnButton) {
-
- offlineButton.setEnabled(true);
- onlineButton.setEnabled(true);
- online = false;
- ontoBox1.setEnabled(false);
- ontoBox2.setEnabled(false);
- ontoRefresh.setEnabled(false);
- alignBox.setEnabled(false);
- alignImportButton.setEnabled(false);
+ JOptionPane pane = new JOptionPane();
+ dialog = pane.createDialog(null, "Input for connection");
+ dialog.setSize(new Dimension(300,120));
- localAlignImportButton.setEnabled(false);
- alignUploadButton.setEnabled(false);
+ Container cont = dialog.getContentPane();
+ Component[] comps = cont.getComponents();
+ for(int i=0;i< comps.length ;i++) { cont.remove(comps[i]);}
- alignFindButton.setEnabled(false);
-
- alignTrimButton.setEnabled(false);
- //alignRetrieveButton.setEnabled(false);
- allAlignButton.setEnabled(false);
- alignStoreButton.setEnabled(false);
-
- //openbutton1.setEnabled(false);
- //openbutton2.setEnabled(false);
- strategy.setEnabled(false);
- mapButton.setEnabled(false);
- disconnButton.setEnabled(false);
- hostField.setEnabled(false);
- portField.setEnabled(false);
- connButton.setEnabled(false);
- //threshold.setEnabled(false);
-
- strategy.removeAllItems();
- alignBox.removeAllItems();
- localAlignBox.removeAllItems();
- ontoBox1.removeAllItems();
- ontoBox2.removeAllItems();
+
+ cont.add(connButton);
+ cont.add(cancelButton);
- ontoList = new String[0];
- NeOnOntoList = new String[0];
- alignIdList = new String[0];
- localAlignIdList = new String[0];
- methodList = new String[0];
+ JPanel jPane = new JPanel (new GridLayout (3, 2, 20, 10));
+
+ jPane.add(hostName); jPane.add(hostField);
+ jPane.add(portName); jPane.add(portField);
+ jPane.add(connButton);
+ jPane.add(cancelButton);
+
+ dialog.setContentPane(jPane);
+ dialog.show();
-
- selectedOnto1 = null;
- selectedOnto2 = null;
- selectedAlign = null;
- selectedNeOnOnto1 = null;
- selectedNeOnOnto2 = null;
}
};
});
+
+
selectedHost = defaultHost;
hostName = new JLabel( "Host name" );
hostField = new JTextField( defaultHost, 15 );
- hostField.setEnabled(false);
+ hostField.setEnabled(true);
hostField.setEditable( true );
- /*
- hostList.setMaximumRowCount(20);
- hostList.addItemListener(new ItemListener() {
- public void itemStateChanged(ItemEvent event)
- {
- if (event.getStateChange()==ItemEvent.SELECTED)
- hostInd = hostList.getSelectedIndex();
- selectedHost = hostNames[hostInd];
-
- }
- });
- */
-
selectedPort = defaultPort;
portName = new JLabel( "Port" );
portField = new JTextField( defaultPort, 4 );
- portField.setEnabled(false);
+ portField.setEnabled(true);
portField.setEditable( true );
- /*
- portList = new JComboBox( ports );
- portList.setEnabled(false);
- portList.setEditable( true );
- portList.setMaximumRowCount(20);
- portList.addItemListener(new ItemListener() {
- public void itemStateChanged(ItemEvent event) {
- if (event.getStateChange()==ItemEvent.SELECTED)
- portInd = portList.getSelectedIndex();
- selectedPort = ports[portInd];
-
- }
- });
- */
-
- //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 );
-
connButton = new JButton("Connect",null);
- connButton.setEnabled(false);
+ connButton.setEnabled(true);
+
connButton.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent e) {
if (e.getSource() == connButton) {
// for connecting to server
+
selectedHost = hostField.getText();
selectedPort = portField.getText();
onAlign = new OnlineAlign(selectedPort, selectedHost);
-
- /*
- if(! onAlign.isConnected() )
- JOptionPane.showMessageDialog(null, "Impossible connection!","Warning",2);
- else {
- */
+
String mt = onAlign.getMethods();
- if(mt == null)
+ if(mt == null) {
JOptionPane.showMessageDialog(null, "Impossible connection!","Warning",2);
- else {
-
+ return;
+ }
+
String[] list = getResultsFromAnswer( mt, "method", null ); //"."
methodList = new String[list.length];
@@ -475,18 +410,17 @@ public class SWTInterface extends JPanel {
for(int i=0; i< list.length; i++){
- methodList[i]= list[i];//"fr.inrialpes.exmo.align.impl.method." + list[i];
+ methodList[i]= list[i];
strategy.addItem(list[i]);
}
- //openbutton1.setEnabled(true);
- //openbutton2.setEnabled(true);
+
ontoBox1.setEnabled(true);
ontoBox2.setEnabled(true);
strategy.setEnabled(true);
ontoRefresh.setEnabled(true);
mapButton.setEnabled(true);
- disconnButton.setEnabled(true);
+
alignBox.setEnabled(true);
localAlignBox.setEnabled(true);
alignImportButton.setEnabled(true);
@@ -495,23 +429,44 @@ public class SWTInterface extends JPanel {
alignFindButton.setEnabled(true);
allAlignButton.setEnabled(true);
- alignTrimButton.setEnabled(true);
- //threshold.setEnabled(true);
- //alignRetrieveButton.setEnabled(true);
alignStoreButton.setEnabled(true);
- hostField.setEnabled(false);
- portField.setEnabled(false);
+ offlineButton.setEnabled(true);
+ onlineButton.setEnabled(false);
+
+ serverAlignTrimButton.setEnabled(true);
+ localAlignTrimButton.setEnabled(true);
+
+ alignStoreButton.setEnabled(true);
+
+ ontoRefresh.setEnabled(true);
+
+ mapButton.setEnabled(true);
+ strategy.setEnabled(true);
+
+ online = true;
+
+ dialog.dispose();
- connButton.setEnabled(false);
-
- }//connect
- }
-
+ }
+
};
});
- alignLabel = new JLabel("Alignments from server");
+
+ cancelButton = new JButton("Cancel",null);
+ cancelButton.setEnabled(true);
+ cancelButton.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource() == cancelButton) {
+ //System.out.println("Cancel");
+ dialog.dispose();
+
+ }
+ };
+ });
+
+ alignLabel = new JLabel("Server alignments");
alignBox = new JComboBox(alignIdList);
alignBox.setEnabled(false);
alignBox = new JComboBox(alignIdList);
@@ -531,10 +486,10 @@ public class SWTInterface extends JPanel {
}
});
- localAlignLabel = new JLabel("Local alignments");
+ localAlignLabel = new JLabel("Local alignments ");
localAlignBox = new JComboBox(localAlignIdList);
localAlignBox.setEnabled(false);
- localAlignBox = new JComboBox(localAlignIdList);
+ localAlignBox = new JComboBox(localAlignIdList);
localAlignBox.setEnabled(false);
localAlignBox.setMaximumRowCount(20);
@@ -556,43 +511,75 @@ public class SWTInterface extends JPanel {
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);
+ if(selectedLocalAlign == null) {
+ JOptionPane.showMessageDialog(null, "Choose an alignment ID from list!","Warning",2);
+ return;
+ }
- File fn = new File(selectedLocalAlign + ".owl");
- //System.out.println("file name off to export :"+ fn.getName());
- String inputName=null;
+ File fn = new File(selectedLocalAlign + ".owl");
+
+ //System.out.println("Filename off to export :"+ fn.getAbsolutePath());
+
+ corrList = getCorresFromAnswer( SWTInterface.alignmentTable.get(selectedLocalAlign) );
+
+ System.out.println("corrList Size="+corrList.size());
+
+ pane2.removeAll();
+ for(int i=0;i< corrList.size();i++) {
+
+ String[] li= (String [])corrList.get(i);
+ String n = "";
+ for(int j=0;j<li.length;j++)
+ {
+ String sep = "";
+ if(n.equals("")) sep = "==>"; else if(n.equals("=")) sep = ""; else sep = "----";
+
+ if (li[j]!=null)
+ n = n + sep+ li[j];
+ }
+
+ System.out.println("line= "+ n);
+ JTextArea header1= new JTextArea(n);
+
+ pane2.add(header1);
+ }
+
+ String inputName=null;
try {
- do {
- inputName = JOptionPane.showInputDialog(null, "Enter a project name", "AlignmentProject");
- }
- while (inputName==null || inputName.equals(""));
+
+ inputName = JOptionPane.showInputDialog(null, "Enter a project name", "AlignmentProject");
+
+ if (inputName==null || inputName.equals("")) return;
String[] projects = DatamodelPlugin.getDefault().getOntologyProjects();
if(projects!=null) {
- boolean found = false;
+ boolean found = false;
- for(int i=0; i < projects.length; i++) {
+ for(int i=0; i < projects.length; i++) {
- if(projects[i].equals(inputName)) {
+ if(projects[i].equals(inputName)) {
found = true;break;
+ }
}
- }
- if(!found)
- ProjectControl.getDefault().createNewOntologyProject(inputName, new String[0]);
- }
+ if(!found) {
+ Properties proper = new Properties();
+ proper.put(IConfig.ONTOLOGY_LANGUAGE.toString(), IConfig.OntologyLanguage.OWL.toString());
+ new CreateProject( inputName, DatamodelTypes.RAM, proper ).run();
+
+ // ProjectControl.getDefault().createNewOntologyProject(inputName, new String[0]);
+ }
ImportExportControl ieControl = new ImportExportControl();
- String[] importedModules = ieControl.importFileSystem(inputName, fn.getAbsolutePath(), null, null);
- ieControl.addOntologies2Project(importedModules, inputName);
+ ieControl.importFileSystem(inputName, "file:"+ fn.getAbsolutePath(), null);
+ //ieControl.addOntologies2Project(importedModules, inputName);
+ }
}
catch ( Exception ex ) { ex.printStackTrace();};
-
}//choose an align
@@ -631,29 +618,105 @@ public class SWTInterface extends JPanel {
public void actionPerformed(ActionEvent e) {
if (e.getSource() == alignImportButton) {
- //the name is originated from the server with slash
- String [] sali = selectedAlign.split("/");
- String uniqueId = sali[sali.length-2].concat(sali[sali.length-1]);
+ if(selectedAlign == null) {
+ JOptionPane.showMessageDialog(null, "Choose an alignment ID from list!","Warning",2);
+ return;
+ }
+ //the name originated from the server is a URL so slashes are used
+ //String [] sali = selectedAlign.split("/");
+ //String uniqueId = sali[sali.length-2].concat(sali[sali.length-1]);
+
+ FileWriter out = null;
+
+ String inputName = null;
- if(online) {
-
- if(selectedAlign == null)
- JOptionPane.showMessageDialog(null, "Choose an alignment ID from list!","Warning",2);
- else {
+
+ //export to local List
+ String rdfalignStr = onAlign.getRDFAlignment( selectedAlign );
+ String alignKey = alignFolder.getAbsolutePath() + File.separator + getNewAlignId();
+
+ String rdfPath = alignKey + ".rdf";
+
+ try {
+
+ File rdfFile = new File( rdfPath );
+ out = new FileWriter( rdfFile );
+ out.write( rdfalignStr );
+ //out.write( answer );
+ out.close();
+ File file = new File(rdfPath);
+ AlignmentParser ap = new AlignmentParser(1);
+ Alignment align = ap.parse(file.toURI().toString());
+
+ SWTInterface.alignmentTable.put( alignKey , (Alignment)align );
+
+ String[] list = offAlign.getAllAlign( );
+
+ if(list!=null) {
+ localAlignIdList = new String[1];
+ localAlignBox.removeAllItems();
+
+ for(int i=0; i< list.length; i++){
+ if(list[i].equals(alignKey)) {
+ localAlignIdList[0]= list[i];
+ localAlignBox.addItem(list[i]);
+ break;
+ }
+ }
+
+ if(localAlignIdList.length > 0) {
+ selectedLocalAlign = localAlignIdList[0];
+ }
+ }
+
+ System.out.println("saved local align. ");
+
+ corrList = getCorresFromAnswer( align );
+
+ System.out.println("corrList Size="+corrList.size());
+
+ pane2.removeAll();
+ for(int i=0;i< corrList.size();i++) {
+
+ String[] li= (String [])corrList.get(i);
+ String n = "";
+ for(int j=0;j<li.length;j++)
+ {
+ String sep = "";
+ if(n.equals("")) sep = "==>"; else if(n.equals("=")) sep = ""; else sep = "----";
+
+ if (li[j]!=null)
+ n = n + sep+ li[j];
+ }
+
+ System.out.println("line= "+ n);
+ JTextArea header1= new JTextArea(n);
+
+ pane2.add(header1);
+ }
+
+ }
+ catch ( Exception ex ) { ex.printStackTrace();};
+
+ //get align from server, then export it as owl onto
+ String owlPath = ontoFolder.getAbsolutePath() + File.separator + getNewAlignId() + ".owl";
+
String owlalignStr = onAlign.getOWLAlignment( selectedAlign );
-
- if(owlalignStr==null) JOptionPane.showMessageDialog(null, "Alignment can not be exported.","Warning",2);
- else {
+
+
+ if(owlalignStr==null) {
+ JOptionPane.showMessageDialog(null, "Alignment cannot be exported.","Warning",2);
+ return;
+ }
- String inputName = null;
- //Store it
- FileWriter out = null;
+
try {
- do {
- inputName = JOptionPane.showInputDialog(null, "Enter a project name", "AlignmentProject");
- }
- while (inputName==null || inputName.equals(""));
+
+
+ inputName = JOptionPane.showInputDialog(null, "Enter a project name", "AlignmentProject");
+
+ if (inputName==null || inputName.equals("")) return;
String[] projects = DatamodelPlugin.getDefault().getOntologyProjects();
if(projects!=null) {
@@ -664,31 +727,31 @@ public class SWTInterface extends JPanel {
if(projects[i].equals(inputName)) {
found = true;break;
}
-
}
- if(!found)
- ProjectControl.getDefault().createNewOntologyProject(inputName, new String[0]);
+ if(!found) {
+
+ Properties proper = new Properties();
+ proper.put(IConfig.ONTOLOGY_LANGUAGE.toString(), IConfig.OntologyLanguage.OWL.toString());
+ new CreateProject( inputName, DatamodelTypes.RAM, proper ).run();
+ }
}
- File owlFile = new File( uniqueId + ".owl");
+ File owlFile = new File( owlPath );
out = new FileWriter( owlFile );
out.write( owlalignStr );
//out.write( answer );
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(inputName, uniqueId + ".owl", null, null);
- ieControl.addOntologies2Project(importedModules, inputName);
+ try {
+ ImportExportControl ieControl = new ImportExportControl();
+ String[] importedModules = ieControl.importFileSystem(inputName, "file:" + owlPath, null);
+
+ //ieControl.addOntologies2Project(importedModules, inputName);
+ } catch ( ControlException ex ) { }
- }
- catch ( Exception ex ) { ex.printStackTrace();};
- }
- }
- }
-
+ }
+ catch ( Exception ex ) { ex.printStackTrace();}
+
}
};
});
@@ -703,15 +766,17 @@ public class SWTInterface extends JPanel {
//onAlign = new OnlineAlign(selectedPort, selectedHost);
if(online) {
String aa = onAlign.getAllAlign();
- if(aa == null)
+ if(aa == null) {
JOptionPane.showMessageDialog(null, "Impossible connection!","Warning",2);
- else {
- String[] list = getResultsFromAnswer( aa , "alid", null );
+ return;
+ }
+
+ 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++){
+ for(int i=0; i< list.length; i++){
alignIdList[i]= list[i];
alignBox.addItem(list[i]);
}
@@ -720,7 +785,23 @@ public class SWTInterface extends JPanel {
selectedAlign = alignIdList[0];
}
- }
+
+
+ String[] list1 = offAlign.getAllAlign( );
+ if(list1!=null) {
+ localAlignIdList = new String[list1.length];
+ localAlignBox.removeAllItems();
+
+ for(int i=0; i< list1.length; i++){
+ localAlignIdList[i]= list1[i];
+ localAlignBox.addItem(list1[i]);
+ }
+
+ if(localAlignIdList.length > 0) {
+ selectedLocalAlign = localAlignIdList[0];
+ }
+ }
+
}
else { //offline
String[] list = offAlign.getAllAlign( );
@@ -750,7 +831,7 @@ public class SWTInterface extends JPanel {
// for connecting to server
//onAlign = new OnlineAlign(selectedPort, selectedHost);
- if(selectedNeOnOnto1 == null || selectedNeOnOnto2 == null )
+ if(selectedOnto1 == null || selectedOnto2 == null )
JOptionPane.showMessageDialog(null, "Choose two ontologies from lists!","Warning",2);
else {
@@ -779,22 +860,22 @@ public class SWTInterface extends JPanel {
};
});
- alignTrimButton = new JButton("Trim an alignment", null);
- alignTrimButton.setEnabled(false);
- alignTrimButton.addActionListener(new ActionListener(){
+ serverAlignTrimButton = new JButton("Trim", null);
+ serverAlignTrimButton.setEnabled(false);
+ serverAlignTrimButton.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent e) {
- if (e.getSource() == alignTrimButton) {
+ if (e.getSource() == serverAlignTrimButton) {
- if(online) {
+
//onAlign = new OnlineAlign(selectedPort, selectedHost);
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(""));
+
+ thres = JOptionPane.showInputDialog(null, "Enter a threshold ", "0.5");
+
+ if (thres==null || thres.equals("")) return;
String at = onAlign.trimAlign(selectedAlign, thres);
@@ -816,16 +897,25 @@ public class SWTInterface extends JPanel {
}
}
}
- }
- else { //offline
+
+ }
+ };
+ });
+
+ localAlignTrimButton = new JButton("Trim", null);
+ localAlignTrimButton.setEnabled(false);
+ localAlignTrimButton.addActionListener(new ActionListener(){
+ public void actionPerformed(ActionEvent e) {
+ if (e.getSource() == localAlignTrimButton) {
+
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 thres = JOptionPane.showInputDialog(null, "Enter a threshold ", "0.5");
+
+ if (thres==null || thres.equals("")) return;
String resId = offAlign.trimAndExportAlign( new Double(thres), selectedLocalAlign );
@@ -838,13 +928,13 @@ public class SWTInterface extends JPanel {
selectedLocalAlign = localAlignIdList[0];
}
- }
+
}
};
- });
+ });
//store an alignment on server or locally
- alignStoreButton = new JButton("Store an alignment in the server", null);
+ alignStoreButton = new JButton("Store", null);
alignStoreButton.setEnabled(false);
alignStoreButton.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent e) {
@@ -872,7 +962,7 @@ public class SWTInterface extends JPanel {
public void actionPerformed(ActionEvent e) {
if (e.getSource() == ontoRefresh) {
- refreshOntoList();
+ onto_proj = refreshOntoList();
}
};
@@ -884,16 +974,24 @@ public class SWTInterface extends JPanel {
mapButton.addActionListener(new ActionListener(){
public void actionPerformed(ActionEvent e) {
if (e.getSource() == mapButton) {
- if (selectedNeOnOnto1 == null || selectedNeOnOnto2 == null )
- {JOptionPane.showMessageDialog(null, "Choose two ontologies from lists ","Warning",2);
- }
- else {
-
- if(online) {
-
+ if (selectedOnto1 == null || selectedOnto2 == null ) {
+ JOptionPane.showMessageDialog(null, "Choose two ontologies from lists ","Warning",2);
+ return;
+ }
+
+
+ if(online) {
+ if (!selectedOnto1.startsWith("http://") || !selectedOnto2.startsWith("http://") ) {
+ JOptionPane.showMessageDialog(null, "URLs for ontologies are required. ","Warning",2);
+ return;
+ }
+
String answer = onAlign.getAlignId( matchMethod, selectedOnto1, selectedOnto2 );
- if(answer==null) JOptionPane.showMessageDialog(null, "Alignment is not produced.","Warning",2);
- else {
+ if(answer==null) {
+ JOptionPane.showMessageDialog(null, "Alignment is not produced.","Warning",2);
+ return;
+ }
+
alignIdList = getResultsFromAnswer( answer, "alid", null );
if(alignIdList==null || alignIdList[0].equals("null")) JOptionPane.showMessageDialog(null, "Alignment is not produced.","Warning",2);
@@ -911,85 +1009,35 @@ public class SWTInterface extends JPanel {
}
}
- //retrieve alignment for displaying
- String res = onAlign.getHTMLAlignment( alignIdList[0] );
- corrList = getCorresFromAnswer( res, "tr", null ); //"#"
-
- System.out.println("corrList Size="+corrList.size());
-
- pane2.removeAll();
- for(int i=0;i< corrList.size();i++) {
-
- String[] li= (String [])corrList.get(i);
- String n = "";
- for(int j=0;j<li.length;j++)
- {
- String sep = "";
- if(n.equals("")) sep = "==>"; else if(n.equals("=")) sep = ""; else sep = "----";
-
- if (li[j]!=null)
- n = n + sep+ li[j];
- }
-
- System.out.println("line= "+ n);
- JTextArea header1= new JTextArea(n);
-
- pane2.add(header1);
- }
- }
+
+
}
else { //offline
- String resId = offAlign.matchAndExportAlign( matchMethod, selectedNeOnOnto1, selectedNeOnOnto2);
+ String resId = offAlign.matchAndExportAlign( matchMethod, onto_proj.get(selectedOnto1), selectedOnto1, onto_proj.get(selectedOnto2), selectedOnto2);
localAlignBox.removeAllItems();
localAlignIdList = new String[1];
//File f1 = new File(resId);
- localAlignIdList[0] = resId;//"file:" + f1.getAbsolutePath();
+ localAlignIdList[0] = resId;//"file:" + f1.getAbsolutePath();
localAlignBox.addItem(localAlignIdList[0]);
selectedLocalAlign = localAlignIdList[0];
-
- String htmlString = OfflineAlign.fileToString(new File ( resId + ".html"));
-
- System.out.println("htmlString =" + htmlString);
- corrList = getCorresFromAnswer( htmlString, "tr", null );
-
- System.out.println("corrList Size="+corrList.size());
-
- pane2.removeAll();
-
- for(int i=0;i< corrList.size();i++) {
- String[] li= (String [])corrList.get(i);
- String n = "";
- for(int j=0;j<li.length;j++)
- {
- String sep = "";
- if(n.equals("")) sep = "==>"; else if(n.equals("=")) sep = ""; else sep = "----";
-
- if (li[j]!=null)
- n = n + sep+ li[j];
- }
-
- System.out.println("line= ="+ n);
- JTextArea header1= new JTextArea(n);
-
- pane2.add(header1);
- }
-
-
+ System.out.println("offline matching done. ");
+
+
} //else for ""offline"
- }
- }
+ } // getsource
+
};
});
//retrieve all available onto. in Ontology Navigator
- ontoLabel1 = new JLabel("Ontology 1 :");
+ ontoLabel1 = new JLabel("Ontology 1 ");
ontoBox1 = new JComboBox(ontoList);
ontoBox1.setEnabled(false);
ontoBox1.setMaximumRowCount(20);
@@ -1001,14 +1049,14 @@ public class SWTInterface extends JPanel {
id = ontoBox1.getSelectedIndex();
selectedOnto1 = ontoList[id];
- selectedNeOnOnto1 = NeOnOntoList[id];
+ //selectedNeOnOnto1 = NeOnOntoList[id];
System.out.println("Onto1 selected =" + selectedOnto1);
}
});
- ontoLabel2 = new JLabel("Ontology 2 :");
+ ontoLabel2 = new JLabel("Ontology 2 ");
ontoBox2 = new JComboBox(ontoList);
ontoBox2.setEnabled(false);
ontoBox2.setMaximumRowCount(20);
@@ -1020,7 +1068,7 @@ public class SWTInterface extends JPanel {
id = ontoBox2.getSelectedIndex();
selectedOnto2 = ontoList[id];
- selectedNeOnOnto2 = NeOnOntoList[id];
+ //selectedNeOnOnto2 = NeOnOntoList[id];
System.out.println("Onto2 selected =" + selectedOnto2);
@@ -1028,7 +1076,7 @@ public class SWTInterface extends JPanel {
});
- strat= new JLabel("Alignment methods");
+ strat= new JLabel("Methods ");
strategy = new JComboBox(methodList);
strategy.setEnabled(false);
strategy.setMaximumRowCount(20);
@@ -1039,9 +1087,9 @@ public class SWTInterface extends JPanel {
ind = strategy.getSelectedIndex();
matchMethod = methodList[ind];
- aux[2] = methodList[ind];
+ //aux[2] = methodList[ind];
- System.out.println("method selected ="+aux[2]);
+ System.out.println("method selected =" + matchMethod);
}
});
@@ -1096,20 +1144,7 @@ private JPanel createPhraseList () {
minusLabel.add(onlineButton);
minusLabel.add(offlineButton);
- //minusLabel.add(alignProjLabel);
- //minusLabel.add(alignProj);
-
- zeroLabel.add(hostName);
-
- zeroLabel.add(hostField);
- zeroLabel.add(portName);
- zeroLabel.add(portField);
-
- zeroLabel.add(connButton);
- zeroLabel.add(disconnButton);
-
- //oneLabel.add(openbutton1);
- //oneLabel.add(fileName1);
+
oneLabel.add(ontoLabel1);
oneLabel.add(ontoBox1);
@@ -1127,25 +1162,25 @@ private JPanel createPhraseList () {
fourLabel.add(alignLabel);
fourLabel.add(alignBox);
fourLabel.add(alignImportButton);
+ fourLabel.add(serverAlignTrimButton);
+ fourLabel.add(alignStoreButton);
four2Label.add(localAlignLabel);
four2Label.add(localAlignBox);
four2Label.add(localAlignImportButton);
+ four2Label.add(localAlignTrimButton);
four2Label.add(alignUploadButton);
- //sixLabel.add(thresLabel);
- //sixLabel.add(threshold);
- sixLabel.add(alignTrimButton);
-
+
fiveLabel.add(alignFindButton);
//sevenLabel.add(alignRetrieveButton);
- eightLabel.add(alignStoreButton);
+ //eightLabel.add(alignStoreButton);
nineLabel.add(allAlignButton);
//label_three.add(resButton);
phrasePane.add(minusLabel);
- phrasePane.add(zeroLabel);
+ //phrasePane.add(zeroLabel);
phrasePane.add(oneLabel);
phrasePane.add(twoLabel);
@@ -1154,11 +1189,10 @@ private JPanel createPhraseList () {
phrasePane.add(four2Label);
phrasePane.add(nineLabel);
- phrasePane.add(sixLabel);
+ //phrasePane.add(sixLabel);
phrasePane.add(fiveLabel);
- //phrasePane.add(sevenLabel);
- phrasePane.add(eightLabel);
+
return phrasePane;
@@ -1167,8 +1201,8 @@ private JPanel createPhraseList () {
public void createThirdPane(){
-Res = createListCharac();
-Res.setBorder(BorderFactory.createEmptyBorder (10, 5, 10, 5) );
+ Res = createListCharac();
+ Res.setBorder(BorderFactory.createEmptyBorder (10, 5, 10, 5) );
}
private JPanel createListCharac () {
@@ -1177,69 +1211,65 @@ return pane2;
}
-
-private void refreshOntoList() {
+//This function fetches all ontologies
+private HashMap<String,String> refreshOntoList() {
- Vector<String> vec = new Vector<String>();
+ HashMap<String,String> vec = new HashMap<String,String>();
try {
String[] projects = DatamodelPlugin.getDefault().getOntologyProjects();
+ if(projects != null) {
for(int i=0; i < projects.length; i++) {
//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]);
+ if(projects[i]!=null) { System.out.printf("Project Onto "+ i +" = " + projects[i] );
+
+ //URI[] uris= DatamodelPlugin.getDefault().getProjectOntologyFiles(projects[i]);
+ KAON2Connection connection = DatamodelPlugin.getDefault().getKaon2Connection(projects[i]);
+ Set<String> strSet = connection.getAvailableOntologyURIs();
+ String[] uris = (String[])strSet.toArray(new String[0]);
+
+ for(int k=0; k < uris.length; k++) {
+
+ System.out.printf(" Onto file = " + uris[k]);
+
+ vec.put(uris[k],projects[i]);
+ //NeOnOntoList = DatamodelPlugin.getDefault().getProjectOntologies(projects[i]);
+ }
}
//}
//}
}
-
+ }
+ else {
+ System.out.printf("No Ontology Project !" );
+ return null;
+ }
} catch ( Exception ex ) { ex.printStackTrace();};
ontoBox1.removeAllItems();
ontoBox2.removeAllItems();
- ontoList = new String[ vec.size() ];
- for(int j=0; j < vec.size(); j++) {
-
- String str = vec.get(j);
-
- String st1 = str.replace('\"',' ');
- st1 = st1.replace('\'',' ');
- st1 = st1.replace('#',' ');
- String[] stSplit = st1.split(" ");
- String st="";
- for(int i=0; i <stSplit.length; i++)
- st=st+stSplit[i];
-
- // rethink !!!
- stSplit = st.split(".owl");
- st = stSplit[0]+ ".owl";
-
- //System.out.printf("res st = " + stSplit[0] );
+ String[] keys = (String[]) vec.keySet().toArray(new String[0]);
+
+ ontoList = new String[ keys.length ];
+
+ for(int j=0; j < keys.length; j++) {
+
+ ontoBox1.addItem(keys[j]);
+ ontoBox2.addItem(keys[j]);
+ ontoList[j] = keys[j];
- /*
- //rethink !!!
- String str1 = str.substring(1, str.length() - 1);
- int ins = str1.lastIndexOf('/');
- String str2 = str1.substring(0, ins + 1);
- String str3 = str1.substring(ins + 4, str1.length());
- String st = str2.concat(str3);
- */
- ontoBox1.addItem(st);
- ontoBox2.addItem(st);
- ontoList[j] = st;
if(ontoList.length > 0) {
selectedOnto1 = ontoList[0];
selectedOnto2 = ontoList[0];
- selectedNeOnOnto1 = NeOnOntoList[0];
- selectedNeOnOnto2 = NeOnOntoList[0];
+ //selectedNeOnOnto1 = NeOnOntoList[0];
+ //selectedNeOnOnto2 = NeOnOntoList[0];
}
}
+ return vec;
}
@@ -1257,7 +1287,7 @@ private void refreshOntoList() {
answer = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" + answer;
System.out.println( answer );
try {
- File messageFile = new File("messageFile");
+ File messageFile = new File(basicFolder.getAbsolutePath() + basicFolder.separator + "messageFile");
FileWriter out = new FileWriter(messageFile);
out.write( answer );
out.close();
@@ -1268,7 +1298,7 @@ private void refreshOntoList() {
try {
System.out.println( "Parsing for getting result: "+ type +" ... ");
- doc = parse(new File("messageFile"));
+ doc = parse(new File(basicFolder.getAbsolutePath() + basicFolder.separator + "messageFile"));
Element e = doc.getDocumentElement();
@@ -1302,6 +1332,43 @@ private void refreshOntoList() {
//System.out.println( answer );
}
+ public static Vector<String[]> getCorresFromAnswer( Alignment align ) {
+
+ ArrayList<Cell> cells = ((BasicAlignment)align).getArrayElements();
+ Vector<String[]> names = new Vector<String[]>(cells.size() + 1 );
+
+ String[] corr = new String[4];
+ corr[0] = "Object1";
+
+ corr[1] = "Relation";
+ corr[2] = "Strength";
+ corr[3] = "Object2";
+
+ names.add(corr);
+
+ for(int i=0; i<cells.size(); i++) {
+ try {
+
+ corr = new String[4];
+
+ corr[0] = cells.get(i).getObject1AsURI().toString();
+ //by default : equivalence
+
+ //corr[1] = cells.get(i).getRelation().toString();
+ corr[1] = "=";
+ corr[2] = (new Double(cells.get(i).getStrength())).toString();
+ corr[3] = cells.get(i).getObject2AsURI().toString();
+ names.add(corr);
+
+ }catch (Exception e) {}
+
+ }
+ return names;
+
+ }
+
+
+
public static Vector<String[]> getCorresFromAnswer( String answer, String type ,String separator) {
Document doc=null;
@@ -1311,7 +1378,7 @@ private void refreshOntoList() {
answer = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>" + answer;
//System.out.println( answer );
try {
- File messageFile = new File("messageFile");
+ File messageFile = new File(basicFolder.getAbsolutePath() + File.separator + "messageFile");
FileWriter out = new FileWriter(messageFile);
out.write( answer );
out.close();
@@ -1322,7 +1389,7 @@ private void refreshOntoList() {
try {
//System.out.println( "parsing ... ");
- doc = parse(new File("messageFile"));
+ doc = parse(new File(basicFolder.getAbsolutePath() + File.separator + "messageFile"));
Element e = doc.getDocumentElement();
NodeList m = e.getElementsByTagName("table");
Element cor = (Element)m.item(1);