Mentions légales du service

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Commit 1a3a3b26 authored by Chan Leduc's avatar Chan Leduc
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--For NTK 1.2.3

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plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/AlignView.java
+ 203
− 133
View file @ 1a3a3b26
......@@ -21,13 +21,15 @@
package fr.inrialpes.exmo.align.plugin.neontk;
import org.eclipse.swt.SWT;
import java.lang.ClassNotFoundException;
import java.io.File;
import java.io.File;
import java.io.FileWriter;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.net.URI;
import java.net.URL;
......@@ -42,6 +44,7 @@ import java.util.jar.Attributes.Name;
import java.util.jar.Attributes;
import java.util.jar.Manifest;
import java.util.jar.JarFile;
import java.util.jar.JarEntry;
import java.util.zip.ZipEntry;
import java.util.Enumeration;
import java.util.Dictionary;
......@@ -66,41 +69,33 @@ import org.eclipse.ui.forms.widgets.TableWrapData;
import org.eclipse.swt.widgets.Composite;
import org.eclipse.swt.widgets.Display;
import org.eclipse.core.resources.IWorkspaceRoot;
import org.eclipse.core.runtime.IPath;
import org.eclipse.core.runtime.Path;
import org.eclipse.core.runtime.FileLocator;
import org.eclipse.jface.dialogs.MessageDialog;
import org.eclipse.core.resources.ResourcesPlugin;
import org.osgi.framework.Bundle;
import org.eclipse.core.runtime.Path;
import org.eclipse.core.runtime.FileLocator;
//import org.eclipse.jface.dialogs.MessageDialog;
//import org.semanticweb.kaon2.api.OntologyManager;
import org.semanticweb.kaon2.api.OntologyManager;
import org.semanticweb.owl.align.Alignment;
import org.semanticweb.owl.align.AlignmentVisitor;
//import com.ontoprise.config.IConfig;
import org.neontoolkit.core.NeOnCorePlugin;
//import org.neontoolkit.datamodel.DatamodelPlugin;
//import org.neontoolkit.core.DatamodelTypes;
//import com.ontoprise.ontostudio.datamodel.exception.ControlException;
import org.neontoolkit.core.command.project.CreateProject;
import org.neontoolkit.core.project.IOntologyProject;
import org.neontoolkit.core.project.OntologyProjectManager;
import org.neontoolkit.io.util.ImportExportUtils;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.OWLOntology;
import com.ontoprise.ontostudio.owl.model.OWLManchesterProjectFactory;
import com.ontoprise.config.IConfig;
import com.ontoprise.ontostudio.datamodel.DatamodelPlugin;
import com.ontoprise.ontostudio.datamodel.DatamodelTypes;
import com.ontoprise.ontostudio.datamodel.exception.ControlException;
import com.ontoprise.ontostudio.gui.commands.project.CreateProject;
import com.ontoprise.ontostudio.io.ImportExportControl;
import fr.inrialpes.exmo.align.impl.ObjectAlignment;
import fr.inrialpes.exmo.align.impl.URIAlignment;
import fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor;
import fr.inrialpes.exmo.align.impl.renderer.OWLAxiomsRendererVisitor;
import fr.inrialpes.exmo.align.onto.OntologyFactory;
//import fr.inrialpes.exmo.align.onto.owlapi10.OWLAPIOntologyFactory;
import fr.inrialpes.exmo.align.parser.AlignmentParser;
import fr.inrialpes.exmo.align.plugin.neontk.AlignFormLayoutFactory;
import fr.inrialpes.exmo.align.plugin.neontk.AlignFormSectionFactory;
......@@ -158,7 +153,6 @@ public class AlignView extends ViewPart
public File ontoFolder = null;
public File alignFolder = null;
public static File basicFolder = null;
@Override
public void createPartControl(final Composite parent) {
......@@ -177,8 +171,6 @@ public class AlignView extends ViewPart
//createMUPSSection(composite, formToolkit);
//createInconsistencyResultSection(composite, formToolkit);
//this.refreshProjectList();
//IWorkbench wb = AlignmentPlugin.getDefault().getWorkbench();
IWorkspaceRoot root = org.eclipse.core.resources.ResourcesPlugin.getWorkspace().getRoot();
IPath location = root.getLocation();
String path = location.toOSString();
......@@ -408,7 +400,7 @@ public class AlignView extends ViewPart
//System.out.println(" html with alignKey="+alignKey);
htmlBrowser.setText("");
formToolkit.paintBordersFor(htmlClient);
//I do not know why it no longer works if URI casting is put here!!!
Alignment align = AlignView.alignmentTable.get(alignKey);
StringWriter htmlMessage = null;
......@@ -641,10 +633,11 @@ public class AlignView extends ViewPart
}
}
else { //offline
String resId = offlineAlign.matchAndExportAlign( selectedMethod, ontoByProj.get(selectedOnto1), selectedOnto1, ontoByProj.get(selectedOnto2), selectedOnto2);
localAlignBox.setEnabled( true );
localAlignBox.add(resId, 0);
localAlignBox.setEnabled( true );
localImportButton.setEnabled( true );
localTrimButton.setEnabled( true );
selectedLocalAlign = resId;
......@@ -767,9 +760,7 @@ public class AlignView extends ViewPart
return;
}
String[] projects = OntologyProjectManager.getDefault().getOntologyProjects();
//String[] projects = DatamodelPlugin.getDefault().getOntologyProjects();
String[] projects = DatamodelPlugin.getDefault().getOntologyProjects();
if(projects!=null) {
boolean found = false;
......@@ -780,15 +771,15 @@ public class AlignView extends ViewPart
}
}
if(!found) {
//Properties proper = new Properties();
//proper.put(IConfig.ONTOLOGY_LANGUAGE.toString(), IConfig.OntologyLanguage.OWL.toString());
new CreateProject( inputName, OWLManchesterProjectFactory.FACTORY_ID, new Properties()).run();
//new CreateProject( inputName, DatamodelTypes.RAM, proper ).run();
if(!found) {
Properties proper = new Properties();
proper.put(IConfig.ONTOLOGY_LANGUAGE.toString(), IConfig.OntologyLanguage.OWL.toString());
new CreateProject( inputName, DatamodelTypes.RAM, proper ).run();
} else {
MessageDialog.openError(this.getSite().getShell(), "Error message", "Project name is already existing!");
return;
}
}
String owlPath = ontoFolder.getAbsolutePath() + File.separator + getNewAlignId() + ".owl";
......@@ -799,13 +790,7 @@ public class AlignView extends ViewPart
out.write( owlalignStr );
out.flush();
out.close();
ImportExportUtils ieControl = new ImportExportUtils();
URI uris[] = new URI[1];
uris[0] = new File(owlPath).toURI();
ieControl.copyOntologyFileToProject(uris[0].toString(), inputName);
/*
try {
ImportExportControl ieControl = new ImportExportControl();
URI uris[] = new URI[1];
......@@ -814,7 +799,7 @@ public class AlignView extends ViewPart
//ieControl.addOntologies2Project(importedModules, inputName);
} catch ( ControlException ex ) { }
*/
}
catch ( Exception ex ) { ex.printStackTrace();}
......@@ -846,7 +831,7 @@ public class AlignView extends ViewPart
return;
}
String[] projects = OntologyProjectManager.getDefault().getOntologyProjects();
String[] projects = DatamodelPlugin.getDefault().getOntologyProjects();
if(projects!=null) {
boolean found = false;
......@@ -858,20 +843,19 @@ public class AlignView extends ViewPart
}
if(!found) {
//Properties proper = new Properties();
//proper.put(IConfig.ONTOLOGY_LANGUAGE.toString(), IConfig.OntologyLanguage.OWL.toString());
new CreateProject( inputName, OWLManchesterProjectFactory.FACTORY_ID, new Properties()).run();
//new CreateProject( inputName, DatamodelTypes.RAM, proper ).run();
Properties proper = new Properties();
proper.put(IConfig.ONTOLOGY_LANGUAGE.toString(), IConfig.OntologyLanguage.OWL.toString());
new CreateProject( inputName, DatamodelTypes.RAM, proper ).run();
} else {
MessageDialog.openError(this.getSite().getShell(), "Error message", "Project name is already existing!");
return;
}
//ImportExportControl ieControl = new ImportExportControl();
ImportExportUtils ieControl = new ImportExportUtils();
ImportExportControl ieControl = new ImportExportControl();
URI uris[] = new URI[1];
uris[0] = new File(fn.getAbsolutePath()).toURI();
ieControl.copyOntologyFileToProject(uris[0].toString(), inputName);
//ieControl.importFileSystem(inputName, uris, null);
ieControl.importFileSystem(inputName, uris, null);
}
}
......@@ -995,35 +979,42 @@ public class AlignView extends ViewPart
}
/**
* This function is taken from Alignment Server
* This function is taken from Alignment Server with processing Jar in Jar
*/
public static void implementations( Class tosubclass, Set<String> list , String cp, boolean debug ){
Set<String> visited = new HashSet<String>();
//String classPath = System.getProperty("java.class.path",".");
String classPath = cp;
int count=0;
// Hack: this is not necessary
//classPath = classPath.substring(0,classPath.lastIndexOf(File.pathSeparatorChar));
//System.out.println("classes="+classPath);
//StringTokenizer tk = new StringTokenizer(classPath,File.pathSeparator);
StringTokenizer tk = new StringTokenizer(classPath, ":" );
StringTokenizer tk = new StringTokenizer(classPath, "," );
//System.out.println("classPath for Impl.="+ classPath );
classPath = "";
while ( tk != null && tk.hasMoreTokens() ){
while ( tk != null && tk.hasMoreTokens() ) {
StringTokenizer tk2 = tk;
tk = null;
//System.out.println( "path" + tk2.toString());
// Iterate on Classpath
while ( tk2.hasMoreTokens() ) {
try {
File file = new File( tk2.nextToken() );
URI nn = new URI( tk2.nextToken() );
//System.out.println("token="+ nn);
File file = new File( nn );
if ( file.isDirectory() ) {
//System.err.println("DIR "+file);
String subs[] = file.list();
for(int index = 0 ; index < subs.length ; index ++ ){
//System.out.println(" "+subs[index]);
//System.out.println("DIR "+file);
String subs[] = file.list();
for(int index = 0 ; index < subs.length ; index ++ ){
//System.out.println("subs= "+subs[index]);
// IF class
if ( subs[index].endsWith(".class") ) {
String classname = subs[index].substring(0,subs[index].length()-6);
//System.out.println("classname= "+classname);
if (classname.startsWith(File.separator))
classname = classname.substring(1);
classname = classname.replace(File.separatorChar,'.');
......@@ -1050,24 +1041,29 @@ public class AlignView extends ViewPart
}
}
}
} else if ( file.toString().endsWith(".jar") &&
} else if ( (file.toString().endsWith(".jar") ) &&
!visited.contains( file.toString() ) &&
file.exists() ) {
if ( debug ) System.err.println("JAR "+file);
visited.add( file.toString() );
try {
JarFile jar = new JarFile( file );
Enumeration enumeration = jar.entries();
while( enumeration.hasMoreElements() ){
String classname = enumeration.nextElement().toString();
if ( debug ) System.err.println(" "+classname);
while( enumeration.hasMoreElements() ) {
JarEntry je = (JarEntry)enumeration.nextElement();
String classname = je.toString();
int len = classname.length()-6;
if( len > 0 && classname.substring(len).compareTo(".class") == 0) {
if( len > 0 && classname.substring(len).compareTo(".class") == 0 ) {
classname = classname.substring(0,len);
// Beware, in a Jarfile the separator is always "/"
// and it would not be dependent on the current system anyway.
//classname = classname.replaceAll(File.separator,".");
classname = classname.replaceAll("/",".");
//System.out.println("classname in jar = "+classname);
try {
if ( classname.equals("org.apache.xalan.extensions.ExtensionHandlerGeneral") ) throw new ClassNotFoundException( "Stupid JAVA/Xalan bug");
Class cl = Class.forName(classname);
......@@ -1086,8 +1082,67 @@ public class AlignView extends ViewPart
} catch (ExceptionInInitializerError eiie) {
// This one has been added for OMWG, this is a bad error
}
}
}
} else if( classname.endsWith(".jar") ) {
//If jarEntry is a jarfile
//System.out.println( "jarEntry is a jarfile="+je.getName() );
InputStream jarSt = jar.getInputStream( (ZipEntry)je );
File f = new File("tmpFileXXX"+ count++);
try {
OutputStream out=new FileOutputStream( f );
byte buf[]=new byte[1024];
int len1 ;
while( (len1 = jarSt.read(buf))>0 )
out.write(buf,0,len1);
out.close();
jarSt.close();
}
catch (IOException e){
System.err.println( "Cannot write tmp data!" );
}
JarFile inJar = new JarFile( f );
Enumeration enumeration2 = inJar.entries();
while( enumeration2.hasMoreElements() ) {
JarEntry je2 = (JarEntry)enumeration2.nextElement();
String classname2 = je2.toString();
int len3 = classname2.length()-6;
if( len3 > 0 && classname2.substring(len3).compareTo(".class") == 0 ) {
classname2 = classname2.substring(0,len3);
// Beware, in a Jarfile the separator is always "/"
// and it would not be dependent on the current system anyway.
//classname = classname.replaceAll(File.separator,".");
classname2 = classname2.replaceAll("/",".");
//System.out.println("classname in jar in jar = "+classname2);
try {
if ( classname2.equals("org.apache.xalan.extensions.ExtensionHandlerGeneral") ) throw new ClassNotFoundException( "Stupid JAVA/Xalan bug");
Class cl = Class.forName(classname2);
Class[] ints = cl.getInterfaces();
for ( int i=0; i < ints.length ; i++ ){
if ( ints[i] == tosubclass ) {
//System.out.println(classname2 + " added");
list.add( classname2 );
}
}
} catch ( NoClassDefFoundError ncdex ) {
} catch ( ClassNotFoundException cnfex ) {
} catch ( UnsatisfiedLinkError ule ) {
} catch (ExceptionInInitializerError eiie) {
// This one has been added for OMWG, this is a bad error
}
}
}//while
f.delete();
} // else If endWith .jar
// Iterate on needed Jarfiles
// JE(caveat): this deals naively with Jar files,
// in particular it does not deal with section'ed MANISFESTs
......@@ -1102,38 +1157,42 @@ public class AlignView extends ViewPart
// Is there a way to make it iterable???
for( StringTokenizer token = new StringTokenizer(path," \t"); token.hasMoreTokens(); )
//classPath += File.pathSeparator+file.getParent()+File.separator+token.nextToken();
classPath += ":"+file.getParent()+File.separator+token.nextToken();
classPath += ","+file.getParent()+File.separator+token.nextToken();
}
} //while
} catch (NullPointerException nullexp) { //Raised by JarFile
System.err.println("Warning "+file+" unavailable");
}
}
} catch( IOException e ) {
} catch( Exception e ) {
continue;
}
}
if ( !classPath.equals("") ) {
//tk = new StringTokenizer(classPath,File.pathSeparator);
tk = new StringTokenizer(classPath,":");
tk = new StringTokenizer(classPath,",");
classPath = "";
}
}
}
}
/**
* This function is taken from Alignment Server
*/
public static Set<String> implementations( String interfaceName, String cp ) {
public static Set<String> implementations( String interfaceName, String cp ) {
Set<String> list = new HashSet<String>();
try {
Class toclass = Class.forName(interfaceName);
Class toclass = Class.forName(interfaceName);
implementations( toclass, list, cp, false );
} catch (ClassNotFoundException ex) {
System.err.println("Class "+interfaceName+" not found!");
}
return list;
}
}
void offlineInit(boolean init) {
online = false;
......@@ -1146,47 +1205,66 @@ public class AlignView extends ViewPart
Bundle bundle = AlignmentPlugin.getDefault().getBundle();
Dictionary dic = bundle.getHeaders();
Set<String> ms = new HashSet<String>();
String classpath = dic.get("Bundle-ClassPath").toString();
//System.out.println("classpath="+ classpath);
URL url = FileLocator.find(AlignmentPlugin.getDefault().getBundle(), new Path(""), null);
try {
url = FileLocator.resolve(url);
}catch (IOException ioe){ }
String[] files = classpath.split(",");
classpath = "";
for(int k=0; k < files.length; k++) {
classpath += url.toString()+files[k]+":";
}
//System.out.println("classpath2="+ classpath);
//System.out.println("url ="+ url.toString() );
Set<String> ms = new HashSet<String>();
ms = implementations( "org.semanticweb.owl.align.AlignmentProcess", classpath );
ms.remove("fr.inrialpes.exmo.align.impl.DistanceAlignment"); // this one is generic
ms.remove("fr.inrialpes.exmo.align.ling.JWNLAlignment"); // requires WordNet
//System.out.println("ms="+ms.size());
String[] methodList = new String[ms.size()];
int j=0;
for(String m : ms) methodList[j++] = m;
if( ! url.toString().startsWith("jar") ) {
String[] files = classpath.split(",");
classpath = "";
for(int k=0; k < files.length; k++) {
//System.out.println("files="+ files[k]);
classpath += url.toString()+files[k]+",";
}
//System.out.println("classpath2="+ classpath);
ms = implementations( "org.semanticweb.owl.align.AlignmentProcess", classpath );
ms.remove("fr.inrialpes.exmo.align.impl.DistanceAlignment"); // this one is generic
ms.remove("fr.inrialpes.exmo.align.ling.JWNLAlignment"); // requires WordNet
//System.out.println("ms="+ms.size());
methodList = new String[ms.size()];
int j=0;
for(String m : ms) methodList[j++] = m;
//methodList[0] = "fr.inrialpes.exmo.align.impl.method.NameEqAlignment";
//methodList[0] = "fr.inrialpes.exmo.align.impl.method.NameEqAlignment";
//methodList[1] = "fr.inrialpes.exmo.align.impl.method.StringDistAlignment";
//methodList[1] = "fr.inrialpes.exmo.align.impl.method.StringDistAlignment";
//methodList[2] = "fr.inrialpes.exmo.align.impl.method.SMOANameAlignment";
//methodList[2] = "fr.inrialpes.exmo.align.impl.method.SMOANameAlignment";
//methodList[3] = "fr.inrialpes.exmo.align.impl.method.SubsDistNameAlignment";
//methodList[3] = "fr.inrialpes.exmo.align.impl.method.SubsDistNameAlignment";
//methodList[4] = "fr.inrialpes.exmo.align.impl.method.StrucSubsDistAlignment";
//methodList[4] = "fr.inrialpes.exmo.align.impl.method.StrucSubsDistAlignment";
//methodList[5] = "fr.inrialpes.exmo.align.impl.method.NameAndPropertyAlignment";
//methodList[5] = "fr.inrialpes.exmo.align.impl.method.NameAndPropertyAlignment";
//methodList[6] = "fr.inrialpes.exmo.align.impl.method.ClassStructAlignment";
//methodList[6] = "fr.inrialpes.exmo.align.impl.method.ClassStructAlignment";
//methodList[7] = "fr.inrialpes.exmo.align.impl.method.EditDistNameAlignment";
} else { // Plugin is a jarfile
//methodList[7] = "fr.inrialpes.exmo.align.impl.method.EditDistNameAlignment";
String path = url.getFile();
//To avoid "!/"
if( ! path.endsWith(".jar") ) path = path.substring( 0, path.length() - 2 );
ms = implementations( "org.semanticweb.owl.align.AlignmentProcess", path);
ms.remove("fr.inrialpes.exmo.align.impl.DistanceAlignment"); // this one is generic
ms.remove("fr.inrialpes.exmo.align.ling.JWNLAlignment"); // requires WordNet
//System.out.println("ms="+ms.size());
methodList = new String[ms.size()];
int j=0;
for(String m : ms) methodList[j++] = m;
}
if(methodList.length > 0) selectedMethod = methodList[0];
methods.removeAll();
......@@ -1270,38 +1348,29 @@ public class AlignView extends ViewPart
HashMap<String,String> vec = new HashMap<String,String>();
//OWLAPIOntologyFactory fact = new OWLAPIOntologyFactory();
OntologyFactory fact = OntologyFactory.getFactory();
try {
String[] projects = OntologyProjectManager.getDefault().getOntologyProjects();
String[] projects = DatamodelPlugin.getDefault().getOntologyProjects();
if(projects != null) {
for(int i=0; i < projects.length; i++) {
if(projects[i]!=null) {
//OntologyManager connection = DatamodelPlugin.getDefault().getKaon2Connection(projects[i]);
//Set<String> strSet = connection.getAvailableOntologyURIs();
IOntologyProject ontoProject = OntologyProjectManager.getDefault().getOntologyProject( projects[i] );
Set<String> strSet = ontoProject.getAvailableOntologyURIs();
OntologyManager connection = DatamodelPlugin.getDefault().getKaon2Connection(projects[i]);
Set<String> strSet = connection.getAvailableOntologyURIs();
String[] uris = (String[])strSet.toArray(new String[0]);
if( !online ) {
for(int k=0; k < uris.length; k++) {
if(uris[k].startsWith("file:"))
if(online) {
for(int k=0; k < uris.length; k++) {
//get only http URL
if(uris[k].startsWith("http://"))
try {
fact.loadOntology(new URI(uris[k]));
vec.put(uris[k],projects[i]);
} catch (Exception ex) {
}
}
} else {
for(int k=0; k < uris.length; k++) {
//get only http URL
//if(uris[k].startsWith("http://")) {
//try {
//fact.loadOntology(new URI(uris[k]));
//vec.put(uris[k],projects[i]);
//} catch (Exception ex) {}
//} else {
vec.put(uris[k],projects[i]);
//}
//vec.put( (uris[k]).toString(), projects[i]);
//vec.put(DatamodelPlugin.getDefault().getPhysicalOntologyUri(projects[i], uris[k]).toString(),projects[i]);
}
vec.put(DatamodelPlugin.getDefault().getPhysicalOntologyUri(projects[i], uris[k]).toString(),projects[i]);
}
}
}
}
......@@ -1331,6 +1400,7 @@ public class AlignView extends ViewPart
return vec;
}
@Override
public void setFocus() {
// TODO Auto-generated method stub
......
plugins/neon/src/fr/inrialpes/exmo/align/plugin/neontk/OnlineAlign.java
+ 4
− 3
View file @ 1a3a3b26
......@@ -319,7 +319,8 @@ public class OnlineAlign {
if(httpConn.HTTP_REQ_TOO_LONG == httpConn.getResponseCode()) System.err.println("Request too long");
}
} catch (Exception ex) {
connected= false; ex.printStackTrace() ; return null;
//connected= false;
ex.printStackTrace() ; return null;
}
return answer;
}
......@@ -371,10 +372,10 @@ public class OnlineAlign {
}
if (in != null) in.close();
String answer = strBuff.toString();
connected = true;
//connected = true;
return answer;
} catch (Exception ex) {
connected = false;
//connected = false;
ex.printStackTrace();
return null;
}
......
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