diff --git a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
index cdc8068e9c63671e50eb048031a7a7aff3b88843..64fec27780a54bba463886c628f146fa75d4f1ae 100644
--- a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
+++ b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
@@ -50,6 +50,9 @@ import java.lang.UnsatisfiedLinkError;
import java.lang.ExceptionInInitializerError;
import java.lang.reflect.InvocationTargetException;
import java.io.ByteArrayOutputStream;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.io.FileOutputStream;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.io.BufferedWriter;
@@ -71,6 +74,7 @@ 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;
/**
@@ -187,10 +191,10 @@ public class AServProtocolManager {
boolean todiscard = false;
Properties params = mess.getParameters();
// load the alignment
- String name = (String)params.getProperty("url");
+ String name = params.getProperty("url");
String file = null;
if ( name == null || name.equals("") ){
- file = (String)params.getProperty("filename");
+ file = params.getProperty("filename");
if ( file != null && !file.equals("") ) name = "file://"+file;
}
//if ( debug > 0 ) System.err.println("Preparing for "+name);
@@ -205,7 +209,7 @@ public class AServProtocolManager {
}
// We preserve the pretty tag within the loaded ontology
String pretty = al.getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
- if ( pretty == null ) pretty = (String)params.getProperty("pretty");
+ if ( pretty == null ) pretty = params.getProperty("pretty");
if ( pretty != null && !pretty.equals("") ) {
al.setExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY, pretty );
}
@@ -259,15 +263,15 @@ public class AServProtocolManager {
*/
private Message retrieveAlignment( Message mess ){
Properties params = mess.getParameters();
- String method = (String)params.getProperty("method");
+ String method = params.getProperty("method");
// find and access o, o'
URI uri1 = null;
URI uri2 = null;
Ontology onto1 = null;
Ontology onto2 = null;
try {
- uri1 = new URI((String)params.getProperty("onto1"));
- uri2 = new URI((String)params.getProperty("onto2"));
+ uri1 = new URI(params.getProperty("onto1"));
+ uri2 = new URI(params.getProperty("onto2"));
} catch (Exception e) {
return new NonConformParameters(newId(),mess,myId,mess.getSender(),"nonconform/params/onto",(Properties)null);
};
@@ -332,7 +336,7 @@ public class AServProtocolManager {
public Message translate(Message mess){
Properties params = mess.getParameters();
// Retrieve the alignment
- String id = (String)params.getProperty("id");
+ String id = params.getProperty("id");
Alignment al = null;
try {
al = alignmentCache.getAlignment( id );
@@ -341,7 +345,7 @@ public class AServProtocolManager {
}
// Translate the query
try {
- String translation = QueryMediator.rewriteSPARQLQuery( (String)params.getProperty("query"), al );
+ String translation = QueryMediator.rewriteSPARQLQuery( params.getProperty("query"), al );
return new TranslatedMessage(newId(),mess,myId,mess.getSender(),translation,(Properties)null);
} catch (AlignmentException e) {
return new ErrorMsg(newId(),mess,myId,mess.getSender(),e.toString(),(Properties)null);
@@ -353,7 +357,7 @@ public class AServProtocolManager {
public Message render( Message mess ){
Properties params = mess.getParameters();
// Retrieve the alignment
- String id = (String)params.getProperty("id");
+ String id = params.getProperty("id");
Alignment al = null;
try {
al = alignmentCache.getAlignment( id );
@@ -361,7 +365,7 @@ public class AServProtocolManager {
return new UnknownAlignment(newId(),mess,myId,mess.getSender(),id,(Properties)null);
}
// Render it
- String method = (String)params.getProperty("method");
+ String method = params.getProperty("method");
AlignmentVisitor renderer = null;
// Redirect the output in a String
ByteArrayOutputStream result = new ByteArrayOutputStream();
@@ -448,7 +452,7 @@ public class AServProtocolManager {
*/
public Message metadata( Message mess ){
// Retrieve the alignment
- String id = (String)mess.getParameters().getProperty("id");
+ String id = mess.getParameters().getProperty("id");
Alignment al = null;
try {
al = alignmentCache.getMetadata( id );
@@ -477,7 +481,7 @@ public class AServProtocolManager {
public Message trim( Message mess ) {
// Retrieve the alignment
- String id = (String)mess.getParameters().getProperty("id");
+ String id = mess.getParameters().getProperty("id");
Alignment al = null;
try {
al = alignmentCache.getAlignment( id );
@@ -485,9 +489,9 @@ public class AServProtocolManager {
return new UnknownAlignment(newId(),mess,myId,mess.getSender(),id,(Properties)null);
}
// get the trim parameters
- String type = (String)mess.getParameters().getProperty("type");
+ String type = mess.getParameters().getProperty("type");
if ( type == null ) type = "hard";
- double threshold = Double.parseDouble((String)mess.getParameters().getProperty("threshold"));
+ double threshold = Double.parseDouble(mess.getParameters().getProperty("threshold"));
al = (BasicAlignment)((BasicAlignment)al).clone();
try { al.cut( type, threshold );}
catch (AlignmentException e) {
@@ -509,7 +513,7 @@ public class AServProtocolManager {
public Message inverse( Message mess ){
Properties params = mess.getParameters();
// Retrieve the alignment
- String id = (String)params.getProperty("id");
+ String id = params.getProperty("id");
Alignment al = null;
try {
al = alignmentCache.getAlignment( id );
@@ -549,7 +553,7 @@ public class AServProtocolManager {
public Message eval( Message mess ){
Properties params = mess.getParameters();
// Retrieve the alignment
- String id = (String)params.getProperty("id");
+ String id = params.getProperty("id");
Alignment al = null;
try {
al = alignmentCache.getAlignment( id );
@@ -557,7 +561,7 @@ public class AServProtocolManager {
return new UnknownAlignment(newId(),mess,myId,mess.getSender(),"unknown/Alignment/"+id,(Properties)null);
}
// Retrieve the reference alignment
- String rid = (String)params.getProperty("ref");
+ String rid = params.getProperty("ref");
Alignment ref = null;
try {
ref = alignmentCache.getAlignment( rid );
@@ -565,7 +569,7 @@ public class AServProtocolManager {
return new UnknownAlignment(newId(),mess,myId,mess.getSender(),"unknown/Alignment/"+rid,(Properties)null);
}
// Set the comparison method
- String classname = (String)params.getProperty("method");
+ String classname = params.getProperty("method");
if ( classname == null ) classname = "fr.inrialpes.exmo.align.impl.eval.PRecEvaluator";
Evaluator eval = null;
try {
@@ -628,7 +632,7 @@ public class AServProtocolManager {
public boolean storedAlignment( Message mess ) {
// Retrieve the alignment
- String id = (String)mess.getParameters().getProperty("id");
+ String id = mess.getParameters().getProperty("id");
Alignment al = null;
try {
al = alignmentCache.getAlignment( id );
@@ -735,7 +739,7 @@ public class AServProtocolManager {
if ( file.isDirectory() ) {
//System.err.println("DIR "+file);
String subs[] = file.list();
- for(int index = 0 ; index < subs.length ; index ++ ){
+ for( int index = 0 ; index < subs.length ; index ++ ){
if ( debug ) System.err.println(" "+subs[index]);
// IF class
if ( subs[index].endsWith(".class") ) {
@@ -743,26 +747,8 @@ public class AServProtocolManager {
if (classname.startsWith(File.separator))
classname = classname.substring(1);
classname = classname.replace(File.separatorChar,'.');
- try {
- // JE: Here there is a bug that is that it is not possible
- // to have ALL interfaces with this function!!!
- // This is really stupid but that's life
- // So it is compulsory that AlignmentProcess be declared
- // as implemented
- Class[] cls = Class.forName(classname).getInterfaces();
- for ( int i=0; i < cls.length ; i++ ){
- if ( cls[i] == tosubclass ) {
- if (debug ) System.err.println(" -j-> "+classname);
- list.add( classname );
- }
- if ( debug ) System.err.println(" I> "+cls[i] );
- }
- // Not one of our classes
- } catch ( NoClassDefFoundError ncdex ) {
- } catch (ClassNotFoundException cnfex) {
- } catch (UnsatisfiedLinkError ule) {
- } catch (ExceptionInInitializerError eiie) {
- // This one has been added for OMWG, this is a bad error
+ if ( implementsInterface( classname, tosubclass, debug ) ) {
+ list.add( classname );
}
}
}
@@ -771,50 +757,19 @@ public class AServProtocolManager {
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 != null && enumeration.hasMoreElements() ){
- String classname = enumeration.nextElement().toString();
- if ( debug ) System.err.println(" "+classname);
- int len = classname.length()-6;
- 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("/",".");
- try {
- if ( classname.equals("org.apache.xalan.extensions.ExtensionHandlerGeneral") ) throw new ClassNotFoundException( "Stupid JAVA/Xalan bug");
- Class cl = Class.forName(classname);
- Class[] ints = cl.getInterfaces();
- for ( int i=0; i < ints.length ; i++ ){
- if ( ints[i] == tosubclass ) {
- if (debug ) System.err.println(" -j-> "+classname);
- list.add( classname );
- }
- if ( debug ) System.err.println(" I> "+ints[i] );
- }
- } catch ( NoClassDefFoundError ncdex ) {
- } catch ( ClassNotFoundException cnfex ) {
- if ( debug ) System.err.println(" ******** "+classname);
- } catch ( UnsatisfiedLinkError ule ) {
- } catch (ExceptionInInitializerError eiie) {
- // This one has been added for OMWG, this is a bad error
- }
- }
- }
+ JarFile jar = null;
+ try {
+ jar = new JarFile( file );
+ exploreJar( list, visited, tosubclass, jar, debug );
// Iterate on needed Jarfiles
// JE(caveat): this deals naively with Jar files,
// in particular it does not deal with section'ed MANISFESTs
- // JE2010: Chan did something for that purpose in the
- // AlignView/OfflineAlign part of the NeOn plug-in that works!
Attributes mainAttributes = jar.getManifest().getMainAttributes();
String path = mainAttributes.getValue( Name.CLASS_PATH );
if ( debug ) System.err.println(" >CP> "+path);
if ( path != null && !path.equals("") ) {
// JE: Not sure where to find the other Jars:
- // in the path or at the local place?
+ // in the path or at the local place?
//classPath += File.pathSeparator+file.getParent()+File.separator + path.replaceAll("[ \t]+",File.pathSeparator+file.getParent()+File.separator);
// This replaces the replaceAll which is not tolerant on Windows in having "\" as a separator
// Is there a way to make it iterable???
@@ -835,6 +790,73 @@ public class AServProtocolManager {
}
}
}
+
+ public static void exploreJar( Set<String> list, Set<String> visited, Class tosubclass, JarFile jar, boolean debug ) {
+ Enumeration enumeration = jar.entries();
+ while( enumeration != null && enumeration.hasMoreElements() ){
+ JarEntry entry = (JarEntry)enumeration.nextElement();
+ String entryName = entry.toString();
+ if ( debug ) System.err.println(" "+entryName);
+ int len = entryName.length()-6;
+ if( len > 0 && entryName.substring(len).compareTo(".class") == 0) {
+ entryName = entryName.substring(0,len);
+ // Beware, in a Jarfile the separator is always "/"
+ // and it would not be dependent on the current system anyway.
+ //entryName = entryName.replaceAll(File.separator,".");
+ entryName = entryName.replaceAll("/",".");
+ if ( implementsInterface( entryName, tosubclass, debug ) ) {
+ list.add( entryName );
+ }
+ } else if( entryName.endsWith(".jar") ) { // a jar in a jar
+ //System.err.println( "jarEntry is a jarfile="+je.getName() );
+ try {
+ InputStream jarSt = jar.getInputStream( (ZipEntry)entry );
+ File f = File.createTempFile( "aservTmpFile", "jar" );
+ 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();
+ JarFile inJar = new JarFile( f );
+ exploreJar( list, visited, tosubclass, inJar, debug );
+ f.delete();
+ } catch (IOException ioex) {
+ System.err.println( "Cannot read embedded jar: "+ioex );
+ }
+ }
+ }
+ }
+
+ public static boolean implementsInterface( String classname, Class tosubclass, boolean debug ) {
+ // It is possible to suppress here abstract classes by:
+ //java.lang.reflect.Modifier.isAbstract( Class.forName(classname).getModifiers );
+ try {
+ if ( classname.equals("org.apache.xalan.extensions.ExtensionHandlerGeneral") ) throw new ClassNotFoundException( "Stupid JAVA/Xalan bug");
+ // JE: Here there is a bug that is that it is not possible
+ // to have ALL interfaces with this function!!!
+ // This is really stupid but that's life
+ // So it is compulsory that AlignmentProcess be declared
+ // as implemented
+ Class[] cls = Class.forName(classname).getInterfaces();
+ for ( int i=0; i < cls.length ; i++ ){
+ if ( cls[i] == tosubclass ) {
+ if ( debug ) System.err.println(" -j-> "+classname);
+ return true;
+ }
+ if ( debug ) System.err.println(" I> "+cls[i] );
+ }
+ // Not one of our classes
+ } catch ( NoClassDefFoundError ncdex ) {
+ } catch (ClassNotFoundException cnfex) {
+ } catch (UnsatisfiedLinkError ule) {
+ if ( debug ) System.err.println(" ******** "+classname);
+ } catch (ExceptionInInitializerError eiie) {
+ // This one has been added for OMWG, this is a bad error
+ }
+ return false;
+ }
/**
* Display all the classes inheriting or implementing a given
@@ -873,14 +895,14 @@ public class AServProtocolManager {
public void run() {
Properties params = mess.getParameters();
- String method = (String)params.getProperty("method");
+ String method = params.getProperty("method");
// find and access o, o'
URI uri1 = null;
URI uri2 = null;
try {
- uri1 = new URI((String)params.getProperty("onto1"));
- uri2 = new URI((String)params.getProperty("onto2"));
+ uri1 = new URI(params.getProperty("onto1"));
+ uri2 = new URI(params.getProperty("onto2"));
} catch (Exception e) {
result = new NonConformParameters(newId(),mess,myId,mess.getSender(),"nonconform/params/onto",(Properties)null);
return;
@@ -892,13 +914,13 @@ public class AServProtocolManager {
try {
//if (debug > 0) System.err.println(" Retrieving init");
try {
- init = alignmentCache.getAlignment( (String)params.getProperty("init") );
+ init = alignmentCache.getAlignment( params.getProperty("init") );
} catch (Exception e) {
- result = new UnknownAlignment(newId(),mess,myId,mess.getSender(),(String)params.getProperty("init"),(Properties)null);
+ result = new UnknownAlignment(newId(),mess,myId,mess.getSender(),params.getProperty("init"),(Properties)null);
return;
}
} catch (Exception e) {
- result = new UnknownAlignment(newId(),mess,myId,mess.getSender(),(String)params.getProperty("init"),(Properties)null);
+ result = new UnknownAlignment(newId(),mess,myId,mess.getSender(),params.getProperty("init"),(Properties)null);
return;
}
}
@@ -919,16 +941,16 @@ public class AServProtocolManager {
long newTime = System.currentTimeMillis();
aresult.setExtension( Namespace.ALIGNMENT.uri, Annotations.TIME, Long.toString(newTime - time) );
aresult.setExtension( Namespace.ALIGNMENT.uri, Annotations.TIME, Long.toString(newTime - time) );
- String pretty = (String)params.getProperty( "pretty" );
+ String pretty = params.getProperty( "pretty" );
if ( pretty != null && !pretty.equals("") )
aresult.setExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY, pretty );
} catch (AlignmentException e) {
// The unreachability test has already been done
// JE 15/1/2009: commented the unreachability test
if ( reachable( uri1 ) == null ){
- result = new UnreachableOntology(newId(),mess,myId,mess.getSender(),(String)params.getProperty("onto1"),(Properties)null);
+ result = new UnreachableOntology(newId(),mess,myId,mess.getSender(),params.getProperty("onto1"),(Properties)null);
} else if ( reachable( uri2 ) == null ){
- result = new UnreachableOntology(newId(),mess,myId,mess.getSender(),(String)params.getProperty("onto2"),(Properties)null);
+ result = new UnreachableOntology(newId(),mess,myId,mess.getSender(),params.getProperty("onto2"),(Properties)null);
} else {
result = new NonConformParameters(newId(),mess,myId,mess.getSender(),"nonconform/params/"+e.getMessage(),(Properties)null);
}