diff --git a/src/fr/inrialpes/exmo/align/util/GroupAlign.java b/src/fr/inrialpes/exmo/align/util/GroupAlign.java
index f67369dc4a20ab79b41f0da7edb55d51e672644b..4ce9257db10eb7acf66a575b5ab31e28cbb6f77f 100644
--- a/src/fr/inrialpes/exmo/align/util/GroupAlign.java
+++ b/src/fr/inrialpes/exmo/align/util/GroupAlign.java
@@ -101,6 +101,9 @@ public class GroupAlign {
static Parameters params = null;
static String filename = "align";
static String paramfile = null;
+ static String urlprefix = null;
+ static String source = "onto1.rdf";
+ static String target = "onto.rdf";
static URI uri1 = null;
static String initName = null;
static Hashtable loadedOntologies = null;
@@ -116,7 +119,7 @@ public class GroupAlign {
public static void run(String[] args) throws Exception {
- LongOpt[] longopts = new LongOpt[9];
+ LongOpt[] longopts = new LongOpt[12];
loadedOntologies = new Hashtable();
params = new BasicParameters();
@@ -128,10 +131,13 @@ public class GroupAlign {
longopts[5] = new LongOpt("impl", LongOpt.REQUIRED_ARGUMENT, null, 'i');
longopts[6] = new LongOpt("params", LongOpt.REQUIRED_ARGUMENT, null, 'p');
longopts[7] = new LongOpt("name", LongOpt.REQUIRED_ARGUMENT, null, 'n');
+ longopts[8] = new LongOpt("prefix", LongOpt.REQUIRED_ARGUMENT, null, 'u');
+ longopts[9] = new LongOpt("source", LongOpt.REQUIRED_ARGUMENT, null, 's');
+ longopts[10] = new LongOpt("target", LongOpt.REQUIRED_ARGUMENT, null, 't');
// Is there a way for that in LongOpt ???
- longopts[8] = new LongOpt("D", LongOpt.REQUIRED_ARGUMENT, null, 'D');
+ longopts[11] = new LongOpt("D", LongOpt.REQUIRED_ARGUMENT, null, 'D');
- Getopt g = new Getopt("", args, "ho:a:d::n:r:i:p:D::", longopts);
+ Getopt g = new Getopt("", args, "ho:a:d::n:u:r:i:s:t:p::D::", longopts);
int c;
String arg;
@@ -170,6 +176,18 @@ public class GroupAlign {
/* Use the given file as a partial alignment */
initName = g.getOptarg();
break;
+ case 'u' :
+ /* Use the given url prefix for fetching the ontologies */
+ urlprefix = g.getOptarg();
+ break;
+ case 's' :
+ /* Use the given filename for source ontology */
+ source = g.getOptarg();
+ break;
+ case 't' :
+ /* Use the given filename for target ontology */
+ target = g.getOptarg();
+ break;
case 'D' :
/* Parameter definition */
arg = g.getOptarg();
@@ -194,42 +212,57 @@ public class GroupAlign {
int i = g.getOptind();
- if (debug > 0) params.setParameter("debug", new Integer(debug));
- // debug = ((Integer)params.getParameter("debug")).intValue();
+ if (debug > 0) params.setParameter("debug", new Integer(debug-1));
iterateDirectories();
}
public static void iterateDirectories (){
- try {
- File [] subdir = (new File(System.getProperty("user.dir"))).listFiles();
- int size = subdir.length;
- for ( int i=0 ; i < size; i++ ) {
- if( subdir[i].isDirectory() ) {
- try {
- // Align
- if ( debug > 0 ) System.err.println("Directory: "+subdir[i]);
- align( subdir[i] );
- } catch (Exception e) { e.printStackTrace(); }
- }
- }
- } catch (Exception e) {
+ File [] subdir = null;
+ try { subdir = (new File(System.getProperty("user.dir"))).listFiles(); }
+ catch (Exception e) {
System.err.println("Cannot stat dir "+ e.getMessage());
usage();
}
+ int size = subdir.length;
+ for ( int i=0 ; i < size; i++ ) {
+ if( subdir[i].isDirectory() ) {
+ try {
+ // Align
+ if ( debug > 0 ) System.err.println("Directory: "+subdir[i]);
+ align( subdir[i] );
+ // Unload the ontologies
+ // (this is a pitty but helps avoiding memory full)
+ try {
+ for ( Enumeration e = loadedOntologies.elements() ; e.hasMoreElements(); ){
+ OWLOntology o = (OWLOntology)e.nextElement();
+ o.getOWLConnection().notifyOntologyDeleted( o );
+ }
+ } catch (Exception ex) { System.err.println(ex); };
+ } catch (Exception e) {
+ if ( debug > 1 ) e.printStackTrace(); }
+ }
+ }
}
public static void align ( File dir ) throws Exception {
- String prefix = dir.toURI().toString()+File.separator;
+ String prefix = null;
+ // toURI(). is not very good
AlignmentProcess result = null;
Alignment init = null;
OWLOntology onto1 = null;
OWLOntology onto2 = null;
+ if ( urlprefix != null ){
+ prefix = urlprefix+"/"+dir.getName()+"/";
+ } else {
+ prefix = "file://localhost"+dir.toString()+"/";
+ }
+
BasicConfigurator.configure();
- if ( uri1 == null ) uri1 = new URI(prefix+"onto1.rdf");
- URI uri2 = new URI(prefix+"onto.rdf");
+ if ( uri1 == null ) uri1 = new URI(prefix+source);
+ URI uri2 = new URI(prefix+target);
handler = new OWLRDFErrorHandler() {
public void owlFullConstruct(int code, String message)
@@ -246,18 +279,22 @@ public class GroupAlign {
}
};
- if (debug > 0) System.err.println(" Handler set");
+ if (debug > 1) System.err.println(" Handler set");
+ if (debug > 1) System.err.println(" URI1: "+uri1);
+ if (debug > 1) System.err.println(" URI2: "+uri2);
try {
if (uri1 != null) onto1 = loadOntology(uri1);
if (uri2 != null) onto2 = loadOntology(uri2);
- if (debug > 0) System.err.println(" Ontology parsed");
+ } catch (Exception e) { return ;};
+ if (debug > 1) System.err.println(" Ontology parsed");
+ try {
if (initName != null) {
- AlignmentParser aparser = new AlignmentParser(debug);
+ AlignmentParser aparser = new AlignmentParser(debug-1);
init = aparser.parse(initName, loadedOntologies);
onto1 = (OWLOntology) init.getOntology1();
onto2 = (OWLOntology) init.getOntology2();
- if (debug > 0) System.err.println(" Init parsed");
+ if (debug > 1) System.err.println(" Init parsed");
}
// Create alignment object
@@ -275,12 +312,12 @@ public class GroupAlign {
throw ex;
}
- if (debug > 0) System.err.println(" Alignment structure created");
+ if (debug > 1) System.err.println(" Alignment structure created");
// Compute alignment
result.align(init, params); // add opts
- if (debug > 0) System.err.println(" Alignment performed");
+ if (debug > 1) System.err.println(" Alignment performed");
// Set output file
PrintWriter writer = new PrintWriter (
@@ -300,11 +337,11 @@ public class GroupAlign {
throw ex;
}
- if (debug > 0) System.err.println(" Outputing result to "+dir+File.separator+filename+".rdf");
+ if (debug > 1) System.err.println(" Outputing result to "+dir+File.separator+filename+".rdf");
// Output
result.render( renderer);
- if (debug > 0) System.err.println(" Done..."+renderer+"\n");
+ if (debug > 1) System.err.println(" Done..."+renderer+"\n");
// It should be useful to unload ontologies
// JE: This instruction is very important
diff --git a/src/fr/inrialpes/exmo/align/util/GroupEval.java b/src/fr/inrialpes/exmo/align/util/GroupEval.java
index e6d08d1148e7cc3e0e6a186fdbaec5fdeb49f6e6..dc5759d698cd49d45c5b915271454edb294fd7e4 100644
--- a/src/fr/inrialpes/exmo/align/util/GroupEval.java
+++ b/src/fr/inrialpes/exmo/align/util/GroupEval.java
@@ -174,34 +174,34 @@ public class GroupEval {
params = new BasicParameters();
if (debug > 0) params.setParameter("debug", new Integer(debug-1));
- // debug = ((Integer)params.getParameter("debug")).intValue();
print( iterateDirectories() );
}
public static Vector iterateDirectories (){
Vector result = null;
+ File [] subdir = null;
try {
- File [] subdir = (new File(System.getProperty("user.dir"))).listFiles();
- int size = subdir.length;
- result = new Vector(size);
- int i = 0;
- for ( int j=0 ; j < size; j++ ) {
- if( subdir[j].isDirectory() ) {
- if ( debug > 0 ) System.err.println("\nEntering directory "+subdir[j]);
- // eval the alignments in a subdirectory
- // store the result
- Object vect = (Object)iterateAlignments( subdir[j] );
- if ( vect != null ){
- result.add(i, vect);
- i++;
- }
- }
- }
+ subdir = (new File(System.getProperty("user.dir"))).listFiles();
} catch (Exception e) {
System.err.println("Cannot stat dir "+ e.getMessage());
usage();
}
+ int size = subdir.length;
+ result = new Vector(size);
+ int i = 0;
+ for ( int j=0 ; j < size; j++ ) {
+ if( subdir[j].isDirectory() ) {
+ if ( debug > 0 ) System.err.println("\nEntering directory "+subdir[j]);
+ // eval the alignments in a subdirectory
+ // store the result
+ Object vect = (Object)iterateAlignments( subdir[j] );
+ if ( vect != null ){
+ result.add(i, vect);
+ i++;
+ }
+ }
+ }
return result;
}
@@ -236,12 +236,12 @@ public class GroupEval {
Evaluator eval = null;
try {
// Load alignments
- AlignmentParser aparser1 = new AlignmentParser( debug );
+ AlignmentParser aparser1 = new AlignmentParser( debug-1 );
Alignment align1 = aparser1.parse( alignName1, loaded );
- if ( debug > 0 ) System.err.println(" Alignment structure1 parsed");
- AlignmentParser aparser2 = new AlignmentParser( debug );
+ if ( debug > 1 ) System.err.println(" Alignment structure1 parsed");
+ AlignmentParser aparser2 = new AlignmentParser( debug-1 );
Alignment align2 = aparser2.parse( alignName2, loaded );
- if ( debug > 0 ) System.err.println(" Alignment structure2 parsed");
+ if ( debug > 1 ) System.err.println(" Alignment structure2 parsed");
// Create evaluator object
eval = new PRecEvaluator( align1, align2 );
// Compare