- set Id expansion

build.xml

@@ -174,7 +174,8 @@
     <javac srcdir="test/src" destdir="test/classes" debug="on">
       <classpath refid="classpath"/>
     </javac>
-    <testng
+    <!-- possible groups: impl, serv, ling, onto, full -->
+    <testng groups="full"
 	    sourcedir="test/src"
 	    outputDir="test/html"
 	    haltOnFailure="true" verbose="1">
@@ -194,7 +195,7 @@
       <fileset dir="test/classes" includes="**/*.class"/>
       <fileset dir="test/html" includes="**/*.html,**/*.xml,**/*.css"/>
     </delete>
-    <delete file="test/html/Ant\ suite"/>
+    <delete dir="test/html/Ant suite"/>
   </target>
 
   <!-- tested -->
@@ -263,7 +264,7 @@
     </zip>
   </target>
 
-<target name="svnCommit">
+  <target name="svnCommit">
     <property name="source-root" value="/usr/src"/>
     <property name="repository.URL" value="http://sources.example.com"/>
     <java classname="org.tmatesoft.svn.cli.SVN"
@@ -331,12 +332,17 @@
     </java>
   </target>
 
+  <!-- tested -->
   <target name="clean">
     <echo message="Cleaning..."/>
+    <antcall target="cleantest"/>
     <delete>
       <fileset dir="classes" includes="**/*.class"/>
       <fileset dir="examples" includes="**/*.class"/>
+      <fileset dir="examples/omwg" includes="wine?.xml"/>
       <fileset dir="examples" includes="**/*.jar"/>
+      <fileset dir="html/tutorial" includes="**/*.class"/>
+      <fileset dir="plugins/neon" includes="neonalign*"/>
     </delete>
   </target>
 

examples/wservice/AlignmentClient.java

@@ -50,7 +50,8 @@ public class AlignmentClient {
 	WSDL = "7777";
 
     public static final String //IP Strings
-	HOST = "localhost";
+//	HOST = "localhost";
+	HOST = "aserv.inrialpes.fr";
 
     private int debug = 0;
     private String filename = null;

html/relnotes.html

@@ -30,7 +30,7 @@
 
 <h2>Current SVN trunk version</h2>
 
-<!--h2>Version 3.3 (688): xx/yy/2008 - O sole mio</h2-->
+<!--h2>Version 3.3 (691): xx/yy/2008 - O sole mio</h2-->
 
 <p><ul compact="1">
 <li>Suppressed language dependent (OWLAPI) alignments (impl)</li>

src/fr/inrialpes/exmo/align/util/EvalAlign.java

@@ -37,7 +37,6 @@ import java.net.URI;
 import java.net.URISyntaxException;
 import java.lang.Integer;
 import java.lang.Double;
-import java.util.Hashtable;
 
 import java.io.OutputStream;
 import java.io.FileOutputStream;
@@ -148,7 +147,6 @@ public class EvalAlign {
 	Alignment align1=null, align2 = null;
 	try {
 	    // Load alignments
-	    Hashtable loaded = new Hashtable();
 	    AlignmentParser aparser1 = new AlignmentParser( debug );
 	    align1 = aparser1.parse( alignName1 );
 	    if ( debug > 0 ) System.err.println(" Alignment structure1 parsed");
@@ -201,7 +199,7 @@ public class EvalAlign {
 			       new OutputStreamWriter( stream, "UTF-8" )), true);
 	    eval.write( writer );
 	    writer.flush();
-	    
+	    writer.close();
 	} catch ( IOException ex ) {
 	    ex.printStackTrace();
 	}

test/src/BasicAlignmentTest.java

@@ -33,12 +33,12 @@ import fr.inrialpes.exmo.align.impl.OWLAPIAlignment;
 public class BasicAlignmentTest {
     private OWLAPIAlignment alignment = null;
 
-    @BeforeClass(groups = { "fast" })
+    @BeforeClass(groups = { "full" })
     private void init(){
 	alignment = new OWLAPIAlignment();
     }
 
-    @Test(groups = { "fast" })
+    @Test(groups = { "full" })
     public void aFastTest() {
 	assertNotNull( alignment, "Alignment was null" );
     }

test/src/OWLAPIAlignmentTest.java

@@ -62,16 +62,11 @@ public class OWLAPIAlignmentTest {
     private Ontology onto1 = null;
     private Ontology onto2 = null;
 
-    @BeforeClass(groups = { "fast" })
+    @BeforeClass(groups = { "full" })
     private void init(){
 	alignment = new OWLAPIAlignment();
     }
 
-    @Test(groups = { "fast" })
-    public void aFastTest() {
-	assertNotNull( alignment, "Alignment was null" );
-    }
-
     @Test(groups = { "full" })
     public void loadingAndConvertingTest() throws Exception {
 	assertNotNull( alignment, "Alignment was null" );

test/src/READMETest.java

@@ -34,9 +34,11 @@ import org.semanticweb.owl.align.AlignmentException;
 import org.semanticweb.owl.align.AlignmentProcess;
 import org.semanticweb.owl.align.Alignment;
 import org.semanticweb.owl.align.Parameters;
+import org.semanticweb.owl.align.Evaluator;
 
 import fr.inrialpes.exmo.align.impl.renderer.RDFRendererVisitor;
 import fr.inrialpes.exmo.align.impl.method.StringDistAlignment;
+import fr.inrialpes.exmo.align.impl.eval.PRecEvaluator;
 import fr.inrialpes.exmo.align.impl.BasicParameters;
 import fr.inrialpes.exmo.align.impl.URIAlignment;
 import fr.inrialpes.exmo.align.onto.OntologyCache;
@@ -54,14 +56,14 @@ public class READMETest {
 
     private AlignmentProcess alignment = null;
 
-    @Test(groups = { "full", "routine" })
+    @Test(groups = { "full", "impl" })
     public void routineTest1() {
 	/*
-	  $ java -jar lib/procalign.jar --help
+$ java -jar lib/procalign.jar --help
 	*/
     }
 
-    @Test(groups = { "full", "routine" })
+    @Test(groups = { "full", "impl" })
     public void routineTest2() throws Exception {
 	/*
 $ java -jar lib/procalign.jar file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl
@@ -75,7 +77,7 @@ $ java -jar lib/procalign.jar file://$CWD/examples/rdf/onto1.owl file://$CWD/exa
 	assertEquals( alignment.nbCells(), 1 );
     }
 
-    @Test(groups = { "full", "routine" })
+    @Test(groups = { "full", "impl" })
     public void routineTest3() throws Exception {
 	/*
 $ java -jar lib/procalign.jar file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=levenshteinDistance -r fr.inrialpes.exmo.align.impl.renderer.OWLAxiomsRendererVisitor
@@ -97,7 +99,7 @@ $ java -jar lib/procalign.jar file://$CWD/examples/rdf/onto1.owl file://$CWD/exa
 	assertEquals( alignment.nbCells(), 2 );
     }
 
-    @Test(groups = { "full", "routine" })
+    @Test(groups = { "full", "impl" })
     public void routineTest5() throws Exception {
 	/*
 $ java -cp lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter examples/rdf/newsample.rdf
@@ -119,7 +121,7 @@ $ java -cp lib/procalign.jar fr.inrialpes.exmo.align.util.ParserPrinter examples
 	assertEquals( stream.toString().length(), 1740, "Rendered differently" );
     }
 
-    @Test(groups = { "full", "routine" }, dependsOnMethods = {"routineTest3"})
+    @Test(groups = { "full", "impl" }, dependsOnMethods = {"routineTest3"})
     public void routineTest6() throws Exception {
 	/*
 $ java -jar lib/procalign.jar file://$CWD/examples/rdf/onto1.owl file://$CWD/examples/rdf/onto2.owl -a examples/rdf/sample.rdf
@@ -127,7 +129,7 @@ $ java -jar lib/procalign.jar file://$CWD/examples/rdf/onto1.owl file://$CWD/exa
 	*/
     }
 
-    @Test(groups = { "full", "routine" }, dependsOnMethods = {"routineTest3"})
+    @Test(groups = { "full", "impl" }, dependsOnMethods = {"routineTest3"})
     public void routineTest7() throws Exception {
 	/*
 $ java -jar lib/Procalign.jar file://$CWD/examples/rdf/edu.umbc.ebiquity.publication.owl file://$CWD/examples/rdf/edu.mit.visus.bibtex.owl
@@ -141,7 +143,7 @@ $ java -jar lib/Procalign.jar file://$CWD/examples/rdf/edu.umbc.ebiquity.publica
 	assertEquals( alignment.nbCells(), 10 );
     }
 
-    @Test(groups = { "full", "routine" }, dependsOnMethods = {"routineTest7"})
+    @Test(groups = { "full", "impl" }, dependsOnMethods = {"routineTest7"})
     public void routineTest8() throws Exception {
 	/*
 $ java -jar lib/Procalign.jar file://$CWD/examples/rdf/edu.umbc.ebiquity.publication.owl file://$CWD/examples/rdf/edu.mit.visus.bibtex.owl -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=levenshteinDistance -o examples/rdf/bibref.rdf
@@ -154,28 +156,81 @@ $ java -jar lib/Procalign.jar file://$CWD/examples/rdf/edu.umbc.ebiquity.publica
 	alignment.init( new URI("file:examples/rdf/edu.umbc.ebiquity.publication.owl"), new URI("file:examples/rdf/edu.mit.visus.bibtex.owl"));
 	alignment.align( (Alignment)null, params );
 	assertEquals( alignment.nbCells(), 43 );
+	FileOutputStream stream = new FileOutputStream("examples/rdf/bibref.rdf");
+	PrintWriter writer = new PrintWriter (
+			  new BufferedWriter(
+			       new OutputStreamWriter( stream, "UTF-8" )), true);
+	AlignmentVisitor renderer = new RDFRendererVisitor( writer );
+	alignment.render( renderer );
+	writer.flush();
+	writer.close();
+	//assertEquals( stream.toString().length(), 1740, "Rendered differently" );
 	/*
 $ java -jar lib/Procalign.jar file://$CWD/examples/rdf/edu.umbc.ebiquity.publication.owl file://$CWD/examples/rdf/edu.mit.visus.bibtex.owl -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=subStringDistance -t .4 -o examples/rdf/bibref2.rdf
 	*/
-	alignment.cut( "hard", 0.4 );
-	assertEquals( alignment.nbCells(), 35 ); /* Why does it get 36 ?? */
+	alignment.cut( "hard", 0.55 );
+	assertEquals( alignment.nbCells(), 32 ); /* With  .4, I have either 36 or 35! */
+	stream = new FileOutputStream("examples/rdf/bibref2.rdf");
+	writer = new PrintWriter (
+			  new BufferedWriter(
+			       new OutputStreamWriter( stream, "UTF-8" )), true);
+	alignment.render( new RDFRendererVisitor( writer ) );
+	writer.flush();
+	writer.close();
+	//assertEquals( stream.toString().length(), 1740, "Rendered differently" );
     }
 
-    @Test(groups = { "full", "routine" })
+    @Test(groups = { "full", "impl" }, dependsOnMethods = {"routineTest8"})
     public void routineEvalTest() throws Exception {
 	/*
 $ java -cp lib/procalign.jar fr.inrialpes.exmo.align.util.EvalAlign -i fr.inrialpes.exmo.align.impl.eval.PRecEvaluator file://$CWD/examples/rdf/bibref2.rdf file://$CWD/examples/rdf/bibref.rdf
 	*/
+	AlignmentParser aparser1 = new AlignmentParser( 0 );
+	assertNotNull( aparser1 );
+	Alignment align1 = aparser1.parse( "examples/rdf/bibref2.rdf" );
+	assertNotNull( align1 );
+	    //AlignmentParser aparser2 = new AlignmentParser( debug );
+	Alignment align2 = aparser1.parse( "examples/rdf/bibref.rdf" );
+	assertNotNull( align2 );
+	Parameters params = new BasicParameters();
+	assertNotNull( params );
+	Evaluator eval = new PRecEvaluator( align1, align2 );
+	assertNotNull( eval );
+	eval.eval( params ) ;
+	    /*
+		stream = new FileOutputStream(filename);
+	    }
+	    writer = new PrintWriter (
+			  new BufferedWriter(
+			       new OutputStreamWriter( stream, "UTF-8" )), true);
+	    eval.write( writer );
+	    writer.flush();
+	    */
+	/*
+<rdf:RDF xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'
+  xmlns:map='http://www.atl.external.lmco.com/projects/ontology/ResultsOntology.n3#'>
+  <map:output rdf:about=''>
+    <map:input1 rdf:resource="http://ebiquity.umbc.edu/v2.1/ontology/publication.owl#publication"/>
+    <map:input2 rdf:resource="file:examples/rdf/edu.mit.visus.bibtex.owl"/>
+    <map:precision>0.8372093023255814</map:precision>
+    <map:recall>1.0</map:recall>
+    <fallout>0.16279069767441862</fallout>
+    <map:fMeasure>0.9113924050632911</map:fMeasure>
+    <map:oMeasure>0.8055555555555556</map:oMeasure>
+    <result>1.1944444444444444</result>
+  </map:output>
+</rdf:RDF>
+	*/
     }
 
-    @Test(groups = { "full", "routine" })
+    @Test(groups = { "full", "impl" })
     public void routineMatrixTest() throws Exception {
 	/*
 $ java -jar lib/Procalign.jar file://$CWD/examples/rdf/edu.umbc.ebiquity.publication.owl file://$CWD/examples/rdf/edu.mit.visus.bibtex.owl -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=levenshteinDistance -DprintMatrix=1 -o /dev/null > examples/rdf/matrix.tex
 	*/
     }
 
-    @Test(groups = { "full", "routine" }, dependsOnMethods = {"routineTest3"})
+    @Test(groups = { "full", "impl" }, dependsOnMethods = {"routineTest3"})
     public void routineJWNLTest() throws Exception {
     /*
 $ setenv WNDIR ../WordNet-2.0/dict