diff --git a/build.xml b/build.xml
index 95a9dff2d4397136b81b664538b251c19af4f9c5..5ece33e3a03a2e3d9974c59a199898faed788210 100644
--- a/build.xml
+++ b/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>
diff --git a/examples/wservice/AlignmentClient.java b/examples/wservice/AlignmentClient.java
index 7e6862790dbc9d59496b5a8c62d9e4f4a3cbfb7c..306d103351a59462759742250058deedc85434a2 100644
--- a/examples/wservice/AlignmentClient.java
+++ b/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;
diff --git a/html/relnotes.html b/html/relnotes.html
index d26a8174db7ca074bea0f253b089c6e7050777a1..d49e96f0a938ea5e663101062716cd92d490b62a 100644
--- a/html/relnotes.html
+++ b/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>
diff --git a/lib/align.jar b/lib/align.jar
index bf4c6b6cdec37c30558b8ba8a97f59292e6405ab..c9b15259d1313867d2903c679f1ad9cd8fa07367 100644
Binary files a/lib/align.jar and b/lib/align.jar differ
diff --git a/lib/alignsvc.jar b/lib/alignsvc.jar
index e6d4b92a80980afa623008c4766c29ce666c60d6..0d02c7c86273d5365d2f138cdc937f222b350c26 100644
Binary files a/lib/alignsvc.jar and b/lib/alignsvc.jar differ
diff --git a/lib/alignwn.jar b/lib/alignwn.jar
index 7756aa426641b6f573aa6fab205bee8d10e5ac60..3b8aa99e3e46ede4e02dfc0a9a54b3302e2ad53b 100644
Binary files a/lib/alignwn.jar and b/lib/alignwn.jar differ
diff --git a/lib/procalign.jar b/lib/procalign.jar
index afb67066d32cdfc5c979e1601c2b2ceaac4c5a7e..ee0f8c86f6494fc885d639da1dfe0c0e5009d7e7 100644
Binary files a/lib/procalign.jar and b/lib/procalign.jar differ
diff --git a/src/fr/inrialpes/exmo/align/util/EvalAlign.java b/src/fr/inrialpes/exmo/align/util/EvalAlign.java
index 4a12203db0af6e9922b1a6e0718894b567fa7ee0..5afa9255d4fc8c77e19ebee9d0d0f1d247a9dbf7 100644
--- a/src/fr/inrialpes/exmo/align/util/EvalAlign.java
+++ b/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();
}
diff --git a/test/src/BasicAlignmentTest.java b/test/src/BasicAlignmentTest.java
index 79da5e746eda3bb4a24c0b3de2742fa928311080..245a703de33e7cbc51197f49d86ac6b0e7403033 100644
--- a/test/src/BasicAlignmentTest.java
+++ b/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" );
}
diff --git a/test/src/OWLAPIAlignmentTest.java b/test/src/OWLAPIAlignmentTest.java
index da64a83117201929972fe79f4806437917b8a012..5022b41f065cbd9c994fff13d759fc333a50fb14 100644
--- a/test/src/OWLAPIAlignmentTest.java
+++ b/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" );
diff --git a/test/src/READMETest.java b/test/src/READMETest.java
index 3f61d2ffaf9f14c1997154cf28d7ee5dc46269fb..7edcf815623c8226799842ab682de4db8d5cbcdd 100644
--- a/test/src/READMETest.java
+++ b/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