/*
* Test_OntoWine.java
*
* Johann Petrak
*
* $Id: Test_OntoWine.java 17080 2013-11-12 19:29:34Z markagreenwood $
*/
package gate.creole.ontology.impl.test;
import gate.Factory;
import gate.FeatureMap;
import gate.Gate;
import gate.creole.ResourceInstantiationException;
import gate.creole.ontology.DatatypeProperty;
import gate.creole.ontology.OClass;
import gate.creole.ontology.OConstants;
import gate.creole.ontology.OConstants.Closure;
import gate.creole.ontology.OInstance;
import gate.creole.ontology.OResource;
import gate.creole.ontology.OURI;
import gate.creole.ontology.ObjectProperty;
import gate.creole.ontology.Ontology;
import gate.creole.ontology.impl.AbstractOntologyImpl;
import gate.util.GateException;
import java.io.File;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import static org.junit.Assert.*;
import org.apache.commons.io.FileUtils;
import org.apache.log4j.Logger;
/**
* Run tests on the wine ontology
*/
public class Test_OntoWine {
static File ontologiesDir = null;
static File configDir = null;
static File tmpDir = null;
// TODO: it seems we cannot use a static as intended here: the
// init code still gets run for each fixture?
static boolean isInitialized = false;
Logger log = Logger.getLogger(this.getClass());
OConstants.Closure DIRECT_CLOSURE = Closure.DIRECT_CLOSURE;
OConstants.Closure TRANSITIVE_CLOSURE = Closure.TRANSITIVE_CLOSURE;
// global preparation stuff - check if stuff already initialized, if
// yes, do nothing
@BeforeClass
public static void init() throws GateException, MalformedURLException {
if(!isInitialized) {
System.out.println("Inititalizing ...");
Gate.init();
File pluginHome =
new File(new File(Gate.getGateHome(), "plugins"),
"Ontology");
System.out.println("Plugin home directory is "+pluginHome.getAbsolutePath());
Gate.getCreoleRegister().registerDirectories(
pluginHome.toURI().toURL());
File testingDir = new File(pluginHome,"test");
assertTrue(testingDir.exists());
ontologiesDir = new File(testingDir, "ontologies");
assertTrue(ontologiesDir.exists());
tmpDir = getUniqueTmpDir();
assertTrue(tmpDir.canWrite());
System.out.println("Init complete");
} else {
isInitialized = true;
}
}
@AfterClass
public static void cleanup() throws Exception {
if(tmpDir != null) {
FileUtils.deleteDirectory(tmpDir);
}
}
@Test
public void testWineOntology() throws MalformedURLException,
ResourceInstantiationException {
FeatureMap fm = Factory.newFeatureMap();
// For local wine:
File demoFile = new File(ontologiesDir,"wine.rdfxml.owl");
URL rdfXmlURL = demoFile.toURI().toURL();
File mappingsFile = new File(ontologiesDir,"winemappings.txt");
URL mappingsURL = mappingsFile.toURI().toURL();
fm.put("rdfXmlURL", rdfXmlURL);
// instead of loading the included food ontology from the web, use
// a mappings file to load it from our ontology directory
fm.put("mappingsURL", mappingsURL);
Ontology ontology = (Ontology)Factory.createResource(
"gate.creole.ontology.impl.sesame.OWLIMOntology", fm);
String dns = ontology.getDefaultNameSpace();
assertEquals("http://www.w3.org/TR/2003/CR-owl-guide-20030818/wine#",dns);
// For remote wine:
//fm.put("repositoryID","owlim-wine");
//fm.put("repositoryLocation","http://localhost:8080/openrdf-sesame");
//Ontology ontology = (Ontology)Factory.createResource(
// "gate.creole.ontology.impl.sesame.ConnectSesameOntology", fm);
long beginTime;
long elapsed1;
beginTime = System.nanoTime();
Set<OClass> allclasses = ontology.getOClasses(false);
elapsed1 = System.nanoTime() - beginTime;
System.out.println("##### all WINE classes: "+allclasses.size());
System.out.println("@@@@@ all WINE classes: "+elapsed1);
assertEquals(661,allclasses.size());
beginTime = System.nanoTime();
Set<OClass> topclasses = ontology.getOClasses(true);
elapsed1 = System.nanoTime() - beginTime;
System.out.println("##### top WINE classes: "+topclasses.size());
System.out.println("@@@@@ top WINE classes: "+elapsed1);
assertEquals(459,topclasses.size());
beginTime = System.nanoTime();
System.out.println("Starting to expand all classes ... ");
Set<OClass> collected = new HashSet<OClass>();
collected.addAll(topclasses);
expandAllClasses(collected, 0);
elapsed1 = System.nanoTime() - beginTime;
System.out.println("Expanding classes complete");
System.out.println("##### expanded WINE classes: "+collected.size());
System.out.println("@@@@@ expanded WINE classes: "+elapsed1);
// NOTE: class WineColor is not found by expanding subclasses, because
// it is a subclass of a oneOf restriction which is not in OWL-Lite and
// cannot be represented by the Ontology API. Therefore, one less.
assertEquals(660,collected.size());
beginTime = System.nanoTime();
Set<OClass> ocbn = ((AbstractOntologyImpl)ontology).getOClassesByName("Wine");
elapsed1 = System.nanoTime() - beginTime;
System.out.println("Classes with name Wine: ");
for(OClass cl : ocbn) {
System.out.println(" "+cl.getONodeID().toTurtle());
}
System.out.println("##### classes by name wine: "+ocbn.size());
System.out.println("@@@@@ classes by name wine: "+elapsed1);
assertEquals("Classes for name Wine",2,ocbn.size());
beginTime = System.nanoTime();
List<OResource> ors = ontology.getOResourcesByName("yearValue");
elapsed1 = System.nanoTime() - beginTime;
System.out.println("Resources with name yearValue: ");
for(OResource or : ors) {
System.out.println(" "+or.getONodeID().toTurtle());
}
System.out.println("##### resources by name yearValue: "+ors.size());
System.out.println("@@@@@ resources by name yearValue: "+elapsed1);
assertEquals("Resources for name yearValue",1,ors.size());
assertTrue("yearValue is a datatype property",ontology.isDatatypeProperty((OURI)ors.get(0).getONodeID()));
beginTime = System.nanoTime();
ors = ontology.getOResourcesByName("Wine");
elapsed1 = System.nanoTime() - beginTime;
System.out.println("Resources with name Wine: ");
for(OResource or : ors) {
System.out.println(" "+or.getONodeID().toTurtle());
}
System.out.println("##### resources by name Wine: "+ors.size());
System.out.println("@@@@@ resources by name Wine: "+elapsed1);
assertEquals("Resources for name Wine",2,ors.size());
assertEquals("Class of resource 1 for wine",
"gate.creole.ontology.impl.OClassImpl",
ors.get(0).getClass().getName());
assertEquals("Class of resource 2 for wine",
"gate.creole.ontology.impl.OClassImpl",
ors.get(1).getClass().getName());
beginTime = System.nanoTime();
ors = ontology.getOResourcesByName("Delicate");
elapsed1 = System.nanoTime() - beginTime;
System.out.println("Resources with name Delicate: ");
for(OResource or : ors) {
System.out.println(" "+or.getONodeID().toTurtle());
}
System.out.println("##### resources by name Delicate: "+ors.size());
System.out.println("@@@@@ resources by name Delicate: "+elapsed1);
assertEquals("Resources for name Delicate",2,ors.size());
assertEquals("Class of resource 1 for Delicate",
"gate.creole.ontology.impl.OInstanceImpl",
ors.get(0).getClass().getName());
beginTime = System.nanoTime();
OClass c_WineColor = ontology.getOClass(getURI4Name(ontology,"WineColor"));
OClass c_WineTaste = ontology.getOClass(getURI4Name(ontology,"WineTaste"));
OClass c_WineSugar = ontology.getOClass(getURI4Name(ontology,"WineSugar"));
OClass c_VintageYear = ontology.getOClass(getURI4Name(ontology,"VintageYear"));
OClass c_WineDescriptor = ontology.getOClass(getURI4Name(ontology,"WineDescriptor"));
ObjectProperty op_hasMaker = ontology.getObjectProperty(getURI4Name(ontology,"hasMaker"));
ObjectProperty op_hasWineDescriptor = ontology.getObjectProperty(getURI4Name(ontology,"hasWineDescriptor"));
ObjectProperty op_hasSugar = ontology.getObjectProperty(getURI4Name(ontology,"hasSugar"));
DatatypeProperty dp_yearValue = ontology.getDatatypeProperty(getURI4Name(ontology,"yearValue"));
elapsed1 = System.nanoTime() - beginTime;
System.out.println("@@@@@ find specific entities: "+elapsed1);
assertNotNull("Find WineColor",c_WineColor);
assertNotNull("Find WineTaste",c_WineTaste);
assertNotNull("Find WineSugar",c_WineSugar);
assertNotNull("Find VintageYear",c_VintageYear);
assertNotNull("Find VintageYear",c_VintageYear);
assertNotNull("Find hasMaker",op_hasMaker);
assertNotNull("Find hasWineDescriptor",op_hasWineDescriptor);
assertNotNull("Find hasSugar",op_hasSugar);
assertNotNull("Find yearValue",dp_yearValue);
Set<OResource> domain_yearValue = dp_yearValue.getDomain();
assertEquals(1, domain_yearValue.size());
assertTrue((domain_yearValue.iterator().next() instanceof OClass));
OClass c_domain_yearValue = (OClass)domain_yearValue.iterator().next();
assertEquals("VintageYear",c_domain_yearValue.getName());
assertEquals(c_VintageYear,c_domain_yearValue);
// Check the directo subclasses of WineDescriptor:
Set<OClass> dsub1 = c_WineDescriptor.getSubClasses(DIRECT_CLOSURE);
System.out.println("Subclasses of WineDescriptor: "+dsub1);
// Again, WineColor not found because it is subclass of a oneOf
// restriction, therefore just one instead of 2 subclasses!
assertEquals(1,dsub1.size());
assertTrue(dsub1.contains(c_WineTaste));
beginTime = System.nanoTime();
Set<OInstance> instances = ontology.getOInstances();
elapsed1 = System.nanoTime() - beginTime;
// NOTE: protege4 gets 207 here because it also finds an instance without
// a type and URI: http://www.w3.org/TR/2003/WD-owl-guide-2003-331/wine
// This is the URI of the prior version of the Ontology
System.out.println("##### number of instances: "+instances.size());
System.out.println("@@@@@ number of instances: "+elapsed1);
assertEquals(206,instances.size());
ontology.cleanup();
}
// ***************************************************************
// ************************** HELPER METHODS
// ***************************************************************
// recursively find the set of all subclasses for a given set of classes
// until no more subclasses are found. We limit the maximum depth at 20.
// The set initially should contain all the classes for which we want to
// find all the subclasses.
public void expandAllClasses(Set<OClass> classes, int depth) {
if(depth > 20) {
assertTrue("Depth must not exceed 20",false);
}
if(classes.isEmpty()) return; // there are no classes to expand!
// number of new classes found
Set<OClass> addclasses = new HashSet<OClass>();
for (OClass c : classes) {
Set<OClass> subclasses = c.getSubClasses(OConstants.Closure.DIRECT_CLOSURE);
if(subclasses.contains(c)) {
System.out.println("Subclass of itself: "+c);
assertTrue(false);
}
addclasses.addAll(subclasses);
}
if(classes.addAll(addclasses)) expandAllClasses(classes,depth+1);
}
protected static File getUniqueTmpDir() {
String tmplocation = System.getProperty("run.java.io.tmpdir");
if(tmplocation == null) {
tmplocation = System.getProperty("java.io.tmpdir");
}
if(tmplocation == null) {
tmplocation = "/tmp";
}
if(tmplocation == null) {
System.err.println("Not temp-directory found, cannot continue");
System.exit(1);
}
File tmpdir = new File(tmplocation);
if(!tmpdir.exists()) {
System.err.println("Temp dir does not exist: "+tmpdir.getAbsolutePath());
System.exit(1);
}
String tmpString = Long.toString(System.currentTimeMillis(),36);
File uniqTmpDir = new File(tmpdir,"gate-towlim-"+tmpString);
uniqTmpDir.mkdir();
return uniqTmpDir;
}
protected OURI getURI(Ontology o, String uri) {
return o.createOURI(uri);
}
protected OURI getURI4Name(Ontology o, String uri) {
return o.createOURIForName(uri);
}
}
