/*
* TestOntologyAPI.java
*
* Niraj Aswani, 09/March/07
*
* $Id: Test_OWLIMOntology.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.AnnotationProperty;
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.OURI;
import gate.creole.ontology.ObjectProperty;
import gate.creole.ontology.Ontology;
import gate.creole.ontology.RDFProperty;
import gate.creole.ontology.SymmetricProperty;
import gate.creole.ontology.TransitiveProperty;
import gate.util.GateException;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.HashSet;
import java.util.Set;
import org.apache.commons.io.FileUtils;
import org.apache.log4j.Logger;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import static org.junit.Assert.*;
/**
* Run various tests ...
*/
public class Test_OWLIMOntology {
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;
@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);
}
}
// testLoadImports: test the loading of an existing ontology, finding the ontology
// URI, import mappings, imports etc.
@Test
public void testLoadImports() throws MalformedURLException,
ResourceInstantiationException {
FeatureMap fm = Factory.newFeatureMap();
File demoFile = new File(ontologiesDir,"protonu.owl");
URL rdfXmlURL = demoFile.toURI().toURL();
fm.put("rdfXmlURL", rdfXmlURL);
fm.put("baseURI", "");
File mappingsFile = new File(ontologiesDir,"mappingsfile1.txt");
URL mappingsFileURL = mappingsFile.toURI().toURL();
fm.put("mappingsURL",mappingsFileURL);
fm.put("persistent","false");
fm.put("loadImports", "true");
Ontology ontology = (Ontology)Factory.createResource(
"gate.creole.ontology.impl.sesame.OWLIMOntology", fm);
// we should now have the protou ontology loaded and the protons ontology
// imported from the local directory. The protont import should have
// been ignored, as specified in the mappings file.
Set<OClass> allClasses = ontology.getOClasses(false);
//for(OClass aClass : allClasses ) {
// System.out.println("Class: "+aClass+" / "+aClass.getONodeID().toTurtle());
//}
// Check if the Base URI was set from the loaded ontology
System.out.println("Found default nameSpace: "+ontology.getDefaultNameSpace());
assertEquals("Default Name Space",
"http://proton.semanticweb.org/2005/04/protonu#",
ontology.getDefaultNameSpace());
//System.out.println("Found ontology URIs: "+ontology.getOntologyURIs());
// make sure we find classes from protonu and protont, but not protons
OClass c1 = ontology.getOClass(ontology.createOURIForName("SportEvent"));
assertNotNull(c1);
ontology.cleanup();
}
/**
* Create lots of ontologies in quick succession to test if the creation
* of temporary storage location directories for them works.
* (many more than 50 ontologies cannot be created here or we would run into
* heap memory problems with the default memory settings used when the
* tests are run)
* @throws ResourceInstantiationException
*/
@Test
public void testFastCreation() throws ResourceInstantiationException {
Set<Ontology> ontologies = new HashSet<Ontology>();
for (int i=0; i<50; i++) {
FeatureMap fm = Factory.newFeatureMap();
Ontology ontology = (Ontology)Factory.createResource(
"gate.creole.ontology.impl.sesame.OWLIMOntology", fm);
ontologies.add(ontology);
}
for(Ontology ontology : ontologies) {
ontology.cleanup();
}
}
// testAccessOldNew: test ontology methods that were already present in the old
// implementation - output measurements and do some benchmarking so
// we can compare.
@Test
public void testAccessOldNew() throws MalformedURLException,
ResourceInstantiationException {
FeatureMap fm = Factory.newFeatureMap();
File demoFile = new File(ontologiesDir,"protonust.owl");
URL rdfXmlURL = demoFile.toURI().toURL();
fm.put("rdfXmlURL", rdfXmlURL);
Ontology ontology = (Ontology)Factory.createResource(
"gate.creole.ontology.impl.sesame.OWLIMOntology", fm);
long beginTime;
long elapsed1;
beginTime = System.nanoTime();
Set<OClass> classes = ontology.getOClasses(false);
elapsed1 = System.nanoTime() - beginTime;
System.out.println("##### all classes: "+classes.size());
System.out.println("@@@@@ all classes: "+elapsed1);
assertEquals(252, classes.size());
//System.out.println("Classes: "+classes);
beginTime = System.nanoTime();
classes = ontology.getOClasses(true);
elapsed1 = System.nanoTime() - beginTime;
System.out.println("##### top classes: "+classes.size());
System.out.println("@@@@@ top classes: "+elapsed1);
assertEquals(15, classes.size());
beginTime = System.nanoTime();
Set<AnnotationProperty> anns = ontology.getAnnotationProperties();
elapsed1 = System.nanoTime() - beginTime;
System.out.println("List ann props: "+anns);
System.out.println("##### ann props: "+anns.size());
System.out.println("@@@@@ ann props: "+elapsed1);
assertEquals(6, anns.size());
beginTime = System.nanoTime();
Set<DatatypeProperty> dats = ontology.getDatatypeProperties();
elapsed1 = System.nanoTime() - beginTime;
System.out.println("##### dat props: "+dats.size());
System.out.println("@@@@@ dat props: "+elapsed1);
assertEquals(11, dats.size());
beginTime = System.nanoTime();
Set<ObjectProperty> obs = ontology.getObjectProperties();
elapsed1 = System.nanoTime() - beginTime;
System.out.println("##### obj props: "+obs.size());
System.out.println("@@@@@ obj props: "+elapsed1);
assertEquals(43, obs.size());
beginTime = System.nanoTime();
@SuppressWarnings("deprecation")
Set<OInstance> insts = ontology.getOInstances();
elapsed1 = System.nanoTime() - beginTime;
System.out.println("##### insts: "+insts.size());
System.out.println("@@@@@ insts: "+elapsed1);
assertEquals(0, insts.size());
beginTime = System.nanoTime();
Set<RDFProperty> props = ontology.getPropertyDefinitions();
elapsed1 = System.nanoTime() - beginTime;
System.out.println("##### propdefs: "+props.size());
System.out.println("@@@@@ propdefs: "+elapsed1);
// assertEquals(0, insts.size());
beginTime = System.nanoTime();
Set<SymmetricProperty> symprops = ontology.getSymmetricProperties();
elapsed1 = System.nanoTime() - beginTime;
System.out.println("##### symprops: "+symprops.size());
System.out.println("@@@@@ symprops: "+elapsed1);
// assertEquals(0, insts.size());
beginTime = System.nanoTime();
Set<TransitiveProperty> transprops = ontology.getTransitiveProperties();
elapsed1 = System.nanoTime() - beginTime;
System.out.println("##### transprops: "+transprops.size());
System.out.println("@@@@@ transprops: "+elapsed1);
// assertEquals(0, insts.size());
OURI cBAURI = ontology.createOURIForName("BusinessAbstraction");
//System.out.println("OUIR: "+cBAURI+" / "+cBAURI.toTurtle());
OClass cBA = ontology.getOClass(cBAURI);
assertNotNull(cBA);
beginTime = System.nanoTime();
classes = cBA.getSubClasses(TRANSITIVE_CLOSURE);
elapsed1 = System.nanoTime() - beginTime;
System.out.println("##### BA subclasses all: "+classes.size());
System.out.println("@@@@@ BA subclasses all: "+elapsed1);
assertEquals(2, classes.size());
beginTime = System.nanoTime();
classes = cBA.getSubClasses(DIRECT_CLOSURE);
elapsed1 = System.nanoTime() - beginTime;
System.out.println("##### BA subclasses direct: "+classes.size());
System.out.println("@@@@@ BA subclasses direct: "+elapsed1);
assertEquals(2, classes.size());
//ontology.getOResourcesWith(null, null);
//ontology.getOResourcesWith(null, null);
//ontology.getDistance(null, null);
// TODO:
// for a couple of classes, get all subclasses, direct subclasses
// get all superclasses ...
ontology.cleanup();
}
@Test
public void testCreateModify() throws MalformedURLException,
ResourceInstantiationException,
FileNotFoundException,
IOException {
FeatureMap fm = Factory.newFeatureMap();
Ontology ontology = (Ontology)Factory.createResource(
"gate.creole.ontology.impl.sesame.OWLIMOntology", fm);
long beginTime;
long elapsed1;
beginTime = System.nanoTime();
Set<OClass> classes = ontology.getOClasses(false);
elapsed1 = System.nanoTime() - beginTime;
System.out.println("##### all classes: "+classes.size());
System.out.println("@@@@@ all classes: "+elapsed1);
assertEquals(0, classes.size());
// set the Base URI
ontology.setDefaultNameSpace("http://gate.ac.uk/Ontology/testCreateModify/#");
// create some classes
ontology.addOClass(getURI4Name(ontology,"Class01"));
OClass c02 = ontology.addOClass(getURI4Name(ontology,"Class02"));
assertNotNull(c02);
OClass c0201 = ontology.addOClass(getURI4Name(ontology,"Class0201"));
assertNotNull(c0201);
c02.addSubClass(c0201);
OClass c020101 = ontology.addOClass(getURI4Name(ontology,"Class020101"));
assertNotNull(c020101);
c0201.addSubClass(c020101);
beginTime = System.nanoTime();
classes = ontology.getOClasses(false);
elapsed1 = System.nanoTime() - beginTime;
System.out.println("##### all classes: "+classes.size());
System.out.println("@@@@@ all classes: "+elapsed1);
assertEquals(4, classes.size());
OClass c02b = ontology.getOClass(getURI4Name(ontology,"Class02"));
assertNotNull("Find Class02 again",c02b);
beginTime = System.nanoTime();
classes = c02b.getSubClasses(DIRECT_CLOSURE);
elapsed1 = System.nanoTime() - beginTime;
System.out.println("##### c02 sub classes: "+classes.size());
System.out.println("@@@@@ c02 sub classes: "+elapsed1);
assertEquals(1, classes.size());
beginTime = System.nanoTime();
classes = c02b.getSubClasses(TRANSITIVE_CLOSURE);
elapsed1 = System.nanoTime() - beginTime;
System.out.println("##### c02 all classes: "+classes.size());
System.out.println("@@@@@ c02 all classes: "+elapsed1);
assertEquals(2, classes.size());
// add annotation, datatype, object properties, subproperties,
// transitive properties
// instances
// restrictions
// delete some of the stuff added and see if it is gone
// save to the tmp dir
File savedOntology = new File(tmpDir,"testCreateModify.rdfxml.owl");
FileOutputStream os = new FileOutputStream(savedOntology);
ontology.writeOntologyData(os, OConstants.OntologyFormat.RDFXML, false);
os.close();
File savedOntologyT = new File(tmpDir,"testCreateModify.turtle.owl");
os = new FileOutputStream(savedOntologyT);
ontology.writeOntologyData(os, OConstants.OntologyFormat.TURTLE, false);
os.close();
savedOntologyT = new File(tmpDir,"testCreateModifyWithImports.turtle.owl");
os = new FileOutputStream(savedOntologyT);
ontology.writeOntologyData(os, OConstants.OntologyFormat.TURTLE, true);
os.close();
ontology.cleanup();
//////////////////////////////////////////////////
URL savedOntoURL = savedOntology.toURI().toURL();
fm.put("rdfXmlURL", savedOntoURL);
ontology = (Ontology)Factory.createResource(
"gate.creole.ontology.impl.sesame.OWLIMOntology", fm);
ontology.setDefaultNameSpace("http://gate.ac.uk/Ontology/testCreateModify/#");
beginTime = System.nanoTime();
classes = ontology.getOClasses(false);
elapsed1 = System.nanoTime() - beginTime;
System.out.println("##### 2 all classes: "+classes.size());
System.out.println("@@@@@ 2 all classes: "+elapsed1);
assertEquals(4, classes.size());
c02b = ontology.getOClass(getURI4Name(ontology,"Class02"));
assertNotNull("Find Class02 again",c02b);
beginTime = System.nanoTime();
classes = c02b.getSubClasses(DIRECT_CLOSURE);
elapsed1 = System.nanoTime() - beginTime;
System.out.println("##### c02 sub classes: "+classes.size());
System.out.println("@@@@@ c02 sub classes: "+elapsed1);
assertEquals(1, classes.size());
beginTime = System.nanoTime();
classes = c02b.getSubClasses(TRANSITIVE_CLOSURE);
elapsed1 = System.nanoTime() - beginTime;
System.out.println("##### c02 all classes: "+classes.size());
System.out.println("@@@@@ c02 all classes: "+elapsed1);
assertEquals(2, classes.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);
}
}
