public HGDBOntology createOntologyInDatabase(IRI ontologyIRI)
throws OWLOntologyCreationException {
try {
HGDBOntologyFormat format = new HGDBOntologyFormat();
IRI hgdbDocumentIRI = HGDBOntologyFormat.convertToHGDBDocumentIRI(ontologyIRI);
OWLOntology o = super.createOntology(ontologyIRI);
setOntologyFormat(o, format);
setOntologyDocumentIRI(o, hgdbDocumentIRI);
saveOntology(o, format, hgdbDocumentIRI);
HGDBOntology result = ontologyRepository.getOntologyByDocumentIRI(hgdbDocumentIRI);
result.setOWLOntologyManager(this);
this.ontologiesByID.put(o.getOntologyID(), result);
return result;
} catch (Exception ex) {
throw new RuntimeException(ex);
}
}
public void storeFromTo(OWLOntology from, HGDBOntology to) {
final Set<OWLAxiom> axioms = from.getAxioms();
int i = 0;
for (OWLAxiom axiom : axioms) {
to.applyChange(new AddAxiom(to, axiom));
i++;
if (i % 5000 == 0) {
System.out.println("storeFromTo: Axioms: " + i);
}
}
System.out.println("storeFromTo: Axioms: " + i);
// manager.addAxioms(newOnto, axioms);
// Add Ontology Annotations
for (OWLAnnotation a : from.getAnnotations()) {
to.applyChange(new AddOntologyAnnotation(to, a));
}
// Add Import Declarations
for (OWLImportsDeclaration im : from.getImportsDeclarations()) {
to.applyChange(new AddImport(to, im));
}
}
public void testRenderAndParse() {
List<File> renderedFiles = new ArrayList<File>();
String dblocation = System.getProperty("java.io.tmpdir") + File.separator + "hgdbtest";
HGDBOntologyManager manager = HGOntologyManagerFactory.getOntologyManager(dblocation);
HGDBOntologyRepository repo = new HGDBOntologyRepository(dblocation);
VersionManager versionManager = manager.getVersionManager();
HyperGraph graph = manager.getOntologyRepository().getHyperGraph();
//
// IMPORT AND RENDER
//
try {
// repo.dropHypergraph();
repo.deleteAllOntologies();
// System.out.println("Running GC");
// CANNOT RUN GC nullHANDLE problem !!! repo.runGarbageCollector();
URL ontologyUrl = this.getClass().getResource("/sampleOntology.owl");
IRI targetIRI = ImportOntologies.importOntology(ontologyUrl, manager);
// IRI targetIRI = ImportOntologies.importOntology(f2, manager);
HGDBOntology o = (HGDBOntology) manager.loadOntologyFromOntologyDocument(targetIRI);
VersionedOntology vo = versionManager.versioned(o.getAtomHandle());
// MANIPULATE REMOVE CHANGED
Object[] axioms = o.getAxioms().toArray();
// remove all axioms 10.
for (int i = 0; i < axioms.length / 10; i++) {
int j = i;
for (; j < i + axioms.length / 100; j++) {
if (j < axioms.length) {
manager.applyChange(new RemoveAxiom(o, (OWLAxiom) axioms[j]));
}
}
i = j;
vo.commit("SameUser", " commit no " + i);
}
// RENDER VERSIONED ONTOLOGY, includes data
// TODO...
VOWLXMLRenderConfiguration c = new VOWLXMLRenderConfiguration();
VOWLXMLVersionedOntologyRenderer r = new VOWLXMLVersionedOntologyRenderer(manager);
File fx = new File(TESTFILE.getAbsolutePath() + " Revision-" + ".xml");
renderedFiles.add(fx);
Writer fwriter = new OutputStreamWriter(new FileOutputStream(fx), Charset.forName("UTF-8"));
r.render(vo, null, fwriter, c);
// for (int i = 0; i < vo.getArity(); i++)
// {
// VOWLXMLRenderConfiguration c = new VOWLXMLRenderConfiguration();
// //c.setLastRevisionIndex(i);
// VOWLXMLVersionedOntologyRenderer r = new VOWLXMLVersionedOntologyRenderer(manager);
// File fx = new File(TESTFILE.getAbsolutePath() + " Revision-" + i + ".xml");
// // File fx = new
// // File("C:\\_CiRM\\testontos\\CountyVersioned-Rev-"+ i +
// // ".vowlxml");
// renderedFiles.add(fx);
// // File fx = new File("C:\\_CiRM\\testontos\\1 csr-Rev-"+ i +
// // ".vowlxml");
// Writer fwriter = new OutputStreamWriter(new FileOutputStream(fx),
// Charset.forName("UTF-8"));
// // Full export
// r.render(vo, fwriter, c);
// }
System.out.println("DELETE ALL ONTOLOGIES");
repo.deleteAllOntologies();
GarbageCollector gc = new GarbageCollector(repo);
gc.runGarbageCollection(GarbageCollector.MODE_DELETED_ONTOLOGIES);
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (OWLRendererException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
//
// PARSE
//
File f = new File(TESTFILE.getAbsolutePath() + " Revision-" + 10 + ".xml");
System.out.println("PARSING: " + f + " length: " + (f.length() / 1024) + " kB");
OWLOntologyDocumentSource source = new FileDocumentSource(f);
VOWLXMLParser parser = new VOWLXMLParser();
OWLOntologyEx onto = new OWLTempOntologyImpl(manager, new OWLOntologyID());
// must have onto for manager in super class
VOWLXMLDocument versionedOntologyRoot = new VOWLXMLDocument(onto);
//
// Create VersionedOntology Revision 10
try {
parser.parse(graph, source, versionedOntologyRoot, new OWLOntologyLoaderConfiguration());
System.out.println("PARSING FINISHED.");
} catch (OWLOntologyChangeException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (UnloadableImportException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (OWLParserException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
if (versionedOntologyRoot.getRenderConfig().heads().isEmpty()
&& versionedOntologyRoot
.getRenderConfig()
.roots()
.contains(versionedOntologyRoot.getRenderConfig().firstRevision())) {
OWLOntologyID ontologyID = versionedOntologyRoot.getRevisionData().getOntologyID();
IRI documentIRI =
IRI.create("hgdb://" + ontologyID.getDefaultDocumentIRI().toString().substring(7));
HGPersistentHandle ontologyUUID =
repo.getHyperGraph().getHandleFactory().makeHandle(versionedOntologyRoot.getOntologyID());
try {
System.out.println("Storing ontology data for : " + ontologyUUID);
HGDBOntology o =
manager
.getOntologyRepository()
.createOWLOntology(ontologyID, documentIRI, ontologyUUID);
storeFromTo(versionedOntologyRoot.getRevisionData(), o);
} catch (HGDBOntologyAlreadyExistsByDocumentIRIException e) {
e.printStackTrace();
} catch (HGDBOntologyAlreadyExistsByOntologyIDException e) {
e.printStackTrace();
} catch (HGDBOntologyAlreadyExistsByOntologyUUIDException e) {
e.printStackTrace();
}
// Add version control with full matching history.
System.out.println("Adding version control history to : " + ontologyUUID);
// VersionedOntology voParsed = new VersionedOntology(versionedOntologyRoot.getRevisions(),
// versionedOntologyRoot.getChangesets(), graph);
// VHGDBOntologyRepository vrepo = (VHGDBOntologyRepository)
// manager.getOntologyRepository();
// System.out.println("Versioned Repository Contents: ");
// for (VersionedOntology vox : vrepo.getVersionControlledOntologies())
// {
// System.out.println("Versioned Ontology: " + vox.getWorkingSetData());
// System.out.println("Versioned Ontology Revs: " + vox.getNrOfRevisions());
// }
// //
// // Rendering FULL Versioned Ontology
// //
// System.out.println("Rendering full versioned ontology after parse and store: " +
// ontologyUUID);
// VOWLXMLVersionedOntologyRenderer r = new VOWLXMLVersionedOntologyRenderer(manager);
// File fx = new File(TESTFILE.getAbsolutePath() + "FULL-afterParse.xml");
// Writer fwriter;
// try
// {
// fwriter = new OutputStreamWriter(new FileOutputStream(fx), Charset.forName("UTF-8"));
// r.render(voParsed, fwriter);
// }
// catch (IOException e)
// {
// e.printStackTrace();
// }
// catch (OWLRendererException e)
// {
// e.printStackTrace();
// }
} else {
System.out.println("ERROR: EXPECTING COMPLETE VERSIONED ONTOLOGY");
}
// }
}