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");
}
// }
}
protected boolean hghandleSaveAs(OWLOntology ont, OWLOntologyFormat format) throws Exception {
PHGDBOntologyManagerImpl man =
(PHGDBOntologyManagerImpl) getModelManager().getOWLOntologyManager();
OWLOntologyFormat oldFormat = man.getOntologyFormat(ont);
IRI oldDocumentIRI = man.getOntologyDocumentIRI(ont);
HGDBOntologyRepository repo = man.getOntologyRepository();
if (oldFormat instanceof PrefixOWLOntologyFormat && format instanceof PrefixOWLOntologyFormat) {
PrefixOWLOntologyFormat oldPrefixes = (PrefixOWLOntologyFormat) oldFormat;
for (String name : oldPrefixes.getPrefixNames()) {
((PrefixOWLOntologyFormat) format).setPrefix(name, oldPrefixes.getPrefix(name));
}
}
if (format instanceof HGDBOntologyFormat) {
// Case A1) OntololgyHGDB -> Repository Same Name: Already in
// repository
// Case A2) OntololgyHGDB -> Repository: Copy Ontology in Repository
// NOT CURRENTLY SUPPORTED DIALOLG
if (ont instanceof HGDBOntology) {
String message =
"This ontology is database backed and does not need to be saved to the database again.\n"
+ "All changes to it are instantly persisted in the Hypergraph Ontology Repository.\n"
+ "A copy operation to a different name in the repository is currently not supported.";
System.err.println(message);
// logger.warn(message);
JOptionPane.showMessageDialog(
getWorkspace(),
message,
"Hypergraph Database Backed Ontology",
JOptionPane.ERROR_MESSAGE);
return false;
} else {
// IN MEMORY ONTOLOGY
// Case B) OntololgyImpl -> Repository: Import
String message =
"This in-memory ontology will be imported into the Hypergraph Ontology Repository.\n"
+ "This process is estimated to take one minute per 35000 Axioms. \n"
+ ont.getOntologyID().toString()
+ " has "
+ ont.getAxiomCount()
+ " Axioms. \n"
+ "Please be patient. A Success Dialog will pop up when the process is finished.";
System.err.println(message);
// logger.info(message);
JOptionPane.showMessageDialog(
getWorkspace(), message, "Hypergraph Database Import", JOptionPane.INFORMATION_MESSAGE);
System.out.println("IMPORTING INTO HYPERGRAPH " + ont.getOntologyID());
// logger.info("IMPORTING INTO HYPERGRAPH " +
// ont.getOntologyID());
long startTime = System.currentTimeMillis();
man.setOntologyFormat(ont, format);
// TODO OPEN A DIALOG FOR SELECTING A documentIRI
IRI documentIri;
if (ont.getOntologyID().isAnonymous()) {
int i = 0;
do {
documentIri = IRI.create("hgdb://" + "anonymous-" + i);
i++;
} while (repo.existsOntologyByDocumentIRI(documentIri));
} else {
// HGDBOntologyFormat.convertToHGDBDocumentIRI(ontologyIRI)
// IRI defaultIri =
// ont.getOntologyID().getDefaultDocumentIRI();
// String defaultIriStr = defaultIri.toString();
// int schemaLength = defaultIri.getScheme().length();
// String hgdbIRIStr = "hgdb" +
// defaultIriStr.toString().substring(schemaLength);
documentIri =
HGDBOntologyFormat.convertToHGDBDocumentIRI(
ont.getOntologyID().getDefaultDocumentIRI());
//
// Check if exists by ID or Document IRI
//
if (repo.existsOntology(ont.getOntologyID())) {
JOptionPane.showMessageDialog(
getWorkspace(),
"An ontology with the same ID already exists in the hypergraph repository."
+ "\r\n "
+ ont.getOntologyID()
+ "\r\n If you wish to replace, delete the old one now using: HypergraphDB/Delete",
"Hypergraph Database Import - Failed",
JOptionPane.ERROR_MESSAGE);
return false;
} else if (repo.existsOntologyByDocumentIRI(documentIri)) {
JOptionPane.showMessageDialog(
getWorkspace(),
"An ontology with the same documentIRI already exists in the hypergraph repository."
+ "\r\n "
+ documentIri
+ "\r\n If you wish to replace, delete the old one now using: HypergraphDB/Delete",
"Hypergraph Database Import - Failed",
JOptionPane.ERROR_MESSAGE);
return false;
} // else continue import
}
System.out.println("Saving with documentIRI: " + documentIri);
// logger.info("Saving with documentIRI: " + documentIri);
// + ont.getOntologyID().getOntologyIRI().getFragment());
man.setOntologyDocumentIRI(ont, documentIri);
getModelManager().save(ont);
int durationSecs = (int) (System.currentTimeMillis() - startTime) / 1000;
message =
"Hypergraph Database Import Success.\n"
+ "Saving took "
+ durationSecs
+ " seconds for "
+ ont.getAxiomCount()
+ " Axioms. \n"
+ "You are still working with the in-memory ontology. \n "
+ "Do you wish to use the database backed ontology now?";
int useHGOnto =
JOptionPane.showConfirmDialog(
getWorkspace(),
message,
"Hypergraph Database Import Success",
JOptionPane.YES_NO_OPTION);
addRecent(documentIri.toURI());
if (useHGOnto == JOptionPane.YES_OPTION) {
// load the ontology from hypergraph and close
getModelManager().reload(ont);
} else {
man.setOntologyFormat(ont, oldFormat);
man.setOntologyDocumentIRI(ont, oldDocumentIRI);
}
return true;
}
} else {
// FILE BASED FORMAT
File file = getSaveAsOWLFile(ont);
if (file != null) {
// Do the following only if not database backed.
man.setOntologyFormat(ont, format);
man.setOntologyDocumentIRI(ont, IRI.create(file));
try {
getModelManager().save(ont);
addRecent(file.toURI());
} finally {
if (ont instanceof HGDBOntology) {
man.setOntologyFormat(ont, oldFormat);
man.setOntologyDocumentIRI(ont, oldDocumentIRI);
}
}
return true;
} else {
System.err.println("No valid file specified for the save as operation - quitting");
// logger.warn("No valid file specified for the save as operation - quitting");
return false;
}
}
}