public HGDBOntology importOntology(IRI documentIRI, HGDBImportConfig config) {
try {
OWLOntology o = loadOntologyFromOntologyDocument(documentIRI);
HGDBOntologyFormat format = new HGDBOntologyFormat();
setOntologyFormat(o, format);
setOntologyDocumentIRI(o, documentIRI);
saveOntology(o, format, documentIRI);
return ontologyRepository.getOntologyByDocumentIRI(documentIRI);
} catch (Exception ex) {
throw new RuntimeException(ex);
}
}
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);
}
}
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;
}
}
}