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BasicStorageConnector.java
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BasicStorageConnector.java
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/**
* Copyright (C) 2016 Czech Technical University in Prague
* <p>
* This program is free software: you can redistribute it and/or modify it under
* the terms of the GNU General Public License as published by the Free Software
* Foundation, either version 3 of the License, or (at your option) any
* later version.
* <p>
* This program is distributed in the hope that it will be useful, but WITHOUT
* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
* FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
* details. You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package cz.cvut.kbss.ontodriver.owlapi.connector;
import cz.cvut.kbss.ontodriver.OntologyStorageProperties;
import cz.cvut.kbss.ontodriver.config.DriverConfigParam;
import cz.cvut.kbss.ontodriver.config.DriverConfiguration;
import cz.cvut.kbss.ontodriver.exception.OntoDriverException;
import cz.cvut.kbss.ontodriver.owlapi.config.OwlapiConfigParam;
import cz.cvut.kbss.ontodriver.owlapi.exception.*;
import cz.cvut.kbss.ontodriver.owlapi.util.DefaultOntologyIriMapper;
import cz.cvut.kbss.ontodriver.owlapi.util.MappingFileParser;
import cz.cvut.kbss.ontodriver.owlapi.util.MutableAxiomChange;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.*;
import org.semanticweb.owlapi.reasoner.OWLReasoner;
import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.FileNotFoundException;
import java.net.URI;
import java.util.List;
import java.util.concurrent.locks.Lock;
import java.util.concurrent.locks.ReentrantReadWriteLock;
import java.util.function.Consumer;
import java.util.function.Function;
import java.util.stream.Collectors;
/**
* Default file-based storage connector.
* <p>
* Each call to {@link #getOntologySnapshot()} returns a new snapshot of the current state of the ontology. The changes
* are the applied to a shared ontology, which represents the current state of the underlying storage.
* <p>
* Note: This connector currently does not handle concurrent updates.
*/
public class BasicStorageConnector extends AbstractConnector {
private static final Logger LOG = LoggerFactory.getLogger(BasicStorageConnector.class);
private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
private static Lock READ = LOCK.readLock();
private static Lock WRITE = LOCK.writeLock();
private OWLOntologyManager ontologyManager;
private OWLOntology ontology;
private OWLReasoner reasoner;
private OWLReasonerFactory reasonerFactory;
private OWLOntologyIRIMapper iriMapper;
BasicStorageConnector(DriverConfiguration configuration) throws OwlapiDriverException {
super(configuration);
}
@Override
protected void initializeConnector() throws OwlapiDriverException {
if (isOpen()) {
return;
}
final OntologyStorageProperties storageProperties = configuration.getStorageProperties();
LOG.debug("Loading ontology {} from {}.", storageProperties.getOntologyURI(),
storageProperties.getPhysicalURI());
resolveIriMapper();
this.ontologyManager = OWLManager.createOWLOntologyManager();
setIriMapper(ontologyManager);
loadOntology(storageProperties);
initializeReasonerFactory();
this.reasoner = getReasoner(ontology);
}
private void resolveIriMapper() {
if (configuration.isSet(OwlapiConfigParam.MAPPING_FILE_LOCATION)) {
this.iriMapper = new DefaultOntologyIriMapper(new MappingFileParser(configuration));
}
}
private void setIriMapper(OWLOntologyManager manager) {
if (iriMapper != null) {
manager.getIRIMappers().add(new DefaultOntologyIriMapper(new MappingFileParser(configuration)));
}
}
private void loadOntology(OntologyStorageProperties storageProperties) throws OwlapiDriverException {
try {
this.ontology =
ontologyManager.loadOntologyFromOntologyDocument(IRI.create(storageProperties.getPhysicalURI()));
if (!ontology.getOntologyID().getOntologyIRI().isPresent() ||
!ontology.getOntologyID().getOntologyIRI().get().equals(
IRI.create(storageProperties.getOntologyURI()))) {
throw new InvalidOntologyIriException(
"Expected ontology with IRI " + storageProperties.getOntologyURI() +
" but the loaded ontology has IRI " + ontology.getOntologyID().getOntologyIRI());
}
} catch (OWLOntologyCreationException e) {
if (e.getCause() instanceof FileNotFoundException) {
LOG.trace("Ontology file {} does not exist.", storageProperties.getPhysicalURI());
} else {
LOG.trace("Unable to load ontology from document.", e);
}
tryCreatingOntology();
}
}
private void tryCreatingOntology() throws OwlapiDriverException {
LOG.trace("Creating new ontology in {}.", configuration.getStorageProperties().getPhysicalURI());
try {
this.ontology = ontologyManager
.createOntology(IRI.create(configuration.getStorageProperties().getOntologyURI()));
ontology.saveOntology(IRI.create(configuration.getStorageProperties().getPhysicalURI()));
} catch (OWLOntologyCreationException | OWLOntologyStorageException e) {
throw new OwlapiDriverException(
"Unable to create ontology in " + configuration.getStorageProperties().getPhysicalURI(), e);
}
}
private void initializeReasonerFactory() {
final String reasonerFactoryClass = configuration.getProperty(DriverConfigParam.REASONER_FACTORY_CLASS);
if (reasonerFactoryClass == null) {
LOG.warn("Reasoner factory class not found. Reasoner won't be available.");
return;
}
try {
this.reasonerFactory = (OWLReasonerFactory) Class.forName(reasonerFactoryClass).newInstance();
} catch (InstantiationException | IllegalAccessException e) {
final String msg = "Unable to instantiate reasoner factory class " + reasonerFactoryClass;
LOG.error(msg);
throw new ReasonerNotAvailableException(msg, e);
} catch (ClassNotFoundException e) {
final String msg = "Reasoner factory class " + reasonerFactoryClass + " not found!";
LOG.error(msg);
throw new ReasonerNotAvailableException(msg, e);
}
}
@Override
public URI getOntologyUri() {
assert ontology.getOntologyID().getOntologyIRI().isPresent();
return ontology.getOntologyID().getOntologyIRI().get().toURI();
}
@Override
public OntologySnapshot getOntologySnapshot() {
ensureOpen();
READ.lock();
try {
final OWLOntology snapshot = ontologyManager.createOntology();
cloneOntologyContent(snapshot);
return new OntologySnapshot(snapshot, ontologyManager, ontologyManager.getOWLDataFactory(),
getReasoner(snapshot));
} catch (OWLOntologyCreationException e) {
throw new OntologySnapshotException("Unable to create ontology snapshot.", e);
} finally {
READ.unlock();
}
}
private void cloneOntologyContent(OWLOntology target) {
ontologyManager.addAxioms(target, ontology.axioms());
ontologyManager
.applyChanges(
ontology.importsDeclarations().map(i -> new AddImport(target, i)).collect(
Collectors.toList()));
}
private OntologySnapshot getLiveOntology() {
ensureOpen();
return new OntologySnapshot(ontology, ontologyManager, ontologyManager.getOWLDataFactory(), reasoner);
}
@Override
public <R> R executeRead(Function<OntologySnapshot, R> function) {
ensureOpen();
READ.lock();
try {
return function.apply(getLiveOntology());
} finally {
READ.unlock();
}
}
@Override
public void executeWrite(Consumer<OntologySnapshot> function) {
ensureOpen();
WRITE.lock();
try {
function.accept(getLiveOntology());
} finally {
WRITE.unlock();
}
}
private OWLReasoner getReasoner(OWLOntology ontology) {
if (reasonerFactory == null) {
LOG.warn(
"Creating ontology snapshot without reasoner, because reasoner factory class was not specified.");
return null;
}
return reasonerFactory.createReasoner(ontology);
}
@Override
public void applyChanges(List<OWLOntologyChange> changes) {
ensureOpen();
assert changes != null;
WRITE.lock();
try {
changes.stream().filter(ch -> ch instanceof MutableAxiomChange)
.forEach(ch -> ((MutableAxiomChange) ch).setOntology(ontology));
ontologyManager.applyChanges(changes);
try {
writeToFile();
} catch (OntologyStorageException e) {
LOG.error("Unable to write out ontology." + e);
}
} finally {
WRITE.unlock();
}
}
@Override
public void closeSnapshot(OntologySnapshot snapshot) {
ensureOpen();
assert snapshot != null;
ontologyManager.removeOntology(snapshot.getOntology());
}
@Override
void reloadData() throws OwlapiDriverException {
WRITE.lock();
try {
loadOntology(configuration.getStorageProperties());
this.reasoner = getReasoner(ontology);
} finally {
WRITE.unlock();
}
}
@Override
public void close() throws OntoDriverException {
if (!isOpen()) {
return;
}
WRITE.lock();
try {
writeToFile();
super.close();
} finally {
WRITE.unlock();
}
}
private void writeToFile() throws OntologyStorageException {
try {
ontologyManager.saveOntology(ontology, IRI.create(configuration.getStorageProperties().getPhysicalURI()));
} catch (OWLOntologyStorageException e) {
throw new OntologyStorageException(
"Error when saving ontology to " + configuration.getStorageProperties().getPhysicalURI(), e);
}
}
}