Modified: incubator/stanbol/trunk/reengineer/xml/src/main/java/org/apache/stanbol/reengineer/xml/XMLExtractor.java URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/reengineer/xml/src/main/java/org/apache/stanbol/reengineer/xml/XMLExtractor.java?rev=1197271&r1=1197270&r2=1197271&view=diff ============================================================================== --- incubator/stanbol/trunk/reengineer/xml/src/main/java/org/apache/stanbol/reengineer/xml/XMLExtractor.java (original) +++ incubator/stanbol/trunk/reengineer/xml/src/main/java/org/apache/stanbol/reengineer/xml/XMLExtractor.java Thu Nov 3 19:03:11 2011 @@ -243,7 +243,7 @@ public class XMLExtractor extends Reengi @Override public boolean canPerformReengineering(OWLOntology schemaOntology) { - OWLDataFactory factory = onManager.getOwlFactory(); + OWLDataFactory factory = OWLManager.getOWLDataFactory(); OWLClass dataSourceClass = factory.getOWLClass(Reengineer_OWL.DataSource); Set<OWLIndividual> individuals = dataSourceClass.getIndividuals(schemaOntology); @@ -370,7 +370,7 @@ public class XMLExtractor extends Reengi log.info("Starting XML Reengineering"); OWLOntologyManager ontologyManager = onManager.getOwlCacheManager(); - OWLDataFactory factory = onManager.getOwlFactory(); + OWLDataFactory factory = OWLManager.getOWLDataFactory(); IRI schemaOntologyIRI = schemaOntology.getOntologyID().getOntologyIRI(); @@ -463,7 +463,7 @@ public class XMLExtractor extends Reengi OWLOntology schemaOntology) throws ReengineeringException { OWLOntologyManager ontologyManager = onManager.getOwlCacheManager(); - OWLDataFactory factory = onManager.getOwlFactory(); + OWLDataFactory factory = OWLManager.getOWLDataFactory(); IRI schemaOntologyIRI = schemaOntology.getOntologyID().getOntologyIRI();
Modified: incubator/stanbol/trunk/reengineer/xml/src/main/java/org/apache/stanbol/reengineer/xml/XSDExtractor.java URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/reengineer/xml/src/main/java/org/apache/stanbol/reengineer/xml/XSDExtractor.java?rev=1197271&r1=1197270&r2=1197271&view=diff ============================================================================== --- incubator/stanbol/trunk/reengineer/xml/src/main/java/org/apache/stanbol/reengineer/xml/XSDExtractor.java (original) +++ incubator/stanbol/trunk/reengineer/xml/src/main/java/org/apache/stanbol/reengineer/xml/XSDExtractor.java Thu Nov 3 19:03:11 2011 @@ -53,6 +53,7 @@ import org.apache.xerces.xs.XSParticle; import org.apache.xerces.xs.XSTerm; import org.apache.xerces.xs.XSTypeDefinition; import org.apache.xerces.xs.datatypes.ObjectList; +import org.semanticweb.owlapi.apibinding.OWLManager; import org.semanticweb.owlapi.model.AddAxiom; import org.semanticweb.owlapi.model.IRI; import org.semanticweb.owlapi.model.OWLAxiom; @@ -553,7 +554,7 @@ public class XSDExtractor extends Reengi XSSimpleTypeDecl m; OWLOntologyManager ontologyManager = onManager.getOwlCacheManager(); - OWLDataFactory factory = onManager.getOwlFactory(); + OWLDataFactory factory = OWLManager.getOWLDataFactory(); log.debug("XSD output IRI : " + outputIRI); Modified: incubator/stanbol/trunk/rules/manager/src/main/java/org/apache/stanbol/rules/manager/changes/RuleStoreImpl.java URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/rules/manager/src/main/java/org/apache/stanbol/rules/manager/changes/RuleStoreImpl.java?rev=1197271&r1=1197270&r2=1197271&view=diff ============================================================================== --- incubator/stanbol/trunk/rules/manager/src/main/java/org/apache/stanbol/rules/manager/changes/RuleStoreImpl.java (original) +++ incubator/stanbol/trunk/rules/manager/src/main/java/org/apache/stanbol/rules/manager/changes/RuleStoreImpl.java Thu Nov 3 19:03:11 2011 @@ -515,7 +515,7 @@ public class RuleStoreImpl implements Ru Recipe recipe = null; if (onManager != null && recipeIRI != null) { - OWLDataFactory factory = onManager.getOwlFactory(); + OWLDataFactory factory = OWLManager.getOWLDataFactory(); OWLIndividual recipeIndividual = factory.getOWLNamedIndividual(recipeIRI); if (recipeIndividual != null) { // String ruleNS = @@ -609,7 +609,7 @@ public class RuleStoreImpl implements Ru Set<IRI> recipeIRIs = null; String ruleNS = owlmodel.getOntologyID().toString().replace("<", "").replace(">", "") + "#"; - OWLDataFactory factory = onManager.getOwlFactory(); + OWLDataFactory factory = OWLManager.getOWLDataFactory(); OWLClass recipeOWLClass = factory.getOWLClass(IRI.create(ruleNS + "Recipe")); Set<OWLIndividual> recipeIndividuals = recipeOWLClass.getIndividuals(owlmodel); Modified: incubator/stanbol/trunk/rules/refactor/src/main/java/org/apache/stanbol/rules/refactor/impl/RefactorerImpl.java URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/rules/refactor/src/main/java/org/apache/stanbol/rules/refactor/impl/RefactorerImpl.java?rev=1197271&r1=1197270&r2=1197271&view=diff ============================================================================== --- incubator/stanbol/trunk/rules/refactor/src/main/java/org/apache/stanbol/rules/refactor/impl/RefactorerImpl.java (original) +++ incubator/stanbol/trunk/rules/refactor/src/main/java/org/apache/stanbol/rules/refactor/impl/RefactorerImpl.java Thu Nov 3 19:03:11 2011 @@ -25,10 +25,14 @@ import org.apache.clerezza.rdf.core.Grap import org.apache.clerezza.rdf.core.MGraph; import org.apache.clerezza.rdf.core.TripleCollection; import org.apache.clerezza.rdf.core.UriRef; +import org.apache.clerezza.rdf.core.access.EntityAlreadyExistsException; import org.apache.clerezza.rdf.core.access.TcManager; import org.apache.clerezza.rdf.core.access.WeightedTcProvider; +import org.apache.clerezza.rdf.core.impl.SimpleGraph; import org.apache.clerezza.rdf.core.impl.SimpleMGraph; import org.apache.clerezza.rdf.core.serializedform.Serializer; +import org.apache.clerezza.rdf.core.sparql.ParseException; +import org.apache.clerezza.rdf.core.sparql.QueryParser; import org.apache.felix.scr.annotations.Activate; import org.apache.felix.scr.annotations.Component; import org.apache.felix.scr.annotations.Deactivate; @@ -45,9 +49,10 @@ import org.apache.stanbol.ontologymanage import org.apache.stanbol.ontologymanager.ontonet.api.session.DuplicateSessionIDException; import org.apache.stanbol.ontologymanager.ontonet.api.session.Session; import org.apache.stanbol.ontologymanager.ontonet.api.session.SessionManager; -import org.apache.stanbol.ontologymanager.ontonet.impl.io.ClerezzaOntologyStorage; import org.apache.stanbol.owl.transformation.JenaToClerezzaConverter; +import org.apache.stanbol.owl.transformation.JenaToOwlConvert; import org.apache.stanbol.owl.transformation.OWLAPIToClerezzaConverter; +import org.apache.stanbol.owl.util.OWLUtils; import org.apache.stanbol.rules.base.api.NoSuchRecipeException; import org.apache.stanbol.rules.base.api.Recipe; import org.apache.stanbol.rules.base.api.Rule; @@ -339,13 +344,39 @@ public class RefactorerImpl implements R } + /** + * Method borrowed from the old ontonet ClerezzaStorage + * + * @param sparql + * @param datasetURI + * @return + */ + private OWLOntology sparqlConstruct(String sparql, String datasetURI) { + + org.apache.clerezza.rdf.core.sparql.query.Query query; + MGraph mGraph = new SimpleMGraph(); + try { + query = QueryParser.getInstance().parse(sparql); + UriRef datasetUriRef = new UriRef(datasetURI); + MGraph dataset = weightedTcProvider.getMGraph(datasetUriRef); + mGraph.addAll((SimpleGraph) tcManager.executeSparqlQuery(query, dataset)); + } catch (ParseException e) { + log.error("Unable to execute SPARQL. ", e); + } + + Model om = JenaToClerezzaConverter.clerezzaMGraphToJenaModel(mGraph); + JenaToOwlConvert converter = new JenaToOwlConvert(); + + return converter.ModelJenaToOwlConvert(om, "RDF/XML"); + } + @Override public void ontologyRefactoring(IRI refactoredOntologyIRI, IRI datasetURI, IRI recipeIRI) throws RefactoringException, NoSuchRecipeException { OWLOntology refactoredOntology = null; - ClerezzaOntologyStorage ontologyStorage = onManager.getOntologyStore(); + // ClerezzaOntologyStorage ontologyStorage = onManager.getOntologyStore(); Recipe recipe; try { @@ -358,8 +389,8 @@ public class RefactorerImpl implements R String fingerPrint = ""; for (Rule kReSRule : kReSRuleList) { String sparql = kReSRule.toSPARQL(); - OWLOntology refactoredDataSet = ontologyStorage - .sparqlConstruct(sparql, datasetURI.toString()); + OWLOntology refactoredDataSet = /* ontologyStorage */this.sparqlConstruct(sparql, + datasetURI.toString()); ByteArrayOutputStream out = new ByteArrayOutputStream(); try { @@ -394,7 +425,7 @@ public class RefactorerImpl implements R refactoredOntology = merger.createMergedOntology(ontologyManager, refactoredOntologyIRI); - ontologyStorage.store(refactoredOntology); + /* ontologyStorage. */store(refactoredOntology); } catch (OWLOntologyCreationException e) { // TODO Auto-generated catch block @@ -411,6 +442,30 @@ public class RefactorerImpl implements R } } + /** + * Method borrowed from the old ontonet ClerezzaStorage + * + * @param o + */ + private void store(OWLOntology o) { + // // Why was it using two converters earlier? + // JenaToOwlConvert converter = new JenaToOwlConvert(); + // OntModel om = converter.ModelOwlToJenaConvert(o, "RDF/XML"); + // MGraph mg = JenaToClerezzaConverter.jenaModelToClerezzaMGraph(om); + TripleCollection mg = OWLAPIToClerezzaConverter.owlOntologyToClerezzaMGraph(o); + MGraph mg2 = null; + IRI iri = OWLUtils.guessOntologyIdentifier(o); + UriRef ref = new UriRef(iri.toString()); + try { + mg2 = tcManager.createMGraph(ref); + } catch (EntityAlreadyExistsException ex) { + log.info("Entity " + ref + " already exists in store. Replacing..."); + mg2 = tcManager.getMGraph(ref); + } + + mg2.addAll(mg); + } + @Override public OWLOntology ontologyRefactoring(OWLOntology inputOntology, IRI recipeIRI) throws RefactoringException, NoSuchRecipeException {
