Modified: stanbol/trunk/ontologymanager/multiplexer/clerezza/src/main/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/ontology/ClerezzaOntologyProvider.java URL: http://svn.apache.org/viewvc/stanbol/trunk/ontologymanager/multiplexer/clerezza/src/main/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/ontology/ClerezzaOntologyProvider.java?rev=1744328&r1=1744327&r2=1744328&view=diff ============================================================================== --- stanbol/trunk/ontologymanager/multiplexer/clerezza/src/main/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/ontology/ClerezzaOntologyProvider.java (original) +++ stanbol/trunk/ontologymanager/multiplexer/clerezza/src/main/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/ontology/ClerezzaOntologyProvider.java Tue May 17 22:20:49 2016 @@ -53,22 +53,18 @@ import java.util.Set; import java.util.SortedSet; import java.util.Stack; import java.util.TreeSet; -import java.util.concurrent.locks.Lock; -import org.apache.clerezza.rdf.core.Literal; -import org.apache.clerezza.rdf.core.LiteralFactory; -import org.apache.clerezza.rdf.core.MGraph; -import org.apache.clerezza.rdf.core.NonLiteral; -import org.apache.clerezza.rdf.core.Resource; -import org.apache.clerezza.rdf.core.Triple; -import org.apache.clerezza.rdf.core.TripleCollection; -import org.apache.clerezza.rdf.core.TypedLiteral; -import org.apache.clerezza.rdf.core.UriRef; +import org.apache.clerezza.commons.rdf.Literal; +import org.apache.clerezza.commons.rdf.Graph; +import org.apache.clerezza.commons.rdf.BlankNodeOrIRI; +import org.apache.clerezza.commons.rdf.RDFTerm; +import org.apache.clerezza.commons.rdf.Triple; +import org.apache.clerezza.commons.rdf.IRI; import org.apache.clerezza.rdf.core.access.EntityAlreadyExistsException; -import org.apache.clerezza.rdf.core.access.LockableMGraph; import org.apache.clerezza.rdf.core.access.TcManager; import org.apache.clerezza.rdf.core.access.TcProvider; -import org.apache.clerezza.rdf.core.impl.TripleImpl; +import org.apache.clerezza.commons.rdf.impl.utils.TripleImpl; +import org.apache.clerezza.rdf.core.LiteralFactory; import org.apache.clerezza.rdf.core.serializedform.Parser; import org.apache.clerezza.rdf.core.serializedform.UnsupportedFormatException; import org.apache.clerezza.rdf.ontologies.OWL; @@ -83,21 +79,20 @@ import org.apache.felix.scr.annotations. import org.apache.felix.scr.annotations.ReferencePolicy; import org.apache.felix.scr.annotations.ReferenceStrategy; import org.apache.felix.scr.annotations.Service; -import org.apache.stanbol.commons.indexedgraph.IndexedMGraph; +import org.apache.stanbol.commons.indexedgraph.IndexedGraph; import org.apache.stanbol.commons.owl.OWLOntologyManagerFactory; import org.apache.stanbol.commons.owl.PhonyIRIMapper; import org.apache.stanbol.commons.owl.transformation.OWLAPIToClerezzaConverter; import org.apache.stanbol.commons.owl.util.OWLUtils; import org.apache.stanbol.commons.owl.util.URIUtils; import org.apache.stanbol.commons.stanboltools.offline.OfflineMode; -import org.apache.stanbol.ontologymanager.multiplexer.clerezza.collector.MGraphMultiplexer; +import org.apache.stanbol.ontologymanager.multiplexer.clerezza.collector.GraphMultiplexer; import org.apache.stanbol.ontologymanager.ontonet.api.OntologyNetworkConfiguration; import org.apache.stanbol.ontologymanager.servicesapi.OfflineConfiguration; import org.apache.stanbol.ontologymanager.servicesapi.collector.ImportManagementPolicy; import org.apache.stanbol.ontologymanager.servicesapi.io.Origin; import org.apache.stanbol.ontologymanager.servicesapi.ontology.Multiplexer; import org.apache.stanbol.ontologymanager.servicesapi.ontology.OntologyHandleException; -import org.apache.stanbol.ontologymanager.servicesapi.ontology.OntologyLoadingException; import org.apache.stanbol.ontologymanager.servicesapi.ontology.OntologyProvider; import org.apache.stanbol.ontologymanager.servicesapi.ontology.OrphanOntologyKeyException; import org.apache.stanbol.ontologymanager.servicesapi.scope.Scope; @@ -106,7 +101,6 @@ import org.apache.stanbol.ontologymanage import org.osgi.service.component.ComponentContext; import org.semanticweb.owlapi.apibinding.OWLManager; import org.semanticweb.owlapi.model.AddImport; -import org.semanticweb.owlapi.model.IRI; import org.semanticweb.owlapi.model.OWLDataFactory; import org.semanticweb.owlapi.model.OWLOntology; import org.semanticweb.owlapi.model.OWLOntologyChange; @@ -145,32 +139,32 @@ public class ClerezzaOntologyProvider im */ private class OntologyToTcMapper { - private MGraph graph; + private Graph graph; OntologyToTcMapper() { if (store == null) throw new IllegalArgumentException("TcProvider cannot be null"); - UriRef graphId = new UriRef(metaGraphId); + IRI graphId = new IRI(metaGraphId); try { - graph = store.createMGraph(graphId); + graph = store.createGraph(graphId); } catch (EntityAlreadyExistsException e) { - graph = store.getMGraph(graphId); + graph = store.getGraph(graphId); } } - void addMapping(OWLOntologyID ontologyReference, UriRef graphName) { + void addMapping(OWLOntologyID ontologyReference, IRI graphName) { if (ontologyReference == null || ontologyReference.isAnonymous()) throw new IllegalArgumentException( "An anonymous ontology cannot be mapped. A non-anonymous ontology ID must be forged in these cases."); Triple tType, tMaps, tHasOiri = null, tHasViri = null; - IRI ontologyIRI = ontologyReference.getOntologyIRI(), versionIri = ontologyReference + org.semanticweb.owlapi.model.IRI ontologyIRI = ontologyReference.getOntologyIRI(), versionIri = ontologyReference .getVersionIRI(); - UriRef entry = buildResource(ontologyReference); + IRI entry = buildResource(ontologyReference); tType = new TripleImpl(entry, RDF.type, ENTRY_URIREF); tMaps = new TripleImpl(entry, MAPS_TO_GRAPH_URIREF, graphName); LiteralFactory lf = LiteralFactory.getInstance(); - tHasOiri = new TripleImpl(entry, HAS_ONTOLOGY_IRI_URIREF, lf.createTypedLiteral(new UriRef( + tHasOiri = new TripleImpl(entry, HAS_ONTOLOGY_IRI_URIREF, lf.createTypedLiteral(new IRI( ontologyIRI.toString()))); if (versionIri != null) tHasViri = new TripleImpl(entry, HAS_VERSION_IRI_URIREF, - lf.createTypedLiteral(new UriRef(versionIri.toString()))); + lf.createTypedLiteral(new IRI(versionIri.toString()))); synchronized (graph) { graph.add(tType); graph.add(tMaps); @@ -179,73 +173,76 @@ public class ClerezzaOntologyProvider im } } - OWLOntologyID buildPublicKey(final UriRef resource) { + OWLOntologyID buildPublicKey(final IRI resource) { // TODO desanitize? LiteralFactory lf = LiteralFactory.getInstance(); - IRI oiri = null, viri = null; + org.semanticweb.owlapi.model.IRI oiri = null, viri = null; Iterator<Triple> it = graph.filter(resource, HAS_ONTOLOGY_IRI_URIREF, null); if (it.hasNext()) { - UriRef s = null; - Resource obj = it.next().getObject(); - if (obj instanceof UriRef) s = ((UriRef) obj); - else if (obj instanceof TypedLiteral) s = lf.createObject(UriRef.class, (TypedLiteral) obj); - oiri = IRI.create(s.getUnicodeString()); + IRI s = null; + RDFTerm obj = it.next().getObject(); + if (obj instanceof IRI) s = ((IRI) obj); + else if (obj instanceof Literal) s = lf.createObject(IRI.class, (Literal) obj); + oiri = org.semanticweb.owlapi.model.IRI.create(s.getUnicodeString()); } else { // Anonymous ontology? Decode the resource itself (which is not null) return OntologyUtils.decode(resource.getUnicodeString()); } it = graph.filter(resource, HAS_VERSION_IRI_URIREF, null); if (it.hasNext()) { - UriRef s = null; - Resource obj = it.next().getObject(); - if (obj instanceof UriRef) s = ((UriRef) obj); - else if (obj instanceof TypedLiteral) s = lf.createObject(UriRef.class, (TypedLiteral) obj); - viri = IRI.create(s.getUnicodeString()); + IRI s = null; + RDFTerm obj = it.next().getObject(); + if (obj instanceof IRI) s = ((IRI) obj); + else if (obj instanceof Literal) s = lf.createObject(IRI.class, (Literal) obj); + viri = org.semanticweb.owlapi.model.IRI.create(s.getUnicodeString()); } if (viri == null) return new OWLOntologyID(oiri); else return new OWLOntologyID(oiri, viri); } /** - * Creates an {@link UriRef} out of an {@link OWLOntologyID}, so it can be used as a storage key for + * Creates an {@link IRI} out of an {@link OWLOntologyID}, so it can be used as a storage key for * the graph. * * @param ontologyReference * @return */ - UriRef buildResource(OWLOntologyID publicKey) { + IRI buildResource(OWLOntologyID publicKey) { /* - * The UriRef is of the form ontologyIRI[:::versionIRI] (TODO use something less conventional e.g. + * The IRI is of the form ontologyIRI[:::versionIRI] (TODO use something less conventional e.g. * the string form of OWLOntologyID objects?) */ - TripleCollection meta = getMetaGraph(TripleCollection.class); + Graph meta = getMetaGraph(Graph.class); if (publicKey == null) throw new IllegalArgumentException( - "Cannot build a UriRef resource on a null public key!"); + "Cannot build a IRI resource on a null public key!"); // XXX should versionIRI also include the version IRI set by owners? Currently not // Remember not to sanitize logical identifiers. - IRI ontologyIri = publicKey.getOntologyIRI(), versionIri = publicKey.getVersionIRI(); + org.semanticweb.owlapi.model.IRI ontologyIri = publicKey.getOntologyIRI(), versionIri = publicKey.getVersionIRI(); if (ontologyIri == null) throw new IllegalArgumentException( - "Cannot build a UriRef resource on an anonymous public key!"); - UriRef match = null; + "Cannot build a IRI resource on an anonymous public key!"); + + log.debug("Searching for a meta graph entry for public key:"); + log.debug(" -- {}", publicKey); + IRI match = null; LiteralFactory lf = LiteralFactory.getInstance(); - TypedLiteral oiri = lf.createTypedLiteral(new UriRef(ontologyIri.toString())); - TypedLiteral viri = versionIri == null ? null : lf.createTypedLiteral(new UriRef(versionIri + Literal oiri = lf.createTypedLiteral(new IRI(ontologyIri.toString())); + Literal viri = versionIri == null ? null : lf.createTypedLiteral(new IRI(versionIri .toString())); for (Iterator<Triple> it = meta.filter(null, HAS_ONTOLOGY_IRI_URIREF, oiri); it.hasNext();) { - Resource subj = it.next().getSubject(); + RDFTerm subj = it.next().getSubject(); log.debug(" -- Ontology IRI match found. Scanning"); - log.debug(" -- Resource : {}", subj); - if (!(subj instanceof UriRef)) { + log.debug(" -- RDFTerm : {}", subj); + if (!(subj instanceof IRI)) { log.debug(" ---- (uncomparable: skipping...)"); continue; } if (viri != null) { // Must find matching versionIRI - if (meta.contains(new TripleImpl((UriRef) subj, HAS_VERSION_IRI_URIREF, viri))) { + if (meta.contains(new TripleImpl((IRI) subj, HAS_VERSION_IRI_URIREF, viri))) { log.debug(" ---- Version IRI match!"); - match = (UriRef) subj; + match = (IRI) subj; break; // Found } else { log.debug(" ---- Expected version IRI match not found."); @@ -254,88 +251,86 @@ public class ClerezzaOntologyProvider im } else { // Must find unversioned resource - if (meta.filter((UriRef) subj, HAS_VERSION_IRI_URIREF, null).hasNext()) { + if (meta.filter((IRI) subj, HAS_VERSION_IRI_URIREF, null).hasNext()) { log.debug(" ---- Unexpected version IRI found. Skipping."); continue; } else { log.debug(" ---- Unversioned match!"); - match = (UriRef) subj; + match = (IRI) subj; break; // Found } } } + log.debug("Matching IRI in graph : {}", match); if (match == null) { - return new UriRef(OntologyUtils.encode(publicKey)); + return new IRI(OntologyUtils.encode(publicKey)); } else { return match; } } - UriRef getMapping(OWLOntologyID reference) { - Set<UriRef> aliases = new HashSet<UriRef>(); + IRI getMapping(OWLOntologyID reference) { + Set<IRI> aliases = new HashSet<IRI>(); aliases.add(buildResource(reference)); for (OWLOntologyID alias : listAliases(reference)) aliases.add(buildResource(alias)); - for (UriRef alias : aliases) { + for (IRI alias : aliases) { // Logical mappings first. Iterator<Triple> it = graph.filter(alias, MAPS_TO_GRAPH_URIREF, null); while (it.hasNext()) { - Resource obj = it.next().getObject(); - if (obj instanceof UriRef) return (UriRef) obj; + RDFTerm obj = it.next().getObject(); + if (obj instanceof IRI) return (IRI) obj; } Literal litloc = LiteralFactory.getInstance().createTypedLiteral( - new UriRef(alias.getUnicodeString())); + new IRI(alias.getUnicodeString())); // Logical mappings failed, try physical mappings. it = graph.filter(null, RETRIEVED_FROM_URIREF, litloc); while (it.hasNext()) { - Resource obj = it.next().getSubject(); - if (obj instanceof UriRef) return (UriRef) obj; + RDFTerm obj = it.next().getSubject(); + if (obj instanceof IRI) return (IRI) obj; } } return null; } - OWLOntologyID getReverseMapping(UriRef graphName) { + OWLOntologyID getReverseMapping(IRI graphName) { // Logical mappings first. - - log.info("GRAPH NAME {}", graphName); - Iterator<Triple> it = graph.filter(null, MAPS_TO_GRAPH_URIREF, graphName); while (it.hasNext()) { - Resource obj = it.next().getSubject(); - if (obj instanceof UriRef) return buildPublicKey((UriRef) obj); + RDFTerm obj = it.next().getSubject(); + if (obj instanceof IRI) return buildPublicKey((IRI) obj); } Literal litloc = LiteralFactory.getInstance().createTypedLiteral( - new UriRef(graphName.getUnicodeString())); + new IRI(graphName.getUnicodeString())); // Logical mappings failed, try physical mappings. it = graph.filter(null, RETRIEVED_FROM_URIREF, litloc); while (it.hasNext()) { - Resource subj = it.next().getSubject(); - if (subj instanceof UriRef) return buildPublicKey((UriRef) subj); + RDFTerm subj = it.next().getSubject(); + if (subj instanceof IRI) return buildPublicKey((IRI) subj); } return null; } - Set<OWLOntologyID> getVersions(IRI ontologyIri) { + Set<OWLOntologyID> getVersions(org.semanticweb.owlapi.model.IRI ontologyIri) { if (ontologyIri == null) throw new IllegalArgumentException("Cannot get versions for a null IRI."); Set<OWLOntologyID> keys = new HashSet<OWLOntologyID>(); LiteralFactory lf = LiteralFactory.getInstance(); - TypedLiteral iri = lf.createTypedLiteral(new UriRef(ontologyIri.toString())); + Literal iri = lf.createTypedLiteral(new IRI(ontologyIri.toString())); // Exclude aliases. for (Iterator<Triple> it = graph.filter(null, HAS_ONTOLOGY_IRI_URIREF, iri); it.hasNext();) { - Resource sub = it.next().getSubject(); - if (sub instanceof UriRef) keys.add(buildPublicKey((UriRef) sub)); + RDFTerm sub = it.next().getSubject(); + if (sub instanceof IRI) keys.add(buildPublicKey((IRI) sub)); } // Also check for physical locations for (Iterator<Triple> it = graph.filter(null, RETRIEVED_FROM_URIREF, iri); it.hasNext();) { - Resource sub = it.next().getSubject(); - if (sub instanceof UriRef) keys.add(buildPublicKey((UriRef) sub)); + RDFTerm sub = it.next().getSubject(); + if (sub instanceof IRI) keys.add(buildPublicKey((IRI) sub)); } return keys; } - void mapLocator(IRI locator, UriRef graphName) { + void mapLocator(org.semanticweb.owlapi.model.IRI locator, IRI graphName) { if (graphName == null) throw new IllegalArgumentException("A null graph name is not allowed."); // Null locator is a legal argument, will remove all locator mappings from the supplied graph Set<Triple> remove = new HashSet<Triple>(); @@ -347,7 +342,7 @@ public class ClerezzaOntologyProvider im graph.removeAll(remove); if (locator != null) { Literal litloc = LiteralFactory.getInstance().createTypedLiteral( - new UriRef(locator.toString())); + new IRI(locator.toString())); graph.add(new TripleImpl(graphName, RETRIEVED_FROM_URIREF, litloc)); } } @@ -357,7 +352,7 @@ public class ClerezzaOntologyProvider im Set<OWLOntologyID> aliases = listAliases(publicKey); aliases.add(publicKey); for (OWLOntologyID alias : aliases) { - UriRef ontologyId = buildResource(alias); + IRI ontologyId = buildResource(alias); // Also removes aliases and dependencies. // XXX Too extreme? for (Iterator<Triple> it = graph.filter(ontologyId, null, null); it.hasNext();) @@ -370,14 +365,12 @@ public class ClerezzaOntologyProvider im void removeMapping(OWLOntologyID ontologyReference) { Iterator<Triple> it = graph.filter(buildResource(ontologyReference), MAPS_TO_GRAPH_URIREF, null); - // To avoid concurrent modification exceptions - Collection<Triple> removeUs = new HashSet<Triple>(); + // I expect a concurrent modification exception here, but we can deal with it later. while (it.hasNext()) - removeUs.add(it.next()); - graph.removeAll(removeUs); + graph.remove(it.next()); } - void setMapping(OWLOntologyID ontologyReference, UriRef graphName) { + void setMapping(OWLOntologyID ontologyReference, IRI graphName) { removeMapping(ontologyReference); addMapping(ontologyReference, graphName); } @@ -392,8 +385,6 @@ public class ClerezzaOntologyProvider im private static final boolean _RESOLVE_IMPORTS_DEFAULT = true; - private static final boolean _MISSING_IMPORTS_FAIL_DEFAULT = true; - protected Multiplexer descriptor = null; @Property(name = OntologyProvider.IMPORT_POLICY, options = { @@ -444,9 +435,6 @@ public class ClerezzaOntologyProvider im @Property(name = OntologyProvider.RESOLVE_IMPORTS, boolValue = _RESOLVE_IMPORTS_DEFAULT) protected boolean resolveImports = _RESOLVE_IMPORTS_DEFAULT; - @Property(name = OntologyProvider.MISSING_IMPORTS_FAIL, boolValue = _MISSING_IMPORTS_FAIL_DEFAULT) - protected boolean failMissingImports = _MISSING_IMPORTS_FAIL_DEFAULT; - /* * Do not use SCR reference here: this might be different from the registered WeightedTcProvider services * : when supplied, it overrides TcManager @@ -467,7 +455,7 @@ public class ClerezzaOntologyProvider im * rule store if running outside an OSGI environment. */ public ClerezzaOntologyProvider() { - supported = new Class<?>[] {MGraph.class, TripleCollection.class, OWLOntology.class}; + supported = new Class<?>[] {Graph.class, Graph.class, OWLOntology.class}; } public ClerezzaOntologyProvider(TcProvider store, OfflineConfiguration offline, Parser parser) { @@ -506,7 +494,7 @@ public class ClerezzaOntologyProvider im // This call will also create the metadata graph. keymap = new OntologyToTcMapper(); - descriptor = new MGraphMultiplexer(keymap.graph); + descriptor = new GraphMultiplexer(keymap.graph); // Parse configuration. prefix = (String) (configuration.get(OntologyProvider.GRAPH_PREFIX)); @@ -517,11 +505,6 @@ public class ClerezzaOntologyProvider im } catch (Exception ex) { resolveImports = _RESOLVE_IMPORTS_DEFAULT; // Should be already assigned though } - try { - failMissingImports = (Boolean) (configuration.get(OntologyProvider.MISSING_IMPORTS_FAIL)); - } catch (Exception ex) { - failMissingImports = _MISSING_IMPORTS_FAIL_DEFAULT; // Should be already assigned though - } Object importPolicy = configuration.get(OntologyProvider.IMPORT_POLICY); if (importPolicy == null) { @@ -531,15 +514,15 @@ public class ClerezzaOntologyProvider im } // TODO replace with DataFileProvider ? - final IRI[] offlineResources; + final org.semanticweb.owlapi.model.IRI[] offlineResources; if (this.offlineConfig != null) { - List<IRI> paths = offlineConfig.getOntologySourceLocations(); - if (paths != null) offlineResources = paths.toArray(new IRI[0]); + List<org.semanticweb.owlapi.model.IRI> paths = offlineConfig.getOntologySourceLocations(); + if (paths != null) offlineResources = paths.toArray(new org.semanticweb.owlapi.model.IRI[0]); // There are no offline paths. - else offlineResources = new IRI[0]; + else offlineResources = new org.semanticweb.owlapi.model.IRI[0]; } // There's no offline configuration at all. - else offlineResources = new IRI[0]; + else offlineResources = new org.semanticweb.owlapi.model.IRI[0]; this.mappers = OWLOntologyManagerFactory.getMappers(offlineResources); } @@ -625,7 +608,7 @@ public class ClerezzaOntologyProvider im */ private void fillImportsReverse(OWLOntologyID importing, List<OWLOntologyID> reverseImports, - List<OWLOntologyID> level1Imports) throws OntologyHandleException { + List<OWLOntologyID> level1Imports) { log.debug("Filling reverse imports for {}", importing); // Add the importing ontology first @@ -633,43 +616,25 @@ public class ClerezzaOntologyProvider im if (level1Imports != null) level1Imports.add(importing); // Get the graph and explore its imports - TripleCollection graph // store.getTriples(importing); - = getStoredOntology(/* getPublicKey */(importing), MGraph.class, false); + Graph graph // store.getTriples(importing); + = getStoredOntology(/* getPublicKey */(importing), Graph.class, false); Iterator<Triple> it = graph.filter(null, RDF.type, OWL.Ontology); if (!it.hasNext()) return; - log.debug("Import list follows:"); Iterator<Triple> it2 = graph.filter(it.next().getSubject(), OWL.imports, null); while (it2.hasNext()) { // obj is the *original* import target - Resource obj = it2.next().getObject(); - log.debug(" * {}", obj); - if (obj instanceof UriRef) { + RDFTerm obj = it2.next().getObject(); + if (obj instanceof IRI) { // Right now getKey() is returning the "private" storage ID - String key = getKey(IRI.create(((UriRef) obj).getUnicodeString())); - log.debug(" ... with key {}", key); - if (key == null) { - if (failMissingImports) throw new OntologyHandleException( - "Failed to retrieve storage key for ontology " - + obj - + ". To prevent these exceptions from being thrown, please unset property " - + "'org.apache.stanbol.ontologymanager.ontonet.failOnMissingImports'"); - else { - log.warn("null key for {}!", obj); - log.warn("Will ignore since 'failOnMissingImports' is unset."); - continue; - } - } + String key = getKey(org.semanticweb.owlapi.model.IRI.create(((IRI) obj).getUnicodeString())); // TODO this will not be needed when getKey() and getPublicKey() return the proper public key. - OWLOntologyID oid = keymap.getReverseMapping(new UriRef(key)); + OWLOntologyID oid = keymap.getReverseMapping(new IRI(key)); // Check used for breaking cycles in the import graph. // (Unoptimized, should not use contains() for stacks.) if (!reverseImports.contains(oid)) { if (level1Imports != null) level1Imports.add(oid); fillImportsReverse(oid, reverseImports, null); } - } else { - log.warn("Unexpected type for resource {}.", obj); - log.warn(" ... Expected {}, found {}", UriRef.class, obj.getClass()); } } } @@ -689,7 +654,7 @@ public class ClerezzaOntologyProvider im @Override @Deprecated - public String getKey(IRI ontologyIri) { + public String getKey(org.semanticweb.owlapi.model.IRI ontologyIri) { // ontologyIri = URIUtils.sanitizeID(ontologyIri); return getPublicKey(new OWLOntologyID(ontologyIri)); } @@ -702,48 +667,48 @@ public class ClerezzaOntologyProvider im @SuppressWarnings("unchecked") @Override - public <O extends TripleCollection> O getMetaGraph(Class<O> returnType) { - if (!TripleCollection.class.isAssignableFrom(returnType)) throw new IllegalArgumentException( - "Only subtypes of " + TripleCollection.class + " are allowed."); - return (O) store.getTriples(new UriRef(metaGraphId)); + public <O extends Graph> O getMetaGraph(Class<O> returnType) { + if (!Graph.class.isAssignableFrom(returnType)) throw new IllegalArgumentException( + "Only subtypes of " + Graph.class + " are allowed."); + return (O) store.getGraph(new IRI(metaGraphId)); } @Override @Deprecated public OWLOntologyID getOntologyId(String storageKey) { - return keymap.getReverseMapping(new UriRef(storageKey)); + return keymap.getReverseMapping(new IRI(storageKey)); } public OntologyNetworkConfiguration getOntologyNetworkConfiguration() { Map<String,Collection<OWLOntologyID>> coreOntologies = new HashMap<String,Collection<OWLOntologyID>>(), customOntologies = new HashMap<String,Collection<OWLOntologyID>>(); Map<String,Collection<String>> attachedScopes = new HashMap<String,Collection<String>>(); - final TripleCollection meta = store.getTriples(new UriRef(metaGraphId)); + final Graph meta = store.getGraph(new IRI(metaGraphId)); // Scopes first for (Iterator<Triple> it = meta.filter(null, RDF.type, SCOPE_URIREF); it.hasNext();) { // for each // scope Triple ta = it.next(); - NonLiteral sub = ta.getSubject(); - if (sub instanceof UriRef) { - String s = ((UriRef) sub).getUnicodeString(), prefix = _NS_STANBOL_INTERNAL + Scope.shortName + BlankNodeOrIRI sub = ta.getSubject(); + if (sub instanceof IRI) { + String s = ((IRI) sub).getUnicodeString(), prefix = _NS_STANBOL_INTERNAL + Scope.shortName + "/"; if (s.startsWith(prefix)) { String scopeId = s.substring(prefix.length()); log.info("Rebuilding scope \"{}\".", scopeId); coreOntologies.put(scopeId, new TreeSet<OWLOntologyID>()); customOntologies.put(scopeId, new TreeSet<OWLOntologyID>()); - UriRef core_ur = null, custom_ur = null; - Resource r; + IRI core_ur = null, custom_ur = null; + RDFTerm r; // Check core space Iterator<Triple> it2 = meta.filter(sub, HAS_SPACE_CORE_URIREF, null); if (it2.hasNext()) { r = it2.next().getObject(); - if (r instanceof UriRef) core_ur = (UriRef) r; + if (r instanceof IRI) core_ur = (IRI) r; } else { it2 = meta.filter(null, IS_SPACE_CORE_OF_URIREF, sub); if (it2.hasNext()) { r = it2.next().getSubject(); - if (r instanceof UriRef) core_ur = (UriRef) r; + if (r instanceof IRI) core_ur = (IRI) r; } } @@ -751,12 +716,12 @@ public class ClerezzaOntologyProvider im it2 = meta.filter(sub, HAS_SPACE_CUSTOM_URIREF, null); if (it2.hasNext()) { r = it2.next().getObject(); - if (r instanceof UriRef) custom_ur = (UriRef) r; + if (r instanceof IRI) custom_ur = (IRI) r; } else { it2 = meta.filter(null, IS_SPACE_CUSTOM_OF_URIREF, sub); if (it2.hasNext()) { r = it2.next().getSubject(); - if (r instanceof UriRef) custom_ur = (UriRef) r; + if (r instanceof IRI) custom_ur = (IRI) r; } } @@ -764,23 +729,23 @@ public class ClerezzaOntologyProvider im if (core_ur != null) { for (it2 = meta.filter(core_ur, null, null); it2.hasNext();) { Triple t = it2.next(); - UriRef predicate = t.getPredicate(); + IRI predicate = t.getPredicate(); if (predicate.equals(MANAGES_URIREF)) { - if (t.getObject() instanceof UriRef) coreOntologies.get(scopeId).add( - keymap.buildPublicKey((UriRef) t.getObject()) // FIXME must be very + if (t.getObject() instanceof IRI) coreOntologies.get(scopeId).add( + keymap.buildPublicKey((IRI) t.getObject()) // FIXME must be very // temporary! - // ((UriRef) t.getObject()).getUnicodeString() + // ((IRI) t.getObject()).getUnicodeString() ); } } for (it2 = meta.filter(null, null, core_ur); it2.hasNext();) { Triple t = it2.next(); - UriRef predicate = t.getPredicate(); + IRI predicate = t.getPredicate(); if (predicate.equals(IS_MANAGED_BY_URIREF)) { - if (t.getSubject() instanceof UriRef) coreOntologies.get(scopeId).add( - keymap.buildPublicKey((UriRef) t.getSubject()) // FIXME must be very + if (t.getSubject() instanceof IRI) coreOntologies.get(scopeId).add( + keymap.buildPublicKey((IRI) t.getSubject()) // FIXME must be very // temporary! - // ((UriRef) t.getSubject()).getUnicodeString() + // ((IRI) t.getSubject()).getUnicodeString() ); } } @@ -788,23 +753,23 @@ public class ClerezzaOntologyProvider im if (custom_ur != null) { for (it2 = meta.filter(custom_ur, null, null); it2.hasNext();) { Triple t = it2.next(); - UriRef predicate = t.getPredicate(); + IRI predicate = t.getPredicate(); if (predicate.equals(MANAGES_URIREF)) { - if (t.getObject() instanceof UriRef) customOntologies.get(scopeId).add( - keymap.buildPublicKey((UriRef) t.getObject()) // FIXME must be very + if (t.getObject() instanceof IRI) customOntologies.get(scopeId).add( + keymap.buildPublicKey((IRI) t.getObject()) // FIXME must be very // temporary! - // ((UriRef) t.getObject()).getUnicodeString() + // ((IRI) t.getObject()).getUnicodeString() ); } } for (it2 = meta.filter(null, null, custom_ur); it2.hasNext();) { Triple t = it2.next(); - UriRef predicate = t.getPredicate(); + IRI predicate = t.getPredicate(); if (predicate.equals(IS_MANAGED_BY_URIREF)) { - if (t.getSubject() instanceof UriRef) customOntologies.get(scopeId).add( - keymap.buildPublicKey((UriRef) t.getSubject()) // FIXME must be very + if (t.getSubject() instanceof IRI) customOntologies.get(scopeId).add( + keymap.buildPublicKey((IRI) t.getSubject()) // FIXME must be very // temporary! - // ((UriRef) t.getSubject()).getUnicodeString() + // ((IRI) t.getSubject()).getUnicodeString() ); } } @@ -819,10 +784,10 @@ public class ClerezzaOntologyProvider im for (Iterator<Triple> it = meta.filter(null, RDF.type, SESSION_URIREF); it.hasNext();) { // for each // scope Triple ta = it.next(); - NonLiteral sub = ta.getSubject(); - if (sub instanceof UriRef) { - UriRef ses_ur = (UriRef) sub; - String s = ((UriRef) sub).getUnicodeString(); + BlankNodeOrIRI sub = ta.getSubject(); + if (sub instanceof IRI) { + IRI ses_ur = (IRI) sub; + String s = ((IRI) sub).getUnicodeString(); String prefix = _NS_STANBOL_INTERNAL + Session.shortName + "/"; if (s.startsWith(prefix)) { String sessionId = s.substring(prefix.length()); @@ -832,27 +797,27 @@ public class ClerezzaOntologyProvider im // retrieve the ontologies if (ses_ur != null) { for (Iterator<Triple> it2 = meta.filter(ses_ur, MANAGES_URIREF, null); it2.hasNext();) { - Resource obj = it2.next().getObject(); - if (obj instanceof UriRef) sessionOntologies.get(sessionId).add( - keymap.buildPublicKey((UriRef) obj) // FIXME must be very temporary! - // ((UriRef) obj).getUnicodeString() + RDFTerm obj = it2.next().getObject(); + if (obj instanceof IRI) sessionOntologies.get(sessionId).add( + keymap.buildPublicKey((IRI) obj) // FIXME must be very temporary! + // ((IRI) obj).getUnicodeString() ); } for (Iterator<Triple> it2 = meta.filter(null, IS_MANAGED_BY_URIREF, ses_ur); it2 .hasNext();) { - Resource subj = it2.next().getSubject(); - if (subj instanceof UriRef) sessionOntologies.get(sessionId).add( - keymap.buildPublicKey((UriRef) subj) // FIXME must be very temporary! - // ((UriRef) subj).getUnicodeString() + RDFTerm subj = it2.next().getSubject(); + if (subj instanceof IRI) sessionOntologies.get(sessionId).add( + keymap.buildPublicKey((IRI) subj) // FIXME must be very temporary! + // ((IRI) subj).getUnicodeString() ); } for (Iterator<Triple> it2 = meta.filter(null, APPENDED_TO_URIREF, ses_ur); it2 .hasNext();) { - Resource subj = it2.next().getSubject(); - if (subj instanceof UriRef) { - String s1 = ((UriRef) subj).getUnicodeString(); + RDFTerm subj = it2.next().getSubject(); + if (subj instanceof IRI) { + String s1 = ((IRI) subj).getUnicodeString(); String prefix1 = _NS_STANBOL_INTERNAL + Scope.shortName + "/"; if (s1.startsWith(prefix1)) { String scopeId = s1.substring(prefix1.length()); @@ -862,9 +827,9 @@ public class ClerezzaOntologyProvider im } for (Iterator<Triple> it2 = meta.filter(ses_ur, HAS_APPENDED_URIREF, null); it2 .hasNext();) { - Resource obj = it2.next().getObject(); - if (obj instanceof UriRef) { - String s1 = ((UriRef) obj).getUnicodeString(); + RDFTerm obj = it2.next().getObject(); + if (obj instanceof IRI) { + String s1 = ((IRI) obj).getUnicodeString(); String prefix1 = _NS_STANBOL_INTERNAL + Scope.shortName + "/"; if (s1.startsWith(prefix1)) { String scopeId = s1.substring(prefix1.length()); @@ -889,7 +854,7 @@ public class ClerezzaOntologyProvider im @Override @Deprecated public String getPublicKey(OWLOntologyID ontologyId) { - UriRef ur = keymap.getMapping(ontologyId); + IRI ur = keymap.getMapping(ontologyId); log.debug("key for {} is {}", ontologyId, ur); return (ur == null) ? null : ur.getUnicodeString(); } @@ -907,14 +872,14 @@ public class ClerezzaOntologyProvider im @Override @Deprecated - public <O> O getStoredOntology(IRI reference, Class<O> returnType) { + public <O> O getStoredOntology(org.semanticweb.owlapi.model.IRI reference, Class<O> returnType) { // reference = URIUtils.sanitizeID(reference); return getStoredOntology(new OWLOntologyID(reference), returnType); } @Override @Deprecated - public <O> O getStoredOntology(IRI reference, Class<O> returnType, boolean merge) { + public <O> O getStoredOntology(org.semanticweb.owlapi.model.IRI reference, Class<O> returnType, boolean merge) { // reference = URIUtils.sanitizeID(reference); return getStoredOntology(new OWLOntologyID(reference), returnType, merge); } @@ -948,7 +913,7 @@ public class ClerezzaOntologyProvider im } /** - * In this implementation the identifier is the Graph Name (e.g. ontonet::blabla) + * In this implementation the identifier is the ImmutableGraph Name (e.g. ontonet::blabla) */ @SuppressWarnings("unchecked") @Override @@ -972,20 +937,20 @@ public class ClerezzaOntologyProvider im + " is not allowed in this implementation. Only allowed return types are " + supported); - TripleCollection tc = store.getTriples(new UriRef(identifier)); + Graph tc = store.getGraph(new IRI(identifier)); if (tc == null) return null; /* * The ontology provider itself does not wrap the returned object into an in-memory graph, therefore * any direct modifications will be propagated. Collectors should wrap them, though. To change this * behaviour, uncomment the line below. */ - // tc = new SimpleMGraph(tc); + // tc = new SimpleGraph(tc); - if (TripleCollection.class.equals(returnType) || MGraph.class.isAssignableFrom(returnType)) { + if (Graph.class.equals(returnType) || Graph.class.isAssignableFrom(returnType)) { return returnType.cast(tc); } else if (OWLOntology.class.isAssignableFrom(returnType)) { try { - return (O) toOWLOntology(new UriRef(identifier), forceMerge); + return (O) toOWLOntology(new IRI(identifier), forceMerge); } catch (OWLOntologyCreationException e) { log.error( "Failed to return stored ontology " + identifier + " as type " @@ -1002,7 +967,7 @@ public class ClerezzaOntologyProvider im } @Override - public boolean hasOntology(IRI ontologyIri) { + public boolean hasOntology(org.semanticweb.owlapi.model.IRI ontologyIri) { // ontologyIri = URIUtils.sanitizeID(ontologyIri); return hasOntology(new OWLOntologyID(ontologyIri)); } @@ -1019,9 +984,9 @@ public class ClerezzaOntologyProvider im if (publicKey == null || publicKey.isAnonymous()) throw new IllegalArgumentException( "Cannot check for an anonymous ontology."); if (!new MetaGraphManager(tcManager, keymap.graph).exists(publicKey)) return Status.NO_MATCH; - UriRef graphName = keymap.getMapping(publicKey); + IRI graphName = keymap.getMapping(publicKey); if (graphName == null) return Status.UNCHARTED; - if (store.listTripleCollections().contains(graphName)) return Status.MATCH; + if (store.listGraphs().contains(graphName)) return Status.MATCH; else return Status.ORPHAN; } @@ -1053,18 +1018,18 @@ public class ClerezzaOntologyProvider im protected void computeAliasClosure(OWLOntologyID publicKey, Set<OWLOntologyID> target) { target.add(publicKey); - TripleCollection meta = getMetaGraph(TripleCollection.class); - UriRef ont = keymap.buildResource(publicKey); - Set<Resource> resources = new HashSet<Resource>(); + Graph meta = getMetaGraph(Graph.class); + IRI ont = keymap.buildResource(publicKey); + Set<RDFTerm> resources = new HashSet<RDFTerm>(); // Forwards for (Iterator<Triple> it = meta.filter(ont, OWL.sameAs, null); it.hasNext();) resources.add(it.next().getObject()); // Backwards for (Iterator<Triple> it = meta.filter(null, OWL.sameAs, ont); it.hasNext();) resources.add(it.next().getSubject()); - for (Resource r : resources) - if (r instanceof UriRef) { - OWLOntologyID newKey = keymap.buildPublicKey((UriRef) r); + for (RDFTerm r : resources) + if (r instanceof IRI) { + OWLOntologyID newKey = keymap.buildPublicKey((IRI) r); if (!target.contains(newKey)) computeAliasClosure(newKey, target); } } @@ -1085,8 +1050,8 @@ public class ClerezzaOntologyProvider im public SortedSet<OWLOntologyID> listOrphans() { SortedSet<OWLOntologyID> result = new TreeSet<OWLOntologyID>(); for (OWLOntologyID key : descriptor.getPublicKeys()) { - UriRef graphName = keymap.getMapping(key); - if (graphName == null || !store.listTripleCollections().contains(graphName)) result.add(key); + IRI graphName = keymap.getMapping(key); + if (graphName == null || !store.listGraphs().contains(graphName)) result.add(key); } return result; } @@ -1101,7 +1066,7 @@ public class ClerezzaOntologyProvider im } @Override - public Set<OWLOntologyID> listVersions(IRI ontologyIri) { + public Set<OWLOntologyID> listVersions(org.semanticweb.owlapi.model.IRI ontologyIri) { return keymap.getVersions(ontologyIri); } @@ -1117,20 +1082,20 @@ public class ClerezzaOntologyProvider im // This method only tries the supplied format once. log.debug("Trying to parse data stream with format {}", formatIdentifier); - TripleCollection rdfData = parser.parse(data, formatIdentifier); + Graph rdfData = parser.parse(data, formatIdentifier); log.debug("SUCCESS format {}.", formatIdentifier); return loadInStore(rdfData, force, references); } @Override - public OWLOntologyID loadInStore(final IRI ontologyIri, + public OWLOntologyID loadInStore(final org.semanticweb.owlapi.model.IRI ontologyIri, String formatIdentifier, boolean force, Origin<?>... origins) throws IOException { log.debug("Loading {}", ontologyIri); if (ontologyIri == null) throw new IllegalArgumentException("Ontology IRI cannot be null."); - IRI location = null; + org.semanticweb.owlapi.model.IRI location = null; if (force) location = null; else for (OWLOntologyIRIMapper mapper : mappers) { location = mapper.getDocumentIRI(ontologyIri); @@ -1162,8 +1127,6 @@ public class ClerezzaOntologyProvider im if (sup != null && !formats.contains(sup)) formats.add(sup); } - log.debug("Will try {} supported formats", formats.size()); - for (String currentFormat : formats) { try { final URLConnection con = location.toURI().toURL().openConnection(); @@ -1183,22 +1146,15 @@ public class ClerezzaOntologyProvider im } catch (UnsupportedFormatException e) { log.debug("FAILURE format {} (unsupported). Trying next one.", currentFormat); continue; - } catch (OntologyLoadingException e) { - throw new OntologyLoadingException(e); } catch (Exception e) { - // From here we should only be expecting parser-specific exceptions. - log.debug("FAILURE format {} (most likely a parse error). Will try next one.", currentFormat); - log.debug("Logged exception was a {} : {}", e.getClass(), e.getLocalizedMessage()); - log.trace("Stack trace follows:", e); + log.debug("FAILURE format {} (parse error). Will try next one.", currentFormat); continue; } } // No parser worked, return null. log.error("All parsers failed, giving up."); - log.error("Failing location was <{}>", location); - throw new OntologyLoadingException("Failed to parse an ontology from location <" + location + ">"); - // return null; + return null; } @Override @@ -1208,17 +1164,17 @@ public class ClerezzaOntologyProvider im checkReplaceability(origins); long before = System.currentTimeMillis(); - TripleCollection targetGraph; // The final graph - TripleCollection rdfData; // The supplied ontology converted to TripleCollection + Graph targetGraph; // The final graph + Graph rdfData; // The supplied ontology converted to Graph if (ontology instanceof OWLOntology) { // This will be in memory! - rdfData = OWLAPIToClerezzaConverter.owlOntologyToClerezzaMGraph((OWLOntology) ontology); - } else if (ontology instanceof TripleCollection) { + rdfData = OWLAPIToClerezzaConverter.owlOntologyToClerezzaGraph((OWLOntology) ontology); + } else if (ontology instanceof Graph) { // This might be in memory or in persistent storage. - rdfData = (TripleCollection) ontology; + rdfData = (Graph) ontology; } else throw new UnsupportedOperationException( - "This ontology provider can only accept objects assignable to " + TripleCollection.class + "This ontology provider can only accept objects assignable to " + Graph.class + " or " + OWLOntology.class); // XXX Force is ignored for the content, but the imports? @@ -1229,9 +1185,9 @@ public class ClerezzaOntologyProvider im /* * Compute aliases */ - UriRef graphName = null; + IRI graphName = null; List<OWLOntologyID> overrides = new ArrayList<OWLOntologyID>(); // Priority aliases. - List<IRI> sources = new ArrayList<IRI>(); // Second-choice aliases. + List<org.semanticweb.owlapi.model.IRI> sources = new ArrayList<org.semanticweb.owlapi.model.IRI>(); // Second-choice aliases. // Scan origins ONCE. for (int i = 0; i < origins.length; i++) { @@ -1259,13 +1215,13 @@ public class ClerezzaOntologyProvider im overrides.add(key); log.debug(" ... assigned as a priority alias for {}", primaryKey); } - } else if (ref instanceof IRI) { - sources.add((IRI) ref); + } else if (ref instanceof org.semanticweb.owlapi.model.IRI) { + sources.add((org.semanticweb.owlapi.model.IRI) ref); log.debug(" ... assigned as a secondary alias (source) for {}", primaryKey); - } else if (ref instanceof UriRef) { - if (graphName != null) log.warn("Graph name already assigned as {}. Skipping.", graphName); + } else if (ref instanceof IRI) { + if (graphName != null) log.warn("ImmutableGraph name already assigned as {}. Skipping.", graphName); else { - graphName = (UriRef) ref; + graphName = (IRI) ref; log.debug(" ... assigned as a graph name for {}", primaryKey); } } else { @@ -1280,34 +1236,34 @@ public class ClerezzaOntologyProvider im if (primaryKey == null) // No overrides, no extracted ID. { - IRI z; + org.semanticweb.owlapi.model.IRI z; // The first IRI found becomes the primary key. if (!sources.isEmpty()) z = sources.iterator().next(); else // Try the graph name - if (graphName != null) z = IRI.create(graphName.getUnicodeString()); + if (graphName != null) z = org.semanticweb.owlapi.model.IRI.create(graphName.getUnicodeString()); else // Extrema ratio : compute a timestamped primary key. - z = IRI.create(getClass().getCanonicalName() + "-time:" + System.currentTimeMillis()); + z = org.semanticweb.owlapi.model.IRI.create(getClass().getCanonicalName() + "-time:" + System.currentTimeMillis()); primaryKey = new OWLOntologyID(z); } // Check if it is possible to avoid reloading the ontology content from its source. boolean mustLoad = true; - if (!force && graphName != null && store.listTripleCollections().contains(graphName)) { + if (!force && graphName != null && store.listGraphs().contains(graphName)) { boolean condition = true; // Any failed check will abort the scan. // Check if the extracted ontology ID matches that of the supplied graph. // XXX note that anonymous ontologies should be considered a match... or should they not? - TripleCollection tc = store.getTriples(graphName); + Graph tc = store.getGraph(graphName); OWLOntologyID idFromStore = OWLUtils.extractOntologyID(tc); condition &= (extractedId == null && idFromStore == null) || extractedId.equals(idFromStore); // Finally, a size check // FIXME not a good policy for graphs that change without altering the size. - if (condition && rdfData instanceof TripleCollection) condition &= tc.size() == rdfData.size(); + if (condition && rdfData instanceof Graph) condition &= tc.size() == rdfData.size(); mustLoad &= !condition; } if (!mustLoad && graphName != null) { - log.debug("Graph with ID {} already in store. Default action is to skip storage.", graphName); - targetGraph = store.getTriples(graphName); + log.debug("ImmutableGraph with ID {} already in store. Default action is to skip storage.", graphName); + targetGraph = store.getGraph(graphName); } else { String iri = null; if (primaryKey.getOntologyIRI() != null) iri = primaryKey.getOntologyIRI().toString(); @@ -1315,13 +1271,13 @@ public class ClerezzaOntologyProvider im // s will become the graph name String s = (iri.startsWith(prefix + "::")) ? "" : (prefix + "::"); s += iri; - graphName = new UriRef(URIUtils.sanitize(s)); + graphName = new IRI(URIUtils.sanitize(s)); log.debug("Storing ontology with graph ID {}", graphName); try { - targetGraph = store.createMGraph(graphName); + targetGraph = store.createGraph(graphName); } catch (EntityAlreadyExistsException e) { - if (graphName.equals(e.getEntityName())) targetGraph = store.getMGraph(graphName); - else targetGraph = store.createMGraph(graphName); + if (graphName.equals(e.getEntityName())) targetGraph = store.getGraph(graphName); + else targetGraph = store.createGraph(graphName); } targetGraph.addAll(rdfData); } @@ -1338,11 +1294,11 @@ public class ClerezzaOntologyProvider im // TODO map unversioned ID as well? Triple t = new TripleImpl(keymap.buildResource(primaryKey), SIZE_IN_TRIPLES_URIREF, LiteralFactory.getInstance().createTypedLiteral(Integer.valueOf(rdfData.size()))); - getMetaGraph(MGraph.class).add(t); + getMetaGraph(Graph.class).add(t); } // Add aliases. - for (IRI source : sources) + for (org.semanticweb.owlapi.model.IRI source : sources) if (source != null) overrides.add(new OWLOntologyID(source)); for (OWLOntologyID alias : overrides) if (alias != null && !alias.equals(primaryKey)) { @@ -1350,61 +1306,43 @@ public class ClerezzaOntologyProvider im mappedIds += " , " + alias; } - // Resolve imports. // Do this AFTER registering the ontology, otherwise import cycles will cause infinite loops. if (resolveImports) { // Scan resources of type owl:Ontology, but only get the first. - NonLiteral ontologySubject = null; - List<UriRef> importTargets = new LinkedList<UriRef>(); - Lock l = null; // There could be locking iterators... - if (targetGraph instanceof LockableMGraph) { - l = ((LockableMGraph) targetGraph).getLock().readLock(); - l.lock(); - } - try { - Iterator<Triple> it = targetGraph.filter(null, RDF.type, OWL.Ontology); - if (it.hasNext()) ontologySubject = it.next().getSubject(); - if (ontologySubject != null) { - // Scan import statements for the one owl:Ontology considered. - it = targetGraph.filter(ontologySubject, OWL.imports, null); - while (it.hasNext()) { - Resource obj = it.next().getObject(); - if (obj instanceof UriRef) importTargets.add((UriRef) obj); - } - } - } finally { - if (l != null) l.unlock(); - } - for (UriRef importTgt : importTargets) - try { - log.info("Resolving import target {}", importTgt); - OWLOntologyID id = new OWLOntologyID(IRI.create(importTgt.getUnicodeString())); - if (keymap.getMapping(id) == null) { // Check if it's not there already. - if (isOfflineMode()) throw new RuntimeException( - "Cannot load imported ontology " + importTgt - + " while Stanbol is in offline mode."); - // TODO manage origins for imported ontologies too? - try { - IRI irimp = IRI.create(importTgt.getUnicodeString()); - OWLOntologyID id2 = loadInStore(irimp, null, false); + Iterator<Triple> it = targetGraph.filter(null, RDF.type, OWL.Ontology); + if (it.hasNext()) { + // Scan import statements for the one owl:Ontology considered. + Iterator<Triple> it2 = targetGraph.filter(it.next().getSubject(), OWL.imports, null); + while (it2.hasNext()) { + RDFTerm obj = it2.next().getObject(); + log.info("Resolving import target {}", obj); + if (obj instanceof IRI) try { + // TODO try locals first + IRI target = (IRI) obj; + OWLOntologyID id = new OWLOntologyID(org.semanticweb.owlapi.model.IRI.create(target.getUnicodeString())); + if (keymap.getMapping(id) == null) { // Check if it's not there already. + if (isOfflineMode()) throw new RuntimeException( + "Cannot load imported ontology " + obj + + " while Stanbol is in offline mode."); + // TODO manage origins for imported ontologies too? + OWLOntologyID id2 = loadInStore(org.semanticweb.owlapi.model.IRI.create(((IRI) obj).getUnicodeString()), + null, false); if (id2 != null) id = id2; - log.info("<== SUCCESS"); - } catch (OntologyLoadingException e) { - log.warn("<== FAIL"); - if (failMissingImports) throw e; - else log.warn("Import from IRI <{}> failed, but will not abort due to permissive failed import handling set for this ontology provider."); + log.info("Import {} resolved.", obj); + log.debug(""); + } else { + log.info("Requested import already stored. Setting dependency only."); } - } else { - log.info("Requested import already stored. Setting dependency only."); + descriptor.setDependency(primaryKey, id); + } catch (UnsupportedFormatException e) { + log.warn("Failed to parse format for resource " + obj, e); + // / XXX configure to continue? + } catch (IOException e) { + log.warn("Failed to load ontology from resource " + obj, e); + // / XXX configure to continue? } - descriptor.setDependency(primaryKey, id); - } catch (UnsupportedFormatException e) { - log.warn("Failed to parse format for resource " + importTgt, e); - // / XXX configure to continue? - } catch (IOException e) { - log.warn("Failed to load ontology from resource " + importTgt, e); - // / XXX configure to continue? } + } } log.debug(" Ontology {}", mappedIds); @@ -1421,14 +1359,14 @@ public class ClerezzaOntologyProvider im if (descriptor.getDependents(publicKey).isEmpty() && descriptor.getHandles(publicKey).isEmpty()) { - UriRef graphName = keymap.getMapping(publicKey); + IRI graphName = keymap.getMapping(publicKey); // TODO propagate everything to the descriptor descriptor.clearDependencies(publicKey); // release dependencies keymap.registerOntologyDeletion(publicKey); // remove metadata // Now the actual deletion - store.deleteTripleCollection(graphName); + store.deleteGraph(graphName); return true; } else throw new OntologyHandleException("There are ontologies or collectors depending on " @@ -1442,7 +1380,7 @@ public class ClerezzaOntologyProvider im } @Override - public void setLocatorMapping(IRI locator, OWLOntologyID publicKey) { + public void setLocatorMapping(org.semanticweb.owlapi.model.IRI locator, OWLOntologyID publicKey) { if (publicKey == null || publicKey.isAnonymous()) throw new IllegalArgumentException( "key must be non-null and non-anonymous."); log.info("Setting {} as the resource locator for ontology {}", locator, publicKey); @@ -1450,17 +1388,17 @@ public class ClerezzaOntologyProvider im } @Override - public void setLocatorMapping(IRI locator, String key) { + public void setLocatorMapping(org.semanticweb.owlapi.model.IRI locator, String key) { if (key == null || key.isEmpty()) throw new IllegalArgumentException( "key must be non-null and non-empty."); - if (!store.listTripleCollections().contains(new UriRef(key))) throw new IllegalArgumentException( + if (!store.listGraphs().contains(new IRI(key))) throw new IllegalArgumentException( "No ontology found with storage key " + key); if (locator == null) log .warn( "Setting null locator for {}. This will remove all physical mappings for the corresponding graph.", key); else log.info("Setting {} as the resource locator for ontology {}", locator, key); - keymap.mapLocator(locator, new UriRef(key)); + keymap.mapLocator(locator, new IRI(key)); } protected void checkReplaceability(Origin<?>... origins) { @@ -1480,32 +1418,28 @@ public class ClerezzaOntologyProvider im * @return * @throws OWLOntologyCreationException */ - protected OWLOntology toOWLOntology(UriRef graphName, boolean forceMerge) throws OWLOntologyCreationException { + protected OWLOntology toOWLOntology(IRI graphName, boolean forceMerge) throws OWLOntologyCreationException { log.debug("Exporting graph to OWLOntology"); - log.debug(" -- Graph name : {}", graphName); + log.debug(" -- ImmutableGraph name : {}", graphName); OWLOntologyManager mgr = OWLManager.createOWLOntologyManager(); // Never try to import - mgr.addIRIMapper(new PhonyIRIMapper(Collections.<IRI> emptySet())); + mgr.addIRIMapper(new PhonyIRIMapper(Collections.<org.semanticweb.owlapi.model.IRI> emptySet())); Set<OWLOntologyID> loaded = new HashSet<OWLOntologyID>(); - TripleCollection graph = store.getTriples(graphName); - UriRef ontologyId = null; + Graph graph = store.getGraph(graphName); + IRI ontologyId = null; // Get the id of this ontology. Iterator<Triple> itt = graph.filter(null, RDF.type, OWL.Ontology); if (itt.hasNext()) { - NonLiteral nl = itt.next().getSubject(); - if (nl instanceof UriRef) ontologyId = (UriRef) nl; + BlankNodeOrIRI nl = itt.next().getSubject(); + if (nl instanceof IRI) ontologyId = (IRI) nl; } List<OWLOntologyID> revImps = new Stack<OWLOntologyID>(); List<OWLOntologyID> lvl1 = new Stack<OWLOntologyID>(); - try { - fillImportsReverse(keymap.getReverseMapping(graphName), revImps, lvl1); - } catch (OntologyHandleException e) { - throw new OWLOntologyCreationException(e); - } + fillImportsReverse(keymap.getReverseMapping(graphName), revImps, lvl1); // If not set to merge (either by policy of by force), adopt the set import policy. if (!forceMerge && !ImportManagementPolicy.MERGE.equals(getImportManagementPolicy())) { @@ -1545,20 +1479,20 @@ public class ClerezzaOntologyProvider im } // FIXME when there's more than one ontology, this way of merging them seems inefficient... - TripleCollection tempGraph = new IndexedMGraph(); + Graph tempGraph = new IndexedGraph(); // The set of triples that will be excluded from the merge Set<Triple> exclusions = new HashSet<Triple>(); // Examine all reverse imports for (OWLOntologyID ref : revImps) if (!loaded.contains(ref)) { // Get the triples - TripleCollection imported = + Graph imported = // store.getTriples(ref); - getStoredOntology(getKey(ref), MGraph.class, false); + getStoredOntology(getKey(ref), Graph.class, false); // For each owl:Ontology Iterator<Triple> remove = imported.filter(null, RDF.type, OWL.Ontology); while (remove.hasNext()) { - NonLiteral subj = remove.next().getSubject(); + BlankNodeOrIRI subj = remove.next().getSubject(); /* * If it's not the root ontology, trash all its triples. If the root ontology is * anonymous, all ontology annotations are to be trashed without distinction.
Modified: stanbol/trunk/ontologymanager/multiplexer/clerezza/src/main/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/ontology/MetaGraphManager.java URL: http://svn.apache.org/viewvc/stanbol/trunk/ontologymanager/multiplexer/clerezza/src/main/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/ontology/MetaGraphManager.java?rev=1744328&r1=1744327&r2=1744328&view=diff ============================================================================== --- stanbol/trunk/ontologymanager/multiplexer/clerezza/src/main/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/ontology/MetaGraphManager.java (original) +++ stanbol/trunk/ontologymanager/multiplexer/clerezza/src/main/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/ontology/MetaGraphManager.java Tue May 17 22:20:49 2016 @@ -22,18 +22,17 @@ import static org.apache.stanbol.ontolog import java.util.Iterator; -import org.apache.clerezza.rdf.core.LiteralFactory; -import org.apache.clerezza.rdf.core.MGraph; -import org.apache.clerezza.rdf.core.Resource; -import org.apache.clerezza.rdf.core.Triple; -import org.apache.clerezza.rdf.core.TypedLiteral; -import org.apache.clerezza.rdf.core.UriRef; +import org.apache.clerezza.commons.rdf.Graph; +import org.apache.clerezza.commons.rdf.RDFTerm; +import org.apache.clerezza.commons.rdf.Triple; +import org.apache.clerezza.commons.rdf.IRI; +import org.apache.clerezza.commons.rdf.Literal; import org.apache.clerezza.rdf.core.access.TcManager; -import org.apache.clerezza.rdf.core.impl.TripleImpl; +import org.apache.clerezza.commons.rdf.impl.utils.TripleImpl; +import org.apache.clerezza.rdf.core.LiteralFactory; import org.apache.clerezza.rdf.ontologies.OWL; import org.apache.clerezza.rdf.ontologies.RDF; import org.apache.stanbol.ontologymanager.servicesapi.util.OntologyUtils; -import org.semanticweb.owlapi.model.IRI; import org.semanticweb.owlapi.model.OWLOntologyID; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -47,47 +46,47 @@ import org.slf4j.LoggerFactory; */ class MetaGraphManager { - private MGraph graph; + private Graph graph; private Logger log = LoggerFactory.getLogger(getClass()); private TcManager tcManager; - public MetaGraphManager(TcManager tcManager, MGraph graph) { + public MetaGraphManager(TcManager tcManager, Graph graph) { this.tcManager = tcManager; this.graph = graph; } - protected UriRef buildResource(final OWLOntologyID publicKey) { + protected IRI buildResource(final OWLOntologyID publicKey) { if (publicKey == null) throw new IllegalArgumentException( - "Cannot build a UriRef resource on a null public key!"); - // The UriRef is of the form ontologyIRI[:::versionIRI] (TODO use something less conventional?) + "Cannot build a IRI resource on a null public key!"); + // The IRI is of the form ontologyIRI[:::versionIRI] (TODO use something less conventional?) // XXX should versionIRI also include the version IRI set by owners? Currently not // Remember not to sanitize logical identifiers. - IRI ontologyIri = publicKey.getOntologyIRI(), versionIri = publicKey.getVersionIRI(); + org.semanticweb.owlapi.model.IRI ontologyIri = publicKey.getOntologyIRI(), versionIri = publicKey.getVersionIRI(); if (ontologyIri == null) throw new IllegalArgumentException( - "Cannot build a UriRef resource on an anonymous public key!"); + "Cannot build a IRI resource on an anonymous public key!"); log.debug("Searching for a meta graph entry for public key:"); log.debug(" -- {}", publicKey); - UriRef match = null; + IRI match = null; LiteralFactory lf = LiteralFactory.getInstance(); - TypedLiteral oiri = lf.createTypedLiteral(new UriRef(ontologyIri.toString())); - TypedLiteral viri = versionIri == null ? null : lf.createTypedLiteral(new UriRef(versionIri + Literal oiri = lf.createTypedLiteral(new IRI(ontologyIri.toString())); + Literal viri = versionIri == null ? null : lf.createTypedLiteral(new IRI(versionIri .toString())); for (Iterator<Triple> it = graph.filter(null, HAS_ONTOLOGY_IRI_URIREF, oiri); it.hasNext();) { - Resource subj = it.next().getSubject(); + RDFTerm subj = it.next().getSubject(); log.debug(" -- Ontology IRI match found. Scanning"); - log.debug(" -- Resource : {}", subj); - if (!(subj instanceof UriRef)) { + log.debug(" -- RDFTerm : {}", subj); + if (!(subj instanceof IRI)) { log.debug(" ---- (uncomparable: skipping...)"); continue; } if (viri != null) { // Must find matching versionIRI - if (graph.contains(new TripleImpl((UriRef) subj, HAS_VERSION_IRI_URIREF, viri))) { + if (graph.contains(new TripleImpl((IRI) subj, HAS_VERSION_IRI_URIREF, viri))) { log.debug(" ---- Version IRI match!"); - match = (UriRef) subj; + match = (IRI) subj; break; // Found } else { log.debug(" ---- Expected version IRI match not found."); @@ -96,32 +95,32 @@ class MetaGraphManager { } else { // Must find unversioned resource - if (graph.filter((UriRef) subj, HAS_VERSION_IRI_URIREF, null).hasNext()) { + if (graph.filter((IRI) subj, HAS_VERSION_IRI_URIREF, null).hasNext()) { log.debug(" ---- Unexpected version IRI found. Skipping."); continue; } else { log.debug(" ---- Unversioned match!"); - match = (UriRef) subj; + match = (IRI) subj; break; // Found } } } - log.debug("Matching UriRef in graph : {}", match); - if (match == null) return new UriRef(OntologyUtils.encode(publicKey)); + log.debug("Matching IRI in graph : {}", match); + if (match == null) return new IRI(OntologyUtils.encode(publicKey)); else return match; } public boolean exists(final OWLOntologyID publicKey) { - UriRef publicKeyUriRef = new UriRef(OntologyUtils.encode(publicKey)); - if (graph.filter(publicKeyUriRef, RDF.type, ENTRY_URIREF).hasNext()) return true; - if (graph.filter(publicKeyUriRef, OWL.sameAs, null).hasNext()) return true; + IRI publicKeyIRI = new IRI(OntologyUtils.encode(publicKey)); + if (graph.filter(publicKeyIRI, RDF.type, ENTRY_URIREF).hasNext()) return true; + if (graph.filter(publicKeyIRI, OWL.sameAs, null).hasNext()) return true; return false; } public void updateAddAlias(OWLOntologyID subject, OWLOntologyID object) { // For now add both owl:sameAs statements - UriRef suben = buildResource(subject), oben = buildResource(object); + IRI suben = buildResource(subject), oben = buildResource(object); synchronized (graph) { graph.add(new TripleImpl(suben, OWL.sameAs, oben)); graph.add(new TripleImpl(oben, OWL.sameAs, suben)); @@ -133,14 +132,14 @@ class MetaGraphManager { if (publicKey == null || publicKey.isAnonymous()) throw new IllegalArgumentException( "An anonymous ontology cannot be mapped. A non-anonymous ontology ID must be forged in these cases."); Triple tType, tHasOiri = null, tHasViri = null; - IRI ontologyIRI = publicKey.getOntologyIRI(), versionIri = publicKey.getVersionIRI(); - UriRef entry = buildResource(publicKey); + org.semanticweb.owlapi.model.IRI ontologyIRI = publicKey.getOntologyIRI(), versionIri = publicKey.getVersionIRI(); + IRI entry = buildResource(publicKey); tType = new TripleImpl(entry, RDF.type, ENTRY_URIREF); LiteralFactory lf = LiteralFactory.getInstance(); - tHasOiri = new TripleImpl(entry, HAS_ONTOLOGY_IRI_URIREF, lf.createTypedLiteral(new UriRef( + tHasOiri = new TripleImpl(entry, HAS_ONTOLOGY_IRI_URIREF, lf.createTypedLiteral(new IRI( ontologyIRI.toString()))); if (versionIri != null) tHasViri = new TripleImpl(entry, HAS_VERSION_IRI_URIREF, - lf.createTypedLiteral(new UriRef(versionIri.toString()))); + lf.createTypedLiteral(new IRI(versionIri.toString()))); synchronized (graph) { graph.add(tType); if (tHasViri != null) graph.add(tHasViri); Modified: stanbol/trunk/ontologymanager/multiplexer/clerezza/src/test/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/collector/TestOntologyNetworkPersistence.java URL: http://svn.apache.org/viewvc/stanbol/trunk/ontologymanager/multiplexer/clerezza/src/test/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/collector/TestOntologyNetworkPersistence.java?rev=1744328&r1=1744327&r2=1744328&view=diff ============================================================================== --- stanbol/trunk/ontologymanager/multiplexer/clerezza/src/test/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/collector/TestOntologyNetworkPersistence.java (original) +++ stanbol/trunk/ontologymanager/multiplexer/clerezza/src/test/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/collector/TestOntologyNetworkPersistence.java Tue May 17 22:20:49 2016 @@ -34,10 +34,10 @@ import java.util.Collection; import java.util.Dictionary; import java.util.Hashtable; -import org.apache.clerezza.rdf.core.TripleCollection; -import org.apache.clerezza.rdf.core.UriRef; +import org.apache.clerezza.commons.rdf.Graph; +import org.apache.clerezza.commons.rdf.IRI; import org.apache.clerezza.rdf.core.access.TcProvider; -import org.apache.clerezza.rdf.core.impl.TripleImpl; +import org.apache.clerezza.commons.rdf.impl.utils.TripleImpl; import org.apache.clerezza.rdf.core.serializedform.SupportedFormat; import org.apache.clerezza.rdf.simple.storage.SimpleTcProvider; import org.apache.stanbol.ontologymanager.core.OfflineConfigurationImpl; @@ -51,7 +51,6 @@ import org.apache.stanbol.ontologymanage import org.apache.stanbol.ontologymanager.sources.clerezza.GraphContentInputSource; import org.junit.Before; import org.junit.Test; -import org.semanticweb.owlapi.model.IRI; import org.semanticweb.owlapi.model.OWLOntology; import org.semanticweb.owlapi.model.OWLOntologyID; import org.slf4j.Logger; @@ -82,10 +81,10 @@ public class TestOntologyNetworkPersiste @Test public void canRetrieveOntologyImported() throws Exception { String pcomics = "http://stanbol.apache.org/ontologies/pcomics/";; - OWLOntologyID foaf = new OWLOntologyID(IRI.create("http://xmlns.com/foaf/0.1/";)), all = new OWLOntologyID( - IRI.create(pcomics + "characters_all.owl")), main = new OWLOntologyID( - IRI.create(pcomics + "maincharacters.owl")), minor = new OWLOntologyID( - IRI.create(pcomics + "minorcharacters.owl")); + OWLOntologyID foaf = new OWLOntologyID(org.semanticweb.owlapi.model.IRI.create("http://xmlns.com/foaf/0.1/";)), all = new OWLOntologyID( + org.semanticweb.owlapi.model.IRI.create(pcomics + "characters_all.owl")), main = new OWLOntologyID( + org.semanticweb.owlapi.model.IRI.create(pcomics + "maincharacters.owl")), minor = new OWLOntologyID( + org.semanticweb.owlapi.model.IRI.create(pcomics + "minorcharacters.owl")); OWLOntology oAll, oMain, oMinor, oFoaf; final int total = 4; @@ -133,7 +132,7 @@ public class TestOntologyNetworkPersiste @Test public void canRetrieveOntologySingleton() throws Exception { - OWLOntologyID foaf = new OWLOntologyID(IRI.create("http://xmlns.com/foaf/0.1/";)); + OWLOntologyID foaf = new OWLOntologyID(org.semanticweb.owlapi.model.IRI.create("http://xmlns.com/foaf/0.1/";)); OWLOntology o1; // Get the fake FOAF and load it into the ontology provider @@ -286,18 +285,18 @@ public class TestOntologyNetworkPersiste public void updatesGraphOnSpaceModification() throws Exception { // Ensure the metadata graph is there. - TripleCollection meta = ontologyProvider.getMetaGraph(TripleCollection.class); + Graph meta = ontologyProvider.getMetaGraph(Graph.class); assertNotNull(meta); String scopeId = "updateTest"; Scope scope = onm.createOntologyScope(scopeId, new GraphContentInputSource(getClass() .getResourceAsStream("/ontologies/test1.owl"))); - UriRef collector = new UriRef(_NS_STANBOL_INTERNAL + OntologySpace.shortName + "/" + IRI collector = new IRI(_NS_STANBOL_INTERNAL + OntologySpace.shortName + "/" + scope.getCoreSpace().getID()); - UriRef test1id = new UriRef("http://stanbol.apache.org/ontologies/test1.owl";); // Has no versionIRI + IRI test1id = new IRI("http://stanbol.apache.org/ontologies/test1.owl";); // Has no versionIRI // Be strict: the whole property pair must be there. - UriRef predicate = MANAGES_URIREF; + IRI predicate = MANAGES_URIREF; assertTrue(meta.contains(new TripleImpl(collector, predicate, test1id))); predicate = IS_MANAGED_BY_URIREF; assertTrue(meta.contains(new TripleImpl(test1id, predicate, collector))); @@ -306,7 +305,7 @@ public class TestOntologyNetworkPersiste scope.getCoreSpace().addOntology( new GraphContentInputSource(getClass().getResourceAsStream("/ontologies/minorcharacters.owl"))); - UriRef minorId = new UriRef("http://stanbol.apache.org/ontologies/pcomics/minorcharacters.owl";); + IRI minorId = new IRI("http://stanbol.apache.org/ontologies/pcomics/minorcharacters.owl";); predicate = MANAGES_URIREF; assertTrue(meta.contains(new TripleImpl(collector, predicate, minorId))); predicate = IS_MANAGED_BY_URIREF; Modified: stanbol/trunk/ontologymanager/multiplexer/clerezza/src/test/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/io/TestStorage.java URL: http://svn.apache.org/viewvc/stanbol/trunk/ontologymanager/multiplexer/clerezza/src/test/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/io/TestStorage.java?rev=1744328&r1=1744327&r2=1744328&view=diff ============================================================================== --- stanbol/trunk/ontologymanager/multiplexer/clerezza/src/test/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/io/TestStorage.java (original) +++ stanbol/trunk/ontologymanager/multiplexer/clerezza/src/test/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/io/TestStorage.java Tue May 17 22:20:49 2016 @@ -28,9 +28,9 @@ import java.util.HashSet; import java.util.Iterator; import java.util.Set; -import org.apache.clerezza.rdf.core.Graph; -import org.apache.clerezza.rdf.core.Triple; -import org.apache.clerezza.rdf.core.UriRef; +import org.apache.clerezza.commons.rdf.ImmutableGraph; +import org.apache.clerezza.commons.rdf.Triple; +import org.apache.clerezza.commons.rdf.IRI; import org.apache.clerezza.rdf.utils.GraphNode; import org.apache.stanbol.ontologymanager.multiplexer.clerezza.Constants; import org.apache.stanbol.ontologymanager.servicesapi.io.OntologyInputSource; @@ -40,7 +40,6 @@ import org.apache.stanbol.ontologymanage import org.junit.After; import org.junit.BeforeClass; import org.junit.Test; -import org.semanticweb.owlapi.model.IRI; import org.semanticweb.owlapi.model.OWLOntology; import org.semanticweb.owlapi.model.OWLOntologyID; import org.slf4j.Logger; @@ -65,7 +64,7 @@ public class TestStorage { @Test public void storageOnScopeCreation() throws Exception { - assertEquals(1, ontologyProvider.getStore().listTripleCollections().size()); + assertEquals(1, ontologyProvider.getStore().listGraphs().size()); // This one has an import that we want to hijack locally, so we use the ParentPathInputSource. OntologyInputSource<?> ois = new ParentPathInputSource(new File(getClass().getResource( "/ontologies/minorcharacters.owl").toURI())); @@ -74,16 +73,16 @@ public class TestStorage { Set<Triple> triples = new HashSet<Triple>(); - for (UriRef iri : ontologyProvider.getStore().listTripleCollections()) { + for (IRI iri : ontologyProvider.getStore().listGraphs()) { log.info("{}", iri.toString()); - UriRef entity = new UriRef(Constants.PEANUTS_MINOR_BASE + "#" + Constants.truffles); - Graph ctx = new GraphNode(entity, ontologyProvider.getStore().getTriples(iri)).getNodeContext(); + IRI entity = new IRI(Constants.PEANUTS_MINOR_BASE + "#" + Constants.truffles); + ImmutableGraph ctx = new GraphNode(entity, ontologyProvider.getStore().getGraph(iri)).getNodeContext(); Iterator<Triple> it = ctx.iterator(); while (it.hasNext()) triples.add(it.next()); } - assertFalse(ontologyProvider.getStore().listTripleCollections().isEmpty()); + assertFalse(ontologyProvider.getStore().listGraphs().isEmpty()); assertEquals(3, triples.size()); } @@ -95,7 +94,7 @@ public class TestStorage { @Test public void storedOntologyOutlivesScope() throws Exception { String ephemeralScopeId = "CaducousScope"; - OntologyInputSource<OWLOntology> ois = new RootOntologySource(IRI.create(getClass().getResource( + OntologyInputSource<OWLOntology> ois = new RootOntologySource(org.semanticweb.owlapi.model.IRI.create(getClass().getResource( "/ontologies/nonexistentcharacters.owl"))); OWLOntologyID ontologyId = ois.getRootOntology().getOntologyID(); Scope scope = onManager.createOntologyScope(ephemeralScopeId); Modified: stanbol/trunk/ontologymanager/multiplexer/clerezza/src/test/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/scope/TestAxiomInterpretation.java URL: http://svn.apache.org/viewvc/stanbol/trunk/ontologymanager/multiplexer/clerezza/src/test/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/scope/TestAxiomInterpretation.java?rev=1744328&r1=1744327&r2=1744328&view=diff ============================================================================== --- stanbol/trunk/ontologymanager/multiplexer/clerezza/src/test/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/scope/TestAxiomInterpretation.java (original) +++ stanbol/trunk/ontologymanager/multiplexer/clerezza/src/test/java/org/apache/stanbol/ontologymanager/multiplexer/clerezza/scope/TestAxiomInterpretation.java Tue May 17 22:20:49 2016 @@ -22,7 +22,7 @@ import static org.junit.Assert.assertNot import java.io.InputStream; -import org.apache.clerezza.rdf.core.Graph; +import org.apache.clerezza.commons.rdf.ImmutableGraph; import org.apache.clerezza.rdf.core.serializedform.SupportedFormat; import org.apache.stanbol.ontologymanager.servicesapi.io.OntologyInputSource; import org.apache.stanbol.ontologymanager.servicesapi.scope.Scope; @@ -51,7 +51,7 @@ public class TestAxiomInterpretation { OntologyInputSource<?> custSrc = new GraphContentInputSource(content, SupportedFormat.TURTLE); scope.getCustomSpace().addOntology(custSrc); - Graph g = scope.export(Graph.class, true); + ImmutableGraph g = scope.export(ImmutableGraph.class, true); // for (Triple t : g) // System.out.println(t);
