Jena 6 ont-api

http-tests/document-hierarchy/GET-namespace-forClass-rdfs.sh

@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+initialize_dataset "$END_USER_BASE_URL" "$TMP_END_USER_DATASET" "$END_USER_ENDPOINT_URL"
+initialize_dataset "$ADMIN_BASE_URL" "$TMP_ADMIN_DATASET" "$ADMIN_ENDPOINT_URL"
+purge_cache "$END_USER_VARNISH_SERVICE"
+purge_cache "$ADMIN_VARNISH_SERVICE"
+purge_cache "$FRONTEND_VARNISH_SERVICE"
+
+# sp:Describe is declared only as rdfs:Class (not owl:Class) in sp.ttl.
+# OntologyFilter must promote rdfs:Class to owl:Class during materialization so
+# that OWL2 profiles recognise third-party vocab terms and return their SPIN constructors.
+
+response=$(curl -k -f -s \
+  -G \
+  -E "$OWNER_CERT_FILE":"$OWNER_CERT_PWD" \
+  -H "Accept: application/rdf+xml" \
+  --data-urlencode "forClass=http://spinrdf.org/sp#Describe" \
+  "${END_USER_BASE_URL}ns")
+
+# response must be non-empty: sp:Describe must be recognised as an OntClass
+echo "$response" | grep -q "http://spinrdf.org/sp#Describe"

pom.xml

@@ -146,7 +146,7 @@
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>twirl</artifactId>
-            <version>1.1.0</version>
+            <version>1.2.0-SNAPSHOT</version>
             <exclusions>
                 <!-- exclude slf4j-reload4j 1.7.x binding; replaced below with 2.0.x matching slf4j-api from Jena -->
                 <exclusion>
@@ -163,13 +163,13 @@
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>client</artifactId>
-            <version>4.3.0</version>
+            <version>4.3.1-SNAPSHOT</version>
             <classifier>classes</classifier>
         </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>client</artifactId>
-            <version>4.3.0</version>
+            <version>4.3.1-SNAPSHOT</version>
             <type>war</type>
         </dependency>
         <dependency>

src/main/java/com/atomgraph/linkeddatahub/resource/Generate.java

@@ -42,7 +42,7 @@
 import jakarta.ws.rs.core.Response.Status;
 import jakarta.ws.rs.core.UriBuilder;
 import jakarta.ws.rs.core.UriInfo;
-import org.apache.jena.ontology.Ontology;
+import org.apache.jena.ontapi.model.OntModel;
 import org.apache.jena.query.ParameterizedSparqlString;
 import org.apache.jena.query.Query;
 import org.apache.jena.query.QueryFactory;
@@ -69,7 +69,7 @@ public class Generate
     private final UriInfo uriInfo;
     private final MediaTypes mediaTypes;
     private final Application application;
-    private final Ontology ontology;
+    private final OntModel ontology;
     private final Optional<AgentContext> agentContext;
     private final com.atomgraph.linkeddatahub.Application system;
     private final ResourceContext resourceContext;
@@ -88,7 +88,7 @@ public class Generate
      */
     @Inject
     public Generate(@Context Request request, @Context UriInfo uriInfo, MediaTypes mediaTypes,
-            com.atomgraph.linkeddatahub.apps.model.Application application, Optional<Ontology> ontology, Optional<AgentContext> agentContext,
+            com.atomgraph.linkeddatahub.apps.model.Application application, Optional<OntModel> ontology, Optional<AgentContext> agentContext,
             com.atomgraph.linkeddatahub.Application system, @Context ResourceContext resourceContext)
     {
         if (ontology.isEmpty()) throw new InternalServerErrorException("Ontology is not specified");
@@ -134,7 +134,7 @@ public Response post(Model model)
                     if (queryRes == null) throw new BadRequestException("Container query string (spin:query) not provided");
 
                     // Lookup query in ontology
-                    Resource queryResource = getOntology().getOntModel().getResource(queryRes.getURI());
+                    Resource queryResource = getOntology().getResource(queryRes.getURI());
                     if (queryResource == null || !queryResource.hasProperty(SP.text))
                         throw new BadRequestException("Query resource not found in ontology: " + queryRes.getURI());
 
@@ -265,7 +265,7 @@ public Application getApplication()
      *
      * @return the ontology
      */
-    public Ontology getOntology()
+    public OntModel getOntology()
     {
         return ontology;
     }

src/main/java/com/atomgraph/linkeddatahub/resource/Namespace.java

@@ -31,7 +31,7 @@
 import com.atomgraph.core.model.impl.dataset.ServiceImpl;
 import com.atomgraph.linkeddatahub.apps.model.Application;
 import com.atomgraph.linkeddatahub.apps.model.EndUserApplication;
-import com.atomgraph.linkeddatahub.server.util.OntologyModelGetter;
+import com.atomgraph.linkeddatahub.server.util.OntologyRepository;
 import java.net.URI;
 import java.util.List;
 import java.util.Optional;
@@ -47,7 +47,7 @@
 import jakarta.ws.rs.core.SecurityContext;
 import jakarta.ws.rs.core.UriInfo;
 import org.apache.jena.irix.IRIx;
-import org.apache.jena.ontology.Ontology;
+import org.apache.jena.ontapi.model.OntModel;
 import org.apache.jena.query.DatasetFactory;
 import org.apache.jena.query.Query;
 import org.apache.jena.query.QueryFactory;
@@ -70,7 +70,7 @@ public class Namespace extends com.atomgraph.core.model.impl.SPARQLEndpointImpl
     private final URI uri;
     private final UriInfo uriInfo;
     private final Application application;
-    private final Ontology ontology;
+    private final OntModel ontology;
     private final com.atomgraph.linkeddatahub.Application system;
 
     /**
@@ -86,10 +86,10 @@ public class Namespace extends com.atomgraph.core.model.impl.SPARQLEndpointImpl
      */
     @Inject
     public Namespace(@Context Request request, @Context UriInfo uriInfo,
-            Application application, Optional<Ontology> ontology, MediaTypes mediaTypes,
+            Application application, Optional<OntModel> ontology, MediaTypes mediaTypes,
             @Context SecurityContext securityContext, com.atomgraph.linkeddatahub.Application system)
     {
-        super(request, new ServiceImpl(DatasetFactory.create(ontology.get().getOntModel()), mediaTypes), mediaTypes);
+        super(request, new ServiceImpl(DatasetFactory.create(ontology.get()), mediaTypes), mediaTypes);
         this.uri = uriInfo.getAbsolutePath();
         this.uriInfo = uriInfo;
         this.application = application;
@@ -128,7 +128,7 @@ public Response get(@QueryParam(QUERY) Query query,
                 Model instances = ModelFactory.createDefaultModel();
 
                 forClasses.stream().
-                    map(forClass -> Optional.ofNullable(getOntology().getOntModel().getOntClass(checkURI(forClass).toString()))).
+                    map(forClass -> Optional.ofNullable(getOntology().getOntClass(checkURI(forClass).toString()))).
                     flatMap(Optional::stream).
                     forEach(forClass -> new Constructor().construct(forClass, instances, getApplication().getBase().getURI()));
 
@@ -141,8 +141,8 @@ public Response get(@QueryParam(QUERY) Query query,
                 String ontologyURI = getApplication().getOntology().getURI();
                 if (log.isDebugEnabled()) log.debug("Returning namespace ontology from OntDocumentManager: {}", ontologyURI);
                 // not returning the injected in-memory ontology because it has inferences applied to it
-                OntologyModelGetter modelGetter = new OntologyModelGetter(getApplication().as(EndUserApplication.class), getSystem(), getSystem().getOntModelSpec(), getSystem().getOntologyQuery());
-                return getResponseBuilder(modelGetter.getModel(ontologyURI)).build();
+                OntologyRepository repository = new OntologyRepository(getApplication().as(EndUserApplication.class), getSystem(), com.atomgraph.linkeddatahub.client.GraphStoreClient.create(getSystem().getClient(), getSystem().getMediaTypes()), getSystem().getOntologyQuery());
+                return getResponseBuilder(org.apache.jena.rdf.model.ModelFactory.createModelForGraph(repository.get(ontologyURI))).build();
             }
             else throw new BadRequestException("SPARQL query string not provided");
         }
@@ -223,7 +223,7 @@ public Application getApplication()
      * 
      * @return application ontology
      */
-    public Ontology getOntology()
+    public OntModel getOntology()
     {
         return ontology;
     }

src/main/java/com/atomgraph/linkeddatahub/resource/admin/ClearOntology.java

@@ -18,9 +18,8 @@
 
 import com.atomgraph.linkeddatahub.apps.model.AdminApplication;
 import com.atomgraph.linkeddatahub.apps.model.EndUserApplication;
-import static com.atomgraph.linkeddatahub.server.filter.request.OntologyFilter.addDocumentModel;
 import com.atomgraph.linkeddatahub.server.filter.response.CacheInvalidationFilter;
-import com.atomgraph.linkeddatahub.server.util.OntologyModelGetter;
+import com.atomgraph.linkeddatahub.server.util.OntologyRepository;
 import java.net.URI;
 import jakarta.inject.Inject;
 import jakarta.ws.rs.BadRequestException;
@@ -31,8 +30,7 @@
 import jakarta.ws.rs.core.MediaType;
 import jakarta.ws.rs.core.Response;
 import jakarta.ws.rs.core.UriBuilder;
-import org.apache.jena.ontology.OntModel;
-import org.apache.jena.ontology.OntModelSpec;
+import com.atomgraph.linkeddatahub.server.filter.request.OntologyFilter;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
 import org.apache.jena.rdf.model.Resource;
@@ -82,11 +80,11 @@ public Response post(@FormParam("uri") String ontologyURI, @HeaderParam("Referer
         if (ontologyURI == null) throw new BadRequestException("Ontology URI not specified");
 
         EndUserApplication endUserApp = getApplication().as(AdminApplication.class).getEndUserApplication(); // we're assuming the current app is admin
-        OntModelSpec ontModelSpec = new OntModelSpec(getSystem().getOntModelSpec(endUserApp));
-        if (ontModelSpec.getDocumentManager().getFileManager().hasCachedModel(ontologyURI))
+        OntologyRepository repository = getSystem().getRepository(endUserApp);
+        if (repository.isCached(ontologyURI))
         {
             if (log.isDebugEnabled()) log.debug("Clearing ontology with URI '{}' from memory", ontologyURI);
-            ontModelSpec.getDocumentManager().getFileManager().removeCacheModel(ontologyURI);
+            repository.remove(ontologyURI);
 
             URI ontologyDocURI = UriBuilder.fromUri(ontologyURI).fragment(null).build(); // skip fragment from the ontology URI to get its graph URI
             // frontend proxy still uses URL-pattern BAN for direct document GETs (until Stage 3 brings xkey tagging to varnish-frontend).
@@ -116,19 +114,7 @@ public Response post(@FormParam("uri") String ontologyURI, @HeaderParam("Referer
             }
 
             // !!! we need to reload the ontology model before returning a response, to make sure the next request already gets the new version !!!
-            // same logic as in OntologyFilter. TO-DO: encapsulate?
-            OntologyModelGetter modelGetter = new OntologyModelGetter(endUserApp, getSystem(), ontModelSpec, getSystem().getOntologyQuery());
-            ontModelSpec.setImportModelGetter(modelGetter);
-            if (log.isDebugEnabled()) log.debug("Started loading ontology with URI '{}' from the admin dataset", ontologyURI);
-            Model baseModel = modelGetter.getModel(ontologyURI);
-            OntModel ontModel = ModelFactory.createOntologyModel(ontModelSpec, baseModel);
-            // materialize OntModel inferences to avoid invoking rules engine on every request
-            OntModel materializedModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); // no inference
-            materializedModel.add(ontModel);
-            ontModel.getDocumentManager().addModel(ontologyURI, materializedModel, true); // make immutable and add as OntModel so that imports do not need to be reloaded during retrieval
-            // make sure to cache imported models not only by ontology URI but also by document URI
-            ontModel.listImportedOntologyURIs(true).forEach((String importURI) -> addDocumentModel(ontModel.getDocumentManager(), importURI));
-            if (log.isDebugEnabled()) log.debug("Finished loading ontology with URI '{}' from the admin dataset", ontologyURI);
+            OntologyFilter.loadOntology(repository, ontologyURI);
         }
 
         if (referer != null) return Response.seeOther(referer).build();

src/main/java/com/atomgraph/linkeddatahub/resource/admin/SignUp.java

@@ -72,7 +72,7 @@
 import jakarta.ws.rs.core.UriInfo;
 import jakarta.ws.rs.ext.Providers;
 import static org.apache.jena.datatypes.xsd.XSDDatatype.XSDhexBinary;
-import org.apache.jena.ontology.Ontology;
+import org.apache.jena.ontapi.model.OntModel;
 import org.apache.jena.query.ParameterizedSparqlString;
 import org.apache.jena.query.Query;
 import org.apache.jena.query.ResultSet;
@@ -144,7 +144,7 @@ public class SignUp extends DocumentHierarchyGraphStoreImpl
     // TO-DO: move to AuthenticationExceptionMapper and handle as state instead of URI resource?
     @Inject
     public SignUp(@Context Request request, @Context UriInfo uriInfo, MediaTypes mediaTypes,
-            com.atomgraph.linkeddatahub.apps.model.Application application, Optional<Ontology> ontology, Optional<Service> service,
+            com.atomgraph.linkeddatahub.apps.model.Application application, Optional<OntModel> ontology, Optional<Service> service,
             @Context SecurityContext securityContext, Optional<AgentContext> agentContext,
             @Context Providers providers, com.atomgraph.linkeddatahub.Application system, @Context ServletConfig servletConfig)
     {

src/main/java/com/atomgraph/linkeddatahub/resource/admin/pkg/InstallPackage.java

@@ -17,7 +17,6 @@
 package com.atomgraph.linkeddatahub.resource.admin.pkg;
 
 import static com.atomgraph.client.MediaType.TEXT_XSL;
-import com.atomgraph.client.util.DataManager;
 import com.atomgraph.linkeddatahub.apps.model.AdminApplication;
 import com.atomgraph.linkeddatahub.apps.model.EndUserApplication;
 import com.atomgraph.linkeddatahub.client.GraphStoreClient;
@@ -60,7 +59,6 @@
 import org.apache.jena.ontology.ConversionException;
 import org.apache.jena.update.UpdateFactory;
 import org.apache.jena.update.UpdateRequest;
-import org.apache.jena.util.FileManager;
 import com.atomgraph.linkeddatahub.vocabulary.DH;
 import com.atomgraph.linkeddatahub.vocabulary.FOAF;
 import com.atomgraph.linkeddatahub.vocabulary.SIOC;
@@ -88,7 +86,6 @@ public class InstallPackage
 
     private final com.atomgraph.linkeddatahub.apps.model.Application application;
     private final com.atomgraph.linkeddatahub.Application system;
-    private final DataManager dataManager;
     private final Optional<AgentContext> agentContext;
 
     @Context ServletContext servletContext;
@@ -105,12 +102,10 @@ public class InstallPackage
     @Inject
     public InstallPackage(com.atomgraph.linkeddatahub.apps.model.Application application,
                    com.atomgraph.linkeddatahub.Application system,
-                   DataManager dataManager,
                    Optional<AgentContext> agentContext)
     {
         this.application = application;
         this.system = system;
-        this.dataManager = dataManager;
         this.agentContext = agentContext;
     }
 
@@ -242,12 +237,12 @@ private com.atomgraph.linkeddatahub.apps.model.Package getPackage(String package
         final Model model;
 
         // check if we have the model in the cache first and if yes, return it from there instead making an HTTP request
-        if (((FileManager)getDataManager()).hasCachedModel(packageURI) ||
-                (getDataManager().isResolvingMapped() && getDataManager().isMapped(packageURI))) // read mapped URIs (such as system ontologies) from a file
+        if (getSystem().getRepository().isCached(packageURI) ||
+                (getSystem().getRepository().isMapped(packageURI))) // read mapped URIs (such as system ontologies) from a file
         {
-            if (log.isDebugEnabled()) log.debug("hasCachedModel({}): {}", packageURI, ((FileManager)getDataManager()).hasCachedModel(packageURI));
-            if (log.isDebugEnabled()) log.debug("isMapped({}): {}", packageURI, getDataManager().isMapped(packageURI));
-            model = getDataManager().loadModel(packageURI);
+            if (log.isDebugEnabled()) log.debug("hasCachedModel({}): {}", packageURI, getSystem().getRepository().isCached(packageURI));
+            if (log.isDebugEnabled()) log.debug("isMapped({}): {}", packageURI, getSystem().getRepository().isMapped(packageURI));
+            model = ModelFactory.createModelForGraph(getSystem().getRepository().get(packageURI));
         }
         else
         {
@@ -284,12 +279,12 @@ private Model downloadOntology(String uri)
         if (log.isDebugEnabled()) log.debug("Downloading ontology from: {}", uri);
 
         // check if we have the model in the cache first and if yes, return it from there instead making an HTTP request
-        if (((FileManager)getDataManager()).hasCachedModel(uri) ||
-                (getDataManager().isResolvingMapped() && getDataManager().isMapped(uri))) // read mapped URIs (such as system ontologies) from a file
+        if (getSystem().getRepository().isCached(uri) ||
+                (getSystem().getRepository().isMapped(uri))) // read mapped URIs (such as system ontologies) from a file
         {
-            if (log.isDebugEnabled()) log.debug("hasCachedModel({}): {}", uri, ((FileManager)getDataManager()).hasCachedModel(uri));
-            if (log.isDebugEnabled()) log.debug("isMapped({}): {}", uri, getDataManager().isMapped(uri));
-            return getDataManager().loadModel(uri);
+            if (log.isDebugEnabled()) log.debug("hasCachedModel({}): {}", uri, getSystem().getRepository().isCached(uri));
+            if (log.isDebugEnabled()) log.debug("isMapped({}): {}", uri, getSystem().getRepository().isMapped(uri));
+            return ModelFactory.createModelForGraph(getSystem().getRepository().get(uri));
         }
         else
         {
@@ -522,15 +517,6 @@ public ServletContext getServletContext()
         return servletContext;
     }
 
-    /**
-     * Returns RDF data manager.
-     *
-     * @return RDF data manager
-     */
-    public DataManager getDataManager()
-    {
-        return dataManager;
-    }
 
     /**
      * Returns JAX-RS resource context.