Seed the ad-hoc ontology repository in Namespace

Namespace built a fresh OntologyRepository without the bundled
vocabulary/ontology mappings, so an empty SPARQL result would fall through
to an HTTP dereference of a bundled URI instead of the shipped file.
Extract Application.createRepository(app) (the seeding done by
getRepository(app)) and use it in both places.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

Author: namedgraph

src/main/java/com/atomgraph/linkeddatahub/Application.java

@@ -1782,15 +1782,25 @@ protected Map<String, OntologyRepository> getEndUserRepositories()
      */
     public OntologyRepository getRepository(EndUserApplication app)
     {
-        return getEndUserRepositories().computeIfAbsent(app.getURI(), uri ->
-        {
-            OntologyRepository appRepository = new OntologyRepository(app, this, GraphStoreClient.create(getClient(), getMediaTypes()), getOntologyQuery());
-            // seed bundled vocabulary/ontology mappings from the global repository
-            getRepository().getLocationMappings().forEach(appRepository::addLocationMapping);
-            getRepository().getPrefixMappings().forEach(appRepository::addPrefixMapping);
+        return getEndUserRepositories().computeIfAbsent(app.getURI(), uri -> createRepository(app));
+    }
 
-            return appRepository;
-        });
+    /**
+     * Creates a fresh ontology repository for an application, seeded with the bundled
+     * vocabulary/ontology mappings from the global repository so that mapped URIs resolve to shipped
+     * files rather than being dereferenced over HTTP.
+     *
+     * @param app end-user application resource
+     * @return ontology repository
+     */
+    public OntologyRepository createRepository(EndUserApplication app)
+    {
+        OntologyRepository appRepository = new OntologyRepository(app, this, GraphStoreClient.create(getClient(), getMediaTypes()), getOntologyQuery());
+        // seed bundled vocabulary/ontology mappings from the global repository
+        getRepository().getLocationMappings().forEach(appRepository::addLocationMapping);
+        getRepository().getPrefixMappings().forEach(appRepository::addPrefixMapping);
+
+        return appRepository;
     }
 
     /**

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

@@ -139,9 +139,10 @@ public Response get(@QueryParam(QUERY) Query query,
             {
                 // the application ontology MUST use a <ns> URI! This is the URI this ontology endpoint is deployed on by the Dispatcher class
                 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
-                OntologyRepository repository = new OntologyRepository(getApplication().as(EndUserApplication.class), getSystem(), com.atomgraph.linkeddatahub.client.GraphStoreClient.create(getSystem().getClient(), getSystem().getMediaTypes()), getSystem().getOntologyQuery());
+                if (log.isDebugEnabled()) log.debug("Returning raw namespace ontology: {}", ontologyURI);
+                // not returning the injected in-memory ontology because it has inferences applied to it;
+                // a fresh, mapping-seeded repository serves the raw SPARQL-loaded ontology
+                OntologyRepository repository = getSystem().createRepository(getApplication().as(EndUserApplication.class));
                 return getResponseBuilder(org.apache.jena.rdf.model.ModelFactory.createModelForGraph(repository.get(ontologyURI))).build();
             }
             else throw new BadRequestException("SPARQL query string not provided");