Add support for EObject creation and deletion

This commit implements the creation and deletion of EObjects in the resource,
including the recursive creation and deletion of their descendants in the
containment hierarchy.

The documentation has been updated to describe the required tweaks to the .rdfres
file when using the resource to create new RDF files. The user should either set a
default namespace IRI for the new instances (which use EMF-generated UUIDs),
whether through the .rdfres, or by setting the namespace IRI of the empty prefix
(e.g. `PREFIX : <http://foo/bar/> .`).

If none of the above are set, the resource will fall back to Jena's default behaviour,
which is to use the absolute IRI of the RDF model (e.g. `file://a/b/c/file.ttl#`).

---------

Co-authored-by: Antonio Garcia-Dominguez <a.garcia-dominguez@york.ac.uk>

Author: OwenR-York

RESOURCE.md

@@ -4,6 +4,10 @@ This repository includes a prototype implementation of an EMF resource for RDF g
 
 It can be installed from the repository's update site: see [`README`](./README.md) for details.
 
+This RDF-EMF resource produces an EMF model representation of an RDF model; this could be an EMF model saved as RDF, or an RDF model from another program.
+One or more RDF model files and schemas can be combined/reasoned before being deserialised against an EMF Ecore metamodel.
+An EMF model instance is composed of `EObject`s for the RDF model element that have `rdf:type` statements that match an `EClass` in the configured Ecore metamodel(s).
+
 ## Differences with emf-triple
 
 This implementation has some major differences with [emf-triple](https://github.com/ghillairet/emftriple):
@@ -15,21 +19,25 @@ These differences are achieved by loading an intermediary `.rdfres` file with al
 
 ## Current limitations
 
-The only modifications that are supported at the moment are:
+Saving has only been tested against file-based locations. We have not tested saving into triple stores.
+
+The resource assumes that the EPackage nsURI and the RDF nsURI used for `rdf:type` subjects and for property statements (e.g. `metamodel:featureName`) are a close match to each other.
+Specifically, we support two options:
 
-* Setting/unsetting single-valued `EAttribute`s with the pre-defined `EDataType`s in Ecore.
+* RDF namespace IRI = EPackage nsURI (including any trailing separator, such as `#` or `/`).
+* RDF namespace IRI = EPackage nsURI + "#".
 
-Saving has only been tested against file-based locations.
-We have not tested saving into triple stores.
+Namespaces for creating EMF models must be configured in the `.rdfres` (see  Default model namespace section below).
+At the moment, the same namespace URI is used for every EObject created by the resource.
 
 ## .rdfres file format
 
 Suppose you have a `model.ttl` Turtle file with some statements of interest, written against an ontology in `schema.ttl`.
 
 Suppose as well that the RDF resources in `model.ttl` follows certain conventions that relate them to an Ecore metamodel, in the [MOF2RDF](https://www.omg.org/spec/MOF2RDF/1.0/About-MOF2RDF) style:
 
-* There are `rdf:type` predicates from the RDF resource to another RDF resource whose URI is `ePackageNamespaceURI#eClassName`.
-* Statements use predicates with URIs of the form `ePackageNamespaceURI#eStructuralFeatureName`:
+* There are `rdf:type` predicates from the RDF resource to another RDF resource whose namespace URI is `ePackageNamespaceURI`, and local name is `eClassName`.
+* Statements use predicates whose namespace URIs are `ePackageNamespaceURI` and local names are `eStructuralFeatureName`:
   * Predicate objects can be other RDF resources (in the case of `EReference`s), or literals (in the case of `EAttribute`s).
   * RDF lists are supported for many-valued features.
 
@@ -83,3 +91,19 @@ schemaModels:
   - schema.ttl
 multiValueAttributeMode: List
 ```
+
+### Default model namespace
+
+A default model namespace URI is required when adding new resources to an RDF model.
+The namespace URI can be configured in the `.rdfres` file as shown below.
+
+```yaml
+defaultModelNamespace: http://foo/bar/example#
+```
+The URI must be absolute, e.g. by starting with `file://` (`/` will become file) or `http://`.
+If you provide an invalid URI, then Jena will revert to using the URI of the named model it loaded the RDF from as the name space. 
+
+The example above results in new RDF node with an IRI composed of the default name space and a UUID for the new EObject. E.g. `http://foo/bar/example#_6sDDMIgJEfC2g6UdYdL1hg`
+
+If a default model namespace is not provided in the `.rdfres` file, the resource will fall back to the blank prefix `PREFIX : <URI>` in the RDF model.
+The last resort is to let Jena decide, which will use the URI that the RDF model was loaded from.

bundles/org.eclipse.epsilon.rdf.emf/src/org/eclipse/epsilon/rdf/emf/RDFDeserializer.java

@@ -63,10 +63,44 @@ public class RDFDeserializer {
 	private final Map<EObject, Resource> eobToResource = new IdentityHashMap<>();
 	private final Multimap<Resource, EObject> resourceToEob = HashMultimap.create();
 
+	private final Map<EObject, Resource> deregisteredEObject = new IdentityHashMap<>();
+
 	public RDFDeserializer(Supplier<EPackage.Registry> packageRegistry) {
 		this.packageRegistry = packageRegistry;
 	}
-
+	
+	/**
+	 * <p>
+	 * Normalise EMF package URI to end in '#' if they don't end in '#' or '/'.
+	 * </p>
+	 *
+	 * <p>
+	 * The resource assumes that the EPackage nsURI and the RDF nsURI used for
+	 * `rdf:type` subjects and for property statements (e.g.
+	 * `metamodel:featureName`) are a close match to each other.
+	 * </p>
+	 *
+	 * <p>
+	 * Specifically, we support two options:
+	 * </p>
+	 *
+	 * <ul>
+	 * <li>RDF namespace IRI = EPackage nsURI (including any trailing separator,
+	 * such as `#` or `/`).</li>
+	 * <li>RDF namespace IRI = EPackage nsURI + "#".</li>
+	 * </ul>
+	 *
+	 * @param namespaceURI EPackage namespace URI to be normalised.
+	 * @return EPackage namespace URI normalised to have a trailing separator (e.g.
+	 *         # or /).
+	 */
+	public String normaliseEPackageNSURI(String namespaceURI) {
+		if (!namespaceURI.endsWith("#") && !namespaceURI.endsWith("/")) {
+			namespaceURI += "#";
+		}
+		return namespaceURI;
+	}
+	
 	/**
 	 * Populates the {@link #getEObjectToResourceMap()} from the contents of
 	 * the {@code ontModel}.
@@ -138,17 +172,15 @@ protected void deserializeProperty(Resource node, EObject eob, EStructuralFeatur
 		}
 	}
 
+	/**
+	 * The resource assumes that the EPackage nsURI and the RDF nsURI used for `rdf:type` subjects and for property statements (e.g. `metamodel:featureName`) are a close match to each other.
+	 * Specifically, we support two options:
+	 * <br>- RDF namespace IRI = EPackage nsURI (including any trailing separator, such as `#` or `/`).
+	 * <br>- RDF namespace IRI = EPackage nsURI + "#".
+	 */
 	@SuppressWarnings("unchecked")
 	protected Object deserializeProperty(Resource node, EStructuralFeature sf) {
-		String sfPackageURI = sf.getEContainingClass().getEPackage().getNsURI();
-		if (!sfPackageURI.endsWith("#") && !sfPackageURI.endsWith("/")) {
-			/*
-			 * We assume that when the EPackage nsURI does not end in # or /, the RDF nsURI ends in #.
-			 *
-			 * TODO make this mapping configurable?
-			 */
-			sfPackageURI += "#";
-		}
+		String sfPackageURI = normaliseEPackageNSURI(sf.getEContainingClass().getEPackage().getNsURI());
 
 		List<Object> values = new ArrayList<>();
 		for (StmtIterator itValue = node.listProperties(new PropertyImpl(sfPackageURI, sf.getName())); itValue.hasNext(); ) {
@@ -305,4 +337,24 @@ protected void deserializeObjectAttributes(Resource node) {
 		}
 	}
 
+	public void deregisterEObject(EObject eob) {
+		Resource node = getRDFResource(eob);
+		eobToResource.remove(eob);
+		resourceToEob.remove(eob, node);
+		deregisteredEObject.put(eob, node);
+	}
+
+	public void registerNewEObject(EObject eob, Resource node) {
+		eobToResource.put(eob, node);
+		resourceToEob.put(node, eob);
+	}
+
+	public Resource restoreEObjectResource(EObject eObject) {
+		Resource node = deregisteredEObject.remove(eObject);
+		if (node != null) {
+			registerNewEObject(eObject, node);
+		}
+		return node;
+	}
+
 }

bundles/org.eclipse.epsilon.rdf.emf/src/org/eclipse/epsilon/rdf/emf/RDFGraphResourceImpl.java

@@ -50,7 +50,7 @@
 
 public class RDFGraphResourceImpl extends ResourceImpl {
 
-	private static final boolean NOTIFICATION_TRACE = true;
+	private static final boolean NOTIFICATION_TRACE = false;
 
 	private RDFResourceConfiguration config;
 	private RDFDeserializer deserializer;
@@ -62,6 +62,16 @@ public class RDFGraphResourceImpl extends ResourceImpl {
 	private Model rdfSchemaModel;
 	private Model rdfDataModel;
 	private OntModel rdfOntModel;
+	
+	private String defaultModelNamespace;
+
+	public String getDefaultModelNamespace() {
+		return defaultModelNamespace;
+	}
+
+	public void setDefaultModelNamespace(String defaultModelNamespace) {
+		this.defaultModelNamespace = defaultModelNamespace;
+	}
 
 	public static enum MultiValueAttributeMode {
 		LIST("List"), CONTAINER("Container");
@@ -108,6 +118,7 @@ protected void doLoad(InputStream inputStream, Map<?, ?> options) throws IOExcep
 		CustomClassLoaderConstructor constructor = new CustomClassLoaderConstructor(this.getClass().getClassLoader(), new LoaderOptions());
 		this.config = new Yaml(constructor).loadAs(inputStream, RDFResourceConfiguration.class);
 		loadRDFModels();
+		setDefaultModelNamespace(config.getDefaultModelNamespace());
 
 		validationMode = config.getRawValidationMode();
 
@@ -124,9 +135,9 @@ protected void doLoad(InputStream inputStream, Map<?, ?> options) throws IOExcep
 		// Apply eAdapters for notifications of changes, and setup the Graph Resource updater
 		if (NOTIFICATION_TRACE) {
 			// Produce a console trace for debugging and development
-			this.eAdapters().add(new RDFGraphResourceNotificationAdapterTrace());
+			this.eAdapters().add(new RDFGraphResourceNotificationAdapterTrace(this));
 		}
-		this.eAdapters().add(new RDFGraphResourceNotificationAdapterChangeRDF());
+		this.eAdapters().add(new RDFGraphResourceNotificationAdapterChangeRDF(this));
 		rdfGraphUpdater = new RDFGraphResourceUpdate(deserializer, this, multiValueAttributeMode);
 	}
 
@@ -239,7 +250,7 @@ public List<Resource> getResourcesForNamedModelsContaining(EObject eObject) {
 
 	public List<Resource> getResourcesForNamedModelsContaining(Resource res) {
 		List<Resource> resources = new ArrayList<Resource>();		
-		if (null != dataModelSet) {
+		if (null != dataModelSet && null != res) {
 			Iterator<Resource> namedModels = dataModelSet.listModelNames();
 			namedModels.forEachRemaining(m -> {
 				Model model = dataModelSet.getNamedModel(m);

bundles/org.eclipse.epsilon.rdf.emf/src/org/eclipse/epsilon/rdf/emf/RDFGraphResourceNotificationAdapterChangeRDF.java

@@ -22,12 +22,20 @@
 import org.eclipse.emf.ecore.util.EContentAdapter;
 
 public class RDFGraphResourceNotificationAdapterChangeRDF extends EContentAdapter {	
+	
+	private final RDFGraphResourceImpl initialRDFGraphResource;
+	
+	public RDFGraphResourceNotificationAdapterChangeRDF(RDFGraphResourceImpl rdfGraphResource) {
+		this.initialRDFGraphResource = rdfGraphResource;
+	}
+
 	@Override
 	public void notifyChanged(Notification notification) {
 		Object feature = notification.getFeature();
 		if (null != feature) {
 			featureNotification(feature, notification);
 		}
+		super.notifyChanged(notification);
 	}
 
 	private void featureNotification (Object feature, Notification notification){		
@@ -47,6 +55,11 @@ private void eStructuralFeatureNotification(EStructuralFeature eStructuralFeatur
 		int position = notification.getPosition();
 
 		RDFGraphResourceImpl graphResource = (RDFGraphResourceImpl) onEObject.eResource();
+		if (null == graphResource) {
+			System.err.println("The Graph resource has been removed, using the initial graph resource instead");
+			graphResource = initialRDFGraphResource;
+		}
+		
 		RDFGraphResourceUpdate rdfUpdater = graphResource.getRDFGraphUpdater();
 		List<Resource> namedModelURIs = graphResource.getResourcesForNamedModelsContaining(onEObject);
 
@@ -76,7 +89,7 @@ private void eStructuralFeatureNotification(EStructuralFeature eStructuralFeatur
 							namedModelURIs.add(first);
 						}
 					}
-					rdfUpdater.newSingleValueEStructuralFeatureStatements(namedModelURIs, onEObject,
+					rdfUpdater.addSingleValueEStructuralFeatureStatements(namedModelURIs, onEObject,
 						changedFeature, newValue);
 				}
 			} else {
@@ -96,8 +109,7 @@ private void eStructuralFeatureNotification(EStructuralFeature eStructuralFeatur
 			break;
 		case Notification.REMOVE_MANY:
 		case Notification.REMOVE:
-			rdfUpdater.removeMultiEStructuralFeature(namedModelURIs, onEObject, changedFeature, 
-					newValue, oldValue);
+			rdfUpdater.removeMultiEStructuralFeature(namedModelURIs, onEObject, changedFeature, oldValue);
 			break;
 		case Notification.UNSET:
 			// Single values, don't need to worry about order