Add option to trigger internal Jena consistency checks during loading (…

…#29)

There are cases where the loaded RDF graph is obviously against the OWL constraints that have been used to define a class: for instance, if someone says "Computers are things that have one motherboard" and then the graph has something said to be a Computer with two motherboards.

This commit adds a checkbox in the model configuration dialog which triggers Jena's internal consistency checks, and will raise an error during model loading if an inconsistency is found.

---------

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

bundles/org.eclipse.epsilon.emc.rdf.dt/src/org/eclipse/epsilon/emc/rdf/dt/RDFModelConfigurationDialog.java

@@ -185,13 +185,17 @@ protected String getModelType() {
 		return "RDF";
 	}
 
+	//
+	// Ordering of Groups in Dialogue window
+
 	@Override
 	protected void createGroups(Composite control) {
 		createNameAliasGroup(control);
 		createDataModelRDFUrlsGroup(control);
 		createSchemaModelRDFUrlsGroup(control);
 		createNamespaceMappingGroup(control);
 		createLanguagePreferenceGroup(control);
+		createValidateModelGroup(control);
 	}
 
 	private Composite createNamespaceMappingGroup(Composite parent) {
@@ -490,7 +494,6 @@ public void widgetSelected(SelectionEvent e) {
 
 	protected Label languagePreferenceLabel;
 	protected Text languagePreferenceText;
-
 	private Composite createLanguagePreferenceGroup(Composite parent) {
 		final Composite groupContent = DialogUtil.createGroupContainer(parent, "Language tag preference", 1);
 
@@ -511,7 +514,24 @@ public void modifyText(ModifyEvent event) {
 		return groupContent;
 	}
 
-	@Override
+
+	protected String validateModel;
+
+	protected Button validateModelCheckBox;
+	private Composite createValidateModelGroup(Composite parent) {
+		final Composite groupContent = DialogUtil.createGroupContainer(parent, "Model validation", 1);
+
+		validateModelCheckBox = new Button(groupContent, SWT.CHECK);
+		validateModelCheckBox.setText("Run Jena's model validation on loaded models");
+		boolean isJenaValidationEnabled = RDFModel.VALIDATION_SELECTION_JENA.equals(validateModel);
+		validateModelCheckBox.setSelection(isJenaValidationEnabled);
+
+		groupContent.layout();
+		groupContent.pack();
+		return groupContent;
+	}
+
+	@Override	
 	protected void loadProperties(){
 		super.loadProperties();
 		if (properties == null) return;
@@ -544,7 +564,11 @@ protected void loadProperties(){
 		}
 
 		languagePreferenceText.setText(properties.getProperty(RDFModel.PROPERTY_LANGUAGE_PREFERENCE));
-
+
+		// Load any saved property and default to Jena if none
+		validateModel = properties.getProperty(RDFModel.PROPERTY_VALIDATE_MODEL, RDFModel.VALIDATION_SELECTION_JENA);
+		validateModelCheckBox.setSelection(RDFModel.VALIDATION_SELECTION_JENA.equals(validateModel));
+
 		this.dataModelUrlListViewer.refresh();
 		this.schemaModelUrlListViewer.refresh();
 		this.nsMappingTable.refresh();
@@ -572,6 +596,12 @@ protected void storeProperties(){
 
 		properties.put(RDFModel.PROPERTY_LANGUAGE_PREFERENCE,
 				languagePreferenceText.getText().replaceAll("\\s", ""));
+
+		if (validateModelCheckBox.getSelection()) {
+			properties.put(RDFModel.PROPERTY_VALIDATE_MODEL, RDFModel.VALIDATION_SELECTION_JENA);
+		} else {
+			properties.put(RDFModel.PROPERTY_VALIDATE_MODEL, RDFModel.VALIDATION_SELECTION_NONE);
+		}
 	}
 
 	protected void validateForm() {

bundles/org.eclipse.epsilon.emc.rdf/src/org/eclipse/epsilon/emc/rdf/RDFModel.java

@@ -22,6 +22,7 @@
 import java.util.Map.Entry;
 
 import org.apache.jena.ontology.OntModel;
+import org.apache.jena.ontology.OntModelSpec;
 import org.apache.jena.rdf.model.InfModel;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
@@ -31,6 +32,8 @@
 import org.apache.jena.rdf.model.Resource;
 import org.apache.jena.reasoner.Reasoner;
 import org.apache.jena.reasoner.ReasonerRegistry;
+import org.apache.jena.reasoner.ValidityReport;
+import org.apache.jena.reasoner.ValidityReport.Report;
 import org.apache.jena.vocabulary.RDF;
 import org.eclipse.epsilon.common.util.StringProperties;
 import org.eclipse.epsilon.eol.exceptions.EolRuntimeException;
@@ -57,9 +60,15 @@ public class RDFModel extends CachedModel<RDFModelElement> {
 	 * pairs will take precedence over existing pairs in the resource.
 	 */
 	public static final String PROPERTY_PREFIXES = "prefixes";
+	public static final String PROPERTY_VALIDATE_MODEL = "enableModelValidation";
+
+	public static final String VALIDATION_SELECTION_JENA = "jena";
+	public static final String VALIDATION_SELECTION_NONE = "none";
+	public static final String VALIDATION_SELECTION_DEFAULT = VALIDATION_SELECTION_JENA;
 
 	protected final List<String> languagePreference = new ArrayList<>();
 	protected final Map<String, String> customPrefixesMap = new HashMap<>();
+	protected String validationMode = VALIDATION_SELECTION_DEFAULT;
 
 	// TODO add to this list to cover reasoner types in the ReasonerRegistry Class
 	public enum ReasonerType {
@@ -169,6 +178,8 @@ public void load(StringProperties properties, IRelativePathResolver resolver) th
 		loadCommaSeparatedProperty(properties, PROPERTY_DATA_URIS, this.dataURIs);
 		loadCommaSeparatedProperty(properties, PROPERTY_SCHEMA_URIS, this.schemaURIs);
 
+		this.validationMode = properties.getProperty(RDFModel.PROPERTY_VALIDATE_MODEL, VALIDATION_SELECTION_JENA);
+
 		this.customPrefixesMap.clear();
 		String sPrefixes = properties.getProperty(PROPERTY_PREFIXES, "").strip();
 		if (!sPrefixes.isEmpty()) {
@@ -201,6 +212,15 @@ public void load(StringProperties properties, IRelativePathResolver resolver) th
 		}
 
 		load();
+
+		// After Loading all scheme, data models and inferring the full model, validate
+		if (VALIDATION_SELECTION_JENA.equals(validationMode)) {
+			try {
+				validateModel();
+			} catch (Exception e) {
+				throw new EolModelLoadingException(e, this);
+			}
+		}
 	}
 
 	protected void loadCommaSeparatedProperty(StringProperties properties, String propertyName, List<String> targetList) {
@@ -322,7 +342,7 @@ protected void loadModel() throws EolModelLoadingException {
 			}
 
 			//Create an OntModel to handle the data model being loaded or inferred from data and schema
-			this.model = ModelFactory.createOntologyModel();
+			this.model = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM_RULE_INF);
 
 			if (reasonerType == ReasonerType.NONE) {
 				// Only the OntModel bits are added to the dataModel being loaded.
@@ -343,6 +363,42 @@ protected void loadModel() throws EolModelLoadingException {
 		}
 	}
 
+	protected void validateModel() throws Exception {
+		/*
+		 * The way the model is validated by Jena depends on how the new OntModel was
+		 * created by the ModelFactory.
+		 */
+
+		ValidityReport modelValidityReport = model.validate();
+		if (!modelValidityReport.isValid() || !modelValidityReport.isClean()) {
+			StringBuilder sb = new StringBuilder("The loaded model is not valid or not clean\n");
+			int i = 1;
+			for (Iterator<Report> o = modelValidityReport.getReports(); o.hasNext();) {
+				ValidityReport.Report report = (ValidityReport.Report) o.next();
+				sb.append(String.format(" %d: %s", i, report.toString()));
+				i++;
+			}
+			throw new Exception(sb.toString());
+		}
+	}
+
+	public String getValidationMode() {
+		return validationMode;
+	}
+
+	/**
+	 * Changes the internal consistency validation mode used during loading.
+	 *
+	 * @param mode New mode. Must be one of {@code RDFModel#VALIDATION_SELECTION_NONE} or
+	 *             {@code RDFModel#VALIDATION_SELECTION_JENA}.
+	 */
+	public void setValidationMode(String mode) {
+		if (!VALIDATION_SELECTION_JENA.equals(mode) && !VALIDATION_SELECTION_NONE.equals(mode)) {
+			throw new IllegalArgumentException("Unknown validation mode " + mode);
+		}
+		this.validationMode = mode;
+	}
+
 	@Override
 	protected void disposeModel() {
 		model = null;

tests/org.eclipse.epsilon.emc.rdf.dt.tests/src/org/eclipse/epsilon/emc/rdf/dt/tests/EclipseRDFModelUrlTest.java

@@ -164,6 +164,12 @@ protected StringProperties createStringProperties(String dataModelUri, String sc
 		props.put(RDFModel.PROPERTY_DATA_URIS, dataModelUri);
 		props.put(RDFModel.PROPERTY_SCHEMA_URIS, schemaModelUri);
 		props.put(RDFModel.PROPERTY_LANGUAGE_PREFERENCE, languagePreference);
+
+		/*
+		 * Throws model validity errors for computer with 2 motherboards (expected to
+		 * fail Jena validation).
+		 */
+		props.put(RDFModel.PROPERTY_VALIDATE_MODEL, RDFModel.VALIDATION_SELECTION_NONE);
 		return props;
 	}
 }

tests/org.eclipse.epsilon.emc.rdf.tests/resources/OWL/owlDemoData_valid.ttl

@@ -0,0 +1,19 @@
+@prefix : <urn:x-hp:eg/> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+
+:alienBox51 a :GamingComputer .
+
+:bigName42 a :Computer ;
+    :bundle :binNameSpecialBundle ;
+    :motherBoard :bigNameSpecialMB .
+
+:whiteBoxZX a :Computer ;
+    :bundle :actionPack ;
+    :motherBoard :nForce .
+
+:actionPack a :GameBundle .
+
+:bigNameSpecialMB owl:differentFrom :nForce2 .
+
+:unknownMB :hasGraphics :gamingGraphics .
+

tests/org.eclipse.epsilon.emc.rdf.tests/src/org/eclipse/epsilon/emc/rdf/CommonQueryTest.java

@@ -201,8 +201,8 @@ public void getPersonInformation() throws Exception {
 			"foaf:Person",
 			model.getTypeNameOf(firstPerson));
 
-		assertEquals("The model should only report the Person type and the rdfs Resource",
-				new HashSet<>(Arrays.asList("foaf:Person", "rdfs:Resource")),
+		assertEquals("The model should only report the foaf Person, rdfs Resource and owl Thing",
+				new HashSet<>(Arrays.asList("foaf:Person", "rdfs:Resource", "owl:Thing")),
 				new HashSet<>(model.getAllTypeNamesOf(firstPerson)));		
 	}
 

tests/org.eclipse.epsilon.emc.rdf.tests/src/org/eclipse/epsilon/emc/rdf/MOF2RDFModelOWLReasonerTest.java

@@ -97,6 +97,7 @@ protected void loadModel(String dataModelUri, String schemaModelUri, String lang
 		props.put(RDFModel.PROPERTY_DATA_URIS, dataModelUri);
 		props.put(RDFModel.PROPERTY_SCHEMA_URIS, schemaModelUri);
 		props.put(RDFModel.PROPERTY_LANGUAGE_PREFERENCE, languagePreference);
+		props.put(RDFModel.PROPERTY_VALIDATE_MODEL, RDFModel.VALIDATION_SELECTION_NONE);
 		model.load(props);
 
 		this.context = new EolContext();

tests/org.eclipse.epsilon.emc.rdf.tests/src/org/eclipse/epsilon/emc/rdf/RDFModelOWLReasonerTest.java

@@ -101,6 +101,9 @@ protected void loadModel(String dataModelUri, String schemaModelUri, String lang
 		props.put(RDFModel.PROPERTY_DATA_URIS, dataModelUri);
 		props.put(RDFModel.PROPERTY_SCHEMA_URIS, schemaModelUri);
 		props.put(RDFModel.PROPERTY_LANGUAGE_PREFERENCE, languagePreference);
+
+		// There is a known issue in the model required for tests
+		props.put(RDFModel.PROPERTY_VALIDATE_MODEL, RDFModel.VALIDATION_SELECTION_NONE);
 		model.load(props);
 
 		this.context = new EolContext();

tests/org.eclipse.epsilon.emc.rdf.tests/src/org/eclipse/epsilon/emc/rdf/RDFModelValidationTest.java

@@ -0,0 +1,62 @@
+/********************************************************************************
+ * Copyright (c) 2024 University of York
+ *
+ * This program and the accompanying materials are made available under the
+ * terms of the Eclipse Public License 2.0 which is available at
+ * http://www.eclipse.org/legal/epl-2.0.
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ *
+ * Contributors:
+ *   Antonio Garcia-Dominguez - initial API and implementation
+ ********************************************************************************/
+package org.eclipse.epsilon.emc.rdf;
+
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import org.eclipse.epsilon.common.util.StringProperties;
+import org.eclipse.epsilon.eol.exceptions.models.EolModelLoadingException;
+import org.junit.Test;
+
+public class RDFModelValidationTest {
+
+	private static final String OWL_DEMO_DATAMODEL_INVALID = "resources/OWL/owlDemoData.ttl";
+	private static final String OWL_DEMO_DATAMODEL_VALID = "resources/OWL/owlDemoData_valid.ttl";
+	private static final String OWL_DEMO_SCHEMAMODEL = "resources/OWL/owlDemoSchema.ttl";
+
+	private static final String LANGUAGE_PREFERENCE_EN_STRING = "en";
+
+	private RDFModel model;
+
+	@Test
+	public void loadInvalidModel() {
+
+		try {
+			loadModel(OWL_DEMO_DATAMODEL_INVALID);
+			fail("An exception was expected");
+		} catch (EolModelLoadingException e) {
+			String sErrors = e.getMessage();
+			assertTrue("The model loaded should FAIL validation (6 errors relating to BigName42 having 2 motherboards)",
+					sErrors.contains("not valid"));
+		}
+	}
+
+	@Test
+	public void loadValidModel() throws EolModelLoadingException {
+		loadModel(OWL_DEMO_DATAMODEL_VALID);
+	}
+
+	// Functions not tests
+
+	protected void loadModel(String dataModelUri) throws EolModelLoadingException {
+		this.model = new RDFModel();
+		StringProperties props = new StringProperties();
+		props.put(RDFModel.PROPERTY_DATA_URIS, dataModelUri);
+		props.put(RDFModel.PROPERTY_SCHEMA_URIS, OWL_DEMO_SCHEMAMODEL);
+		props.put(RDFModel.PROPERTY_LANGUAGE_PREFERENCE, LANGUAGE_PREFERENCE_EN_STRING);
+		props.put(RDFModel.PROPERTY_VALIDATE_MODEL, RDFModel.VALIDATION_SELECTION_JENA);
+		model.load(props);
+	}
+
+}