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Use same logic to remove blank nodes from reasoner's internal model as used in RDFService (#397)

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* Refactor blank-nodes-as-variables behavior from RDFServiceJena to JenaModelUtils; use this logic when removing triples from the TBox reasoner's internal assertions model.  Add unit test.

* Remove complication of datasets and remove blank nodes directly from models

* Remove temporary debugging logging

* Simplify original blank node tree logic

* Remove unneeded imports
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Brian Lowe 2023-06-15 13:55:23 +03:00 • committed by GitHub
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commit fb9d86a57d
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102
api/src/test/java/edu/cornell/mannlib/vitro/webapp/tboxreasoner/impl/jfact/JFactTBoxReasonerTest.java Normal file
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package edu.cornell.mannlib.vitro.webapp.tboxreasoner.impl.jfact;
import java.io.StringReader;
import org.apache.jena.ontology.OntModel;
import org.apache.jena.ontology.OntModelSpec;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.rdf.model.RDFNode;
import org.junit.Assert;
import org.junit.Test;
import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils;
import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
import edu.cornell.mannlib.vitro.webapp.tboxreasoner.ReasonerConfiguration;
import edu.cornell.mannlib.vitro.webapp.tboxreasoner.impl.BasicTBoxReasonerDriver;
public class JFactTBoxReasonerTest {
private final static String axioms = "@prefix obo: <http://purl.obolibrary.org/obo/> .\r\n" +
"@prefix owl: <http://www.w3.org/2002/07/owl#> .\r\n" +
"@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .\r\n" +
"@prefix xml: <http://www.w3.org/XML/1998/namespace> .\r\n" +
"@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .\r\n" +
"@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .\r\n" +
"\r\n" +
"<http://vivo.mydomain.edu/individual/class_c> rdf:type owl:Class ;\r\n" +
" \r\n" +
" rdfs:subClassOf [ rdf:type owl:Class ;\r\n" +
" owl:intersectionOf ( <http://vivo.mydomain.edu/individual/class_a>\r\n" +
" <http://vivo.mydomain.edu/individual/class_b>\r\n" +
" )\r\n" +
" ] .\r\n" +
"\r\n" +
"<http://vivo.mydomain.edu/individual/class_a>\r\n" +
" a owl:Class ;\r\n" +
" rdfs:label \"Class A\"@en-US .\r\n" +
"\r\n" +
"<http://vivo.mydomain.edu/individual/class_b>\r\n" +
" a owl:Class ;\r\n" +
" rdfs:label \"Class B\"@en-US .\r\n" +
"\r\n" +
"<http://vivo.mydomain.edu/individual/class_c>\r\n" +
" a owl:Class ;\r\n" +
" rdfs:label \"Class C\"@en-US .\r\n";
/**
* Test that axioms containing blank nodes can be removed from the reasoner
* even if the internal blank node IDs are different from when first added.
*/
@Test
public void testRemoveAxiomsWithBlankNodes() {
OntModel tboxAssertions = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
OntModel tboxInferences = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
OntModel tboxUnion = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,
ModelFactory.createUnion(tboxAssertions, tboxInferences));
JFactTBoxReasoner reasoner = new JFactTBoxReasoner();
BasicTBoxReasonerDriver driver = new BasicTBoxReasonerDriver(
tboxAssertions, tboxInferences.getBaseModel(), tboxUnion, reasoner,
ReasonerConfiguration.DEFAULT);
Model additions = ModelFactory.createDefaultModel();
additions.read(new StringReader(axioms), null, "TTL");
// Reading again will generate new internal blank node IDs
Model subtractions = ModelFactory.createDefaultModel();
subtractions.read(new StringReader(axioms), null, "TTL");
// Confirm that directly subtracting the models doesn't work because
// the blank node IDs do not match
Model incorrectSubtraction = additions.difference(subtractions);
Assert.assertFalse(incorrectSubtraction.isEmpty());
tboxAssertions.getBaseModel().add(additions);
tboxAssertions.getBaseModel().notifyEvent(new EditEvent(null, false));
waitForTBoxReasoning(driver);
// Confirm that union model now contains inferred triples
Assert.assertTrue(tboxUnion.size() > additions.size());
JenaModelUtils.removeWithBlankNodesAsVariables(subtractions, tboxAssertions.getBaseModel());
tboxAssertions.getBaseModel().notifyEvent(new EditEvent(null, false));
waitForTBoxReasoning(driver);
// Confirm that no statements related to classes a, b or c remain in the
// TBox union model. (The inference model may not be completely empty, because
// the reasoner may supply unrelated triples related to OWL and RDFS vocabulary.)
Assert.assertFalse(tboxUnion.contains(tboxUnion.getResource(
"http://vivo.mydomain.edu/individual/class_a"), null, (RDFNode) null));
Assert.assertFalse(tboxUnion.contains(tboxUnion.getResource(
"http://vivo.mydomain.edu/individual/class_b"), null, (RDFNode) null));
Assert.assertFalse(tboxUnion.contains(tboxUnion.getResource(
"http://vivo.mydomain.edu/individual/class_c"), null, (RDFNode) null));
}
private void waitForTBoxReasoning(BasicTBoxReasonerDriver driver) {
int sleeps = 0;
// sleep at least once to make sure the TBox reasoning gets started
while ((0 == sleeps) || ((sleeps < 1000) && driver.getStatus().isReasoning())) {
try {
Thread.sleep(200);
} catch (InterruptedException e) {
throw new RuntimeException(e);
}
sleeps++;
}
}
}