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Fix: Mixed ontology level annotations #20

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Fix: Mixed ontology level annotations #20

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b58dfce
Merge remote-tracking branch 'upstream/master' into upstream
syphax-bouazzouni Dec 21, 2022
5a17c74
add test to count annotions of the source ontology vs generated one
syphax-bouazzouni Dec 21, 2022
168cb9b
remove sourceOwlManager.getOntologies() loop for addOntologyAnnotations
syphax-bouazzouni Dec 21, 2022
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81 changes: 40 additions & 41 deletions src/main/java/org/stanford/ncbo/owlapi/wrapper/OntologyParser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -206,65 +206,64 @@ private boolean buildOWLOntology(OWLOntology masterOntology, boolean isOBO) {
return false;
}


for (OWLOntology sourceOnt : sourceOwlManager.getOntologies()) {
IRI documentIRI = sourceOwlManager.getOntologyDocumentIRI(sourceOnt);

addGroundMetadata(documentIRI, fact, sourceOnt);
generateGroundTriplesForAxioms(allAxioms, fact, sourceOnt);

if (isOBO) {
if (!documentIRI.toString().startsWith("owlapi:ontology")) {
generateSKOSInObo(allAxioms, fact, sourceOnt);
}
if (isOBO && !documentIRI.toString().startsWith("owlapi:ontology")) {
generateSKOSInObo(allAxioms, fact, sourceOnt);
}

boolean isPrefixedOWL = sourceOwlManager.getOntologyFormat(sourceOnt).isPrefixOWLOntologyFormat();
log.info("isPrefixOWLOntologyFormat: {}", isPrefixedOWL);
if (isPrefixedOWL == true && !isOBO) {
if (isPrefixedOWL && !isOBO) {
generateSKOSInOwl(allAxioms, fact, sourceOnt);
}
}

targetOwlManager.addAxioms(targetOwlOntology, allAxioms);
for (OWLAnnotation ann : targetOwlOntology.getAnnotations()) {
targetOwlManager.addAxioms(targetOwlOntology, allAxioms);
for (OWLAnnotation ann : targetOwlOntology.getAnnotations()) {
AddOntologyAnnotation addAnn = new AddOntologyAnnotation(targetOwlOntology, ann);
targetOwlManager.applyChange(addAnn);
}

if (isOBO) {
String oboVersion = parserInvocation.getOBOVersion();
if (oboVersion != null) {
log.info("Adding version: {}", oboVersion);
OWLAnnotationProperty prop = fact.getOWLAnnotationProperty(IRI.create(OWLRDFVocabulary.OWL_VERSION_INFO.toString()));
IRI versionSubjectIRI = IRI.create(VERSION_SUBJECT);
OWLAnnotationAssertionAxiom annVersion = fact.getOWLAnnotationAssertionAxiom(prop, versionSubjectIRI, fact.getOWLLiteral(oboVersion));
targetOwlManager.addAxiom(targetOwlOntology, annVersion);
}
}

addOntologyAnnotations(masterOntology);
escapeXMLLiterals(targetOwlOntology);

OWLReasonerFactory reasonerFactory = new StructuralReasonerFactory();
OWLReasoner reasoner = reasonerFactory.createReasoner(targetOwlOntology);
InferredSubClassAxiomGenerator isc = new InferredSubClassAxiomGenerator();
Set<OWLSubClassOfAxiom> subAxs = isc.createAxioms(targetOwlOntology.getOWLOntologyManager().getOWLDataFactory(), reasoner);
targetOwlManager.addAxioms(targetOwlOntology, subAxs);
deprecateBranch();

log.info("isOBO: {}", isOBO);
if (isOBO) {
replicateHierarchyAsTreeview(fact);
}
return true;
}

private void addOntologyAnnotations(OWLOntology masterOntology){
for (OWLAnnotation ann : masterOntology.getAnnotations()) {
AddOntologyAnnotation addAnn = new AddOntologyAnnotation(targetOwlOntology, ann);
targetOwlManager.applyChange(addAnn);
}

if (isOBO) {
String oboVersion = parserInvocation.getOBOVersion();
if (oboVersion != null) {
log.info("Adding version: {}", oboVersion);
OWLAnnotationProperty prop = fact.getOWLAnnotationProperty(IRI.create(OWLRDFVocabulary.OWL_VERSION_INFO.toString()));
IRI versionSubjectIRI = IRI.create(VERSION_SUBJECT);
OWLAnnotationAssertionAxiom annVersion = fact.getOWLAnnotationAssertionAxiom(prop, versionSubjectIRI, fact.getOWLLiteral(oboVersion));
targetOwlManager.addAxiom(targetOwlOntology, annVersion);
}
}

for (OWLOntology sourceOnt : sourceOwlManager.getOntologies()) {
for (OWLAnnotation ann : sourceOnt.getAnnotations()) {
AddOntologyAnnotation addAnn = new AddOntologyAnnotation(targetOwlOntology, ann);
targetOwlManager.applyChange(addAnn);
}
}

escapeXMLLiterals(targetOwlOntology);

OWLReasonerFactory reasonerFactory = new StructuralReasonerFactory();
OWLReasoner reasoner = reasonerFactory.createReasoner(targetOwlOntology);
InferredSubClassAxiomGenerator isc = new InferredSubClassAxiomGenerator();
Set<OWLSubClassOfAxiom> subAxs = isc.createAxioms(targetOwlOntology.getOWLOntologyManager().getOWLDataFactory(), reasoner);
targetOwlManager.addAxioms(targetOwlOntology, subAxs);
deprecateBranch();

log.info("isOBO: {}", isOBO);
if (isOBO) {
replicateHierarchyAsTreeview(fact);
}
return true;
}

private void replicateHierarchyAsTreeview(OWLDataFactory fact) {
Set<OWLAxiom> treeViewAxs = new HashSet<OWLAxiom>();
for (OWLAxiom axiom : targetOwlOntology.getAxioms()) {
Expand Down
20 changes: 20 additions & 0 deletions src/test/java/org/stanford/ncbo/owlapi/wrapper/OntologyParserTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
import org.junit.Before;
import org.junit.Test;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLOntology;

import java.io.File;

Expand Down Expand Up @@ -144,6 +145,25 @@ public void parse_DetectsOntologyIRI_ReturnsTrue() throws Exception {
assertEquals(sourceIRI, targetIRI);

}
@Test
public void parse_OntologyAnnotationCount_ReturnsTrue() throws Exception {
String outputRepositoryFolder = "./src/test/resources/repo/output/cno";
ParserInvocation pi = new ParserInvocation("./src/test/resources/repo/input/cno",
outputRepositoryFolder, "cnov0_5.owl", true);
assertTrue(pi.valid());

OntologyParser parser = new OntologyParser(pi);
assertTrue(parser.parse());
assertEquals(1, parser.getLocalOntologies().size());

OWLOntology targetOwlOntology = parser.getTargetOwlOntology();
OWLOntology sourceOntology = parser.getParsedOntologies().stream().findFirst().orElse(null);

assertNotNull(sourceOntology);
assertEquals(sourceOntology.getAnnotations().size(), targetOwlOntology.getAnnotations().size());

}


@After
public void tearDown() throws Exception {
Expand Down