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Merged
goneall merged 3 commits into from
Jul 20, 2026
Merged

Migrate OntModel to use Jena 5 jena-ontapi #308

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8c4421e
Migrate to Jena new ontapi OntModel
bact Jul 20, 2026
3725afd
Remove unused imports
bact Jul 20, 2026
487d1ec
Add OWL->JSON context / schema tests
bact Jul 20, 2026
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5 changes: 5 additions & 0 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -150,6 +150,11 @@
<artifactId>json-schema-validator</artifactId>
<version>1.5.9</version>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-ontapi</artifactId>
<version>5.6.0</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
Expand Down
8 changes: 4 additions & 4 deletions src/main/java/org/spdx/tools/RdfSchemaToJsonContext.java
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Expand Up @@ -26,9 +26,9 @@
import java.io.InputStream;
import java.util.Objects;

import org.apache.jena.ontology.OntModel;
import org.apache.jena.ontology.OntModelSpec;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.ontapi.OntModelFactory;
import org.apache.jena.ontapi.OntSpecification;
import org.apache.jena.ontapi.model.OntModel;
import org.spdx.tools.schema.OwlToJsonContext;

import com.fasterxml.jackson.core.JsonGenerator;
Expand Down Expand Up @@ -68,7 +68,7 @@ public static void main(String[] args) {
OwlToJsonContext owlToJsonContext = null;
try {
is = new FileInputStream(fromFile);
OntModel model = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
OntModel model = OntModelFactory.createModel(OntSpecification.OWL2_DL_MEM);
model.read(is, "RDF/XML");
owlToJsonContext = new OwlToJsonContext(model);
} catch (FileNotFoundException e) {
Expand Down
8 changes: 4 additions & 4 deletions src/main/java/org/spdx/tools/RdfSchemaToJsonSchema.java
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Expand Up @@ -26,9 +26,9 @@
import java.io.InputStream;
import java.util.Objects;

import org.apache.jena.ontology.OntModel;
import org.apache.jena.ontology.OntModelSpec;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.ontapi.OntModelFactory;
import org.apache.jena.ontapi.OntSpecification;
import org.apache.jena.ontapi.model.OntModel;
import org.spdx.tools.schema.OwlToJsonSchema;

import com.fasterxml.jackson.core.JsonGenerator;
Expand Down Expand Up @@ -70,7 +70,7 @@ public static void main(String[] args) {
OntModel model = null;
try {
is = new FileInputStream(fromFile);
model = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
model = OntModelFactory.createModel(OntSpecification.OWL2_DL_MEM);
model.read(is, "RDF/XML");
} catch (FileNotFoundException e) {
System.err.println("File not found for "+fromFile.getName());
Expand Down
8 changes: 4 additions & 4 deletions src/main/java/org/spdx/tools/RdfSchemaToXsd.java
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Expand Up @@ -27,9 +27,9 @@
import java.io.OutputStream;
import java.util.Objects;

import org.apache.jena.ontology.OntModel;
import org.apache.jena.ontology.OntModelSpec;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.ontapi.OntModelFactory;
import org.apache.jena.ontapi.OntSpecification;
import org.apache.jena.ontapi.model.OntModel;
import org.apache.ws.commons.schema.XmlSchema;
import org.apache.ws.commons.schema.XmlSchemaSerializer.XmlSchemaSerializerException;
import org.spdx.tools.schema.OwlToXsd;
Expand Down Expand Up @@ -68,7 +68,7 @@ public static void main(String[] args) {
OntModel model = null;
try {
is = new FileInputStream(fromFile);
model = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
model = OntModelFactory.createModel(OntSpecification.OWL2_DL_MEM);
model.read(is, "RDF/XML");
} catch (FileNotFoundException e) {
System.err.println("File not found for "+fromFile.getName());
Expand Down
186 changes: 100 additions & 86 deletions src/main/java/org/spdx/tools/schema/AbstractOwlRdfConverter.java
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Expand Up @@ -30,19 +30,15 @@
import java.util.Optional;
import java.util.Set;

import org.apache.jena.ontology.Individual;
import org.apache.jena.ontology.OntClass;
import org.apache.jena.ontology.OntModel;
import org.apache.jena.ontology.OntProperty;
import org.apache.jena.ontology.OntResource;
import org.apache.jena.ontology.Ontology;
import org.apache.jena.ontology.Restriction;
import org.apache.jena.ontology.UnionClass;
import org.apache.jena.rdf.model.NodeIterator;
import org.apache.jena.ontapi.model.OntClass;
import org.apache.jena.ontapi.model.OntID;
import org.apache.jena.ontapi.model.OntModel;
import org.apache.jena.ontapi.model.OntProperty;
import org.apache.jena.rdf.model.Property;
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.util.iterator.ExtendedIterator;
import org.apache.jena.rdf.model.Statement;
import org.apache.jena.rdf.model.StmtIterator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.spdx.library.model.v2.SpdxConstantsCompatV2;
Expand Down Expand Up @@ -104,25 +100,25 @@ public PropertyRestrictions(OntClass ontClass, OntProperty property) {
Objects.requireNonNull(ontClass, "Missing required ontology class");
Objects.requireNonNull(property, "Missing required property");
this.property = property;
List<Restriction> restrictions = getRestrictionsFromSuperclasses(ontClass, property);
List<OntClass.Restriction> restrictions =
getRestrictionsFromSuperclasses(ontClass, property);
interpretRestrictions(restrictions);
}

/**
* Convert a list of restrictions for this property into the field values
* @param restrictions
*/
private void interpretRestrictions(List<Restriction> restrictions) {
for (Restriction r:restrictions) {
RDFNode typePropertyValue = r.getPropertyValue(owlClassProperty);
private void interpretRestrictions(List<OntClass.Restriction> restrictions) {
for (OntClass.Restriction r:restrictions) {
Statement typeStmt = r.getProperty(owlClassProperty);
RDFNode typePropertyValue = typeStmt != null ? typeStmt.getObject() : null;
if (Objects.nonNull(typePropertyValue) && typePropertyValue.isURIResource()) {
typeUri = typePropertyValue.asResource().getURI();
// check to see if this type is an enumeration type
OntClass typeClass = model.getOntClass(typeUri);
if (Objects.nonNull(typeClass)) {
ExtendedIterator<Individual> individualIter = model.listIndividuals(typeClass);
while (individualIter.hasNext()) {
Individual individual = individualIter.next();
typeClass.individuals().forEach(individual -> {
if (individual.isURIResource()) {
Enum<?> e = SpdxEnumFactoryCompatV2.uriToEnum.get(individual.getURI());
if (Objects.nonNull(e)) {
Expand All @@ -132,13 +128,13 @@ private void interpretRestrictions(List<Restriction> restrictions) {
logger.warn("Missing enum value for " + individual.getLocalName());
}
}
}
});
}
} else {
// Check for enumeration types as a direct restriction
NodeIterator hasValueIter = r.listPropertyValues(hasValueProperty);
StmtIterator hasValueIter = r.listProperties(hasValueProperty);
while (hasValueIter.hasNext()) {
RDFNode hasValue = hasValueIter.next();
RDFNode hasValue = hasValueIter.next().getObject();
if (hasValue.isURIResource()) {
Enum<?> e = SpdxEnumFactoryCompatV2.uriToEnum.get(hasValue.asResource().getURI());
if (Objects.nonNull(e)) {
Expand All @@ -149,12 +145,30 @@ private void interpretRestrictions(List<Restriction> restrictions) {
}
}
// cardinality
RDFNode qualCardPropValue = r.getPropertyValue(qualCardProperty);
RDFNode cardPropValue = r.getPropertyValue(cardProperty);
RDFNode maxQualCardPropValue = r.getPropertyValue(maxQualCardProperty);
RDFNode maxCardPropValue = r.getPropertyValue(maxCardProperty);
RDFNode minCardPropValue = r.getPropertyValue(minCardProperty);
RDFNode minQualCardPropValue = r.getPropertyValue(minQualCardProperty);
Statement qualCardStmt = r.getProperty(qualCardProperty);
RDFNode qualCardPropValue = qualCardStmt != null
? qualCardStmt.getObject() : null;

Statement cardStmt = r.getProperty(cardProperty);
RDFNode cardPropValue = cardStmt != null
? cardStmt.getObject() : null;

Statement maxQualCardStmt = r.getProperty(maxQualCardProperty);
RDFNode maxQualCardPropValue = maxQualCardStmt != null
? maxQualCardStmt.getObject() : null;

Statement maxCardStmt = r.getProperty(maxCardProperty);
RDFNode maxCardPropValue = maxCardStmt != null
? maxCardStmt.getObject() : null;

Statement minCardStmt = r.getProperty(minCardProperty);
RDFNode minCardPropValue = minCardStmt != null
? minCardStmt.getObject() : null;

Statement minQualCardStmt = r.getProperty(minQualCardProperty);
RDFNode minQualCardPropValue = minQualCardStmt != null
? minQualCardStmt.getObject() : null;

if (Objects.nonNull(qualCardPropValue) && qualCardPropValue.isLiteral()) {
absoluteCardinality = qualCardPropValue.asLiteral().getInt();
if (absoluteCardinality > 0) {
Expand Down Expand Up @@ -205,14 +219,23 @@ private void interpretRestrictions(List<Restriction> restrictions) {
}
if (Objects.isNull(typeUri)) {
// get the type from the range of the property
ExtendedIterator<? extends OntResource> rangeIter = property.listRange();
while (rangeIter.hasNext()) {
OntResource range = rangeIter.next();
property.ranges().forEach(range -> {
if (range.isURIResource()) {
if (Objects.isNull(typeUri) || typeUri.equals("http://www.w3.org/2000/01/rdf-schema#Literal")) {
typeUri = range.asResource().getURI();
}
}
});
}
if (Objects.isNull(typeUri)) {
try {
Optional<Resource> propType = getPropertyType(property);
if (propType.isPresent()) {
typeUri = propType.get().getURI();
}
} catch (Exception e) {
logger.warn("Error getting property type for "
+ property.getLocalName(), e);
}
}
if (Objects.isNull(typeUri) && ("comment".equals(property.getLocalName()) || "seeAlso".equals(property.getLocalName()))) {
Expand All @@ -221,38 +244,38 @@ private void interpretRestrictions(List<Restriction> restrictions) {
}
}

private List<Restriction> getRestrictionsFromSuperclasses(OntClass ontClass, OntProperty property) {
List<Restriction> retval = new ArrayList<>();
ExtendedIterator<OntClass> superClasses = ontClass.listSuperClasses();
while (superClasses.hasNext()) {
OntClass superClass = superClasses.next();
if (superClass.isUnionClass()) {
UnionClass uClass = superClass.asUnionClass();
ExtendedIterator<? extends OntClass> unionClassiter = uClass.listOperands();
while (unionClassiter.hasNext()) {
OntClass operand = unionClassiter.next();
if (operand.isRestriction() && property.equals(operand.asRestriction().getOnProperty())) {
retval.add(operand.asRestriction());
private List<OntClass.Restriction> getRestrictionsFromSuperclasses(
OntClass ontClass, OntProperty property) {
List<OntClass.Restriction> retval = new ArrayList<>();
ontClass.superClasses(false).forEach(superClass -> {
if (superClass instanceof OntClass.UnionOf) {
OntClass.UnionOf uClass = (OntClass.UnionOf) superClass;
uClass.components().forEach(operand -> {
if (operand instanceof OntClass.UnaryRestriction
&& property.equals(
((OntClass.UnaryRestriction<?>) operand)
.getProperty())) {
retval.add((OntClass.Restriction) operand);
}
}
} else if (superClass.isRestriction()) {
if (property.equals(superClass.asRestriction().getOnProperty())) {
retval.add(superClass.asRestriction());
});
} else if (superClass instanceof OntClass.UnaryRestriction) {
OntClass.UnaryRestriction<?> r =
(OntClass.UnaryRestriction<?>) superClass;
if (property.equals(r.getProperty())) {
retval.add(r);
}
} else {
retval.addAll(getRestrictionsFromSuperclasses(superClass, property));
}
}
});
return retval;
}

public PropertyRestrictions(OntProperty property) {
Objects.requireNonNull(property, "Missing required property");
this.property = property;
List<Restriction> propertyRestrictions = new ArrayList<>();
ExtendedIterator<Restriction> restrictionIter = property.listReferringRestrictions();
while (restrictionIter.hasNext()) {
propertyRestrictions.add(restrictionIter.next());
List<OntClass.Restriction> propertyRestrictions = new ArrayList<>();
if (property instanceof org.apache.jena.ontapi.model.OntRelationalProperty) {
((org.apache.jena.ontapi.model.OntRelationalProperty) property)
.referringRestrictions().forEach(propertyRestrictions::add);
}
interpretRestrictions(propertyRestrictions);
}
Expand Down Expand Up @@ -342,7 +365,7 @@ public boolean isSingleProperty() {
Property restResource;
Property intersectionOfProperty;

Ontology ontology;
OntID ontology;

public AbstractOwlRdfConverter(OntModel model) {
Objects.requireNonNull(model, "Model must not be null");
Expand All @@ -360,13 +383,8 @@ public AbstractOwlRdfConverter(OntModel model) {
intersectionOfProperty = model.createProperty("http://www.w3.org/2002/07/owl#intersectionOf");
firstResource = model.createProperty("http://www.w3.org/1999/02/22-rdf-syntax-ns#first");
restResource = model.createProperty("http://www.w3.org/1999/02/22-rdf-syntax-ns#rest");
ontology = null;
ExtendedIterator<Ontology> ontIter = model.listOntologies();
if (!ontIter.hasNext()) {
throw new RuntimeException("No ontologies defined in RDF OWL");
}
ontology = ontIter.next();
if (ontIter.hasNext()) {
ontology = model.getID();
if (Objects.isNull(ontology)) {
throw new RuntimeException("No ontologies defined in RDF OWL");
}
}
Expand Down Expand Up @@ -417,13 +435,7 @@ public int compare(OntProperty arg0, OntProperty arg1) {
private void removeSuperProperties(Collection<OntProperty> properties) {
List<OntProperty> superProperties = new ArrayList<>();
for (OntProperty property:properties) {
if (property.isProperty()) {
OntProperty op = property.asProperty();
ExtendedIterator<? extends OntProperty> superIter = op.listSuperProperties();
while (superIter.hasNext()) {
superProperties.add(superIter.next());
}
}
property.superProperties(false).forEach(superProperties::add);
}
for (OntProperty superProp:superProperties) {
if (properties.contains(superProp)) {
Expand All @@ -446,9 +458,10 @@ protected Collection<OntProperty> propertiesFromClassRestrictions(OntClass oClas
* @throws SchemaException
*/
protected Optional<Resource> getPropertyType(OntProperty property) throws SchemaException {
ExtendedIterator<? extends OntResource> rangeIter = property.listRange();
java.util.Iterator<? extends Resource> rangeIter =
property.ranges().iterator();
while (rangeIter.hasNext()) {
OntResource range = rangeIter.next();
Resource range = rangeIter.next();
if (range.isURIResource()) {
return Optional.of(range);
} else if (range.hasProperty(unionOfProperty)) {
Expand Down Expand Up @@ -502,30 +515,31 @@ private void collectPropertiesFromRestrictions(OntClass oClass,
return;
}
reviewedClasses.add(oClass);
if (oClass.isUnionClass()) {
UnionClass uClass = oClass.asUnionClass();
ExtendedIterator<? extends OntClass> unionClassiter = uClass.listOperands();
while (unionClassiter.hasNext()) {
collectPropertiesFromRestrictions(unionClassiter.next(), properties,
if (oClass instanceof OntClass.UnionOf) {
OntClass.UnionOf uClass = (OntClass.UnionOf) oClass;
uClass.components().forEach(nextClass -> {
collectPropertiesFromRestrictions(nextClass, properties,
reviewedClasses, excludeSuperClassProperties);
}
} else if (oClass.isRestriction()) {
Restriction r = oClass.asRestriction();
OntProperty property = r.getOnProperty();
});
} else if (oClass instanceof OntClass.UnaryRestriction) {
OntClass.UnaryRestriction<?> r = (OntClass.UnaryRestriction<?>) oClass;
OntProperty property = r.getProperty();
if (Objects.nonNull(property)) {
properties.add(property);
}
} else {
ExtendedIterator<OntClass> subClassIter = oClass.listSuperClasses(excludeSuperClassProperties);
java.util.stream.Stream<OntClass> superClassStream =
oClass.superClasses(excludeSuperClassProperties);
if (excludeSuperClassProperties) {
subClassIter = subClassIter.filterDrop(sc -> {
return sc.isURIResource() &&
!"http://www.w3.org/2000/01/rdf-schema#Container".equals(sc.getURI());
superClassStream = superClassStream.filter(sc -> {
return !sc.isURIResource() ||
"http://www.w3.org/2000/01/rdf-schema#Container".equals(sc.getURI());
});
}
while (subClassIter.hasNext()) {
collectPropertiesFromRestrictions(subClassIter.next(), properties, reviewedClasses, excludeSuperClassProperties);
}
superClassStream.forEach(sc -> {
collectPropertiesFromRestrictions(sc, properties,
reviewedClasses, excludeSuperClassProperties);
});
}
}
}
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