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Upgrade to OWL API 5 #1295

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1b25b71
First pass at upgrade to OWLAPI 5
jamesaoverton Oct 7, 2026
77f55a4
Update owl-diff and diff-based tests
jamesaoverton Oct 7, 2026
a9be301
Fix more unit tests
jamesaoverton Oct 7, 2026
efb358b
Use Imports.INCLUDED when replacing ReferencedEntitySetProvider
jamesaoverton Oct 7, 2026
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28 changes: 5 additions & 23 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -154,35 +154,17 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-api</artifactId>
<version>4.5.29</version>
<exclusions>
<exclusion>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
</exclusion>
</exclusions>
<version>5.5.1</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-apibinding</artifactId>
<version>4.5.29</version>
<exclusions>
<exclusion>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
</exclusion>
</exclusions>
<version>5.5.1</version>
</dependency>
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-rio</artifactId>
<version>4.5.29</version>
<exclusions>
<exclusion>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
</exclusion>
</exclusions>
<version>5.5.1</version>
</dependency>
<dependency>
<groupId>junit</groupId>
Expand Down Expand Up @@ -221,7 +203,7 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>org.semanticweb.hermit</artifactId>
<version>1.4.5.456</version>
<version>1.4.5.519</version>
<exclusions>
<exclusion>
<groupId>net.sourceforge.owlapi</groupId>
Expand Down Expand Up @@ -256,7 +238,7 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>jfact</artifactId>
<version>4.0.4</version>
<version>5.0.3</version>
<exclusions>
<exclusion>
<groupId>net.sourceforge.owlapi</groupId>
Expand Down
8 changes: 4 additions & 4 deletions robot-command/src/main/java/org/obolibrary/robot/AnnotateCommand.java
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Original file line number Diff line number Diff line change
Expand Up @@ -314,7 +314,7 @@ public CommandState execute(CommandState state, String[] args) throws Exception
ontology
.getOntologyID()
.getVersionIRI()
.or(ontology.getOntologyID().getOntologyIRI().orNull());
.orElse((ontology.getOntologyID().getOntologyIRI().orElse(null)));
if (provenanceIRI != null) {
OWLAnnotationProperty annotationProp =
ontology
Expand All @@ -331,7 +331,7 @@ public CommandState execute(CommandState state, String[] args) throws Exception
boolean definedBy = CommandLineHelper.getBooleanValue(line, "annotate-defined-by", false);
if (definedBy) {
hasAnnotation = true;
IRI ontIRI = ontology.getOntologyID().getOntologyIRI().orNull();
IRI ontIRI = ontology.getOntologyID().getOntologyIRI().orElse(null);
if (ontIRI != null) {
OWLAnnotationProperty rdfsIsDefinedBy =
ontology.getOWLOntologyManager().getOWLDataFactory().getRDFSIsDefinedBy();
Expand Down Expand Up @@ -369,8 +369,8 @@ public CommandState execute(CommandState state, String[] args) throws Exception
* @return the updated string
*/
private String expandValue(String value, OWLOntology ontology) {
IRI ontologyIRI = ontology.getOntologyID().getOntologyIRI().orNull();
IRI versionIRI = ontology.getOntologyID().getVersionIRI().orNull();
IRI ontologyIRI = ontology.getOntologyID().getOntologyIRI().orElse(null);
IRI versionIRI = ontology.getOntologyID().getVersionIRI().orElse(null);
if (ontologyIRI != null) {
value = value.replace("%{ontology_iri}", ontologyIRI.toString());
}
Expand Down
6 changes: 3 additions & 3 deletions robot-command/src/main/java/org/obolibrary/robot/ExtractCommand.java
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Expand Up @@ -288,7 +288,7 @@ private static OWLOntology mireotExtract(
// Get the output IRI and create the output ontology
IRI outputIRI = CommandLineHelper.getOutputIRI(line);
if (outputIRI == null) {
outputIRI = inputOntology.getOntologyID().getOntologyIRI().orNull();
outputIRI = inputOntology.getOntologyID().getOntologyIRI().orElse(null);
}
OWLOntology outputOntology = MergeOperation.merge(outputOntologies);
if (outputIRI != null) {
Expand Down Expand Up @@ -344,7 +344,7 @@ private static OWLOntology slmeExtract(
// Get the output IRI
IRI outputIRI = CommandLineHelper.getOutputIRI(line);
if (outputIRI == null) {
outputIRI = inputOntology.getOntologyID().getOntologyIRI().orNull();
outputIRI = inputOntology.getOntologyID().getOntologyIRI().orElse(null);
}

return ExtractOperation.extract(
Expand Down Expand Up @@ -397,7 +397,7 @@ private static OWLOntology subsetExtract(
// Get the output IRI
IRI outputIRI = CommandLineHelper.getOutputIRI(line);
if (outputIRI == null) {
outputIRI = inputOntology.getOntologyID().getOntologyIRI().orNull();
outputIRI = inputOntology.getOntologyID().getOntologyIRI().orElse(null);
}

return ExtractOperation.extractSubset(
Expand Down
2 changes: 1 addition & 1 deletion robot-command/src/main/java/org/obolibrary/robot/FilterCommand.java
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Expand Up @@ -255,7 +255,7 @@ private static OWLOntology getOutputOntology(CommandLine line, OWLOntology input
outputIRI = IRI.create(outputIRIString);
} else {
// If it is not provided, copy the input IRI
outputIRI = inputOntology.getOntologyID().getOntologyIRI().orNull();
outputIRI = inputOntology.getOntologyID().getOntologyIRI().orElse(null);
}

// Create the output ontology
Expand Down
2 changes: 1 addition & 1 deletion robot-command/src/main/java/org/obolibrary/robot/RepairCommand.java
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Expand Up @@ -120,7 +120,7 @@ public CommandState execute(CommandState state, String[] args) throws Exception

IRI outputIRI = CommandLineHelper.getOutputIRI(line);
if (outputIRI == null) {
outputIRI = inputOntology.getOntologyID().getOntologyIRI().orNull();
outputIRI = inputOntology.getOntologyID().getOntologyIRI().orElse(null);
}

boolean repairInvalidReferences =
Expand Down
4 changes: 3 additions & 1 deletion robot-command/src/main/java/org/obolibrary/robot/ValidateProfileCommand.java
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Expand Up @@ -113,7 +113,9 @@ public CommandState execute(CommandState state, String[] args) throws Exception
if (!report.isInProfile()) {
throw new Exception(
String.format(
profileViolationError, ontology.getOntologyID().getOntologyIRI().orNull(), profile));
profileViolationError,
ontology.getOntologyID().getOntologyIRI().orElse(null),
profile));
}
return state;
}
Expand Down
52 changes: 6 additions & 46 deletions robot-core/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -33,47 +33,7 @@
</plugin>

<!-- Ensure backward compatibility -->
<plugin>
<groupId>com.github.siom79.japicmp</groupId>
<artifactId>japicmp-maven-plugin</artifactId>
<version>0.15.4</version>
<configuration>
<oldVersion>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>${project.artifactId}</artifactId>
<version>1.9.11</version> <!-- japicmp target -->
<type>jar</type>
</dependency>
</oldVersion>
<newVersion>
<file>
<path>${project.build.directory}/${project.artifactId}-${project.version}.${project.packaging}</path>
</file>
</newVersion>
<parameter>
<!-- see documentation: http://siom79.github.io/japicmp/MavenPlugin.html -->
<breakBuildOnBinaryIncompatibleModifications>true</breakBuildOnBinaryIncompatibleModifications>
<breakBuildOnSourceIncompatibleModifications>true</breakBuildOnSourceIncompatibleModifications>
<!-- include on breaking changes
<excludes></excludes>
-->
<ignoreMissingClassesByRegularExpressions>
<!-- To handle sesame-rio-api-2.7.16.jar -> rdf4j-rio-api-2.4.2.jar lib change on owlapi 4.5.25 upgrade: -->
<!-- This ignore can be removed in consecutive releases -->
<ignoreMissingClassesByRegularExpression>org.openrdf.rio.*</ignoreMissingClassesByRegularExpression>
</ignoreMissingClassesByRegularExpressions>
</parameter>
</configuration>
<executions>
<execution>
<phase>verify</phase>
<goals>
<goal>cmp</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- Remove for ROBOT 2 update -->
</plugins>
</build>

Expand All @@ -86,7 +46,7 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-api</artifactId>
<version>4.5.29</version>
<version>5.5.1</version>
<exclusions>
<exclusion>
<groupId>com.google.code.findbugs</groupId>
Expand All @@ -97,7 +57,7 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-apibinding</artifactId>
<version>4.5.29</version>
<version>5.5.1</version>
<exclusions>
<exclusion>
<groupId>com.google.code.findbugs</groupId>
Expand All @@ -108,7 +68,7 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-rio</artifactId>
<version>4.5.29</version>
<version>5.5.1</version>
<exclusions>
<exclusion>
<groupId>com.google.code.findbugs</groupId>
Expand Down Expand Up @@ -241,7 +201,7 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlexplanation</artifactId>
<version>2.0.0</version>
<version>5.0.1</version>
<exclusions>
<exclusion>
<groupId>net.sourceforge.owlapi</groupId>
Expand Down Expand Up @@ -275,7 +235,7 @@
<dependency>
<groupId>org.geneontology</groupId>
<artifactId>owl-diff_${scala.version}</artifactId>
<version>1.3.0</version>
<version>2.0.0</version>
<exclusions>
<exclusion>
<groupId>net.sourceforge.owlapi</groupId>
Expand Down
12 changes: 12 additions & 0 deletions robot-core/src/main/java/org/obolibrary/robot/DiffOperation.java
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Expand Up @@ -6,6 +6,7 @@
import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Stream;
import javax.annotation.Nonnull;
import org.geneontology.owl.differ.Differ;
import org.geneontology.owl.differ.render.BasicDiffRenderer;
Expand Down Expand Up @@ -201,6 +202,17 @@ public DualOntologySetProvider(OWLOntologySetProvider left, OWLOntologySetProvid
public Set<OWLOntology> getOntologies() {
return Collections.unmodifiableSet(ontologies);
}

/**
* Get the ontologies in the provider.
*
* @return Set of OWLOntologies
*/
@Nonnull
@Override
public Stream<OWLOntology> ontologies() {

@jamesaoverton jamesaoverton Oct 7, 2026

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This method is required to implement HasGetOntologies.

return ontologies.stream();
}
}

/**
Expand Down
4 changes: 2 additions & 2 deletions robot-core/src/main/java/org/obolibrary/robot/ExpandOperation.java
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Expand Up @@ -101,7 +101,7 @@ public static void expand(
ax ->
executeConstruct(
dataset,
ax.getValue().asLiteral().orNull().getLiteral(),
ax.getValue().asLiteral().orElse(null).getLiteral(),
(IRI) (ax.getSubject()),
config.getAnnotateExpansionAxioms()))
.reduce(ExpandOperation::combine)
Expand All @@ -126,7 +126,7 @@ private static Set<OWLAxiom> executeConstruct(
OWLManager.getOWLDataFactory().getOWLAnnotation(dctSource, definitionTerm));
annotatedAxioms =
axioms.stream()
.map(ax -> ax.getAnnotatedAxiom(sourceAnnotation))
.map(ax -> (OWLAxiom) ax.getAnnotatedAxiom(sourceAnnotation))
.collect(Collectors.toSet());
} else {
annotatedAxioms = axioms;
Expand Down
14 changes: 9 additions & 5 deletions robot-core/src/main/java/org/obolibrary/robot/ExplainOperation.java
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Expand Up @@ -52,7 +52,8 @@ public static Set<Explanation<OWLAxiom>> explain(
logger.debug("Explaining: " + axiom);

ExplanationGeneratorFactory<OWLAxiom> genFac =
ExplanationManager.createExplanationGeneratorFactory(reasonerFactory);
ExplanationManager.createExplanationGeneratorFactory(
reasonerFactory, OWLManager::createOWLOntologyManager);
ExplanationGenerator<OWLAxiom> gen = genFac.createExplanationGenerator(ontology);
return gen.getExplanations(axiom, maxExplanations);
}
Expand All @@ -68,7 +69,11 @@ public static Set<Explanation<OWLAxiom>> explain(
public static Set<Explanation<OWLAxiom>> explainInconsistent(
OWLOntology ontology, OWLReasonerFactory reasonerFactory, int max) {
InconsistentOntologyExplanationGeneratorFactory igf =
new InconsistentOntologyExplanationGeneratorFactory(reasonerFactory, 10000);
new InconsistentOntologyExplanationGeneratorFactory(
reasonerFactory,
OWLManager.getOWLDataFactory(),
OWLManager::createOWLOntologyManager,
10000);
ExplanationGenerator<OWLAxiom> generator = igf.createExplanationGenerator(ontology);
OWLAxiom entailment = df.getOWLSubClassOfAxiom(df.getOWLThing(), df.getOWLNothing());
return generator.getExplanations(entailment, max);
Expand Down Expand Up @@ -126,8 +131,7 @@ public static Set<Explanation<OWLAxiom>> explainUnsatisfiableClasses(
public static Set<Explanation<OWLAxiom>> explainRootUnsatisfiableClasses(
OWLOntology ontology, OWLReasoner reasoner, OWLReasonerFactory reasonerFactory, int max) {
RootDerivedReasoner rootReasoner =
new StructuralRootDerivedReasoner(
ontology.getOWLOntologyManager(), reasoner, reasonerFactory);
new StructuralRootDerivedReasoner(ontology.getOWLOntologyManager(), reasoner);
List<OWLClass> unsatisfiable_classes =
new ArrayList<>(rootReasoner.getRootUnsatisfiableClasses());
return getUnsatExplanationsForClasses(ontology, reasonerFactory, max, unsatisfiable_classes);
Expand Down Expand Up @@ -221,7 +225,7 @@ Determine source ontologies (if imports are present).
sb.append("\n\n" + "# Ontologies used: " + "\n");
for (OWLOntologyID oid : ontologyIdAbbreviation.keySet()) {
String soid = ontologyIdAbbreviation.get(oid);
String oiri = oid.getOntologyIRI().or(IRI.create("unknown.iri")).toString();
String oiri = oid.getOntologyIRI().orElse(IRI.create("unknown.iri")).toString();
sb.append("- ").append(soid).append(" (").append(oiri).append(")\n");
}
return sb.toString();
Expand Down
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