Bump net.sourceforge.owlapi:owlapi-distribution from 3.4.10 to 5.5.1

[dependabot]

Bumps net.sourceforge.owlapi:owlapi-distribution from 3.4.10 to 5.5.1.

Commits

• f760b3a OWLAPI version 5.5.1
• a7daa84 Remove org.openrdf.rio.RDFParserFactory #1125
• 372d61b Fix #1126 Handle exception when comparing integer literals.
• 6d95fe2 jaxb-ap dropped in OWLAPI 5.1 causes failure running on Java 11 #1150
• 9e4b6f5 Clarify "Entity not properly recognized" #1152
• 1ea3aca Provide a BOM for owlapi #1148
• 750d455 fix test error GH-1145
• 2d54418 Fix case sensitive extensions in ZipIRIMapper
• 2ef0667 GH-1145 verify both ignore and throw exception behaviours
• b296ff5 GH-1145 add jakarta.json and no.hasmac to the osgi config
• Additional commits viewable in compare view

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[greptile-apps]

Greptile Summary

This Dependabot PR bumps net.sourceforge.owlapi:owlapi-distribution from 3.4.10 to 5.5.1 — a two-major-version jump that includes significant breaking API changes. While the diff itself is a single-line version change in pom.xml, the upgrade is not safe to merge as-is because it breaks both a co-dependency and several compile-time API usages in the existing codebase.

Key issues:

• HermiT runtime incompatibility: com.hermit-reasoner:org.semanticweb.hermit:1.3.8.4 (the OWL DL reasoner) was built against OWLAPI 3.x/4.x and is binary-incompatible with OWLAPI 5.x. It must be replaced with net.sourceforge.owlapi:org.semanticweb.HermiT:1.4.3.456, which was repackaged specifically for OWLAPI 5.x (note the different groupId and artifactId).
• Compile-time failures in Ontology.java: Six uses of removed OWLAPI 3.x/4.x APIs (OWLOntologyFormat, OWLXMLOntologyFormat, getOntologyFormat(), isPrefixOWLOntologyFormat(), asPrefixOWLOntologyFormat(), copyPrefixesFrom()) must be migrated to their OWLAPI 5.x equivalents (OWLDocumentFormat, OWLXMLDocumentFormat, getOntologyDocumentFormat(), PrefixDocumentFormat, etc.).

Confidence Score: 1/5

Not safe to merge — will cause compilation failures and runtime errors in the OWL reasoning stack.

Score of 1 reflects that the single-line version bump is blocked by two P0 issues: a co-dependency that is binary-incompatible with OWLAPI 5.x, and six removed API usages in Ontology.java that will prevent the module from compiling. Both must be resolved before the upgrade can land.

klab.services.reasoner/pom.xml (HermiT dependency must be updated) and klab.services.reasoner/src/main/java/org/integratedmodelling/klab/services/reasoner/owl/Ontology.java (six removed API usages must be migrated to OWLAPI 5.x equivalents).

Important Files Changed

Filename	Overview
klab.services.reasoner/pom.xml	Version bump from OWLAPI 3.4.10 → 5.5.1 breaks the bundled HermiT reasoner dependency and requires source-level migration of removed APIs.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[pom.xml: owlapi-distribution 3.4.10 → 5.5.1] --> B{Breaking changes?}
    B -->|HermiT co-dependency| C[com.hermit-reasoner:hermit:1.3.8.4\nBuilt against OWLAPI 3.x/4.x]
    C --> D[❌ NoClassDefFoundError / IncompatibleClassChangeError at runtime]
    D --> E[Fix: replace with\nnet.sourceforge.owlapi:org.semanticweb.HermiT:1.4.3.456]
    B -->|Removed API classes| F[Ontology.java uses:\nOWLOntologyFormat\nOWLXMLOntologyFormat\ngetOntologyFormat\nisPrefixOWLOntologyFormat\nasPrefixOWLOntologyFormat]
    F --> G[❌ Compilation failure]
    G --> H[Fix: migrate to\nOWLDocumentFormat\nOWLXMLDocumentFormat\ngetOntologyDocumentFormat\nPrefixDocumentFormat]

Loading

Comments Outside Diff (1)

1. klab.services.reasoner/pom.xml, line 63-73 (link)

   HermiT reasoner is incompatible with OWLAPI 5.x

   com.hermit-reasoner:org.semanticweb.hermit:1.3.8.4 was compiled against OWLAPI 3.x/4.x and is not binary-compatible with OWLAPI 5.x. At runtime this will throw NoClassDefFoundError or IncompatibleClassChangeError because the internal class hierarchy changed between major versions.

   For OWLAPI 5.x, the compatible HermiT repackage is published under a different Maven coordinate:

   <dependency>
       <groupId>net.sourceforge.owlapi</groupId>
       <artifactId>org.semanticweb.HermiT</artifactId>
       <version>1.4.3.456</version>
   </dependency>

   Note that both the groupId and artifactId change from the current entry.

_{Reviews (1): Last reviewed commit: "Bump net.sourceforge.owlapi:owlapi-distr..." | Re-trigger Greptile}

[greptile-apps]

OWLAPI 5.x removes several APIs used in Ontology.java

The version bump will cause compilation failures because Ontology.java still uses classes and methods that were removed in OWLAPI 5.x:

Old (3.x/4.x)	Replacement in 5.x
org.semanticweb.owlapi.io.OWLXMLOntologyFormat (line 35)	org.semanticweb.owlapi.formats.OWLXMLDocumentFormat
OWLOntologyFormat (line 241)	OWLDocumentFormat
OWLOntologyManager.getOntologyFormat(ontology) (line 242)	OWLOntologyManager.getOntologyDocumentFormat(ontology)
new OWLXMLOntologyFormat() (line 243)	new OWLXMLDocumentFormat()
format.isPrefixOWLOntologyFormat() (line 245)	format instanceof PrefixDocumentFormat
format.asPrefixOWLOntologyFormat() (line 246)	(PrefixDocumentFormat) format

All six usages are in klab.services.reasoner/src/main/java/org/integratedmodelling/klab/services/reasoner/owl/Ontology.java and must be updated before this dependency bump can be used.