Imported ontologies in turtle format have odd RDF artifacts when saved

[nickdrummond]

Heyup! Fantastic tool you have there!! One tiny niggle...

The problem with roundtripping turtle format ontologies in #609 still occurs on imported ontologies...

tiny-turtle-imports.zip

1. Open b.owl
2. change the active ontology to a.owl
3. modified it (add an ontology annotation for example)
4. saved a.owl

a.owl has blank nodes and odd comments (see below) - other more complex ontologies expose RDF structures

The fix looks like just running the DocumentFormatUpdater on the imports closure of the loaded ontologies to prevent Rio being used for serialisation.

I have a pull request - will try to link that. Couldn't come up with a reasonable test as it would be a large integration test.

@prefix : <http://null.com/a#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
# 
# 
# #################################################################
# #
# #    Object Properties
# #
# #################################################################
# 
# 
# http://null.com/a#p
# 
# 
# 
# #################################################################
# #
# #    Classes
# #
# #################################################################
# 
# 
# http://null.com/a#X
# 
# http://null.com/a#Y
# 
# Generated by the OWL API (version 5.1.17.2020-11-07T15:03:35Z) https://github.com/owlcs/owlapi/

<http://null.com/a> a owl:Ontology;
  rdfs:comment "sss" .

:p a owl:ObjectProperty .

:X a owl:Class;
  rdfs:subClassOf _:genid1 .

_:genid1 a owl:Restriction;
  owl:someValuesFrom :Y;
  owl:onProperty :p .

:Y a owl:Class .

Checking the impact of the Rio ttl serialisation:

package com.nickd.sw;

import junit.framework.TestCase;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.formats.RioTurtleDocumentFormat;
import org.semanticweb.owlapi.io.FileDocumentSource;
import org.semanticweb.owlapi.io.OWLOntologyDocumentSource;
import org.semanticweb.owlapi.model.*;

import java.io.File;
import java.net.URISyntaxException;

public class TtlRoundtripTest extends TestCase {

    public void testCorruptA () throws OWLOntologyCreationException, OWLOntologyStorageException, URISyntaxException {
        OWLOntologyManager mngr = new OWLManager().get();
        File a = new File(getClass().getClassLoader().getResource("a.owl.ttl").toURI());
        OWLOntologyDocumentSource docSource = new FileDocumentSource(a, new RioTurtleDocumentFormat());
        OWLOntology ontA = mngr.loadOntologyFromOntologyDocument(docSource);
        OWLDocumentFormat format = new RioTurtleDocumentFormat();
        ontA.saveOntology(format, System.out);
    }
}

[nickdrummond]

Sorry, can't work out how to link the pull request - #1025

[jmkeil]

@gouttegd This is still an issue in Protege 5.6.3. Would be great, if it gets fixed.