The functionality copyOntology(..) does not work correctly in case of cyclic imports and OntologyCopy.SHALLOW

[sszuev]

The testcase:

    public static void main(String ... args) {
        OntologyManager m1 = OntManagers.createONT();
        Ontology a = m1.createOntology(IRI.create("A"));
        Ontology b = m1.createOntology(IRI.create("B"));
        a.asGraphModel().addImport(b.asGraphModel());
        b.asGraphModel().addImport(a.asGraphModel());

        testManager(m1);

        OntologyManager m2 = OntManagers.createONT();
        m1.ontologies().forEach(x -> m2.copyOntology(x, OntologyCopy.SHALLOW));

        testManager(m2);
    }

    private static void testManager(OntologyManager m) {
        Assert.assertEquals(2, m.ontologies().peek(x -> {
            System.out.println("TEST: " + x);
            Assert.assertEquals(2, Graphs.baseGraphs(((Ontology)x).asGraphModel().getGraph()).count());
        }).count());
    }

Additional info: The method copyOntology with OntologyCopy.SHALLOW is used in RDF Protege. The example of ontology with cyclic imports is http://www.w3.org/TR/owl-guide/wine.rdf

[sszuev]

fixed

[sszuev]

Reopen: fix causes an error when the manager contains anonymous ontologies:

java.lang.NullPointerException: Must be named ontology

    at java.util.Objects.requireNonNull(Objects.java:228)
    at com.github.owlcs.ontapi.jena.utils.OntModels.insert(OntModels.java:91)
    at com.github.owlcs.ontapi.OntologyManagerImpl.lambda$syncImports$28(OntologyManagerImpl.java:1142)
    at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
    at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    at java.util.concurrent.ConcurrentHashMap$ValueSpliterator.forEachRemaining(ConcurrentHashMap.java:3566)
    at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
    at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
    at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
    at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
    at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
    at com.github.owlcs.ontapi.OntologyManagerImpl.syncImports(OntologyManagerImpl.java:1142)
    at com.github.owlcs.ontapi.OntologyManagerImpl.copyOntology(OntologyManagerImpl.java:1411)