Major bug in punning detection, concealing major performance problem in filterAxioms

[sesuncedu]

Whilst looking in to the issue of why some parts of ontology rendering were non-deterministic, I discovered a major problem in the faster punning detection code

public Set<IRI> getPunnedIRIs(Imports includeImportsClosure) {
        Set<IRI> punned = new HashSet<>();
        Set<IRI> test = new HashSet<>();
  [includeImportsClosure case omitted]
       for (OWLEntity e : getClassesInSignature(EXCLUDED)) {
            punned.add(e.getIRI());
        }
        for (OWLEntity e : getDataPropertiesInSignature(EXCLUDED)) {
            if (test.add(e.getIRI())) {
                punned.add(e.getIRI());
            }
        }
        for (OWLEntity e : getObjectPropertiesInSignature(EXCLUDED)) {
            if (test.add(e.getIRI())) {
                punned.add(e.getIRI());
            }
        }
        [etc.]
        return punned;

This defines defines a punned IRI as one that names a class, a data property, an object property that is not also a data property, etc.

In some ways this is a good thing, as correcting the error causes saving the Gene Ontology as RDF/XML to take half an hour, almost all of the time being in MapPointer.filterAxioms.

Investigation continues.

Also, Annotation Assertions are not sorted. Also, predicates in triples are not totally ordered.

[sesuncedu]

Ah... this would be the filter Axioms by doing a linear search through every single annotation property assertion axiom instead of using the index approach.

[sesuncedu]

Internals::filterAxioms is about to get a minimalist hack.

[sesuncedu]

After, 3.5s. That's a bit better. Now to see what broke

[ignazio1977]

Rings a bell, I think I fixed something similar a month or two ago. Core Developer Misusing Own API Badge Of Shame: ASSIGNED :-(

[ignazio1977]

I've changed a number of calls to Filters.annotations that I had missed first time around. Really that filter should go. I won't touch the area at the moment, if you're making changes as well.

[sesuncedu]

Change made. I didn't pull request because I was feeling too tired, and I hit a weird writer bug in a non test suite run against some modded translated obo - FSS files with imports that didn't fire on related files without imports, and the was too tired to test.

Also: A pun? I mean a palindrome. A palindrome of Bolton would be Notlob.

[ignazio1977]

I've had a peek on your repo, everything looks fine to me. Big boner, the punning test that does the opposite check <shame/>

[sesuncedu]

I'm going to see what a merge looks like .

[sesuncedu]

And I see why the RDF/XML rendering is exploding:

In RDFRenderBase, we create a graph for all annotations for this entity, from anywhere in the imports closure.

    private boolean createGraph(@Nonnull OWLEntity entity,
            Collection<IRI> illegalPuns) {
            ...
            for (OWLOntology o : ontology.getImportsClosure()) {
                axioms.addAll(o.getAnnotationAssertionAxioms(entity.getIRI()));
            }
           ...

In RDFXMLNamespaceManager we get all the annotation properties in the axiom signature that we are going to define namespaces for, but with imports EXCLUDED .

    protected Set<OWLEntity> getEntitiesThatRequireNamespaces() {
        ...
        entities.addAll(getOntology().getAnnotationPropertiesInSignature(
                EXCLUDED));
        ...
    }

And in XMLWriterImpl, we explode if there is no namespace defined (or for absolutely no reason, if there is a namespace defined whose length is equal to the prefix part of the iri)

    public void writeStartElement(IRI name) throws IOException {
        String qName = xmlWriterNamespaceManager.getQName(name);
        if (qName.length() == name.length()) {
            // Could not generate a valid QName, therefore, we cannot
            // write valid XML - just throw an exception!
            throw new IllegalElementNameException(name.toString());
        }

Cause it's all about the base, the base, the base no prefix.

[sesuncedu]

This will move to a new issue and fix after I've had my supper.

[ignazio1977]

Fixed last month.