RDFLibGenid not matched by Graph.query()

[white-gecko]

When I have a Graph object with a blank node in it and perform a skolemization on it, the graph generates RDFLibGenid instances which are not matched by IRIs in a query. To reproduce this I have created the following MWE.
As can be seen, after serializing and parsing the graph, the node is a URIRef that is matched by the same query.

from rdflib import Graph, __version__

print("rdflib version:", __version__)

g = Graph()
g.parse(data='[] <urn:prop> "val" .', format="turtle")
for s, p, o in g:
    print(type(s), s)

gs = g.skolemize()
for s, p, o in gs:
    print(type(s), s)

query_with_iri = 'select ?p ?o {{ <{}> ?p ?o }}'.format(s)
query_for_all = 'select ?s ?p ?o { ?s ?p ?o }'

print(query_with_iri)
print(query_for_all)

print("Get by IRI")
for row in gs.query(query_with_iri):
    print(row)

print("??? ^^^ Why is this empty? ^^^")

print("Get everything")
for row in gs.query(query_for_all):
    print(row)

gp = Graph()
gp.parse(data=gs.serialize(format='turtle'), format='turtle')

print("Get from parsed graph by IRI")
for row in gp.query(query_with_iri):
    print(row)

print("Get everything from parsed graph")
for row in gp.query(query_for_all):
    print(row)

The Output of the MWE:

rdflib version: 6.1.1
<class 'rdflib.term.BNode'> nbdebdd66e4a84a64b29c66ecfc019d5fb1
<class 'rdflib.term.RDFLibGenid'> http://rdlib.net/.well-known/genid/rdflib/nbdebdd66e4a84a64b29c66ecfc019d5fb1
select ?p ?o { <http://rdlib.net/.well-known/genid/rdflib/nbdebdd66e4a84a64b29c66ecfc019d5fb1> ?p ?o }
select ?s ?p ?o { ?s ?p ?o }
Get by IRI
??? ^^^ Why is this empty? ^^^
Get everything
(RDFLibGenid('http://rdlib.net/.well-known/genid/rdflib/nbdebdd66e4a84a64b29c66ecfc019d5fb1'), rdflib.term.URIRef('urn:prop'), rdflib.term.Literal('val'))
Get from parsed graph by IRI
(rdflib.term.URIRef('urn:prop'), rdflib.term.Literal('val'))
Get everything from parsed graph
(rdflib.term.URIRef('http://rdlib.net/.well-known/genid/rdflib/nbdebdd66e4a84a64b29c66ecfc019d5fb1'), rdflib.term.URIRef('urn:prop'), rdflib.term.Literal('val'))

[ghost]

Mmm. The issue is related to the genid's type. Skolemization of a BNode used to return a URIRef until issue #1404 when it was first changed in commit e63450a ("Fix BNode.skolemize() returning a URIRef instead of a Genid.") and then again in 8ea101d "Use RDFLibGenid instead of Genid to maintain original blank node id when performing de-skolemization."

A quick recursive grep for skolemize in tests returns only one reference - that of test_issue1404.py -

    # Check the BNode is now an RDFLibGenid after skolemization.
    skolem_bnode = skolemized_graph.value(**query)
    assert type(skolem_bnode) == RDFLibGenid

Other than that, there aren't any tests of skolemized graphs/bnodes

Looks we need to re-visit the implemented solution to issue #1404 and add some more tests.

fwiw, just to confirm the origin of the issue, temporarily changing BNode.skolemize() to wrap the returned RDFLibGenid in a URIRef enables the query to succeed, albeit at the cost of the assertion in test_issue1404.py failing.

[white-gecko]

I assume the issue is due to the situation, that the terms are matched with a simple object lookup in a dictionary:
https://github.com/RDFLib/rdflib/blob/master/rdflib/plugins/stores/memory.py#L87
i.e. instance of URIRef not equal to instance of RDFLibGenid

[ghost]

Yes, I think you nailed where the fault lies (L#87 is SimpleMemory.triples(), need to look at L#330 in Memory.triples()):

        elif subject is not None:  # subject is given
            spo = self.__spo
            logger.debug(f"TRIPLES\nsubject=“{subject}” {type(subject)}\nspo=“{spo}”")
            if subject in spo:
...
            else:  # given subject not found
                logger.debug(f"Given subject {subject} not found")
                pass

logger reports:

DEBUG    rdflib:memory.py:332 TRIPLES
subject=“http://rdlib.net/.well-known/genid/rdflib/n7938b043fd5d4c76b2bd3c38053fdabbb1” <class 'rdflib.term.URIRef'>
spo=“{RDFLibGenid('http://rdlib.net/.well-known/genid/rdflib/n7938b043fd5d4c76b2bd3c38053fdabbb1'): {rdflib.term.URIRef('urn:prop'): {rdflib.term.Literal('val'): 1}}}”
DEBUG    rdflib:memory.py:366 Given subject http://rdlib.net/.well-known/genid/rdflib/n7938b043fd5d4c76b2bd3c38053fdabbb1 not found

Inspecting the call stack reveals that the call is from evalBGP.

[aucampia]

This issue may also be related:

• A URIRef subclass breaks SPARQL querying #1332