sbol-shacl validation fails when inherited properties are set

[jakebeal]

For classes derived from SBOL classes other than the roots, the sbol-shacl validation fails when inherited properties are set. This seems to be because sbol-shacl is not aware of the sub-class relationship.

A minimal reproduction showing the generality of the failure mode:

TTL file:

@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix sbol: <http://sbols.org/v3#> .
@prefix sep054: <http://sbols.org/SEP054#> .
@base <http://sbols.org/SEP054#> .

sep054: rdf:type owl:Ontology ; owl:imports sbol: ; rdfs:comment "failure test" ; owl:versionInfo "1.0-alpha1" .

sep054:SequenceX rdf:type owl:Class ;
        rdfs:comment  '''Subclass failure''' ;
        rdfs:subClassOf sbol:Sequence  .

sep054:CollectionX rdf:type owl:Class ;
        rdfs:comment  '''Subclass failure''' ;
        rdfs:subClassOf sbol:Collection  .

Python code:

from pathlib import Path
from sbol_factory import SBOLFactory
import sbol3

sbol3.set_namespace('http://foo.org/bar/')
sep_054 = SBOLFactory('sep_054', Path(__file__).parent / 'scratch.ttl', 'http://sbols.org/SEP054#')

doc = sbol3.Document()
seq = sep_054.SequenceX('seqOK')
doc.add(seq)
doc.add(sep_054.SequenceX('seqFail', encoding=sbol3.IUPAC_DNA_ENCODING))
doc.add(sep_054.CollectionX('colOK'))
doc.add(sep_054.CollectionX('colFail', members=seq))

for e in doc.validate().errors:
    print(str(e))
assert not doc.validate().errors and not doc.validate().warnings