some ObjectProperties from EMMO-beta-4.0 cause errors in OntoGraph

[MBueschelberger]

Dear EMMO-Python developers,

I came across the issue that my EMMO-python v0.3.1 on Python 3.9 (Windows 10 ) has troubles plotting some ObjectProperties with EMMO-beta-4.0 from public Github.

Here is my example serialization:

@prefix : <http://my_exp.info#> .
@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 emmo: <http://emmo.info/emmo#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@base <http://my_exp.info> .

<http://my_exp.info> rdf:type owl:Ontology ;
                                 owl:versionIRI <http://my_exp.info/v0.1> ;
                                 owl:imports <https://emmo-repo.github.io/versions/1.0.0-beta4/emmo-inferred.ttl> .

:EMMO_822408b4_c473_4433_8cd0_21e54e82a812 rdf:type owl:Class ;
                                           rdfs:subClassOf emmo:EMMO_22522299_4091_4d1f_82a2_3890492df6db ,
                                                           [ rdf:type owl:Restriction ;
                                                             owl:onProperty emmo:EMMO_c4bace1d_4db0_4cd3_87e9_18122bae2840 ;
                                                             owl:someValuesFrom emmo:EMMO_cd2cd0de_e0cc_4ef1_b27e_2e88db027bac
                                                           ] ;
                                           skos:prefLabel "my_exp" .

If one tries to import it into emmo-python with the following script ...

from ontopy import get_ontology
from ontopy.graph import OntoGraph
import os

PATH = os.getcwd()
onto_file = os.path.join(PATH, "example.ttl")
new = get_ontology(onto_file).load()


graph = OntoGraph(new, new.my_exp, parents=1, addnodes=True, relations="all")

... the following traceback is returned:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
~\ontology_viszalizaion.ipynb Cell 9' in <cell line: 6>()

----> 6 graph = OntoGraph(new, new.my_exp, parents=1, addnodes=True, relations="all")


File ~\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.9_qbz5n2kfra8p0\LocalCache\local-packages\Python39\site-packages\ontopy\graph.py:293, in OntoGraph.__init__(self, ontology, root, leafs, entities, relations, style, edgelabels, addnodes, addconstructs, included_namespaces, included_ontologies, parents, excluded_nodes, graph, imported, **kwargs)
    286     self.add_entities(
    287         relations=relations,
    288         edgelabels=edgelabels,
    289         addnodes=addnodes,
    290         addconstructs=addconstructs,
    291     )
    292 elif root:
--> 293     self.add_branch(
    294         root,
    295         leafs,
    296         relations=relations,
    297         edgelabels=edgelabels,
    298         addnodes=addnodes,
    299         addconstructs=addconstructs,
    300         included_namespaces=included_namespaces,
    301         included_ontologies=included_ontologies,
    302     )
    303     if parents:
    304         self.add_parents(
    305             root,
    306             levels=parents,
   (...)
    310             addconstructs=addconstructs,
    311         )

File ~\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.9_qbz5n2kfra8p0\LocalCache\local-packages\Python39\site-packages\ontopy\graph.py:390, in OntoGraph.add_branch(self, root, leafs, include_leafs, strict_leafs, exclude, relations, edgelabels, addnodes, addconstructs, included_namespaces, included_ontologies, include_parents, **attrs)
    387 for leaf in leafs:
    388     nodeattrs[get_label(leaf)] = self.style.get("leaf", {})
--> 390 self.add_entities(
    391     entities=classes,
    392     relations=relations,
    393     edgelabels=edgelabels,
    394     addnodes=addnodes,
    395     addconstructs=addconstructs,
    396     nodeattrs=nodeattrs,
    397     **attrs,
    398 )
    400 parents = self.ontology.get_ancestors(
    401     classes, include=include_parents, strict=True
    402 )
    403 if parents:

File ~\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.9_qbz5n2kfra8p0\LocalCache\local-packages\Python39\site-packages\ontopy\graph.py:341, in OntoGraph.add_entities(self, entities, relations, edgelabels, addnodes, addconstructs, nodeattrs, **attrs)
    339     entities = self.ontology.classes(imported=self.imported)
    340 self.add_nodes(entities, nodeattrs=nodeattrs, **attrs)
--> 341 self.add_edges(
    342     relations=relations,
    343     edgelabels=edgelabels,
    344     addnodes=addnodes,
    345     addconstructs=addconstructs,
    346     **attrs,
    347 )

File ~\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.9_qbz5n2kfra8p0\LocalCache\local-packages\Python39\site-packages\ontopy\graph.py:608, in OntoGraph.add_edges(self, sources, relations, edgelabels, addnodes, addconstructs, **attrs)
    606     sources = self.nodes
    607 for source in sources.copy():
--> 608     self.add_source_edges(
    609         source,
    610         relations=relations,
    611         edgelabels=edgelabels,
    612         addnodes=addnodes,
    613         addconstructs=addconstructs,
    614         **attrs,
    615     )

File ~\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.9_qbz5n2kfra8p0\LocalCache\local-packages\Python39\site-packages\ontopy\graph.py:573, in OntoGraph.add_source_edges(self, source, relations, edgelabels, addnodes, addconstructs, **attrs)
    571             continue
    572         pred = asstring(relation, exclude_object=True)
--> 573         self.add_edge(
    574             label, pred, obj, edgelabel=edgelabels, **attrs
    575         )
    577 # inverse
    578 if isinstance(relation, owlready2.Inverse):

File ~\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.9_qbz5n2kfra8p0\LocalCache\local-packages\Python39\site-packages\ontopy\graph.py:504, in OntoGraph.add_edge(self, subject, predicate, obj, edgelabel, **attrs)
    501 elif edgelabel:
    502     label = predicate
--> 504 kwargs = self.get_edge_attrs(predicate, attrs=attrs)
    505 self.dot.edge(subject, obj, label=label, **kwargs)
    506 self.edges.add(key)

File ~\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.9_qbz5n2kfra8p0\LocalCache\local-packages\Python39\site-packages\ontopy\graph.py:725, in OntoGraph.get_edge_attrs(self, predicate, attrs)
    723         break
    724 else:
--> 725     raise ValueError(
    726         f"Relation {relation} not found in entity.mro()."
    727     )
    728 # object property
    729 if isinstance(
    730     entity,
    731     (owlready2.ObjectPropertyClass, owlready2.ObjectProperty),
    732 ):

ValueError: Relation <class 'object'> not found in entity.mro().

The problem occurs for all ObjectProperties, which are a subproperty of hasHolisticRelation, but e.g. does not occur for other relations such as hasPart, hasParticipant, hasSign etc.

Do you have an idea what might be the cause?

[francescalb]

Hi, thanx for pointing this out. I have changed so that relations that do not have a default style will use the overall default style (olive, solid line). At the same time a warning is printed.

I suggest that you add edgelabel=True if you want to check more what is what.

I will make a new issue about adding defaults for new relations in EMMO 1.0.0-beta4.

Note that this change is not added to the pypi package just yet, but it will happen soon.