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fix(export): address review findings on the ontology schema fix

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Four findings from the automated review, all reproduced first.

1. The name fallback minted invalid IRIs. `_term_iri` pasted a raw name
   onto the ontology base, so a class named "Customer Account" produced
   <https://example.org/onto/Customer Account>. rdflib only warns about
   the space, Oxigraph rejects it with "Invalid IRI code point". That is
   the same class of defect this PR set out to fix, introduced by the fix
   itself. Local names are now percent-encoded.

2. `improve_coherence` raised AttributeError. It lives on
   OntologyOptimizer, which holds no namespace manager, so the URI
   fallback I added there crashed on any ontology carrying a class
   without a URI. It now mints from the ontology's own base through a
   shared module-level helper.

3. `owl:Thing` was treated as an absolute IRI. It matches the generic
   scheme grammar, so `_is_absolute_iri` accepted it and domains and
   ranges came out as the term <owl:Thing> rather than
   <http://www.w3.org/2002/07/owl#Thing>. This is the live path: stage 4
   of the generator assigns ["owl:Thing"] to object properties with no
   inferred endpoints. Absoluteness is now decided on a real scheme, and
   the well-known prefixes expand.

4. Unusable property entries were dropped in silence. Non-dictionary
   entries and definitions carrying no type are now named in a warning.

6 further tests, including a strict-parser check through Oxigraph, which
is what catches the space that rdflib waves through.
This commit is contained in:
FABIOTESS
2026-08-19 17:35:06 +01:00
parent c30ec14858
commit 9ca83d397f
3 changed files with 206 additions and 7 deletions
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semantica/export/owl_exporter.py
+70 -4
View File
@@ -25,6 +25,7 @@ License: MIT
import re
from datetime import datetime
from pathlib import Path
from urllib.parse import quote
from typing import Any, Dict, List, Optional, Union
from ..utils.exceptions import ProcessingError, ValidationError
@@ -38,6 +39,9 @@ from ..utils.progress_tracker import get_progress_tracker
# PROV-exported URIs co-resolve under one shared namespace by default.
from ..provenance.manager import DEFAULT_BASE_URI
#: Module-level logger, for the classmethod helpers that have no instance.
logger = get_logger("owl_exporter")
class OWLExporter:
"""
@@ -374,15 +378,61 @@ class OWLExporter:
_XSD_NS = "http://www.w3.org/2001/XMLSchema#"
#: Prefixes the generator and hand-authored ontologies actually use. A
#: prefixed name is not an absolute IRI: `owl:Thing` matches the generic
#: scheme grammar, so treating it as one produced <owl:Thing> as a domain,
#: which is a different term from http://www.w3.org/2002/07/owl#Thing.
_KNOWN_PREFIXES = {
"owl": "http://www.w3.org/2002/07/owl#",
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"xsd": _XSD_NS,
"skos": "http://www.w3.org/2004/02/skos/core#",
"dc": "http://purl.org/dc/elements/1.1/",
"dcterms": "http://purl.org/dc/terms/",
"foaf": "http://xmlns.com/foaf/0.1/",
"sem": "https://semantica.dev/ns#",
"semantica": "https://semantica.dev/ns#",
}
#: Schemes that really do introduce an absolute IRI without `//`.
_ABSOLUTE_SCHEMES = ("urn:", "doi:", "mailto:", "tag:", "uuid:")
@classmethod
def _is_absolute_iri(cls, value: str) -> bool:
if not isinstance(value, str):
return False
value = value.strip()
if "://" in value:
return bool(re.match(r"^[A-Za-z][A-Za-z0-9+.\-]*://", value))
return value.lower().startswith(cls._ABSOLUTE_SCHEMES)
@classmethod
def _expand_prefixed_name(cls, value: str) -> str:
"""Expand a known prefixed name, or return "" when it cannot be expanded."""
prefix, _, local = value.partition(":")
namespace = cls._KNOWN_PREFIXES.get(prefix)
return f"{namespace}{local}" if namespace and local else ""
@staticmethod
def _is_absolute_iri(value: str) -> bool:
return bool(re.match(r"^[A-Za-z][A-Za-z0-9+.\-]*:", value))
def _iri_safe(local: str) -> str:
"""
Percent-encode a local name so it can sit inside <>.
A name is free text. "Customer Account" pasted onto a base gives an IRI
with a space in it, which rdflib only warns about and Oxigraph rejects
with "Invalid IRI code point".
"""
return quote(local.strip(), safe="~._-!$&'()*+,;=:@/?")
@classmethod
def _join_iri(cls, base: str, local: str) -> str:
"""Append a local name to a base IRI, respecting hash and slash bases."""
if not base:
return ""
local = cls._iri_safe(local)
if not local:
return ""
separator = "" if base.endswith(("#", "/", ":")) else "#"
return f"{base}{separator}{local}"
@@ -438,8 +488,8 @@ class OWLExporter:
return value
if value in index:
return index[value]
if ":" in value: # a prefixed name we cannot expand
return ""
if ":" in value:
return cls._expand_prefixed_name(value)
return cls._join_iri(base, value)
@classmethod
@@ -497,16 +547,32 @@ class OWLExporter:
if isinstance(prop, dict):
data_props.append(prop)
skipped = 0
untyped = []
for prop in ontology.get("properties", []) or []:
if not isinstance(prop, dict):
skipped += 1
continue
kind = str(prop.get("type") or "").strip().lower()
owl_type = str(prop.get("@type") or "").strip().lower()
if kind in ("object", "objectproperty") or owl_type.endswith("objectproperty"):
object_props.append(prop)
else:
if not kind and not owl_type:
untyped.append(prop.get("name") or prop.get("uri") or "<unnamed>")
data_props.append(prop)
if skipped:
logger.warning(
f"Skipped {skipped} entr(y/ies) in 'properties' that are not "
"dictionaries and cannot be exported"
)
if untyped:
logger.warning(
"Exported as data properties because they declare no type or "
f"@type: {', '.join(str(name) for name in untyped)}"
)
return object_props, data_props
@staticmethod
semantica/ontology/ontology_generator.py
+26 -3
View File
@@ -33,6 +33,7 @@ License: MIT
from dataclasses import dataclass, field, replace as dataclass_replace
from datetime import datetime
from typing import Any, Dict, List, Optional
from urllib.parse import quote
from ..utils.exceptions import ProcessingError, ValidationError
from ..utils.logging import get_logger
@@ -698,12 +699,15 @@ class OntologyOptimizer:
# Ensure all classes have required fields. Both guards used `not in`,
# which misses a key that is present and None, and the URI fallback
# assigned a bare class name where an absolute IRI is required (#1103).
#
# The base comes from the ontology being optimized. OntologyOptimizer
# holds no namespace manager, so reaching for one here would raise
# AttributeError on every ontology carrying a class with no URI.
base_uri = ontology.get("uri") or DEFAULT_ONTOLOGY_BASE_URI
classes = ontology.get("classes", [])
for cls in classes:
if not cls.get("uri"):
cls["uri"] = self.namespace_manager.generate_class_iri(
cls.get("name", "Entity")
)
cls["uri"] = _mint_term_iri(base_uri, cls.get("name", "Entity"))
if not cls.get("label"):
cls["label"] = cls.get("name", "Entity")
@@ -751,6 +755,25 @@ class NodeShape:
severity: str = "Violation"
#: Used when an ontology carries no URI of its own.
DEFAULT_ONTOLOGY_BASE_URI = "https://semantica.dev/ontology/"
def _mint_term_iri(base_uri: str, name: str) -> str:
"""
Mint an absolute IRI for a term from a base and a name.
The name is percent-encoded: names are free text, and "Customer Account"
pasted onto a base gives an IRI with a space in it, which strict parsers
reject outright.
"""
local = quote(str(name).strip(), safe="~._-!$&'()*+,;=:@")
if not local:
local = "Entity"
separator = "" if base_uri.endswith(("#", "/", ":")) else "#"
return f"{base_uri}{separator}{local}"
@dataclass
class SHACLGraph:
"""Internal model representing the complete SHACL shapes graph."""
tests/export/test_owl_exporter_generator_schema.py
+110
View File
@@ -179,3 +179,113 @@ def test_a_class_without_any_identifier_is_skipped_not_emitted_as_empty():
assert set(graph.subjects(RDF.type, OWL.Class)) == set()
assert (URIRef("https://example.org/onto/"), RDF.type, OWL.Ontology) in graph
# ── Review findings on the first revision of this fix ────────────────────────
def test_a_name_with_a_space_still_mints_a_valid_iri():
"""The name fallback pasted free text onto a base, producing `<... ...>`."""
import pyoxigraph
ontology = {
"uri": "https://example.org/onto/",
"name": "Spaces",
"classes": [{"name": "Customer Account"}],
}
turtle = OWLExporter()._export_owl_turtle(ontology)
graph = Graph()
graph.parse(data=turtle, format="turtle")
subjects = [str(s) for s in graph.subjects(RDF.type, OWL.Class)]
assert subjects, "the class was dropped entirely"
assert " " not in subjects[0], subjects[0]
# rdflib only warns about a space in an IRI; a strict parser refuses it.
pyoxigraph.Store().load(
turtle.encode(), format=pyoxigraph.RdfFormat.TURTLE, base_iri=None
)
def test_owl_thing_expands_instead_of_becoming_its_own_scheme():
"""`owl:Thing` matches the generic scheme grammar but is a prefixed name."""
ontology = {
"uri": "https://example.org/onto/",
"name": "Thing",
"classes": [{"name": "Person", "uri": "https://example.org/onto/Person"}],
"object_properties": [
{
"name": "relatedTo",
"uri": "https://example.org/onto/relatedTo",
"domain": ["owl:Thing"],
"range": ["owl:Thing"],
}
],
}
graph = Graph()
graph.parse(data=OWLExporter()._export_owl_turtle(ontology), format="turtle")
subject = URIRef("https://example.org/onto/relatedTo")
for predicate in (RDFS.domain, RDFS.range):
values = [str(v) for v in graph.objects(subject, predicate)]
assert values == ["http://www.w3.org/2002/07/owl#Thing"], values
def test_the_generators_owl_thing_fallback_round_trips():
"""stage 4 assigns domain/range of ["owl:Thing"], so this is the live path."""
ontology = {
"uri": "https://example.org/onto/",
"name": "Generated",
"classes": [{"name": "Person", "uri": "https://example.org/onto/Person"}],
"properties": [
{"name": "linkedTo", "type": "object", "uri": "https://example.org/onto/linkedTo",
"domain": ["owl:Thing"], "range": ["owl:Thing"], "@type": "owl:ObjectProperty"}
],
}
graph = Graph()
graph.parse(data=OWLExporter()._export_owl_turtle(ontology), format="turtle")
assert (
URIRef("https://example.org/onto/linkedTo"),
RDFS.domain,
URIRef("http://www.w3.org/2002/07/owl#Thing"),
) in graph
def test_optimizing_a_class_without_a_uri_does_not_raise():
"""improve_coherence lives on OntologyOptimizer, which owns no namespace manager."""
from semantica.ontology.ontology_generator import OntologyOptimizer
result = OntologyOptimizer().improve_coherence(
{"uri": "https://example.org/onto/", "classes": [{"name": "Person"}], "properties": []}
)
minted = result["classes"][0]["uri"]
assert minted.startswith("https://example.org/onto/"), minted
assert " " not in minted
def test_optimizing_falls_back_to_a_base_when_the_ontology_has_no_uri():
from semantica.ontology.ontology_generator import OntologyOptimizer
result = OntologyOptimizer().improve_coherence(
{"classes": [{"name": "Customer Account"}], "properties": []}
)
minted = result["classes"][0]["uri"]
assert minted.startswith("http"), minted
assert " " not in minted, minted
def test_unusable_property_entries_are_reported_not_silently_dropped(caplog):
import logging
ontology = {
"uri": "https://example.org/onto/",
"name": "Malformed",
"classes": [],
"properties": ["not a dict", {"name": "untyped", "uri": "https://example.org/onto/untyped"}],
}
with caplog.at_level(logging.WARNING):
OWLExporter()._export_owl_turtle(ontology)
messages = " ".join(record.getMessage() for record in caplog.records)
assert "not dictionaries" in messages or "not\ndictionaries" in messages or "dictionaries" in messages
assert "untyped" in messages