Merge pull request #1156 from 13g4d0/fix/ontology-ingestor-named-graph

Read JSON-LD named graphs in OntologyIngestor (#1129)

semantica/ingest/ontology_ingestor.py

@@ -40,7 +40,7 @@ from pathlib import Path
 from typing import Any, Dict, List, Optional, Union
 
 import rdflib
-from rdflib import RDF, RDFS, OWL, Graph
+from rdflib import RDF, RDFS, OWL, Dataset, Graph
 
 from ..utils.exceptions import ProcessingError, ValidationError
 from ..utils.logging import get_logger
@@ -106,15 +106,24 @@ class OntologyIngestor:
                 raise ValidationError(f"File not found: {file_path}")
 
             self.progress.update_tracking(tracking_id, message="Parsing RDF graph...")
-            g = Graph()
+            # `Dataset`, not `Graph`: a JSON-LD document with a top-level `@id` *and*
-            
+            # `@graph` places its terms in a NAMED graph. `Graph.parse()` loads only the
+            # default graph and discards the rest without an error, so every class and
+            # property in such a document was dropped while the load reported success.
+            # Same migration #757 made for JenaStore; the ingest path was not covered by it.
+            # `default_union=True` makes the Dataset itself present triples from every
+            # graph as one merged view (it is an rdflib.Graph subclass, so it satisfies
+            # _convert_to_dict()'s Graph-typed contract directly) instead of copying every
+            # quad into a second in-memory Graph.
+            ds = Dataset(default_union=True)
+
             # Use provided format or let rdflib guess based on extension
             parse_kwargs = kwargs.copy()
             if format:
                 parse_kwargs['format'] = format
-            
+
             try:
-                g.parse(file_path, **parse_kwargs)
+                ds.parse(file_path, **parse_kwargs)
             except Exception as e:
                 # Fallback: try to guess format from extension if not provided and initial parse failed
                 if not format:
@@ -130,12 +139,14 @@ class OntologyIngestor:
                     guessed_fmt = fmt_map.get(ext)
                     if guessed_fmt:
                         self.logger.info(f"Retrying with guessed format: {guessed_fmt}")
-                        g.parse(file_path, format=guessed_fmt, **kwargs)
+                        ds.parse(file_path, format=guessed_fmt, **kwargs)
                     else:
                         raise e
                 else:
                     raise e
 
+            g = ds
+
             self.progress.update_tracking(tracking_id, message="Converting to internal format...")
             
             # Determine format for metadata

tests/ingest/test_ontology_named_graph.py

@@ -0,0 +1,92 @@
+"""A JSON-LD ontology whose terms live in a named graph must not be silently dropped.
+
+A JSON-LD document with a top-level ``@id`` *and* ``@graph`` places its terms in a NAMED
+graph. ``rdflib.Graph.parse()`` loads only the default graph and discards the rest without
+raising, so every class and property in such a document disappeared while the load reported
+success — see issue #1129 for the reproduction through the public API.
+
+This is the same ``Graph`` -> ``Dataset`` migration #757 made for ``JenaStore`` (#756); the
+ingest path was not covered by it.
+"""
+
+from __future__ import annotations
+
+import json
+
+import pytest
+
+from semantica.ingest.ontology_ingestor import OntologyIngestor
+
+NAMED_GRAPH_ONTOLOGY = {
+    "@context": {
+        "ex": "https://example.org/ns#",
+        "owl": "http://www.w3.org/2002/07/owl#",
+        "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+    },
+    "@id": "https://example.org/ns",
+    "@type": "owl:Ontology",
+    "@graph": [
+        {"@id": "ex:Thing", "@type": "owl:Class", "rdfs:label": "Thing"},
+        {"@id": "ex:Other", "@type": "owl:Class", "rdfs:label": "Other"},
+        {
+            "@id": "ex:relatesTo",
+            "@type": "owl:ObjectProperty",
+            "rdfs:domain": {"@id": "ex:Thing"},
+            "rdfs:range": {"@id": "ex:Other"},
+        },
+    ],
+}
+
+DEFAULT_GRAPH_ONTOLOGY = {
+    "@context": NAMED_GRAPH_ONTOLOGY["@context"],
+    "@graph": [
+        {"@id": "ex:Thing", "@type": "owl:Class", "rdfs:label": "Thing"},
+        {"@id": "ex:Other", "@type": "owl:Class", "rdfs:label": "Other"},
+    ],
+}
+
+
+def _write(tmp_path, name, document):
+    path = tmp_path / name
+    path.write_text(json.dumps(document), encoding="utf-8")
+    return path
+
+
+def test_terms_in_a_named_graph_are_ingested(tmp_path):
+    """The regression: two classes and one object property, all inside the named graph."""
+    path = _write(tmp_path, "named.jsonld", NAMED_GRAPH_ONTOLOGY)
+
+    data = OntologyIngestor().ingest_ontology(path).data
+
+    assert len(data["classes"]) == 2, (
+        "classes inside a JSON-LD named graph were dropped; the ingestor is reading only "
+        "the default graph"
+    )
+    assert len(data["properties"]) == 1
+    assert {c["uri"] for c in data["classes"]} == {
+        "https://example.org/ns#Thing",
+        "https://example.org/ns#Other",
+    }
+
+
+def test_terms_in_the_default_graph_still_work(tmp_path):
+    """Canary for the test above: a document *without* a top-level ``@id`` keeps its terms
+    in the default graph and always parsed correctly. If this stopped passing, the fix would
+    have traded one blind spot for another."""
+    path = _write(tmp_path, "default.jsonld", DEFAULT_GRAPH_ONTOLOGY)
+
+    data = OntologyIngestor().ingest_ontology(path).data
+
+    assert len(data["classes"]) == 2
+
+
+@pytest.mark.parametrize("document", [NAMED_GRAPH_ONTOLOGY, DEFAULT_GRAPH_ONTOLOGY])
+def test_metadata_reports_what_was_actually_read(tmp_path, document):
+    """Whatever the shape of the document, the counts reported have to match the terms
+    returned — a load that says it succeeded while returning nothing is what made #1129
+    cost an afternoon to find."""
+    path = _write(tmp_path, "any.jsonld", document)
+
+    result = OntologyIngestor().ingest_ontology(path)
+
+    assert result.data["classes"], "reported success with zero classes"